Please also consider that the T1, f.nii and ROI.ii.gz (obtained by label2vol) are nice overlapped. The brain.mni305.2mm.nii seem to be strange (see the image attached). In the sig.nii.gz the cluster are bad coregistered and some of those out are of the brain. Thanks Stefano
----Messaggio originale----
Da: stdp82@virgilio.it
Data: 12-feb-2016 0.23
A: "Freesurfer support list"freesurfer@nmr.mgh.harvard.edu
Ogg: [Freesurfer] R: Re: To use a ROI.label as seed in FS-FAST
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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