Differences between revisions 21 and 31 (spanning 10 versions)

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Although the reconstruction process is broken down into three different stages, this workflow suggests the user to run all these steps at once before beginning to inspect the data. This allows the user to see the final complete output before deciding on any interventions. Any manual intervention needed can be all done at once (with the exception of the talairach and the skullstrip) which can save both time and use of computer power. See the ReconAllDevTable for a list of all the steps associated with each recon stage, or ReconAllBlockDiagram for a different presentation, and OtherUsefulFlags for a list of other flags that you can use with recon-all.

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 all the steps of recon-all. See the ReconAllDevTable for individual steps that will be run during the whole process.
- recon-all -all -subjid your_subject_name
After your subject finishes running, do the following to make sure the recon was successful.
Check the talairach transform:
- tkregister2 --mgz --s your_subject_name --fstal
- For instructions 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 steps -autorecon-cp (this will run -normalization, using control points, and everything else through the end of -autorecon2) and -autorecon3 (this will update all your stat tables with the new changes).
  - FsTutorial/SkullStripFix
    - After adjusting the skullstrip, run the steps -autorecon2 and -autorecon3.
Check the white and pial surfaces:
- tkmedit your_subject_name brainmask.mgz -aux wm.mgz -surfs
- For instructions on editing the final surfaces, refer to:
  - FsTutorial/WhiteMatterEdits
    - After editing the wm.mgz volume run the steps -autorecon2-wm (this will run -fill, using new wm.mgz volume, and everything else through the end of -autorecon2) and -autorecon3.
  - FsTutorial/PialEdits
    - After editing the brainmask.mgz volume to adjust the pial surface, run the steps -autorecon-pial (this will run -finalsurfs, using new brainmask.mgz volume, and everything else through the end of -autorecon3.)
  - FsTutorial/FinalSurfEx
Next, check the segmentations:
- tkmedit your_subject_name brainmask.mgz -surfs -aseg
- For instructions on editing the aseg, refer to:
  - TkMeditGuide/TkMeditWorkingWithData/TkMeditSegmentations
    - After editing the wm.mgz volume run the following steps: -normalization -maskbfs -segmentation -autorecon2-wm -autorecon3.

-  ⇤ ← Revision 21 as of 2011-07-05 15:40:14 → 
  Size: 3526
  Editor: KhoaNguyen
  Comment:
+   ← Revision 31 as of 2011-07-05 16:30:00 → ⇥
  Size: 3955
  Editor: KhoaNguyen
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
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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.
+Although the reconstruction process is broken down into three different stages, this workflow suggests the user to run all these steps at once before beginning to inspect the data. This allows the user to see the final complete output before deciding on any interventions. Any manual intervention needed can be all done at once (with the exception of the talairach and the skullstrip) which can save both time and use of computer power. See the ReconAllDevTable for a list of all the steps associated with each recon stage, or ReconAllBlockDiagram for a different presentation, and OtherUsefulFlags for a list of other flags that you can use with recon-all.
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+Line 23:
-After your subject finishes running, do the following to make sure the recon was successful.
+   After your subject finishes running, do the following to make sure the recon was successful.
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-  For intructions on how to fix bad talairachs tranforms, refer to:
+  For instructions on how to fix bad talairachs tranforms, refer to:
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-      After adding control points run the step [[OtherUsefulFlags|-autorecon-cp]] (this will run -normalization, using control points, and everything else through the end of -autorecon2.)
+      After adding control points run the steps [[OtherUsefulFlags|-autorecon-cp]] (this will run -normalization, using control points, and everything else through the end of -autorecon2) and -autorecon3 (this will update all your stat tables with the new changes).
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+      After adjusting the skullstrip, run the steps -autorecon2 and -autorecon3.
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+Line 41:
-. 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''` brainmask.mgz -aux wm.mgz -surfs`'''
-Line 43:
+Line 44:
-. 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:
+  For instructions on editing the final surfaces, refer to:
-Line 48:
+Line 46:
-      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.)
+      After editing the wm.mgz volume run the steps [[OtherUsefulFlags|-autorecon2-wm]] (this will run -fill, using new wm.mgz volume, and everything else through the end of -autorecon2) and -autorecon3.
-Line 50:
+Line 48:
-      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.)
+      After editing the brainmask.mgz volume to adjust the pial surface, run the steps [[OtherUsefulFlags|-autorecon-pial]] (this will run -finalsurfs, using new brainmask.mgz volume, and everything else through the end of -autorecon3.)
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+Line 51:
-. After you have accurate pial and white surfaces run the final step of recon-all:
     '''`recon-all -autorecon3 -subjid `''your_subject_name'''''
+. Next, check the segmentations:
   '''`tkmedit `''your_subject_name''` brainmask.mgz -surfs -aseg`'''

  For instructions on editing the aseg, refer to:
   * TkMeditGuide/TkMeditWorkingWithData/TkMeditSegmentations
      After editing the wm.mgz volume run the following steps: -normalization -maskbfs -segmentation -autorecon2-wm -autorecon3.