'''!ReconAll Output File Descriptions'''

<<TableOfContents>>

*WORK IN PROGRESS- more details needed

= -all Output Files =
== /mri/orig ==
=== 001.mgz ===
The input to recon-all (i.e. the MPRAGE) gets converted to the mgz file format using mri_convert and is called 001.mgz. If you ever wanted to start over and rerun this subject from scratch, you only need the files in the orig directory to do so (and not the dicoms). Be sure to copy the entire directory structure elsewhere so that you have: subj001/mri/orig/001.mgz all together before you run: recon-all -all -s subj001

=== 002.mgz ===
Occassionally some datasets have a second structural run which is converted to mgz format and called 002.mgz (and if there's a third run it'll be called 003.mgz etc..) and saved in subj001/mri/orig/ directory.

=== T1raw.mgz ===
=== FLAIRraw.mgz ===
== /mri ==
=== rawavg.mgz ===
this is the file that's generated after averaging (if there are more than 1 run) the volumes in mri/orig/ . If there's just one run, then the rawavg.mgz file will be the same as 001.mgz. This is unconformed volume.

=== orig.mgz ===
This is the conformed output of rawavg.mgz as a result of running mri_convert.

=== orig_nu.mgz ===
=== nu.mgz ===
This is a intensity normalized volume generated after correcting for non-uniformity in the orig.mgz. If there are any errors in the recon-all stream in the later steps, it sometimes helps to check and compare nu.mgz in that dataset and check if the intensity values don't look normal. If the values are too high, then scaling down the intensity a little bit and rerunning recon-all usually corrects that error. In some cases, this scaling down can also be done for the orig.mgz volume.

{{{
mri_convert --scale 0.3 nu_copy.mgz nu.mgz
}}}
=== T1.mgz ===
=== brainmask.mgz ===
=== norm.mgz ===
=== aseg.auto.mgz ===
=== aseg.presurf.mgz ===
=== brain.mgz ===
=== brain.finalsurfs.mgz ===
=== wm.mgz ===
=== filled.mgz ===
=== aparc+aseg.mgz ===
=== aparc.a2009s+aseg.mgz ===
=== aparc.DKTatlas+aseg.mgz ===
=== aseg.mgz ===
=== wmparc.mgz ===
== /mri/transforms ==
=== talairach.xfm ===
Transform file generated with orig.mgz as input. If there's ever any suspicion about the accuracy of transform or any talairach error, appply this transform file to the volume to check with the image orientation looks okay. If coronal looks like coronal and so on, then it means that the transform file is correct.

=== talairach_with_skull.lta ===
=== talairach.lta ===
=== talairach.m3z ===
== /surf ==
=== ?h.orig.nofix ===
=== ?h.smoothwm.nofix ===
=== ?h.inflated.nofix ===
=== ?h.qsphere.nofix ===
=== ?h.orig ===
=== ?h.inflated ===
?h.sphere

?h.pial

?h.thickness



== /labels ==
=== ?h.aparc.annot ===
=== ?h.cortex.label ===
=== ?h.*_exvivo.label ===
== /stats ==
=== ?h.aparc.stats ===
These files are generated during the last stage of recon-all (-autorecon3). It's a summary table of cortical parcellation statistics for each structure created as a result of the output of mris_anatomical_stats.

=== aseg.stats ===
Statistical file generated by running mris_anatomical_stats on the segmented subcortical volume mri/aseg.mgz.

=== wmparc.stats ===
=== ?h.BA_exvivo.stats ===
== /scripts ==
=== recon-all.log ===
An extremely helpful log file which records all the commands that the recon-all stream runs. If recon-all exits with errors, this log file gives more details as to what the error is and where in the stream the error occurs.

=== build-stamp.txt ===
=== lastcall.build-stamp.txt ===
=== recon-all.env ===
=== recon-all.cmd ===
=== recon-all.done ===
=== recon-all-status.log ===
= -qcache Output Files =
== /surf ==
=== ?h. ===
= -long Output Files =
= -gems Output Files =