you can change formats with mri_convert:
mri_convert vol.nii.gz vol.mgz
but you shouldn't need to - all our tools will read nifti just fine. Doug's
question was whether your mask was in the right coordinates, regardless of
whether it was in mgz or nifti.
cheers
Bruce
On Sun, 12 Jul 2015,
std...@virgilio.it wrote:
Thank you very much.My mask is in .nii.gz. How can I transform it in .mgz?
Should I do it?
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
>
>
> _______________________________________________
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> 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
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www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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