Hi Pieter,
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.
Best,
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
>
> [log in to unmask] tel: +32 (0)9 332 48 20
> http://gifmi.ugent.be fax: +32 (0)9 332 49 69
>
>
>
>
--
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
*http://www.restfmri.net/forum/yanchaogan*
http://scholar.google.com/citations?user=lJQ9B58AAAAJ&hl=en
