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FreeSurfer Release Notes

These Release Notes cover what's new in a release, and known issues.

See also DownloadAndInstall, and BugReporting.

Stable v4.5.0

11 Aug 2009

Stable release version 4.5.0 is a minor release containing bug fixes and new features affecting both the default (cross-sectional) and longitudinal analysis streams.

What's New

  • Bug fixes:
    • fixed mri_glmfit-sim, mri_glmfit, and mri_surfcluster: when sign was set to abs, gave the same significance for all clusters.
    • fixed mris_volmask (the -cortribbon stage of recon-all): segfaulted if not enough memory was available. a memory leak was plugged.
  • New features:

    • improvements to the longitudinal stream further reducing bias found between cross-sectional and longitudinal runs. See LongitudinalChangeLog.

    • updated C.Destrieux atlas (aparc.a2009s). See DestrieuxAtlasChanges.

    • -norandomness is the the default. The binaries in the recon-all stream which are subject to variability due to usage of a random number generator (mris_smooth, mris_sphere, mris_topology_fixer, mris_topo_fixer and mris_ca_label) are now seeded with the same number, with the result being that repeated runs of the recon-all stream on a subject on the same platform will always give identical results. The -randomness flag can be used to allow usage of a random seed.
    • updated versions of aparcstats2table and asegstats2table have:
      • ability to choose common segmentations or all segmentations in asegstats2table
      • different invocations of these scripts produce outputs which have segs/parcs in the same order

      • better debug information ( with the -v or --debug switch )

    • support for reading .vtk surface format, and writing patch files in gifti (.gii) format
    • built against static libtiff, negating the problem of some systems having shared lib libtiff.so.3 and others libtiff.so.4

Known Issues

  • mri_ca_label: this message might appear: "GCA sequential renormalization: label 28 not consistently computed." prior to exiting. This error is invalid (an exit should not occur). There is no work-around. A fix will appear in the next release. Or users can download a new mri_ca_label for their platform here.

  • mris_make_surfaces: where wm lesions exist, even if the lesion is filled in wm.mgz volume, when mris_make_surfaces is run to create the final surfaces, because it uses brain.finalsurfs.mgz for its intensity info, and doesnt consider the fill data in wm.mgz, its possible for surfaces to not follow grey matter on the perimeter of the lesion. A fix will appear in a future release. There is no work-around.
  • make_average_volume: can exit with 'Cannot alloc memory' error if there are a lot of subjects. The work-around is to include the flag '-no-aseg', which will prevent creating the aseg.mgz.
  • mris_make_face_parcellations: creates labels with spaces in the name, which causes table parsing in aparcstats2table to fail. a fix (using underscores) will appear in the next release.

  • aparcstats2table, asegstats2table: output the parcellations/segmentations in a random order compared to the input aseg.stats/?h.aparc.stats files. A fix will appear in the next release. For 4.5.0 users, they can be downloaded from here. Copy the files asegstats2table, aparcstats2table and datastruct_utils.py to your $FREESURFER_HOME/bin.

  • mris_volmask: the VTK library dependency can be problematic on some systems, particularly clusters. The next release will include a new mris_volmask with the VTK library dependency removed.
  • mri_watershed: some subjects will fail the skull-strip stage with a message containing "GLOBAL region of the brain empty !". A fix for this will appear in the next release. A work-around is to include the -no-wsgcaatlas flag at the end of recon-all.

Upcoming features (release v5.0.0)

  • mris_volmask completely rewritten, eliminating dependency on the VTK library (a bane to usage in many clusters). results (?h.ribbon.mgz files) are identical.
  • QDEC:
    • added Nuisance Factor menu in Design tab, allowing selection of any number of continuous variables of which will be treated as 'nuisance variables' in the glm (contrast matrix will have value '0' for these)

    • added FindClustersAndGotoMax button to run mri_surfcluster on a selected result, which will find clusters based on currently selected display threshold, output a table of results to the terminal, and move the cursor to the max vertex in the #1 cluster. 'Next' and 'Prev' buttons allow cycling movement of the cursor through the found clusters.

    • added QuickSnapsTIFF option to automatically take snapshots of medial/lateral pial/inflated and save these four pics to an automatically generated filename
    • added optional parsing of an 'ignore.factors' file to allow specifying columns in the qdec.table.dat to ignore (as would be case for columns containing alternate subject IDs)
    • added optional parsing of an 'ordinal.factors' file to allow specifying which continuous factors are ordinals (integers, not floating point). only affects 'Save Data Table' menu option where the qdec.table.dat is written to disk (ordinals are not written as floats).
    • added usage of NaN (or nan) to indicate missing data point, allowing automatic exclusion of that subject from an analysis
  • mri_nu_correct.mni will use float internally instead of uchar. It will also rescale the output so that the global mean is the same as that of the input. These two changes are linked and can be turned off with --no-float.

  • the skull-strip stage will include a new step following mri_watershed, where the new utility 'mri_gcut' is run to refine the skull-strip, resulting in removal of dura and skull in some cases where it might otherwise remain after the mri_watershed step. see Skull Stripping Using Graph Cuts.

  • support for reading/writing annotation/colortable data in Gifti LabelTable format

  • 32b Linux now produces the same results as 64b Linux. this requires that the processor support SSE2 instructions, which became available in the Pentium 4 series (around 2004).
  • mri_robust_template now used to do motion correction (production of the rawavg.mgz file when two input structurals are present), replacing usage of the FSL 'flirt' tool. the recon-all flag -motioncor-flirt can be used to revert back to flirt over robust_template for motion correction stage.
  • GPU support:

    • mri_em_register will make use of a GPU card, reducing runtime from 30-40 minutes down to 3 minutes. Adding the flag -use-gpu to recon-all will enable GPU support on CUDA-compatible Nvidia cards for this and future freesurfer executables.

  • -show-edits command will show 'persistent' edits. see Edits.

  • -cw256 works better than -cropsize256 so -cropsize256 has been removed
  • reconciled ?h.cortex.label with Desikan and Destrieux parcellations: ?h.cortex.label is used as the template defining cortex, and is used in mris_ca_label to correct any medial wall discrepancies, and is used in mris_anatomical_stats as a mask.
  • tksurfer will now load multiple overlays from the command-line.

Stable v4.4.0

11 June 2009

Stable release version 4.4.0 is a minor release containing bug fixes affecting the longitudinal analysis stream.

What's New

  • Bug fixes:

    • longitudinal processing (recon-all -long) was biased toward the timepoint selected as the base. The new longitudinal processing stream is described in the --help output of recon-all, and extensively here: LongitudinalProcessing.

Known Issues

  • mris_make_surfaces: where wm lesions exist, even if the lesion is filled in wm.mgz volume, when mris_make_surfaces is run to create the final surfaces, because it uses brain.finalsurfs.mgz for its intensity info, and doesnt consider the fill data in wm.mgz, its possible for surfaces to not follow grey matter on the perimeter of the lesion. A fix will appear in a future release. There is no work-around.
  • make_average_volume: can exit with 'Cannot alloc memory' error if there are a lot of subjects. The work-around is to include the flag '-no-aseg', which will prevent creating the aseg.mgz.
  • mri_glmfit-sim, mri_glmfit, and mri_surfcluster: when sign is set to abs, gives the same significance for all clusters. This has been fixed for the next version.
  • mris_volmask (the -cortribbon stage of recon-all) will segfault if not enough memory is available. A fix will appear in the next release. The workaround is to run a single subject at a time and ensure that 4GB of ram is available.

Stable v4.3.1

19 May 2009

Stable release version 4.3.1 is a minor release containing bug fixes (but the changes do not change the results in the default analysis stream relative to v4.3.0), and new features.

What's New

  • Bug fixes:

    • fixed FS-FAST GUI bug.

    • fixed mri_nu_correct.mni bug: incorrectly used the -distance flag when --fwhm is passed.
    • fixed mri_normalize bug on Mac OS X: using the -no1d flag caused segfault.
    • some files supporting aparcstats2table and asegstats2table that were missing are now included.
  • New features:
    • fsaverage (the default common-space subject) now contains the insula label.

Known Issues

  • mris_make_surfaces: where wm lesions exist, even if the lesion is filled in wm.mgz volume, when mris_make_surfaces is run to create the final surfaces, because it uses brain.finalsurfs.mgz for its intensity info, and doesnt consider the fill data in wm.mgz, its possible for surfaces to not follow grey matter on the perimeter of the lesion. A fix will appear in a future release. There is no work-around.
  • make_average_volume: can exit with 'Cannot alloc memory' error if there are a lot of subjects. The work-around is to include the flag '-no-aseg', which will prevent creating the aseg.mgz.
  • longitudinal processing (recon-all -long) is biased toward the timepoint selected as the base. There is no work-around. A new longitudinal processing scheme will appear in a future release.

Stable v4.3.0

26 March 2009

Stable release version 4.3.0 is a minor release containing bug fixes (that change some results in the default analysis stream) and new features.

What's New

  • Bug fixes:
    • fixed aparcstats2table bug: if some of the subjects in a group had missing values of a certain label, aparcstats2table failed to designate a 0 for them, leaving the number of columns for that subject short by one (or specifically, by the number of missing labels relative to the other subjects), thereby making the table nearly useless.
    • fixed isxconcat-sess bug: used --projfrac-avg 0 1 0.2 regardless of what is specified, which meant it would average across the cortical ribbon along the surface normal. The new default is to use a projection fraction of 0.5.

    • fixed wmparc.stats - the BrainSeg, !BrainSegNVox and BrainSegNotVent values are now correct.

    • fixed mri_convert bug: when using the -oc flag (which is used during make_average_subject) during make_average_subject, the tal transform and the centering (-oc 0 0 0) were applied in consecutive transforms instead of being composed into one. The first translated it out of the FOV and the 2nd translated it back-in, exposing the cropped FOV (typically posterior) from the first transform.
    • fixed tkmedit bug: seg-faulted on some systems when scrolling and middle-button clicking at the same time over the tkmedit volume image.
    • the estimated Total Intracranial Volume (eTIV) calculation has been found to be more accurate if the talairach.xfm transform is used instead of the talaiarch_with_skull.lta transform. in this release (4.3.0), the new corrected value will appear in the aseg.stats file, and will be output by mri_segstats and mri_label_volume. there is no simple scale factor to correct existing measures.
    • fixed mri_average bug: -sqr option would overflow for short data-type images.
    • fixed recon-all -make all bug: the -finalsurfs stage incorrectly depended on brain.mgz instead of brain.finalsurfs.mgz, so if brain.finalsurfs.mgz is edited, recon-all -make all wont detect the changed file.
  • New features:
    • new insula label in cortical parcellation atlas

Known Issues

  • aparcstats2table and asegstats2table: are missing four helper scripts which raises a Python import error. These can be downloaded from the following locations and put in $FREESURFER_HOME/bin/. This will be fixed in the next version. ( Note that since these are scripts, they work on all platforms without the need for compilation. )

  • mris_make_surfaces: where wm lesions exist, even if the lesion is filled in wm.mgz volume, when mris_make_surfaces is run to create the final surfaces, because it uses brain.finalsurfs.mgz for its intensity info, and doesnt consider the fill data in wm.mgz, its possible for surfaces to not follow grey matter on the perimeter of the lesion. A fix will appear in a future release. There is no work-around.
  • make_average_volume: can exit with 'Cannot alloc memory' error if there are a lot of subjects. The work-around is to include the flag '-no-aseg', which will prevent creating the aseg.mgz.
  • mri_nu_correct.mni incorrectly uses the -distance flag when --fwhm is passed. The work-around is to edit the script to correct this copy and paste error. A fix will appear in the next release.
  • longitudinal processing (recon-all -long) is biased toward the timepoint selected as the base. There is no work-around. A new longitudinal processing scheme will appear in a future release.

  • FS-FAST GUI bug

Stable v4.2.0

21 Jan 2009

Stable release version 4.2.0 is a minor release containing bug fixes (that change some results in the default analysis stream) and new features.

What's New

  • Bug fixes:
    • aseg.stats/wmparc.stats bug fix: structure volumes, such as hippocampus, were reported as being about 2% smaller in wmparc.stats compared to the same structure in aseg.stats.
    • mri_ca_train bug fix: this message appeared: "GCAupdateNodeCovariance: could not find label".

    • mri_surfcluster bug fix: problem was in the way mri_surfcluster reported the area of a cluster when using a group surface such as fsaverage. fyi, see GroupAverageSurface for info on Freesurfer's group average surfaces.

    • mri_em_register bug fix: a bug prevented the full searching over rotation angles so the solution it found might not be optimal. this bug would manifest itself during mri_watershed, outputing the error message: "GLOBAL region of the brain empty !". this fix may change the results of the analysis stream in some regions by a very small amount.
    • tksurfer minor bug fixes:
      • The text in the colorbar when an overlay is loaded now reflects the Min and Max fields in the Overlay options.
      • A bug in tksurfer was responsible the labels drawn in tkmedit being outside the actual regions ( scattered )
      • A bug in tksurfer gave an "invalid command name" error when switching between overlays.
      • Due to a minor bug, the histogram in "Configure Window Overlay" dialog didn't include an entry for the values at 1.
      • Bug which stopped displaying annotation units after the 3000th was fixed.
  • New features:
    • mri_glmfit-sim: utility to more easily perform cluster-based correction for multiple-comparisons
    • tksurfer : a button to write all 4 views ( medial, lateral, inferior and superior ) of the current surface in the window to a file.

Known issues

  • aparcstats2table bug: if some of the subjects in a group have missing values of a certain label, aparcstats2table fails to designate a 0 for them, leaving the number of columns for that subject short by one (or specifically, by the number of missing labels relative to the other subjects), thereby making the table nearly useless. there is no workaround. a fix will appear in the next release, or can be downloaded here. ( extract the file to $FREESURFER_HOME/bin/ directory )

  • isxconcat-sess: will use --projfrac-avg 0 1 0.2 regardless of what is specified. This means it will average across the cortical ribbon along the surface normal. This has been fixed, and the fix will appear in the next release. The new default will be to use a projection fraction of 0.5. This new version is already in place in both the dev and stable versions in the Martinos Center.

  • wmparc.stats - the BrainSeg, !BrainSegNVox and BrainSegNotVent values are incorrect. Use the values from aseg.stats

  • mri_convert: a bug in using the -oc flag (which is used during make_average_subject) exists: during make_average_subject, the tal transform and the centering (-oc 0 0 0) were applied in consecutive transforms instead of being composed into one. The first translated it out of the FOV and the 2nd translated it back-in, exposing the cropped FOV (typically posterior) from the first transform. A fix will appear in the next release. There is no work-around.

  • tkmedit: seg-faults on some systems when scrolling and middle-button clicking at the same time over the tkmedit volume image. A fix will appear in the next release, or can be downloaded here.

  • the estimated Total Intracranial Volume (eTIV) calculation has been found to be more accurate if the talairach.xfm transform is used instead of the talaiarch_with_skull.lta transform. in the next release, the new corrected value will appear in the aseg.stats file, and will be output by mri_segstats and mri_label_volume. there is no simple scale factor to correct existing measures.
  • mri_average: -sqr option will overflow for short data-type images. A fix will appear in the next release.
  • mris_make_surfaces: where wm lesions exist, even if the lesion is filled in wm.mgz volume, when mris_make_surfaces is run to create the final surfaces, because it uses brain.finalsurfs.mgz for its intensity info, and doesnt consider the fill data in wm.mgz, its possible for surfaces to not follow grey matter on the perimeter of the lesion. A fix will appear in a future release. There is no work-around.
  • make_average_volume: can exit with 'Cannot alloc memory' error if there are a lot of subjects. The work-around is to include the flag '-no-aseg', which will prevent creating the aseg.mgz.
  • recon-all -make all bug: the -finalsurfs stage incorrectly depends on brain.mgz instead of brain.finalsurfs.mgz, so if brain.finalsurfs.mgz is edited, recon-all -make all wont detect the changed file. a fixed recon-all.makefile will appear in the next release.

Upcoming features

  • The next release will contain a new cortical atlas containing the insula label.

Stable v4.1.0

14 Oct 2008

Stable release version 4.1.0 is a minor release containing bug fixes (that change some results in the default analysis stream) and new features.

What's New

  • Bug fixes:

    • Problems with the longitudinal analysis stream (affecting recon-all, mri_ca_label, mri_ca_register, and FSL's flirt) have been fixed. Refer to the help text output from recon-all -help for new usage instructions of the longitudinal stream.

    • mri_segstats and mris_wm_volume bugs fixed. Users of the ?h-cerebral-white-matter stats in the aseg.stats and wmparc.stats files should re-run recon-all -segstats -wmparc.

    • mris_make_surfaces problem causing a 'spike' feature in the pial surface in the insula has been fixed.
    • mri_mergelabel bug fixed: added -n to tail usage, as Fedora Core 5 needs -n to specify the number of lines to tail. mri_mergelabel is called by make_average_surface (which is called by make_average_subject).
  • New features:
    • Qdec is now built against vtk v5.2.

    • Detection of images having a FOV > 256. If detected, recon-all exits. Users must add the -cw256 flag to recon-all, which will crop the image to no greater than 256 voxels.

Known issues

  • aparcstats2table bug: if some of the subjects in a group have missing values of a certain label, aparcstats2table fails to designate a 0 for them, leaving the number of columns for that subject short by one (or specifically, by the number of missing labels relative to the other subjects), thereby making the table nearly useless. there is no workaround. a fix will appear in a future release.
  • aseg.stats/wmparc.stats problem: structure volumes, such as hippocampus, are reported as being about 2% smaller in wmparc.stats compared to the same structure in aseg.stats. the difference is due to differing partial-voluming compensation methods. a fix will appear in the next release. the values in aseg.stats are the correct values.
  • mri_ca_train bug: this message may appear: "GCAupdateNodeCovariance: could not find label". a fix for this bug will appear in the next release. there is no work-around.
  • mri_surfcluster bug: problem in the way mri_surfcluster reports the area of a cluster when using a group surface such as fsaverage. The bottom line is that the area reported is about 25% too big. However, the cluster-wise p-values reported by mri_surfcluster based on simulations from mri_glmfit ARE NOT AFFECTED. Volume clustering is unaffected. A fix will appear in the next release.

  • See GroupAverageSurface for info on Freesurfers group average surfaces.

  • mri_em_register bug: a bug prevented the full searching over rotation angles so the solution it found might not be optimal. A fix will appear in the next release.

Stable v4.0.5

15 June 2008

Stable release version 4.0.5 is a new feature and bug fix release.

What's New

  • New features:

    • Now supports Gifti v1.0 surface format read and write (.gii file extension) for exchanging surface files with Caret, AFNI, BrainVisa, BrainVoyager and Vistrails.

    • Updated Qdec v1.1: has aseg/aparc stats tables import; miscellaneous user features.
    • New volume and surface viewing app: freeview (beta). Note: freeview is not yet available for the Mac.
  • Bug fixes:

    • Qdec now uses VTK v5.0 instead of v5.1, to fix the problem with message: "TclTk error: invalid command name "vtkTemp349"

Known issues

  • Same issues as v4.0.4
  • Bug in mri_segstats: some input data exposes a problem which results in a huge (GB) recon-all.log file, and incorrect results for ?h-cerebral-white-matter in the wmparc.stats file. this bug will be fixed in the next release.

  • It is possible for a 'spike' to appear in the pial surface near the insula, like this image, in some subject data. A fix for mris_make_surfaces will appear in the next release.

  • White matter parcellation (mris_wm_volume) bug:
    • isthmus cingulate segmentation appears between thalamus and pallidum.
    • parahippocampal segmentation appears next to ventralDC.
    • white matter extending into cortex (affects 4.0.3 and 4.0.4).
    • ASeg.stats: white matter volume way too low.
    • A fix for mris_wm_volume will appear in the next release.
  • A bug in the longitudinal analysis stream has been found. A fix will appear in the next release.

Stable v4.0.4

6 May 2008

Stable release version 4.0.4 is a bug fix release.

What's New

  • Bug fixes:
    • The tksurfer bug, where the text on the color-scalebar, and the caption text, may not appear, or appear dim, has been fixed.
    • The tksurfer bug, where it can exit with an error 'alloc: invalid block' when an overlay is loaded, has been fixed.
    • The recon-all -localGI bugs have been fixed.

Known issues

  • mris_make_surfaces can let the pial surface extend inward toward the insular cortex in cases where the extreme capsule is so thin that no voxels are labeled as white matter (and no significant gm/wm contrast boundary exists). There is no work-around.

  • The qdec app produces a 'Bad Match' error when started on some Linux platforms. The work-around is to add this to your /etc/X11/xorg.conf file: 

Section "Extensions"
   Option "Composite" "false"
EndSection

  • Input data having a FOV greater than 256 will fail in the -autorecon2 stage during mri_fill, because the wm.mgz file is 2563 while the norm.mgz and aseg.mgz files are FOV3 (where FOV > 256). The work-around is to use the --cropsize256 flag with recon-all with -autorecon1.

  • The surface files ?h.volume are not produced by recon-all yet, but are mentioned in mris_preproc. Production of the ?h.volume files by recon-all (calculating ?h.area * ?h.thickness) will be available in a future release.

Stable v4.0.3

31 March 2008

Stable release version 4.0.3 is a bug fix and new feature release.

What's New

  • Bug fixes:
    • The -log option of mris_anatomical_stats was fixed.

    • In qdec, the problem where a popup window appeared containing the message 'FsgdfPlot_IsWindowShowing' has been fixed.

    • The problem where make_average_subject failed with the message 'Cannot allocate memory' has been fixed.
    • The mri_ca_register and mri_ca_label segfault bug on the Mac OS has been fixed.
    • In tkmedit, the problem where the cursor goes to the wrong location when tal coords are entered has been fixed.
    • mris_preproc fixed: can now transform multiple volumes from the same subject.
  • New features:
    • Updated qdec, now allows saving/loading a project data file.

    • A new option, -lGI, will calculate a local gyrification index. See localGI.

    • New Brodmann area labels for the 'fsaverage' subject. See BA Maps.

    • talairach_with_skull.lta generation is now robust in presence of increased background noise levels.

Known issues

  • mris_make_surfaces can let the pial surface extend inward toward the insular cortex in cases where the extreme capsule is so thin that no voxels are labeled as white matter (and no significant gm/wm contrast boundary exists). There is no work-around.

  • The qdec app produces a 'Bad Match' error when started on some Linux platforms. The work-around is to add this to your /etc/X11/xorg.conf file: 

Section "Extensions"
   Option "Composite" "false"
EndSection

  • Input data having a FOV greater than 256 will fail in the -autorecon2 stage during mri_fill, because the wm.mgz file is 2563 while the norm.mgz and aseg.mgz files are FOV3 (where FOV > 256). The work-around is to use the --cropsize256 flag with recon-all with -autorecon1.

  • The surface files ?h.volume are not produced by recon-all yet, but are mentioned in mris_preproc. Production of the ?h.volume files by recon-all (calculating ?h.area * ?h.thickness) will be available in a future release.
  • In tksurfer, the text on the color-scalebar, and the caption text, may not appear, or appear dim. A fix for this will appear in the next release. There is no work-around.
  • The -localGI feature is broken, in particular, the mris_fill utility. The effect is a shifted filled.mgz relative to the true surfaces. A fix will appear in the next release.
  • tksurfer can exit with an error 'alloc: invalid block' when an overlay is loaded. A fix will appear in the next release.

Stable v4.0.2

16 December 2007

Stable release version 4.0.2 is a bug fix and new feature release.

What's New

  • Bug fixes:
    • Fixed mris_flatten bug where the map did not unfold properly.

    • Fixed unpacksdcmdir (mri_convert) issue, string: "syngo MR B15".

    • Fixed bug where mri_fill might fail with the message "could not find any points where lh and rh wm are nbrs".

    • mris_thickness_diff and mris_surface_stats now properly handle .mgh file io.
  • New features:
    • Improved -tal-check option, for checking the Talairach alignment.
    • The FSL package is no longer included in the distribution (except for the binary 'flirt', found in freesurfer/bin).

Known issues

  • mris_make_surfaces can let the pial surface extend inward toward the insular cortex in cases where the extreme capsule is so thin that no voxels are labeled as white matter (and no significant gm/wm contrast boundary exists). There is no work-around.

  • The qdec app produces a 'Bad Match' error when started on some Linux platforms. The work-around is to setenv XLIB_SKIP_ARGB_VISUALS 1 if using tcsh, or export XLIB_SKIP_ARGB_VISUALS=1 if using bash.

  • Input data having a FOV greater than 256 will fail in the -autorecon2 stage during mri_fill, because the wm.mgz file is 2563 while the norm.mgz and aseg.mgz files are FOV3 (where FOV > 256). The work-around is to use the --cropsize256 flag with recon-all with -autorecon1.

  • The surface files ?h.volume are not produced by recon-all yet, but are mentioned in mris_preproc. Production of the ?h.volume files by recon-all (calculating ?h.area * ?h.thickness) will be available in a future release.
  • The -log option of mris_anatomical_stats does not work. A fix will appear in the next release.

  • In qdec, a popup window containing the message 'FsgdfPlot_IsWindowShowing' may appear. To fix this, copy this script to your $FREESURFER_HOME/lib/tcl directory: fsgdfPlot.tcl. This fix will appear in the next release.

  • make_average_subject can fail with the message 'Cannot allocate memory'. A fix will appear in the next release.
  • mri_ca_register and mri_ca_label can segfault on the Mac OS. A fix will appear in the next release.
  • In tkmedit, when tal coords are entered, the cursor goes to the wrong location. A fix will appear in the next release.
  • mris_preproc, when transforming multiple volumes from the same subject, each file converted overwrites the previous. A fix will appear in the next release.

Stable v4.0.1

18 September 2007

Stable release version 4.0.1 is a bug fix release.

What's New

  • Bug fixes:
    • Fixed seg-faulting mri_convert in unpacksdcmdir.
    • Fixed tkmedit problem whereby volume display after loading talairach.xfm was incorrect.
    • Fixed seg-faulting mris_annot_to_segmentation.
    • Fixed tksurfer problem whereby curvature and overlay displays could not be turned off.
    • Fixed qdec problem where the display could be hidden on small screens (now has scroll bars).

    • Updated spatialsmooth-sess such that it no longer uses FSL's 'ip' binary.

Known issues

  • When making flatmaps with mris_flatten, sometimes the map never unfolds properly (where there can be a section where it folds over itself). The fix for this bug will appear in a future release.

  • The qdec app produces a 'Bad Match' error when started on some Linux platforms. The work-around is to setenv XLIB_SKIP_ARGB_VISUALS 1 if using tcsh, or export XLIB_SKIP_ARGB_VISUALS=1 if using bash.

  • Input data having a FOV greater than 256 will fail in the -autorecon2 stage during mri_fill, because the wm.mgz file is 2563 while the norm.mgz and aseg.mgz files are FOV3 (where FOV > 256). The work-around is to use the --cropsize256 flag with recon-all with -autorecon1.

  • The surface files ?h.volume are not produced by recon-all yet, but are mentioned in mris_preproc. Production of the ?h.volume files by recon-all (calculating ?h.area * ?h.thickness) will be available in a future release.
  • mris_make_surfaces will let a surface in callosal regions extend across midline in some cases. This bug will be fixed in the next release. There is no work-around.

  • unpacksdcmdir (mri_convert) issue: "ERROR: incorrectly formatted version string syngo MR B15". A fix for this problem will appear in the next release.

  • The -tal-check option for checking the Talairach alignment step does not always catch failures. An improved checker will appear in the next release.

  • mri_fill might fail with the message "could not find any points where lh and rh wm are nbrs". A fix will appear in the next release.

Stable v4.0.0

21 August 2007

Stable release version 4.0.0 is a major release with new features and bug fixes.

What's New

  • New features:
    • The corpus callosum is now segmented into five separate labels in the subcortical segmentation volume 'aseg.mgz'
    • White matter is now parcellated for gyral regions
    • mris_wm_volume - calculates the total white matter volume
    • Improved talairach alignment, with automatic failure detection
    • Improved atlas-based skull-strip
    • Longitudinal analysis (recon-all -long, see help section in recon-all --help)

    • Qdec - group analysis GUI tool

    • DTI recon stream: see dt_recon --help, also new: dmri_poistats (see --help) Linux Centos only
    • FSFast:
      • Full NIFTI compliance
      • mkanalysis GUI -- set up analysis AND contrasts
      • selxavg3-sess -- now replaces stxgrinder, implicit intensity normalization, better whitening
      • tksurfer-sess -- replaces paint-sess and surf-sess
      • tkmedit-sess -- accepts multiple contrasts
      • isxconcat-sess + mri_glmfit -- intersubject averaging (RFx, FFx, weighted RFx), replaces func2sph-sess, func2tal-sess, and isxavg-??-sess, GRF
      • No longer needed: stxgrinder-sess, paint-sess, func2sph, fun2tal, isxavg-??, mkcontrast, inorm-sess
    • Average subject subcortical segmentation
    • Updated numerics libraries (NRC and GSL replaced by VXL), paving the way for an open-source release.
  • Bug fixes:
    • Corrected midline parcellation (during cortical parcellation, areas of the anterior cingulate cortex (rostral anterior cingulate in the parcellation atlas), were mislabeled as corpus callosum or "unlabeled subcortical")
    • Corrected aseg: removal of grey matter around callosum
    • Corrected average subject surface area
    • Corrected problem with average subject thickness generation (mismatched number of vertices)
    • Corrected problem with mris_anatomical_stats, where incorrect results were reported for the measures 'average integrated rectified mean curvature', 'average integrated rectified Gaussian curvature', 'folding index', and 'intrinsic curvature index'.

Known issues

  • When using unpacksdcmdir, mri_convert will fail with a segmentation fault. A fix will appear in the next release.
  • In tkmedit, the displayed volume after loading the talairach.xfm file is not correct. The work-around is to either load the talairach.lta file, or use tkregister2 instead. This will be fixed in the next release.
  • mris_annot_to_segmentation may segfault. A fixed version will appear in the next release.
  • In tksurfer, if you have both curvature and an overlay loaded, and you turn both off, the overlay stays on. This will be fixed in the next release.
  • When making flatmaps with mris_flatten, sometimes the map never unfolds properly (where there can be a section where it folds over itself). The fix for this bug will appear in a future release.
  • In qdec, the Analyze button can be hidden on small screens. This will be fixed in the next release.
  • The qdec app produces a 'Bad Match' error when started on some Linux platforms. There is no work-around at this time.

  • Input data having a FOV greater than 256 will fail in the -autorecon2 stage during mri_fill, because the wm.mgz file is 2563 while the norm.mgz and aseg.mgz files are FOV3 (where FOV > 256). The work-around is to use the --cropsize256 flag with recon-all with -autorecon1.

  • The surface files ?h.volume are not produced by recon-all yet, but are mentioned in mris_preproc. Production of the ?h.volume files by recon-all (calculating ?h.area * ?h.thickness) will be available in a future release.

Stable v3.0.5

7 Feb 2007

Stable release version 3.0.5 is a bug-fix release.

What's New

  • Bug fixes:

    • Fixed bug in NIFTI reader in FreeSurfer (see details below in v3.0.4 Known Issues).

    • Fixed bug in 'unpacksdcmdir' and 'mri_convert' commands on the Intel Mac distribution.
    • Fixed bug in recon-all such that now xopts is correctly processed by mri_nu_correct.mni.

Known Issues

  • Input data having a FOV greater than 256 will fail in the -autorecon2 stage during mri_fill, because the wm.mgz file is 2563 while the norm.mgz and aseg.mgz files are FOV3 (where FOV > 256). The work-around is to use the --cropsize option of mri_convert (see its --help for details) to convert the orig.mgz file to 2563.

  • During cortical parcellation, areas of the anterior cingulate cortex (rostral anterior cingulate in the parcellation atlas), are mislabelled as corpus callosum or "unlabelled subcortical". A fix for this is in the works, possibly for the next release.
  • When making flatmaps with mris_flatten, sometimes the map never unfolds properly (where there can be a section where it folds over itself). The fix for this bug will appear in a future release.
  • On the Mac, make_average_subject (and make_average_volume and make_average_surface) will fail if more than 252 subjects are specified. The work-around is to type 'limit descriptors unlimited' before running these scripts. A fix will appear in the next release.
  • mris_anatomical_stats, as executed by recon-all, reports incorrect results for the measures 'average integrated rectified mean curvature', 'average integrated rectified Gaussian curvature', 'folding index', and 'intrinsic curvature index'. The other reported measures ('total white matter volume', 'total surface area', 'total gray matter volume' and 'average cortical thickness') are correct as reported by recon-all's execution of mris_anatomical_stats. There is no work-around. A fix will appear in the next release.

Stable v3.0.4

25 Nov 2006

Stable release version 3.0.4 is a bug-fix release.

What's New

  • Bug fixes:
    • Fixed problem with left hemi of fsaverage subject (see v3.0.3 Known Issues, below, for details).
    • Fixed bug whereby the pial surface can cross the midline in the cingulate/callosum area to the other hemisphere. The change [attachment:bert-medial-wall-diffs.tiff affects this area].
    • Fixed 'glutInit' bug occuring on Fedora Core and Debian Linux installations using tksurfer.
    • Fixed bug in mri_normalize which core dumped for low SNR input volumes.
    • Fixed bug in tksurfer with "Don't cross functional threshold" parameter.
    • Fixed problem with public declaration of Tcl/Tk/Tix/BLT environment variables which caused problems with FSL and 3D Slicer.
  • New features:

    • Label file named <subjid>/label/?h.cortex.label is a single label for all of cortex.

Known Issues

  • Input data having a FOV greater than 256 will fail in the -autorecon2 stage during mri_fill, because the wm.mgz file is 2563 while the norm.mgz and aseg.mgz files are FOV3 (where FOV > 256). The work-around is to use the --cropsize option of mri_convert (see its --help for details) to convert the orig.mgz file to 2563.

  • The 'unpacksdcmdir' command, and 'mri_convert' of some DICOM formatted data, will fail on the Intel Mac distribution v3.0.4, due to a byte-endian issue. The v3.0.4b distribution has a fix for these problems.
  • recon-all does not process xopts for mri_nu_correct.mni. The fix will appear in the next release.

  • There is a small bug in the NIFTI reader in FreeSurfer, which causes the sform/qfrom matrix to be slightly off for oblique volumes that are non-isotropic (the more oblique and the more non-isotropic, the worse). Part of the error involves the matrix being slightly non-orthogonal. The fix for this bug will appear in the next release. There is NO effect of this bug if any of the following apply:

    1. You use mri_convert to convert from DICOM (or any other non-NIFTI format) to NIFTI
    2. Your volumes are not oblique
    3. Your volumes are isotropic
  • During cortical parcellation, areas of the anterior cingulate cortex (rostral anterior cingulate in the parcellation atlas), are mislabelled as corpus callosum or "unlabelled subcortical". A fix for this is in the works, possibly for the next release.
  • When making flatmaps with mris_flatten, sometimes the map never unfolds properly (where there can be a section where it folds over itself). The fix for this bug will appear in a future release.

Stable v3.0.3

24 May 2006

Stable release version 3.0.3 is a bug-fix and feature-addition release.

What's New

  • Bug fixes:
    • Fixed a bug in tksurfer in which if an overlay and the curvature was loaded, the curvature would draw under the overlay even if the curvature display was turned off.
    • Modified the way NIFTI1 files are stored (these are the single .nii and .nii.gz files). The change is somewhat esoteric: the vox_offset is now 352 instead of 348. 352 is the NIFTI spec, so we were technically out of compliance before, although AFNI, FSL, and SPM did not seem to have a problem with 348.
    • Fixed bug in make_average_surface and make_average_volume scripts which limited the number of subjects that could be specified on the command line.
  • New features:
    • asegstats2table and aparcstats2table - scripts to generate text/ascii tables of freesurfer stats data (eg, aseg.stats). This can then be easily imported into a stats program.

Known Issues

  • In tksurfer, if using the -fthresh option, specify the number as a float (-fthresh 2.0) not an integer (don't use -fthresh 2).
  • There is a problem with the left hemi of the fsaverage subject, specifically lh.sphere.reg. This will cause some inaccuracies in the visualization of maps on the left hemi of fsaverage and other average subjects (but the statistics themselves should be ok). The corrected lh.sphere.reg for fsaverage will be included in the next release. Or, if you have an average subject that you want to correct, you do not have to rebuild it. Rather, you can simply: 

cd youraveragesubject/surf
cp lh.sphere.reg lh.sphere.reg.old # backup
cp rh.sphere.reg lh.sphere.reg # copy rh.sphere to lh.sphere
  • There is a bug whereby the pial surface can cross the midline in the cingulate/callosum area to the other hemisphere. There is no workaround. The bug will be fixed in the next release. This change will [attachment:bert-medial-wall-diffs.tiff affect this area].
  • tksurfer will fail on Fedora Core and Debian Linux installations which use freeglut, as 'glutInit' is not executed. This bug will be fixed in the next release.
  • mri_normalize may core dump for low SNR input volumes. This bug will be fixed in the next release.
  • In tksurfer, fills that use the "Don't cross functional threshold" parameter do not correctly fill negative functional areas. This bug will be fixed in the next release (v3.0.4).
  • Tcl/Tk/Tix/BLT environment variables declared in freesurfer setup file causes problems with other apps, like FSL and 3D Slicer. This problem will be fixed in the next release. The workaround is to not call the Freesurfer setup script when using the other apps.

Stable v3.0.2

18 April 2006

Stable release version 3.0.2 is a bug-fix and feature-addition release.

What's New

  • Bug fixes:
    • The --all-info or --version command-line corrupting bug has been fixed.
    • The mris_fix_topology mrisDefectAnalysis bug has been fixed.
    • The bug where control points were being truncated instead of rounded by mri_normalize, which could offset them by 1 voxel, has been fixed.
    • The bug where curvature was being computed incorrectly for RH9 binaries has been fixed (affected spherical morph, and curvature overlay).
    • eTIV calculations are now correct (they were ~25% too large, specifically, multiply pre v3.0.2 eTIV values by .744 to get the correct eTIV).
    • mri_label2vol - fixed bug for segmentation IDs over 999. Runs much faster now.
  • New features:
    • bem directory is created in subjects dir (for the MEG people)
    • Better integration with FSL (compatible with FSL-nifti)
    • Uses robust estimates of class statistics in mri_normalize, mri_segment and mris_make_surfaces. Helps in low contrast (such as SPGR-based) images in which the gray matter is oversegmented.

Known Issues

  • None at this time.

Stable v3.0.1

13 March 2006

Stable release version 3.0.1 is a bug-fix release.

What's New

  • FIX_VERTEX_AREA no longer need be set in the environment outside of recon-all.
  • In tkmedit, while loading a functional overlay or time course, the registration file name is now read properly.
  • The FSFast utility mkanalysis-sess.new now accepts only sequence names matching "TR " (instead of all occurrences of TR).

Known Issues

  • When running mri_surfcluster with average7 inside your csd file, make sure to specify --subject average7 --really-use-average7 or else it will underestimate the clustersize and cause the significances to be too low.

  • mris_fix_topology may exit recon-all with the following message in the log: mrisDefectAnalysis : defect 123 overlap defect 119, where your defect numbers will be different. If this happens for one of your subjects, there is no work-around. A fix will appear in the next release.

  • If the flags --all-info or --version are included at the beginning of a command-line, it will corrupt the subsequent command-line arguments. The work-around is to not include --all-info or --version with other command-line arguments. A fix will appear in the next release.

  • On the rh9 distribution, sometimes the ?h.curv files produced are incorrect, displaying as nearly all red (instead of green and red, indicating gyri and sulci). This produces incorrect cortical parcellation data. There is no known work-around at this time. This problem does not appear when using the Centos or Mac distributions.
  • tkmedit saves control points for intensity normalization in floating point RAS coordinates, but mri_normalize truncated these when they are read in with the -f command (the default behavior when the tmp/control.dat file exists). This can result in the control points being displaced by a voxel from the location that tkmedit displays them.
  • mri_label_volume estimated TIV calculation are about 25% too large. This will be fixed in the next release.

  • Be sure to read about the changes to recon-all, detailed below, and also read about the new fsaverage subject.

Stable v3.0.0

5 March 2006

Stable release version 3.0.0 is a major release containing many new features over the prior stable release (version 2.2).

Important! The recon-all script has been updated. Please read the ReconAllChanges page which describes these changes! Users of prior 'dev' releases should also take note of the changes.

  • COR file format is no longer accepted by recon-all. mgz file's have replaced this old format.

  • brainmask.mgz has replaced what was the brain volume. You should visualize and make all edits to brainmask.mgz and not to brain.mgz

  • recon-all will now save all your changes by default. Any manual changes/edits to the talairach, setting of control points, edits to volumes etc will be saved and used by default and you must specify when you wish to ignore these changes.

  • Data processed with an older release should make use of the -legacy flag in recon-all.

What's New

  • Sub-cortical segmentation - Each MRI volume voxel is assigned one of 37 possible neuroanatomical labels, including left and and right caudate, putamen, pallidum, thalamus, lateral ventricles, hippocampus, and amygdala. The labeling allows for volumetric measurement of these structures. The segmentation information also improves the ability to create a filled white-matter volume.

  • Automated filling of ventricles and basal ganglia - Improves the ability to create a filled white-matter volume (which is used in the surface creation process). Note: this requires the use of the new average subject fsaverage because the surface registration changes.

  • Improved automation - The need to conduct manual edits to account for skull-stripping and cutting-plane problems is reduced. The topology fixer is much better at handling temporal lobe strands. Overall, greater than 90% of hemispheres processed by recon-all do not require manual intervention.

  • Improved GUI tools - The GUI tools tkmedit and tksurfer incorporate many usability improvements requested by the user-base.

  • New cortical parcellation - A neuroanatomical label is assigned to each location on the cortical surface model based on probabilistic information estimated from a manually labeled training set.

  • Surface-based GLM analysis - Utilities for conducting group analysis studies with GLM.

  • Multiple comparison correction for surface analysis - False discovery rate (FDR), permutation and Monte Carlo simulations.

  • New average subject. $FREESURFER_HOME/subjects/fsaverage. Keeps info about average surface area.

  • Average subject customization. Make your own average subject from your cohort.

  • Extensive testing - The recon-all processing stream has been tested against several hundred subjects, different pulse-sequence types, and different MRI system platforms.

  • Online tutorial of the Freesurfer work-flow - This release is compatible with the on-line tutorial. Tutorial data must be downloaded separately.

  • Simplified distribution download and installation - The critical library and toolkit dependencies (MNI, FSL, GSL, Tcl/Tk/Tix/BLT, and Qt) are included to ease installation. These third-party open-sourced packages can be removed if they are already installed on the target system (although full Freesurfer functionality is no longer assured). For Mac OS X, a GUI installation package is provided.

  • Compatible with all mouse pads

  • Now Y2K compliant!

Known Issues

  • Make sure to run "setenv FIX_VERTEX_AREA" if using any commands outside of recon-all, particularly the mri_glmfit and mri_surfcluster programs. To be safe, you can just add the line "setenv FIX_VERTEX_AREA" into FreeSurferEnv.csh or your .cshrc file. This will only affect those downloading the new version. This will automatically be done for those in the Martinos Center.

  • In tkmedit, while loading a functional overlay or time course, the registration file name may not be read properly. A workaround is to load the overlay or time course from the command line (see tkmedit for details).

  • The surface registration curvature target has changed with the new automatic filling of ventricles and basal ganglia. Do not mix newly reconstructed subjects with those that used the old target. For new data recons, display overlay maps on the new average subject fsaverage. For older data, use average7.

  • There are some changes in the way that mri_surfcluster and mri_glmfit computes cluster sizes and how these interact with the average subject (and average7) see the notes fsaverage for more detail.

ReleaseNotes (last edited 2026-01-16 13:38:36 by DougGreve)