Hi Iwo,
can you send us the recon-all.log file (probably better to send it to the
freesurfer list)
Bruce
On Wed, 27 May 2009, Iwo Bohr wrote:
>
> That's true, I realized I should have run recon-all , so I did, but to my frustration the error message is still the same!
>
> Still no brainmask file!
>
> What can I do now?
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> Many thanks,
>
> Iwo
>
>
>
> Date: Wed, 27 May 2009 08:38:49 -0500
> From: [log in to unmask]
> Subject: Re: [FSL] brainmask.mgz - how to produce for Freeesurfer ?
> To: [log in to unmask]
>
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> That is on if the outputs of the default freesurfer analysis pipeline. Did you run recon-all --all yet?
>
> Peace,
>
> Matt.
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> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Iwo Bohr
> Sent: Wednesday, May 27, 2009 7:04 AM
> To: [log in to unmask]
> Subject: [FSL] brainmask.mgz - how to produce for Freeesurfer ?
>
> Dear FSL-Freesurfer experts,
>
> I would like to use Freesurfer to segment functional time series images.
> To do so, first I have to register example_func.nii to anatamical using routine:
>
> reg-feat2anat
>
> however I can't run it, since I don't have this mask file, the complain is as follows:
>
> FeatDir is 1_Left+.feat
> template volume is 1_Left+.feat/example_func.nii.gz
> ERROR: cannot find brainmask for test
>
> How can I produce this mask? I thought that following the tutorial on FLIRT will help me , but the mask produced by FLIRT:
>
> ------------------
> http://www.fmrib.ox.ac.uk/fslcourse/lectures/practicals/reg/index.html:
>
> Standard-space masking - a useful application
> Now let's use a saved FLIRT transform to mask out the ventricles, cerebellum and brain stem in example_func, using a crude standard-space mask which excludes those regions.
> The registration from example_func to the standard-space template has already been done and is saved as exfunc2std.mat. We want to take this matrix and transform a standard-space mask to the functional space.
> ---------------------
>
> The description above sounds like the relevant procedure, but did not change anything
>
> Can anybody please advice me on this matter?
>
>
> Iwo Bohr, PhD
> School of Computing Science
> Newcastle University
> UK
>
>
>
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