open-discussion > shape analysis on freesurfer data
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Apr 3, 2017  07:04 AM | Qiao Jun Liew
shape analysis on freesurfer data
Hi everyone.

I can run SPHARM_Tutorial_Data_July2015 without any error and get the same result. When i try run the data that i segmentation manual from the aseg.mgz file,there is  not any error but i cant see anything when i open the file. The number of euler is 0. Any solution and suggestion?
Apr 5, 2017  11:04 AM | Beatriz Paniagua
RE: shape analysis on freesurfer data
Hi Quiao,

Do you see any output data in your Mesh/PostProcess folder?
Thank you,
Beatriz
Apr 6, 2017  12:04 AM | Qiao Jun Liew
RE: shape analysis on freesurfer data
Hi Beatriz,

Yes,there is output data in the folder,same like the output data when i run the tutorial. But when i open it, there is nothing to show. Is my input file problem? I using nifti format and the dimension is 256*256*256.
Apr 6, 2017  04:04 AM | Beatriz Paniagua
RE: shape analysis on freesurfer data
Hi Qiao,


Could you please send us an example of your dataset so we can diagnose/correct the problem?
Thank you so much,


Beatriz
Apr 6, 2017  09:04 AM | Qiao Jun Liew
RE: shape analysis on freesurfer data
Hi Beatriz,

This is one of the dataset that i segmented from aseg.mgz file.
Attachment: 6308_l_hippo.nii.gz
Apr 7, 2017  08:04 AM | Beatriz Paniagua
RE: shape analysis on freesurfer data
Hi Qiao,


We found a problem that we will solve in our new Shape Analysis Module release. In the meantime, you can save your data to nrrd using Slicer before running the module.
Please let us know if you need assistance with that task.


Best regards,
Beatriz
Apr 7, 2017  09:04 AM | Qiao Jun Liew
RE: shape analysis on freesurfer data
Thanks profusely for your help. So, by converting the nifti to nrrd format, will SPHARM-PDM accept this format for processing?
Apr 7, 2017  09:04 AM | Beatriz Paniagua
RE: shape analysis on freesurfer data
Yes. Please let us know if this is not the case.
Apr 7, 2017  11:04 AM | Beatriz Paniagua
RE: shape analysis on freesurfer data
Hi Qiao,

One of the SPHARM developers has pointed out that your nii file will work if you disable the rescale parameter in SegPostProcess (see attachment).
I hope this helps!


Beatriz
Attachment: 2017-04-07.png
Apr 7, 2017  01:04 PM | Qiao Jun Liew
RE: shape analysis on freesurfer data
Hi Beatriz,

It works perfectly!!!!!Thank you very much. You save my FYP . Really thanks a lot.