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It does not appear your attempt at running
recon-all was successful, as there should be many more files than that.
Peace,
Matt.
From: FSL - FMRIB's
Software Library [mailto:[log in to unmask]] On
Behalf Of Iwo Bohr
Sent: Wednesday, May 27, 2009 1:41
PM
To: [log in to unmask]
Subject: [FSL] FW: [FSL]
brainmask.mgz - how to produce for Freeesurfer ?
Sorry the following files were created while executing recon-all not
reg-feat2anat- this failed to execute
From: [log in to unmask]
To: [log in to unmask]
Subject: RE: [FSL] brainmask.mgz - how to produce for Freeesurfer ?
Date: Wed, 27 May 2009 18:33:01 +0000
These are the only new files created in
subject/test/mri
while trying to execute the reg-feat2anat command:
May 27 15:54 mri_nu_correct.mni.log
May 27 15:54 tmp.mri_nu_correct.mni.6289
May 27 15:54 orig.mgz
May 27 15:53 rawavg.mgz
What can you make up of it?
Does it matter here .feat files are located? Should they be in any specific
place?
Date: Wed, 27 May 2009 11:07:25
-0500
From: [log in to unmask]
Subject: Re: [FSL] brainmask.mgz - how to produce for Freeesurfer ?
To: [log in to unmask]
Can you find it in
$FreeSurferDir/subjects/$YourSubject/mri?
Peace,
Matt.
From: FSL - FMRIB's
Software Library [mailto:[log in to unmask]] On
Behalf Of Iwo Bohr
Sent: Wednesday, May 27, 2009
10:27 AM
To: [log in to unmask]
Subject: Re: [FSL] brainmask.mgz -
how to produce for Freeesurfer ?
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?
Many thanks,
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]
That is on if the outputs of the default
freesurfer analysis pipeline. Did you run recon-all --all yet?
Peace,
Matt.
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?
School of Computing Science
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