There is a semi-automatic way to reduce the burden for reorienting the images in DPARSF (
www.restfmri.net), called reorient functional images interactively or reorient T1 images interactively.
With that module, you don't need to select the individual files manually, DPARSF just pop up the T1 images files subject by subject. In addition, you don't need to set 'right {mm}', 'forward {mm}' and 'up {mm}' values to reset the origin, but just click the where the origin you want instead.
Hope this information helps.
Chao-Gan
On Tue, Jan 29, 2013 at 5:57 AM, Pieter Vandemaele
<[log in to unmask]> wrote:
Thanks for the feedback.
The screenshots were taken with MRICRON.
This is the result with CheckReg in spm.
I did not check out all anatomicals, but it would be a huge burden
to adjust all subjects manually.
I normalised the same data with the Normalisation module and did
not have to reorient the images. Normalisation with the Segment
module fails.
Do you have suggestions to do this fast?
Thx
Pieter
Op 29/01/2013 11:38, Marko Wilke schreef:
Pieter,
I would expect that they are all looking into the wrong direction
:) but I suggest using spm to check that. If you first call up one
of the templates coming with spm, and then your image, they should
look similar with regard to their overall orientation. If not so,
you can use the pitch, roll, yaw fields to enter multiples (or
halves) of pi to reorient your image. Once you're happy with the
result, you can apply the transformation to all your images, using
"reorient images". This changes the header, so you may want to
make sure you have backups first.
Cheers,
Marko
Pieter Vandemaele wrote:
Dear SPM'ers,
I used the Segment module to segment and normalize anatomical
scans and
got strange results, see attachments.
Is this due to the origin localisation?
What is the easiest way to deal with this? I have 80 subjects so
a
(semi)automatic solution would be ideal.
Best
Pieter
--
Pieter
Vandemaele, MSc-Ing
GIfMI Site Manager
Ghent Institute for Functional and Metabolic Imaging
MR Department -1K12
Ghent University Hospital
De Pintelaan 185
9000 Ghent - BELGIUM
--
Chao-Gan YAN, Ph.D.
Research Scientist
The Nathan Kline Institute for Psychiatric Research, 140 Old Orangeburg Road, Orangeburg, NY 10962
Center for the Developing Brain, Child Mind Institute, 445 Park Avenue, New York, NY 10022
The Phyllis Green and Randolph Cowen Institute for Pediatric Neuroscience, New York University Child Study Center, New York, NY 10016
