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Statistical NonParametric Mapping, development version
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Handling .gii files #24

Open IndrajeetPatil opened 8 years ago

IndrajeetPatil commented 8 years ago

Hi,

I am currently working with cortical thickness data and want to compare two groups with highly unequal sample sizes. To protect against false positives, I wanted to carry put non-parametric tests using SnPM13. But I realized that it currently doesn't accept GIfTI files.

Will future release be able to handle these images? Is this something that you are thinking of including?

Thanks, Indrajeet

nicholst commented 8 years ago

SnPM makes use of the file I/O tools of SPM. If SPM can support GIFTI, I don't see why SnPM couldn't. Have you tried your analysis in SPM? Does it work OK?

IndrajeetPatil commented 8 years ago

Yes, that's why it's surprising!

Analysis worked with SPM, but when I selected the .gii files to enter into SnPM, it doesn't accept any of the files: capture

nicholst commented 8 years ago

Ah... yes, we do ask SPM just for 'image' file types, and not {'image','mesh'} file types (which would include GIFTI). But, from just a quick look at the corresponding SPM code (spm_spm.m) there are many many changes that would be required to facilitate reading and writing surfaces.

In the mean time, may I suggest you look at PALM? http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM - Permutation Analysis of Linear Models, a tool developed by a student of mine, @andersonwinkler. It is based entirely in Matlab/Octave, and can read meshes. It will take a little getting used to (it is entirely command line driven) but it is very powerful and should be able to do what you need to do.

IndrajeetPatil commented 8 years ago

Ah! Okay, thanks a lot for the reference! I'll download it and figure out how to carry out the needed analysis.

IndrajeetPatil commented 7 years ago

Hi, Couple of quick follow-up questions:

  1. Is there any possibility that the next release of SnPM will be able to handle the .gii images? Having exclusively worked with SPM thus far, I found it difficult to get around PALM and finally gave up. It'll be great if I can do this with SPM.
  2. Also, is there a planned extension of SnPM to include multiple regression models?

Thanks!

nicholst commented 7 years ago

Hi,

I'm afraid no update on .gii reading... still not likely soon.

As for multiple regression, look at "Simple Regression", where you can then add nuisance regressors, giving you the same functionality, right?

IndrajeetPatil commented 7 years ago

Ah, right, that makes sense. I'll add them to nuisance regressors.

Never mind about gifti reading then, will explore some other alternatives with CAT12.

Thanks!

On Mon, Mar 27, 2017 at 4:24 AM, Thomas Nichols notifications@github.com wrote:

Hi,

I'm afraid no update on .gii reading... still not likely soon.

As for multiple regression, look at "Simple Regression", where you can then add nuisance regressors, giving you the same functionality, right?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/nicholst/SnPM-devel/issues/24#issuecomment-289386110, or mute the thread https://github.com/notifications/unsubscribe-auth/AKzjlQnx1y65T4uO8Fmq6U_AcagoBM1wks5rp3I8gaJpZM4Jq-6j .