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6. Check your surfaces and talairach transform. For examples of editing surfaces and troubleshooting, refer to: |
6. Check your surfaces and talairach transform. 6.1 Make sure the talairach subject is linked to `$SUBJECTS_DIR` if not: '''`ln -s $FREESURFER_HOME/subjects/talairach $SUBJECTS_DIR/.`''' 6.2 '''`tkregister2 --mgz --s `''your_subject_name''` --fstal`''' For intructions on how to fix bad talairachs tranforms, refer to: * ["FsTutorial/Talairach"] 6.3 Check the white and pial surfaces: '''`tkmedit `''your_subject_name''` wm.mgz rh.white -aux brain.mgz`''' '''`tkmedit `''your_subject_name''` wm.mgz lh.white -aux brain.mgz`''' For examples of editing surfaces, refer to: |
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* ["FsTutorial/Talairach"] |
For instructions on how to fix poor normalizations or skull strips, refer to: |
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6. Check the talairach transform: 6.1 Make sure the talairach subject is linked to `$SUBJECTS_DIR` if not: '''`ln -s $FREESURFER_HOME/subjects/talairach $SUBJECTS_DIR/.`''' 6.2 '''`tkregister2 --mgz --s `''your_subject_name''` --fstal`''' For intructions on how to fix bad talairachs tranforms, refer to: * ["FsTutorial/Talairach"] 7. Check the skull strip: '''`tkmedit `''your_subject_name''` brain.mgz -aux T1.mgz`''' * FsTutorial/ControlPoints * FsTutorial/SkullStripTutorial 8. After you have an accurate brain volume, run the next step of recon-all: '''`recon-all -autorecon2 -subjid `''your_subject_name''''' 9. 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: * FsTutorial/FixingDefects * FsTutorial/PialEdits * FsTutorial/FinalSurfEx 10. After you have accurate pial and white surfaces run the final step of recon-all: '''`recon-all -autorecon3 -subjid `''your_subject_name''''' |
[wiki:FreeSurferWorkFlows top] | [wiki:FreeSurferWorkFlows previous] | [wiki:TroubleshootingReconstruction next]
FreeSurfer Basic 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
5. Start the script recon-all. See the BasicReconTable for individual steps that will be run.
recon-all -autorecon-all -subjid your_subject_name
6. Check your surfaces and talairach transform.
6.1 Make sure the talairach subject is linked to $SUBJECTS_DIR
if not: ln -s $FREESURFER_HOME/subjects/talairach $SUBJECTS_DIR/.
6.2 tkregister2 --mgz --s your_subject_name --fstal
For intructions on how to fix bad talairachs tranforms, refer to:
- ["FsTutorial/Talairach"]
- 6.3 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 examples of editing surfaces, refer to:
For instructions on how to fix poor normalizations or skull strips, refer to:
6. Check the talairach transform:
6.1 Make sure the talairach subject is linked to $SUBJECTS_DIR
if not: ln -s $FREESURFER_HOME/subjects/talairach $SUBJECTS_DIR/.
6.2 tkregister2 --mgz --s your_subject_name --fstal For intructions on how to fix bad talairachs tranforms, refer to:
- ["FsTutorial/Talairach"]
- Check the skull strip:
tkmedit your_subject_name brain.mgz -aux T1.mgz
- After you have an accurate brain volume, run the next step of recon-all:
recon-all -autorecon2 -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:
- After you have accurate pial and white surfaces run the final step of recon-all:
recon-all -autorecon3 -subjid your_subject_name