Thank you!

I run mri_label2vol but I got this error.

mri_label2vol --label D99_atlas_in_NMT_v2.0_asym_fh.nii.gz --temp /usr/local/freesurfer/fsfast/Monkeys/MonkeyCassis-FF-event-sm03-AVGmonkey/bold/template.nii.gz --reg registerNMT2toCassis.dat --fillthresh .3 --proj frac 0 1 .1 --subject MonkeyCassis --hemi lh --o D99_atlas_in_NMT_v2.0_asym_fh_Cassis_lh.nii.gz

Number of labels: 1
D99_atlas_in_NMT_v2.0_asym_fh.nii.gz
Annot File: (null)
Template Volume: /usr/local/freesurfer/fsfast/Monkeys/MonkeyCassis-FF-event-sm03-AVGmonkey/bold/template.nii.gz
Outut Volume: D99_atlas_in_NMT_v2.0_asym_fh_Cassis_lh.nii.gz
Registration File: registerNMT2toCassis.dat
Fill Threshold: 0.3
Label Vox Vol: 1
ProjType: frac
ProjTypeId: 2
ProjStart: 0
ProjStop: 1
ProjDelta: 0.1
Subject: MonkeyCassis
Hemi: lh
UseNewASeg2Vol: 0
DoLabelStatVol 0
LabelCodeOffset 0
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
$Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $
Template RAS-to-Vox: --------
-0.49612 -0.00000 -0.00000 32.00000;
-0.00000 -0.00000 -0.49612 32.00000;
-0.00000 0.50000 -0.00000 10.00000;
-0.00000 -0.00000 -0.00000 1.00000;
Template Voxel Volume: 8.12549
nHits Thresh: 2.43765
Loading registration from registerNMT2toCassis.dat
RegMat: --------
-0.99904 -0.03839 0.02093 -1.00375;
0.02331 -0.06274 0.99776 -29.26276;
0.03699 -0.99729 -0.06358 -8.60775;
0.00000 0.00000 0.00000 1.00000;
Label RAS-to-Vox: --------
0.49565 0.01905 -0.01038 32.49799;
-0.01835 0.49478 0.03154 36.27051;
0.01166 -0.03137 0.49888 -4.63138;
0.00000 0.00000 0.00000 1.00000;
INFO: loading surface /usr/local/freesurfer/subjects/MonkeyCassis/surf/lh.white
nvertices = 16975
Reading thickness /usr/local/freesurfer/subjects/MonkeyCassis/surf/lh.thickness
nlabels = 1
Allocating Hit Volume (81920) voxels
Loading D99_atlas_in_NMT_v2.0_asym_fh.nii.gz

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mri_label2vol: could not scan # of lines from label file
ERROR reading D99_atlas_in_NMT_v2.0_asym_fh.nii.gz

Il giorno lun 30 nov 2020 alle ore 00:03 Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> ha scritto:

Use mri_label2vol to map the segmentation into the fMRI space, then use mri_segstats using the --avgwf option to get time courses. Run it with --help to get examples

On 11/26/2020 9:16 AM, Francesca Strappini wrote:
External Email - Use Caution

Dear FreeSurfer experts,

I'm trying to use the monkey atlas D99. First, I registered the segmentation atlas to the monkey anatomy through bbregister. Now, I need to resample the segmentation to the functional data and extract the mean value from each functional run using the ROIs contained in the segmentation as masks. I suppose I should mri_segstats but I'm not sure how. Any suggestion?

Thank you

Francesca

--

Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail: francesca.strappini@weizmann.ac.il
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