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This workflow uses the older version of FreeSurfer, in which manual editting of the wm volume was required and subcortical segmentations were not a part of the regular processing stream. See HistoricalReconTable for the steps run by this script. Continue using this workflow if you've already begun processing your subjects this way.
FreeSurfer Historical Reconstruction Work Flow
Source the correct version of FreeSurfer:
source your_freesurfer_dir/SetUpFreeSurfer.csh
- Set your SUBJECTS_DIR variable to your subjects directory:
setenv SUBJECTS_DIR your_subjects_dir
- Make a subjects directory within your SUBJECTS_DIR:
mksubjdirs your_subject_name
- 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
- 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
- Start the recon-all script:
recon-all -stage1 -subjid your_subject_name
- 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"]
- 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:
- Edit the wm.mgz volume For instructions on editing the wm.mgz, refer to:
recon-all -stage2 -subjid your_subject_name
- (Possibly make more edits to wm.mgz volume)
recon-all -stage3 -stage4a -stage4b ?!!!!-avgtif -gcs!!!!? -subjid your_subject_name
- Check the white and pial surfaces:
tkmedit your_subject_name wm.mgz rh.white -aux brain.mgz
tkmedit your_subject_name wm.mgz lh.white -aux brain.mgz For intructions on editing the final surfaces, refer to:
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 |
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-motioncor |
orig/001.mgz |
["mri_motion_correct2"] -i orig/001.mgz -i orig/002.mgz -o rawavg.mgz |
rawavg.mgz |
|
orig/002.mgz |
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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 |
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-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. |
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["recon-all"] stage2 -subjid subj |
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-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 |
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-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 |
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["recon-all"] stage3 -subjid subj |
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-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 |
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-finalsurfs |
brain.mgz |
["mris_make_surfaces"] -w 0 subj ?h |
?h.white |
|
?h.orig |
?h.pial |
|||
?h.thickness |
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-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 |
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["recon-all"] stage4b -subjid subj |
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-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 |
|