Ananth,
> 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.
Yes, I get that a lot :)
> I assume that we should perform 2 steps.
> 1. Estimate Regression Parameters
> 2. Create new template
Yes (and no). These are the two steps to perform, but you do not need to
do both of them yourselves.
> 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?
Sure: on the website you downloaded the toolbox from, there is also a
download of the already estimated regression parameters from the NIH
dataset. We decided to make this an extra download since it is several
hundred MB and some people may not need it.
> 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?
Yes. After you downloaded the nih regression parameters (including the
TOM8.mat in there), you can select this and enter the values you want to
enter. These will need to be within the range of the original data.
Hope this helps,
Marko
PS: Aujourd'hui, je suis Charlie.
> On Thu, Dec 18, 2014 at 2:07 AM, Marko Wilke
> <[log in to unmask]
> <mailto:[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
> <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 <tel:%2B49%207071%2029-83416>
> Fax +49 7071 29-5473 <tel:%2B49%207071%2029-5473>
> [log in to unmask]
> <mailto:[log in to unmask]>
>
> http://www.medizin.uni-__tuebingen.de/kinder/epn/
> <http://www.medizin.uni-tuebingen.de/kinder/epn/>
> ______________________________________________________
>
>
--
____________________________________________________
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]
http://www.medizin.uni-tuebingen.de/kinder/epn/
____________________________________________________
|