Dear Matt
I removed the sform from the t1.nii, before mri_convert makes it
001.mgz, so at the start of Freesurfer (sform_code='0').
But do I understand correctly from your mail that both sform and qform
should be removed? (i.e., sform_code='0' and qform_code='0' in the
header). If so then that might be the reason.
Best,
Ruthger
Le 2014-03-28 18:00, [email protected] a écrit :
Send caret-users mailing list submissions to
[email protected]
To subscribe or unsubscribe via the World Wide Web, visit
http://brainvis.wustl.edu/mailman/listinfo/caret-users
or, via email, send a message with subject or body 'help' to
[email protected]
You can reach the person managing the list at
[email protected]
When replying, please edit your Subject line so it is more specific
than "Re: Contents of caret-users digest..."
Today's Topics:
1. Re: Surface-Volume registration (Matt Glasser)
----------------------------------------------------------------------
Message: 1
Date: Fri, 28 Mar 2014 09:58:32 -0500
From: Matt Glasser <[email protected]>
To: "Caret, SureFit, and SuMS software users"
<[email protected]>
Subject: Re: [caret-users] Surface-Volume registration
Message-ID: <cf5af822.c414e%[email protected]>
Content-Type: text/plain; charset="US-ASCII"
Did you remove the sform and qform at the beginning of the process
(i.e.
before FreeSurfer)?
Peace,
Matt.
On 3/28/14, 9:04 AM, "Righart, Ruthger" <[email protected]>
wrote:
Dear Caret experts,
I am working on myelin mapping but encounter errors in surface-volume
registration, as previously reported in this list.
I have removed oblique sforms from the t1.nii and t2.nii files
(sform_code='0' and qform='1', the new headers have equal matrices
for s
and q).
I have the impression that the first error occurs after the command:
applywarp --interp=spline -i OrigT2w.nii.gz -r T1w.nii.gz
--premat=T2w2T1wbb.mat -o T2w2T1w_translated.nii.gz
Please find attached an fslview for the translated and non-translated
images. The translated image is not centered and from the
non-translated
images a piece of the left hemisphere is cut-off (I wondered if this
has
anything to do with the coordinate space, Scanner Anat(1) or Aligned
Anat(2) in the headers?). I would welcome your suggestions to solve
this
problem. I am working with Caret v5.65 on a Linux machine. Thank you
very much in advance!
Ruthger_______________________________________________
caret-users mailing list
[email protected]
http://brainvis.wustl.edu/mailman/listinfo/caret-users
------------------------------
_______________________________________________
caret-users mailing list
[email protected]
http://brainvis.wustl.edu/mailman/listinfo/caret-users
End of caret-users Digest, Vol 124, Issue 15
********************************************
_______________________________________________
caret-users mailing list
[email protected]
http://brainvis.wustl.edu/mailman/listinfo/caret-users
