You should map the fmri volume to the surface with mri_vol2surf. Then run mri_segstats with --vox vertexno 0 0 and use the --avgwf output option. doug
YUMI MAEDA wrote:
when I want to get the timecourse from vertex number, what is the option name can I use?
YUMI
Yes, that is correct. You can have it produce one time course with --id
1
doug
YUMI MAEDA wrote:
Doug, thank you very much. I tried with --ctab-out my timecourse data and annot has different dimention and I got this
message.
ERROR: dimension mismatch between input volume and seg input 96 32 96 seg 119778 1 1 Then I tried this to get the same dimension, mri_label2vol --label ./ROI.label --temp ./filtered_func_data.nii --reg
reg.dat --fillthresh 0.5 --o ./ROI_func.mgz
mri_segstats --i ./filtered_func_data.nii --seg ROI_func.mgz --avgwf
output
I got the output which contains 2 columns. the second one seems to be
timecourese but I am not quite sure it is correct or not. and also I dont
know what is the first column. will you tell me about the output ? thank you very much. YUMI
You have specified two segmentations (an annotation and a segmentation). Just use one (probably the annot). There will be a column for each label in the annot. Use the --ctab-out to get a color table that indicates
which column belongs to which region.
doug YUMI MAEDA wrote:
HI, I am trying to get timecourse from each subject within a ROI with GUI as follows, in tksurfer GUI, Tools > timecourse > Write summary of marked vetices/label, I would like to do it command line, would you tell me what line I can
use?
I tried to use mri_segstats --i ./filtered_func_data.nii --subject subj1 --sum ./test_summary --avgwf test_output --annot subj1 aparc lh --seg ./testaseg-in-func.img the
output has 7 columns and does not seems to be timecourse and also it
is different from the one that I get when I use GUI as I described
above.
thank you very much. YUMI _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer