Hi Stefano, sorry for the delay, I was traveling. It sounds like you just need to run fcseed-config and specify -seg ROI_MASK.mgz and -segid 1 (assuming your ROI_MASK is in $SUBJECTS_DIR/subject/mri). If the mask is in the orig.mgz space, then everything should work ok, but you can look at it with
tkmedit -f orig.mgz -aux ROI_MASK.mgz You can also run mri_label2vol --seg $SUBJECTS_DIR/subject/mri/ROI_MASK.mgz --reg register.dof6.dat --temp template.nii.gz --fillthresh 0.5 --o func.ROI_MASK.nii where template.nii.gz and register.dof6.dat are in the functional run folder doug On 06/12/2015 04:39 PM, std...@virgilio.it wrote: > Hi list, > I working on the combination of MRS and FS-FAST analysis. > I have extracted the grey matter within voxel (I will call it > "ROI_MASK") by using FSL tools and now it is in the same space of > orig.mgz (the roi mask is perfectly overlapped on orig.nii.gz when I > use fslview). > > I'd like to import it to FS for performing seed-based FS-FAST > functional connectivity. > The seed should the ROI MASK (GM within voxel). > > I know that the FSL and FS operate in different space and orientation. > I think to have resolved the problem of different space by using > orig.nii.gz to create ROI mask by FSL. > However, I'm strongly worried for orientation issues. > I have read the guidelines in FSL and FS sites, but I'm quite confused. > In detail, I'd like to ask whether I should use "mri_cor2label" to > transform ROI mask created by FSL to label. > > Furthmore, I'd like to be sure of the position of the ROI. How can I > visualize it to be sure that the seed of my FS-FAST analysis is > effectively the my ROI_MASK? > > I hope in your help. > > Thanks in advanced. > > > Stefano > > > _______________________________________________ > 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
