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== Recon-all steps and stages == ||<rowbgcolor='#80FF80'>'''recon-all step'''||'''Individual Flag'''||'''Input'''||'''Command Line'''||'''Output'''|| ||<bgcolor='#FFFFE0'>none||<bgcolor='#FFFFE0'>none||<bgcolor='#E0E0FF'>file.dcm||<bgcolor='#E0E0FF'>["mri_convert"] file.dcm orig/001.mgz||<bgcolor='#E0E0FF'>orig/001.mgz|| ||<|17(bgcolor='#FFFFE0'>["recon-all"] -stage1 -subjid subj|| ||<|3(bgcolor='#FFFFE0'>-motioncor||<bgcolor='#E0E0FF'>orig/001.mgz||<|2(bgcolor='#E0E0FF'>["mri_motion_correct2"] -i orig/001.mgz -i orig/002.mgz -o rawavg.mgz||<|2(bgcolor='#E0E0FF'>rawavg.mgz|| ||<rowbgcolor='#E0E0FF'>orig/002.mgz|| ||<rowbgcolor='#E0E0FF'>rawavg.mgz||["mri_convert"] rawavg.mgz orig.mgz --conform||orig.mgz|| ||<|3(bgcolor='#FFFFE0'>-nuintensitycor||<bgcolor='#E0E0FF'>orig.mgz||<bgcolor='#E0E0FF'>["mri_convert"] orig.mgz orig.mnc||<bgcolor='#E0E0FF'>orig.mnc|| ||<rowbgcolor='#E0E0FF'>orig.mnc||(4 iterations of) ["nu_correct"] -clobber nu0.mnc nu1.mnc||nu4.mnc|| ||<rowbgcolor='#E0E0FF'>nu4.mnc||["mri_convert"] nu4.mnc nu.mgz||nu.mgz|| ||<bgcolor='#FFFFE0'>-talairach||<bgcolor='#E0E0FF'>nu.mgz||<bgcolor='#E0E0FF'>["talairach2"] subjid -mgz||<bgcolor='#E0E0FF'>transforms/talairach.xfm|| ||<bgcolor='#FFFFE0'>-normalization||<bgcolor='#E0E0FF'>nu.mgz||<bgcolor='#E0E0FF'>["mri_normalize"] nu.mgz T1.mgz||<bgcolor='#E0E0FF'>T1.mgz|| ||<bgcolor='#FFFFE0'>-skullstrip||<bgcolor='#E0E0FF'>T1.mgz||<bgcolor='#E0E0FF'>["mri_watershed"] T1.mgz brain.mgz||<bgcolor='#E0E0FF'>brain.mgz|| ||<bgcolor='#FFFFE0'>-segmentation||<bgcolor='#E0E0FF'>brain.mgz||<bgcolor='#E0E0FF'>["mri_segment"] brain.mgz wm.mgz||<bgcolor='#E0E0FF'>wm.mgz|| ||<|2(bgcolor='#FFFFE0'>-fill||<bgcolor='#E0E0FF'>wm.mgz||<|2(bgcolor='#E0E0FF'>["mri_fill"] -a ../scripts/ponscc.cut.log -xform transforms/talairach.xfm -segmentation aseg.mgz wm.mgz filled.mgz||<bgcolor='#E0E0FF'>filled.mgz|| ||<rowbgcolor='#E0E0FF'>aseg.mgz||../scripts/ponscc.cut.log|| ||<|2((bgcolor='#FFFFE0'>-tessellate||<|2(bgcolor='#E0E0FF'>filled.mgz||<bgcolor='#E0E0FF'>["mri_tessellate"] filled.mgz 255 ../surf/lh.orig||<bgcolor='#E0E0FF'>lh.orig|| ||<rowbgcolor='#E0E0FF'>["mri_tessellate"] filled.mgz 128 ../surf/rh.orig||rh.orig|| ||<bgcolor='#FFFFE0'>-smooth1||<bgcolor='#E0E0FF'>?h.orig||<bgcolor='#E0E0FF'>["mris_smooth"] ?h.orig ?h.smoothwm||<bgcolor='#E0E0FF'>?h.smoothwm|| ||<bgcolor='#FFFFE0'>-inflate1||<bgcolor='#E0E0FF'>?h.smoothwm||<bgcolor='#E0E0FF'>["mris_inflate"] ?h.smoothwm ?h.inflated||<bgcolor='#E0E0FF'>?h.inflated|| |
[wiki:FreeSurferWorkFlows top] | [wiki:TroubleshootingReconstruction previous] | [wiki:SubcorticalSegmentation next]
FreeSurfer Historical Reconstruction Work Flow
1. source your_freesurfer_dir/SetUpFreeSurfer.csh
2. setenv SUBJECTS_DIR your_subjects_dir
3. mksubjdirs your_subject_name`
4. 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
5. a.If you have multiple scans from the same session, motion correct and average them to produce the orig.mgz volume:
mri_motion_correct2 -i your_subject_name/mri/orig/001.mgz -i your_subject_name/mri/orig/002.mgz -o your_subject_name/mri/rawavg.mgz
mri_convert --conformyour_subject_name/mri/rawavg.mgz your_subject_name/mri/orig.mgz
- b.If you have a single scan, conform the volume to 1 mm^3 and 256x256x256:
mri_convert --conformyour_subject_name/mri/orig/002.mgz your_subject_name/mri/orig.mgz
6. recon-all -stage1 -subjid your_subject_name
7. Check the talairach transform:
Make sure the talairach subject is linked to $SUBJECTS_DIR
if not: ln -s $FREESURFER_HOME/subjects/talairach $SUBJECTS_DIR/.
b. tkregister2 --mgz --s your_subject_name --fstal --surf orig For instructions on how to fix bad talairachs tranforms, refer to:
- FsTutorial/Talairach
8. 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:
9. Edit the wm.mgz volume
- For instructions on editing the wm.mgz, refer to:
- FsTutorial/
10. recon-all -stage2 -subjid your_subject_name
11. (Possibly make more edits to wm.mgz volume)
12. recon-all -stage3 -stage4a -stage4b ?!!!!-avgtif -gcs!!!!? -subjid your_subject_name
13. 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:
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 |