Dear Tim and Matt,
thanks for your replies.
I did check the headers myself with fslhd and yes, there are oblique sforms.
I think I'll first try out one of Tim suggestions, i.e. faking the
header sforms to be plumb and then applying an equivalent transform to
the surfaces.
Best,
Irene
Timothy Coalson wrote:
To dump the header info, there is fslhd from fsl, or wb_command
-nifti-information (part of connectome workbench), or 3dinfo (from
afni). caret5 is allergic to obliques, and may not have a utility to
tell you about them.
wb_command can handle oblique volumes, so if you have a suitable
volume space to resample them into (or create one with caret_command
-volume-create), you can resample the T1 and T2, and then use those.
Alternatively, you could fake the header sforms to be plumb
(fsledithd?), apply an equivalent transform to the surfaces, and use
those. Or, you could do the equivalent of the myelin mapping method
using wb_command operations, since it doesn't object to oblique volumes.
Tim
On Tue, Apr 30, 2013 at 10:16 AM, Irene Altarelli
<[email protected] <mailto:[email protected]>> wrote:
Dear Caret experts,
I'd like to use the myelin mapping processing stream. I have processed
my T1 scans with Freesurfer 5.0 some time ago, finely correcting the
segmentation for a number of subjects (these are children).
>From what I have read from the documentation it appears that oblique
s/qforms might be creating some problems. I am afraid that I have them
in my already processed T1s, given the output of mri_info.
I also got two versions of the T2 sequence from the scanner, one
apparently being somewhat filtered.
May I ask you to have a look at these images and their headers and
give
me some advice on how to proceed? I can upload them wherever you think
is easy to access.
Thank you very much in advance.
Best,
Irene
--
Irene Altarelli, PhD student
Laboratoire de Sciences Cognitives et Psycholinguistique
Ecole Normale Supérieure
29, rue d'Ulm
75230 Paris Cedex 05
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