Hi Ben,
I was able to reproduce the core dump. In my case, it was because a mismatch of color scheme between input annotation file and the color table loaded with the surface.
I suspect it might be the same issue for you too. But I’m not sure what the right action is to work around this.
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu>
On Behalf Of Benjamin Deck
Sent: Friday, June 10, 2022 11:47 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] mri_label2vol fill-ribbon segmentation fault
External Email - Use Caution
Hi there,
Having issues with the following command:
mri_label2vol --annot lh.yeo_2011.annot --temp /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/orig.mgz --hemi lh --fill-ribbon --identity --subject sub-DAEK --o lh.sub-DAEK_annot_nat.nii.gz
produces the following error:
Number of labels: 0
Annot File: lh.yeo_2011.annot
Template Volume: /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/orig.mgz
Outut Volume: lh.sub-DAEK_annot_nat.nii.gz
Registration File: (null)
Fill Threshold: 0
Label Vox Vol: 1
ProjType: (null)
ProjTypeId: 0
ProjStart: 0
ProjStop: 0
ProjDelta: 0.1
Subject: sub-DAEK
Hemi: lh
UseNewASeg2Vol: 0
DoLabelStatVol 0
LabelCodeOffset 0
setenv SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects
7.2.0
Template RAS-to-Vox: --------
-1.25000 -0.00000 -0.00000 160.00000;
-0.00000 -0.00000 -1.25000 160.00000;
-0.00000 1.25000 -0.00000 160.00000;
-0.00000 -0.00000 -0.00000 1.00000;
Template Voxel Volume: 0.512
nHits Thresh: 0
Using Identity Matrix
RegMat: --------
1.00000 0.00000 0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000;
0.00000 0.00000 1.00000 0.00000;
0.00000 0.00000 0.00000 1.00000;
Label RAS-to-Vox: --------
-1.25000 0.00000 0.00000 160.00000;
0.00000 0.00000 -1.25000 160.00000;
0.00000 1.25000 0.00000 160.00000;
0.00000 0.00000 0.00000 1.00000;
INFO: loading surface /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.white
nvertices = 253237
Reading thickness /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.thickness
Loading annotations from lh.yeo_2011.annot
annotidmax = 48
nlabels = 48
Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/ribbon.mgz
Mapping
Segmentation fault
But when I run the same command without fill-ribbon the process runs to completion.
Not sure if this is a memory issue or something else.
Ben
--
Benjamin L. Deck
Doctoral Student
Applied Cognitive and Brain Sciences
Department of Psychological and Brain Sciences
Drexel University
