I have used:mri_label2vol --label RIGHT_ROI.label --temp subj/rest/001/f.nii --reg subj/rest/001/register.dof6.dat --fillthresh .5 --o RIGHT_ROI.nii.gz When I open with freeview the f.nii.gz and the RIGHT_ROI they are fine overlapped.But, after FS-FAST the sig.ii.gz seem to be wrong, probably bad reoriented, especially I have noted this on subcortical connectivity (MNI2mm). Thanks
Stefano
----Messaggio originale----
Da: Douglas Greve greve@nmr.mgh.harvard.edu
Data: 11-feb-2016 4.48
A: freesurfer@nmr.mgh.harvard.edu
Ogg: Re: [Freesurfer] To use a ROI.label as seed in FS-FAST
I may have gotten the exact form of the flag wrong. When it says an option is not known, you should try running the command with --help to see if something similar is there. In this way, you might be able to figure it out for yourself rather than have to wait a day or so for us to respond.
doug
On 2/10/16 4:20 PM, stdp82@virgilio.it wrote:
If I use:
mri_label2vol --label ramgseed_rhsurf.label --temp $SUBJECTS_DIR/subj/mri/orig.mgz --identity --subject fsaverage --hemi rh --o RIGHT_ROI.nii.gz --fill-ribbon ERROR: Option --fill-ribbon unknown
----Messaggio originale----
Da: stdp82@virgilio.it
Data: 8-feb-2016 20.35
A: "Freesurfer support list"freesurfer@nmr.mgh.harvard.edu
Ogg: [Freesurfer] R: Re: To use a ROI.label as seed in FS-FAST
Thanks. I have down a right ad left ROI on the surface. Next, I have run:
mri_label2vol --label ramgseed_rhsurf.label --temp $SUBJECTS_DIR/fsaverage/mri/orig.mgz --identity --subject fsaverage --hemi rh --o RIGHT_ROI.nii.gz
mri_label2vol --label ramgseed_lhsurf.label --temp $SUBJECTS_DIR/fsaverage/mri/orig.mgz --identity --subject fsaverage --hemi rh --o LEFT_ROI.nii.gz
mri_convert RIGHT_ROI.nii.gz RIGHT_ROI.mgz mri_convert LEFT_ROI.nii.gz LEFT_ROI.mgz
fcseed-config -segid 1 -seg RIGHT_ROI.mgz -fsd rest -mean -cfg RIGHT_ROI.config fcseed-config -segid 1 -seg LEFT_ROI.mgz -fsd rest -mean -cfg LEFT_ROI.config
fcseed-sess -s subj1_FS -cfg RIGHT_ROI.config fcseed-sess -s subj1_FS -cfg LEFT_ROI.config
but during fcseed-sess this error occurs:
$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --i /Applications/freesurfer/subjects/fMRI/subj1/rest/001/fmcpr.nii.gz --seg /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/mask.nii.gz --id 1 --sum /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/junk.sum --avgwfvol /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/avgwf.mgh sysname Darwin hostname iMac-di-Stefano.local machine x86_64 user Stefano UseRobust 0 Loading /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/mask.nii.gz Loading /Applications/freesurfer/subjects/fMRI/subj1/rest/001/fmcpr.nii.gz Voxel Volume is 64.5752 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 0 0.000 MRIalloc(0, 1, 1): bad parm
Reporting on 0 segmentations Computing spatial average of each frame
Writing to /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/avgwf.mgh Segmentation fault
----Messaggio originale----
Da: Douglas Greve greve@nmr.mgh.harvard.edu
Data: 8-feb-2016 4.38
A: freesurfer@nmr.mgh.harvard.edu
Ogg: Re: [Freesurfer] To use a ROI.label as seed in FS-FAST
Use mri_label2vol to convert the label into a volume in the anatomical space and store it in $SUBJECTS_DIR/subject/mri. Make sure to use --fill-ribbon if the label is surface-based. When running fcseed-config, specify the volume with the -seg option and use -segid 1
On 2/7/16 3:16 PM, stdp82@virgilio.it wrote:
Hi list,
I would like to use as seed in FS-FAST a ROI.label which I have drawn on a cluster in tksurfer. How can I do it? Should I use mri_label2vol?
Thanks.
Stefano
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