Hi Anna
Where did you install FreeSurfer? That is where the env variable
FREESURFER_HOME should point. What does:
ls $FREESURFER_HOME
show you?
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Pusok, Anna
Sent: Thursday, February 17, 2022 6:40 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter
segmentation (7.1.1, 7.2.0)
External Email - Use Caution
Hi there,
Here's an issue that keeps coming up:
source $FREESURFER_HOME/SetUpFreeSurfer.sh
source: no such file or directory: /Applications/freesurfer/SetUpFreeSurfer.sh
Could you help with this?
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>>
Sent: Thursday, February 17, 2022 6:06 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter
segmentation (7.1.1, 7.2.0)
The edits you are making only change the initial surface; the surface placement
then refines the placement. Sometimes the surface placement can be quite
stubborn. If this is the case, the ?h.orig.nofix and ?h.orig will reflect your
edits (nofix exactly; ?h.orig to some extent). Also check the the
white.preaparc is where the problem starts.
When you say that v6 did better, do you mean on this same data or on different
data? The surface placement has not changed that much since v6.
On 2/14/2022 12:50 PM, Edan Daniel wrote:
External Email - Use Caution
We have been having issues with recreating the final surfaces after editing the
white matter segmentation, which used to work smoothly in version 6.
After running a subject through recon-all (version 7.1.1 *without* the parallel
flag) and then editing the white matter, we run the following command (w
v7.1.1):
recon-all -autorecon2-wm -autorecon3 -subjid ' freesurferfoldername ' -cc-crs '
num2str(corpus_point)
The ribbon file and surfaces do update *very slightly* but it's largely
ignoring our (sometimes large) edits. This pipeline worked well for us in
version 6- do you have any idea what might be going on?
Would love to hear your thoughts about this.
Many thanks!!
Edan, Braindevlab@Princeton
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