Differences between revisions 2 and 20 (spanning 18 versions)

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This workflow completes the reconstruction process in three different steps, allowing the user to check the outputs before proceeding. See the ReconAllDevTable for a list of the steps run with this command, or ReconAllBlockDiagram for a different presentation. OtherUsefulFlags for a list of other flags that you can use with recon-all. Any manual intervention that is needed is done before moving on to the next step, which can save both time and use of computer power.

FreeSurfer Troubleshooting Reconstruction Work Flow

Source the correct version of FreeSurfer:
- source your_freesurfer_dir/SetUpFreeSurfer.csh
Set your SUBJECTS_DIR variable to your subjects directory:
- setenv SUBJECTS_DIR your_subjects_dir
Import your data and create a subject data directory. This is done once using the following command:
- recon-all -i invol1 -i invol2 -subjid your_subject_name
  where invol1 and invol2 are paths to your input files. You can use as many as necessary (i.e., -i invol3 -i invol4) and they can be in any format that is accepted by mri_convert. The command above will create an empty directory named your_subject_name, except the mri/orig directory will contain files named 001.mgz and 002.mgz, which are your imported structurals. Once your input files are imported, you do not need to use the -i flags again.
Run the first step of recon-all. See the ReconAllDevTable for individual steps that will be run during the whole process.
- recon-all -autorecon1 -subjid your_subject_name
Check the talairach transform:
- 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 brainmask.mgz -aux T1.mgz
- For instructions on how to fix poor normalizations or skull strips, refer to:
  - FsTutorial/ControlPoints
    - After adding control points run the step -autorecon2-cp (this will run -normalization, using control points, and everything else through the end of -autorecon2.)
  - FsTutorial/SkullStripFix
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 brainmask.mgz -aux-surface lh.white
- For intructions on editing the final surfaces, refer to:
  - FsTutorial/WhiteMatterEdits
    - After editing the wm.mgz volume run the step -autorecon2-wm (this will run -fill, using new wm.mgz volume, and everything else through the end of -autorecon2.)
  - FsTutorial/PialEdits
    - After editing the brainmask.mgz volume run the step -autorecon2-pial (this will run -finalsurfs, using new brainmask.mgz volume, and everything else through the end of -autorecon2.)
  - FsTutorial/FinalSurfEx
After you have accurate pial and white surfaces run the final step of recon-all:
- recon-all -autorecon3 -subjid your_subject_name

-  ⇤ ← Revision 2 as of 2005-09-06 15:12:46 → 
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+   ← Revision 20 as of 2008-04-29 11:45:24 → ⇥
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  Comment: converted to 1.6 markup
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-[wiki:Self:FreeSurferWorkFlows top] | [wiki:Self:BasicReconstruction previous] | [wiki:Self:HistoricalReconstruction next]
+#acl AdminGroup:read,write,delete,revert All:read
[[FreeSurferWorkFlows|top]] | [[BasicReconstruction|previous]] | [[HistoricalReconstruction|next]]
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-This workflow completes the reconstruction process in three different steps, allowing the user to check the outputs before proceeding. See the RecommendedReconTable for a list of the steps run with this command. Any manual intervention that is needed is done before moving on to the next step, which can save both time and use of computer power.
+This workflow completes the reconstruction process in three different steps, allowing the user to check the outputs before proceeding. See the ReconAllDevTable for a list of the steps run with this command, or ReconAllBlockDiagram for a different presentation. OtherUsefulFlags for a list of other flags that you can use with recon-all. Any manual intervention that is needed is done before moving on to the next step, which can save both time and use of computer power.
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-. Make a subjects directory within your SUBJECTS_DIR:
    '''`mksubjdirs `''your_subject_name'''''
+. Import your data and create a subject data directory.  This is done '''once''' using the following command:
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-. 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`'''
+    '''`recon-all -i `''invol1''`  -i `''invol2''` -subjid `''your_subject_name'''''
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+    where ''invol1'' and ''invol2'' are paths to your input files.  You can use as many as necessary (i.e., '''-i ''invol3'' -i ''invol4''''') and they can be in any format that is accepted by mri_convert.  The command above will create an empty directory named ''your_subject_name'', except the mri/orig directory will contain files named 001.mgz and 002.mgz, which are your imported structurals.  Once your input files are imported, you do not need to use the -i flags again.
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-  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`'''
+. Run the first step of recon-all. See the ReconAllDevTable for individual steps that will be run during the whole process.
    '''`recon-all  -autorecon1 -subjid `''your_subject_name'''''
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-. Run the first step of recon-all. See the TroubleshootingReconTable for individual steps that will be run during the whole process.
    '''`recon-all -autorecon1 -subjid `''your_subject_name'''''

 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`'''
+. Check the talairach transform:
   '''`tkregister2 --mgz --s `''your_subject_name''` --fstal`'''
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-   * ["FsTutorial/Talairach"]
+   * [[FsTutorial/Talairach]]
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-. Check the skull strip:
   '''`tkmedit `''your_subject_name''` brain.mgz -aux T1.mgz`'''
+. Check the skull strip:
   '''`tkmedit `''your_subject_name''` brainmask.mgz -aux T1.mgz`'''
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-   * FsTutorial/SkullStripTutorial
+      After adding control points run the step [[OtherUsefulFlags|-autorecon2-cp]] (this will run -normalization, using control points, and everything else through the end of -autorecon2.)
   * FsTutorial/SkullStripFix
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 . After you have an accurate brain volume, run the next step of recon-all:
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-. 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`'''
+. Check the white and pial surfaces:
   '''`tkmedit `''your_subject_name''` wm.mgz rh.white -aux brainmask.mgz -aux-surface lh.white`'''
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-   * FsTutorial/FixingDefects
+   * FsTutorial/WhiteMatterEdits
      After editing the wm.mgz volume run the step [[OtherUsefulFlags|-autorecon2-wm]] (this will run -fill, using new wm.mgz volume, and everything else through the end of -autorecon2.)
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+      After editing the brainmask.mgz volume run the step [[OtherUsefulFlags|-autorecon2-pial]] (this will run -finalsurfs, using new brainmask.mgz volume, and everything else through the end of -autorecon2.)
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 . After you have accurate pial and white surfaces run the final step of recon-all: