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Lilla,
It worked for the CC into the aseg.
How would I get the CC into the aparc+aseg?
Jim
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu>
On Behalf Of Zollei, Lilla,Ph.D.
Sent: Thursday, October 21, 2021 3:39 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Using only a aparc+aseg input file for TRACULA
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Jim,
You could run
set cmd = (mri_cc -aseg aseg.mgz -o aseg_CCseg.mgz $subj)
to get the CC lables.
Lilla
From:
freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Alexopoulos, Dimitrios <dimitriosalexopoulos@wustl.edu>
Sent: Thursday, October 21, 2021 2:59 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Using only a aparc+aseg input file for TRACULA
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Anastasia,
Upon closer inspection the aparc+aseg we have are analogous to the FS labeling, however, the CC is not segmented, it is simply labelled as cortical WM (labels
2/41). Will using Tracula even work at all or will it generate the other tracts but not include the CC minor/major tracts?
Jim
From:
freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu>
On Behalf Of Yendiki, Anastasia
Sent: Wednesday, October 20, 2021 2:12 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Using only a aparc+aseg input file for TRACULA
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Hi Jim - If the file was called $SUBJECTS_DIR/$subj/mri/aparc+aseg.mgz, included the same labels and followed the same lookup table as the OG aparc+aseg, this could work. Note
that, for the new TRACULA (in FS 7.2), we recommend also running the thalamic nuclei segmentation, as it helps with the accuracy of the tracts that terminate or neighbor the thalamus.
Anastasia.
From:
freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Alexopoulos, Dimitrios <dimitriosalexopoulos@wustl.edu>
Sent: Wednesday, October 20, 2021 2:54 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Using only a aparc+aseg input file for TRACULA
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Hi,
It was my understanding that TRACULA only uses the aparc+aseg segmentation from the standard structural output from FS 7.1.1., and specifically for the relative positions (left, right, anterior, etc.) of each tract with respect
to the segmentation labels in the aparc+aseg.
Is this correct?
How would we run trac-all if we only had an aprc+aseg from another pipeline that generates FS-compatible outputs?
For example, trac-all -preproc -bedp -path -c (where c = dmrirc config file).
Jim
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