Print

Print
Hi Marko,

My colleague and I downloaded the TOM8 toolbox as you suggested, and installed it in our spm8/Toolbox folder. However, we have some questions about this as the instructions aren't fully clear to us.

I assume that we should perform 2 steps.
1. Estimate Regression Parameters
2. Create new template

When we do step1, it is asking for GM images. Are these the GM images from the NIH dataset? We aren't able to find it in the website. Could you please point us in the right direction?

In the second step, I assume that we should use the TOM8.mat file generated from the first step and then feed into it, the age and gender information from our dataset. Is this the right procedure?

We are having trouble executing this, so we'd appreciate any input you might have. Thank you.
'Sincerely,
- Ananth

On Thu, Dec 18, 2014 at 2:07 AM, Marko Wilke <[log in to unmask]> wrote:
Hi Ananth,

We are doing a study on adolescent females, and we need to install the
adolescent template to SPM. My colleague and I settled on using the
following:

 CCHMC2*_old*
(66 children, aged 13-18.8)

(from https://irc.cchmc.org/software/pedbrain/downloads.php)

thanks for choosing a template from our collection :) However, I would advise you to move on from that one and use the TOM8-toolbox instead. It is much more recent and will generate a much better output, to be used as priors in the segmentation routines (not DARTEL, though). You will find it on the same webpage. When downloading, don't forget to also download the regression parameters from the NIH dataset.

What is the difference between the original apriori directory and the
original tpm directory? I know during regular segmentation, spm8 uses
files within the spm8/tpm directory. However, the installation
instructions don't cover changing anything within the spm8/tpm directory.

 The instructions were written before spm8 was published :) We really should make this clearer but as another version is already under development, I am kind of hesitant to give it a big makeover right now (and no, that new version is not yet ready for deployment :)

Will hdr/img images I downloaded from the above mentioned link work with
the .nii files in the spm directory?

 No, the segmentation routine expects priors in another format, which, however, will be generated by the TOM toolbox.

Cheers,
Marko
--
____________________________________________________
PD Dr. med. Marko Wilke
 Facharzt für Kinder- und Jugendmedizin
 Leiter, Experimentelle Pädiatrische Neurobildgebung
 Universitäts-Kinderklinik
 Abt. III (Neuropädiatrie)

Marko Wilke, MD, PhD
 Pediatrician
 Head, Experimental Pediatric Neuroimaging
 University Children's Hospital
 Dept. III (Pediatric Neurology)

Hoppe-Seyler-Str. 1
 D - 72076 Tübingen, Germany
 Tel. +49 7071 29-83416
 Fax  +49 7071 29-5473
 [log in to unmask]de

 http://www.medizin.uni-tuebingen.de/kinder/epn/
____________________________________________________