On 07/20/2015 02:10 AM, std...@virgilio.it wrote: > Hi list, > > in the previous mail you have suggested to run fcseed-config and > specify -seg ROI_MASK.mgz and -segid 1 (assuming my ROI_MASK is in > $SUBJECTS_DIR/subject/mri). > I have two question please. > A- my mask is on vmPFC, thus it include the both hemispheres. Should I > divide it in right and left? If yes, how can I do? You do not need to, just specify the appropriate index value. If they were divided between lh and rh and you wanted to merge them, you would just list the lh and rh indices. > B- I have difficulties to run the fcseed-conf command: what do you mean by "difficulties"?
> fcseed-config -segid 1 -seg ROI_MASK. -fsd rest -mean -cfg > mean.ROI_MASK.config > fcseed-sess -s SessXXX -cfg mean.ROI_MASK.config > Is these command lines corrected? > > Thanks, > > > Stefano > > ----Messaggio originale---- > Da: std...@virgilio.it > Data: 13-lug-2015 10.16 > A: <freesurfer@nmr.mgh.harvard.edu> > Ogg: [Freesurfer] R: Re: Import mask from FSL to FS for performing > seed-based FS-FAST functional connectivity > > Hi list, > > When I use tkmedit the overlap between orig and ROI_MASK.nii.gz seem > to correspond. However, when I added the ROI_MASK.nii.gz, the orig is > vanished, and is remained the ROI_MASK in correct position (and in > white) and around all black. My concern is the correct binarization of > ROI_MASK which it seem correct when I use fslview. > > fslview orig.nii.gz ROI_MASK.nii.gz produce perfect outputs. > > > > After > mri_label2vol --seg $SUBJECTS_DIR/ROI_MASK.nii.gz --reg > $FUNCTIONAL_DATA/Sess102/rest/001/register.dof6.dat --temp > $FUNCTIONAL_DATA/Sess102/rest/001/template.nii.gz --fillthresh 0.5 --o > func.vmPFC_MASK.nii > > The func.vmPFC_MASK.nii (344MB) seem to be empty when I open it with > tkmedit and too big (a red bar which cover the whole) when I use fslview. > With MRIcron, is screen is irregularly divided in half in black and white. > > Which should be the advised folder for func.vmPFC_MASK.nii? > > > Thank you very much > > > Stefano > > > ----Messaggio originale---- > Da: gr...@nmr.mgh.harvard.edu > Data: 30-giu-2015 0.36 > A: <freesurfer@nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] Import mask from FSL to FS for performing > seed-based FS-FAST functional connectivity > > 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. > > > > > > > > _______________________________________________ > 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
