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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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| 1. '''`source `''your_freesurfer_dir''`/SetUpFreeSurfer.csh`''' | = FreeSurfer Basic Reconstruction Work Flow = |
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| 2. '''`setenv SUBJECTS_DIR `''your_subjects_dir''''' | 1. Source the correct version of FreeSurfer: |
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| 3. '''`mksubjdirs `''your_subject_name''`''' | '''`source `''your_freesurfer_dir''`/SetUpFreeSurfer.csh`''' |
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| 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`''' |
2. Set your SUBJECTS_DIR variable to your subjects directory: |
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| 5. '''`recon-all -all -subjid `''your_subject_name''''' | '''`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. '''`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 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. recon-all -autorecon-all -subjid your_subject_name
See the BasicReconTable for individual steps that will be run.
6. Check your surfaces and talairach transform. For examples of editing surfaces and troubleshooting, refer to:
- ["FsTutorial/Talairach"]