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 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 intructions on how to fix bad talairachs tranforms, refer to:

["FsTutorial/Talairach"]

For examples of editing surfaces, refer to:

For instructions on how to fix poor normalizations or skull strips, refer to:

-  ⇤ ← Revision 1 as of 2005-08-11 18:59:04 → 
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  Editor: BrianQuinn
  Comment:
+   ← Revision 17 as of 2005-08-20 21:31:24 → ⇥
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  Editor: JenniPacheco
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
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-## Note: This page was created with the WorkFlowTemplate
##
## If you're modifying this page please take a look at the
## latest version of WorkFlowTemplate to ensure that you're
## using the latest version of the template
##
## Note that the use of 2 commas is not a typo.
+[wiki:Self:FreeSurferWorkFlows top] | [wiki:Self:FreeSurferWorkFlows previous] | [wiki:Self:TroubleshootingReconstruction next]
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-. '''`source `''your_freesurfer_dir''`/SetUpFreeSurfer.csh`'''
+= FreeSurfer Basic Reconstruction Work Flow =
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+Line 5:
-. '''`setenv SUBJECTS_DIR `''your_subjects_dir'''''
+. Source the correct version of FreeSurfer:
    '''`source `''your_freesurfer_dir''`/SetUpFreeSurfer.csh`'''
-Line 13:
+Line 8:
-. '''`mksubjdirs `''your_subject_name''`'''
+. Set your SUBJECTS_DIR variable to your subjects directory:
    '''`setenv SUBJECTS_DIR `''your_subjects_dir'''''
-Line 15:
+Line 11:
-. '''`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`'''
+. Make a subjects directory within your SUBJECTS_DIR:
    '''`mksubjdirs `''your_subject_name'''''
-Line 19:
+Line 14:
-. '''`recon-all -all -subjid `''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`'''
-Line 21:
+Line 17:
-. Check your surfaces and talairach transform. For examples of editing surfaces and troubleshooting, refer to:
+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`'''

  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 intructions on how to fix bad talairachs tranforms, refer to:
    * ["FsTutorial/Talairach"]

For examples of editing surfaces, refer to:
-Line 24:
+Line 40:
-    * FsTutorial/Talairach
+For instructions on how to fix poor normalizations or skull strips, refer to:
-Line 28:
+Line 45: