Giuseppe,
Is it possible that your FreeSurfer created ROIs were not saved as
NIFTI's, but rather as old Analyze format, which assumed a particular
orientation or which code the orientation in an associated .mat file?
cheers,
-MH
On Thu, 2012-05-31 at 04:05 +0000, Christine Zakrzewski wrote:
> Sorry that i cannot provide any solutions from this description. Just
> wanted to say good luck--may be a bitch to fix!!
> One point you could bear in mind is that the information in
> orientation field of your structural, t1 (nifti?) header provides the
> template for the information contained in the header of your ROI.
> Insure that everything has gone as it should in preprocessing
> sequence, and check orientation field of ROI header--fslhd.
> Christine
>
>
> > Date: Wed, 30 May 2012 17:30:35 +0100
> > From: [log in to unmask]
> > Subject: [FSL] Fslswapdim problems for the ROIs created with
> freesurfer
> > To: [log in to unmask]
> >
> > Hi Experts,
> > i have some problems in reorienting the ROIs that i have created
> with freesurfer using fslswapdim. I did not have any problems in
> reorienting the T1 of my subject but when i tried to use the same
> sequence that i used for the T1 (e.g LR PA IS) the ROIs did never
> change in the right way. I have tried every possible combination and
> it did not seem to work, the LPFC for example it was always out of
> place.
> > I don't know if i was completely clear but any suggestions would be
> very appreciated.
> > Thanks a lot,
> > Giuseppe
>
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