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Hello Jenna,
First, I think your problem arises when you use REST, not TOM :) Second,
I don't think that TOM routinely generates a brain mask at all. The
error you report from REST is that the dimensions of your brain mask do
not match those of your imaging data, which is either due to different
voxel sizes or because you analyzed native space data while supplying a
normalized mask. I would suggest you generate a brain mask from your
fMRI images you wish to analyze (using ImCalc on all images with
something like 'mean(X) > 0.2' or so, after setting the read images into
matrix flag to yes), which should solve your first issue. I am sure
there are options within REST to help you with that, but I am not that
familiar with it.
The second part of the problem you report is not necessarily due to the
difference between spm5 and spm8, but between unified segmentation
(which exists in spm5 and spm8) and new segment (only in spm8). The
former requires gm, wm, csf priors in single files, while the latter
requires a single nifti prior with several additional classes encoding
background tissue. Hence, if you want to generate a new segment prior,
you have to enter the additional background class images for each subject.
With regard to covariates, these do not have to be binary (does make
sense for gender, but does not make sense for age, for example).
I hope this helps,
Marko
J. Traynor wrote:
> Hello,
>
> I have created a custom matched-pairs mask using the SPM8 toolbox
> Template-O-Matic because of the uniqueness of my clinical sample.
> Following creating the template, I am using the REST tool in order to
> analyze resting state functional connectivity. However, when I go to run
> the analysis...I get this error:
> Error using rest_loadmask (line 64)
> Mask does not match.
> Mask size is 192 x 240 x 256, not same with required size 79 x95 x 68.
>
> I believe this is because, during the step 'create new template' in the
> TOM8 toolbox that requires you to specify the output as either "priors
> for SPM8 new segment 6 volume TPM file and T1" or "priors for SPM5
> unified segmentation", I am choosing SPM5....even though I am using
> SPM8. The reason for this is because when loading the mask into the REST
> program, you must load a ".img" template....which is not produced when I
> click on the "SPM8 new segment...." option, however a resulting .mat and
> .hdr/.img file for the template creation IS produced when I specify the
> priors as SPM5. So my questions is...
> a) has anyone run into this error and what did you do?
> b) how do I get the resulting .hdr/.img and .mat files to be produced
> when I use the SPM8 option? Thus far I only get a .gif animated file,
> and that is only if I ask for it....otherwise it seems as though there
> is no output for this option. In the TOM8 manual it says to save the
> resulting .mat file as the computer will disregard it when using this
> option....but how do I save the file and where can I find it?
>
> I also tried making sure all of my covariate vectors were in 0s and 1s
> (I found this change in the error code), and that did not work.
>
> Thank you so much in advance,
>
> Jenna
>
>
>
> --
> Jenna Traynor, B.A (Hons.), PhD Cand.
>
> Developmental Neuroscience Lab
> McMaster University
> phone: 905.525.9140 ext. 24784
> email: [log in to unmask] <mailto:[log in to unmask]>
> webpage:
> http://www.science.mcmaster.ca/psychology/devneuro/aboutus/aboutus.html
--
____________________________________________________
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/
____________________________________________________
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