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||<-5(rowbgcolor='#FF8080'>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.||
||<|7(bgcolor='#FFFFE0'>["recon-all"] –stage2 -subjid subj||
||<|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:

  1. 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:

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:

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

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