Differences between revisions 4 and 11 (spanning 7 versions)
⇤ ← Revision 4 as of 2005-08-12 13:12:38 →
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[wiki:Self:FreeSurferWorkFlows top] | [wiki:Self:FreeSurferWorkFlows previous] | [wiki:Self:IntermediateReconstruction next] [wiki:Self:FreeSurferWorkFlows top] | [wiki:Self:FreeSurferWorkFlows previous] | [wiki:Self:TroubleshootingReconstruction next]
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3. '''`mksubjdirs `''your_subject_name''`''' 3. '''`mksubjdirs `''your_subject_name'''''
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5. '''`recon-all -all -subjid `''your_subject_name''''' 5. '''`recon-all -autorecon-all -subjid `''your_subject_name'''''
   See the BasicReconTable for individual steps that will be run.
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    * FsTutorial/Talairach     * ["FsTutorial/Talairach"]

[wiki:FreeSurferWorkFlows top] | [wiki:FreeSurferWorkFlows previous] | [wiki:TroubleshootingReconstruction next]

FreeSurfer Basic 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. recon-all -autorecon-all -subjid your_subject_name

6. Check your surfaces and talairach transform. For examples of editing surfaces and troubleshooting, refer to:

BasicReconstruction (last edited 2008-04-29 11:45:31 by localhost)