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 1. '''`source `''your_freesurfer_dir''`/SetUpFreeSurfer.csh`'''  1. Source the correct version of FreeSurfer:
   
'''`source `''your_freesurfer_dir''`/SetUpFreeSurfer.csh`'''
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 2. '''`setenv SUBJECTS_DIR `''your_subjects_dir'''''  2. Set your SUBJECTS_DIR variable to your subjects directory:
   
'''`setenv SUBJECTS_DIR `''your_subjects_dir'''''
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 3. '''`mksubjdirs `''your_subject_name'' '''  3. Make a subjects directory within your SUBJECTS_DIR:
   
'''`mksubjdirs `''your_subject_name'' '''
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 4. '''`mri_convert `''your_dicom_file'' ''your_subject_name''`/mri/orig/001.mgz`'''  4. Convert the DICOM files to .mgz files in the $SUBJECTS_DIR/your_subjects_name/mri/orig directory:
   
'''`mri_convert `''your_dicom_file'' ''your_subject_name''`/mri/orig/001.mgz`'''
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  If you have multiple scans from the same session, convert additional scans like:
  '''`mri_convert `''your_other_dicom_file'' ''your_subject_name''`/mri/orig/002.mgz`'''
 5.
  5.1 If you have multiple scans from the same session, motion correct and average them to produce the orig.mgz volume:
If you have multiple scans from the same session, convert additional scans like:
   '''`mri_convert `''your_other_dicom_file'' ''your_subject_name''`/mri/orig/002.mgz`'''
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  '''`mri_motion_correct2 -i `''your_subject_name''`/mri/orig/001.mgz` \'''  5. If you have a single scan, conform the volume to 1 mm^3 and 256x256x256:
    '''`mri_convert --conform `''your_subject_name''`/mri/orig/002.mgz `''your_subject_name''`/mri/orig.mgz`'''
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   '''-i ''your_subject_name''`/mri/orig/002.mgz` \'''

   '''-o ''your_subject_name''`/mri/rawavg.mgz` '''

  '''`mri_convert --conform `''your_subject_name''`/mri/rawavg.mgz `''your_subject_name''`/mri/orig.mgz`'''

  5.2 If you have a single scan, conform the volume to 1 mm^3 and 256x256x256:

  '''`mri_convert --conform `''your_subject_name''`/mri/orig/002.mgz `''your_subject_name''`/mri/orig.mgz`'''

 6. '''`recon-all -stage1 -subjid `''your_subject_name'''''
 6. Start the recon-all script:
    '''`recon-all -stage1 -subjid `''your_subject_name'''''

[wiki:FreeSurferWorkFlows top] | [wiki:TroubleshootingReconstruction previous] | [wiki:SubcorticalSegmentation next]

FreeSurfer Historical Reconstruction Work Flow

  1. Source the correct version of FreeSurfer:

    • source your_freesurfer_dir/SetUpFreeSurfer.csh

  2. Set your SUBJECTS_DIR variable to your subjects directory:
    • setenv SUBJECTS_DIR your_subjects_dir

  3. Make a subjects directory within your SUBJECTS_DIR:
    • mksubjdirs your_subject_name

  4. Convert the DICOM files to .mgz files in the $SUBJECTS_DIR/your_subjects_name/mri/orig directory:
    • mri_convert your_dicom_file your_subject_name/mri/orig/001.mgz

If you have multiple scans from the same session, convert additional scans like:

  • mri_convert your_other_dicom_file your_subject_name/mri/orig/002.mgz

  1. If you have a single scan, conform the volume to 1 mm^3 and 256x256x256:
    • mri_convert --conform your_subject_name/mri/orig/002.mgz your_subject_name/mri/orig.mgz

  2. Start the recon-all script:
    • recon-all -stage1 -subjid your_subject_name

  3. Check the talairach transform:
    • 7.1 Make sure the talairach subject is linked to $SUBJECTS_DIR

      • if not: ln -s $FREESURFER_HOME/subjects/talairach $SUBJECTS_DIR/.

      7.2 tkregister2 --mgz --s your_subject_name --fstal --surf orig For instructions on how to fix bad talairachs tranforms, refer to:

      • ["FsTutorial/Talairach"]
  4. Check the skull strip:

    tkmedit your_subject_name brain.mgz -aux T1.mgz For intructions on how to fix poor normalizations or skull strips, refer to:

  5. Edit the wm.mgz volume For instructions on editing the wm.mgz, refer to:
  6. recon-all -stage2 -subjid your_subject_name

  7. (Possibly make more edits to wm.mgz volume)
  8. recon-all -stage3 -stage4a -stage4b ?!!!!-avgtif -gcs!!!!?  -subjid your_subject_name

  9. Check the white and pial surfaces: Note: these Tutorial sections show data processed using Basic workflow, so large defects were autofilled.

Recon-all steps and stages

recon-all step

Individual Flag

Input

Command Line

Output

none

none

file.dcm

["mri_convert"] file.dcm orig/001.mgz

orig/001.mgz

["recon-all"] -stage1 -subjid subj

-motioncor

orig/001.mgz

["mri_motion_correct2"] -i orig/001.mgz -i orig/002.mgz -o rawavg.mgz

rawavg.mgz

orig/002.mgz

rawavg.mgz

["mri_convert"] rawavg.mgz orig.mgz --conform

orig.mgz

-nuintensitycor

orig.mgz

["mri_convert"] orig.mgz orig.mnc

orig.mnc

orig.mnc

(4 iterations of) ["nu_correct"] -clobber nu0.mnc nu1.mnc

nu4.mnc

nu4.mnc

["mri_convert"] nu4.mnc nu.mgz

nu.mgz

-talairach

nu.mgz

["talairach2"] subjid -mgz

transforms/talairach.xfm

-normalization

nu.mgz

["mri_normalize"] nu.mgz T1.mgz

T1.mgz

-skullstrip

T1.mgz

["mri_watershed"] T1.mgz brain.mgz

brain.mgz

-segmentation

brain.mgz

["mri_segment"] brain.mgz wm.mgz

wm.mgz

-fill

wm.mgz

["mri_fill"] -a ../scripts/ponscc.cut.log -xform transforms/talairach.xfm -segmentation aseg.mgz wm.mgz filled.mgz

filled.mgz

aseg.mgz

../scripts/ponscc.cut.log

-tessellate

filled.mgz

["mri_tessellate"] filled.mgz 255 ../surf/lh.orig

lh.orig

["mri_tessellate"] filled.mgz 128 ../surf/rh.orig

rh.orig

-smooth1

?h.orig

["mris_smooth"] ?h.orig ?h.smoothwm

?h.smoothwm

-inflate1

?h.smoothwm

["mris_inflate"] ?h.smoothwm ?h.inflated

?h.inflated

Check skullstrip (brain.mgz), talairach (transforms/talairach.xfm), and normalization (brain.mgz or T1.mgz - mean wm voxel value = 110). Perform manual edits to wm.mgz volume.

["recon-all"] –stage2 -subjid subj

-fill

wm.mgz

["mri_fill"] -a ../scripts/ponscc.cut.log -xform transforms/talairach.xfm -segmentation aseg.mgz wm.mgz filled.mgz

filled.mgz

aseg.mgz

../scripts/ponscc.cut.log

-tessellate

filled.mgz

["mri_tessellate"] filled.mgz 255 ../surf/lh.orig

lh.orig

["mri_tessellate"] filled.mgz 128 ../surf/rh.orig

rh.orig

-smooth1

?h.orig

["mris_smooth"] ?h.orig ?h.smoothwm

?h.smoothwm

-inflate1

?h.smoothwm

["mris_inflate"] ?h.smoothwm ?h.inflated

?h.inflated

Check inflated surface and wm volume, make more edits if necessary

["recon-all"] –stage3 -subjid subj

-fill

wm.mgz

["mri_fill"] -a ../scripts/ponscc.cut.log -xform transforms/talairach.xfm -segmentation aseg.mgz wm.mgz filled.mgz

filled.mgz

aseg.mgz

../scripts/ponscc.cut.log

-tessellate

filled.mgz

["mri_tessellate"] filled.mgz 255 ../surf/lh.orig

lh.orig

["mri_tessellate"] filled.mgz 128 ../surf/rh.orig

rh.orig

-smooth1

?h.orig

["mris_smooth"] ?h.orig ?h.smoothwm

?h.smoothwm

-inflate1

?h.smoothwm

["mris_inflate"] ?h.smoothwm ?h.inflated

?h.inflated

-qsphere

?h.inflated

["mris_sphere"] -w 0 -inflate -in 200 -q ?h.inflated ?h.qsphere

?h.qsphere

-fix

?h.qsphere

["mris_fix_topology"] subj ?h

?h.orig

-euler

?h.orig

["mris_euler_number"] ?h.orig

?h.orig.euler

-smooth2

?h.orig

["mris_smooth"] ?h.orig ?h.smoothwm

?h.smoothwm

-inflate2

?h.smoothwm

["mris_inflate"] ?h.smoothwm ?h.inflated

?h.inflated

["recon-all"] –stage4a -subjid subj

-finalsurfs

brain.mgz

["mris_make_surfaces"] -w 0 subj ?h

?h.white

?h.orig

?h.pial

?h.thickness

-cortribbon

orig.mgz

["mri_surf2vol"] --mkmask --hemi ?h --fillribbon --template orig.mgz --volregidentity subj --outvol ?h.ribbon.mgz

?h.ribbon.mgz

?h.white

?h.pial

["recon-all"] –stage4b -subjid subj

-sphere

?h.inflated

["mris_sphere"] -w 0 ?h.inflated ?h.sphere

?h.sphere

-surfreg

?h.sphere

["mris_register"] -w 0 -curv ?h.sphere $AvgTif ?h.sphere.reg

?h.sphere.reg

-contrasurfreg

rh.sphere

["mris_register"] -w 0 -curv -reverse rh.sphere $AvgTif rh.lh.sphere.reg

rh.lh.sphere.reg

lh.sphere

["mris_register"] -w 0 -curv -reverse lh.sphere $AvgTif lh.rh.sphere.reg

lh.rh.sphere.reg

-avgcurv

?h.sphere.reg

["mrisp_paint"] -a 5 $AvgTif#6 ?h.sphere.reg ?h.avg_curv

?h.avg_curv

HistoricalReconstruction (last edited 2021-09-22 11:45:30 by DevaniCordero)