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Ok thanks. I need to extract the mean signal from the regions contained in this nifti file. I suppose I need first to resample it in functional space and then use mri_segstats, but I'm not sure which is the right way to do it. Any suggestion? 



On Wed, Dec 23, 2020, 19:05 Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> wrote:
The argument to the --label flag should be a freesurfer label file, this is a text file not an nii.gz file.

On 12/21/2020 10:52 AM, Francesca Strappini wrote:

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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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                                                                                                                                                          �s��9� �A�d��A��e��A/�;����:���Lr0�y��<��d�s�QѪ���^�Ou����̂]��
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:

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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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--
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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