Hello, white matter hyperintensities are very easy to see and segment in T2 FLAIR MRI imaging in humans. T1 structural imaging similarly shows hypointensities in the white matter.

Does anyone know if there is some automatic or semi-automatic way to segment the hypointensities on T1 MRI images?

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Hi, you may like to have a look at this package:
https://github.com/NIF-au/w2mhs-itk

Hello 
Now I want to do the WM segmentation with SPM but I have and error and can not solve it. Did you have any suggestion for me?

Tnaks a lot 
Vania

Hi Vania,

I'll try to answer both of your posts. To address your last forum post (and maybe this one, too), it's not clear what you mean by "raw" vs. "processed" images. I'm not familiar with the OASIS dataset, but you should not be using raw DICOM images. SPM can only handle NIFTI (.nii) or image and header (.img / .hdr) file types. I use dcm2niix to convert DICOM files to NIFTI format but you can also use SPM's DICOM conversion tool (though it's slower than dcm2nii). 

Using SPM's segmentation tool should give you six new volumes. The second of those (the c2 image) should be your White Matter volume. This youtube video should be helpful to familiarize yourself with segmentation in SPM: https://www.youtube.com/watch?v=_SSzN9KL_qw

If this does not address the issue, and you're still getting an error message, it would be helpful if you could copy and paste the error from the matlab window into your next forum post. 

Good luck!

Hello Evan
Very very thanks for your time and response. Actually, I did what you told and with other images, I have results I think the problem is for my dataset and maybe need an extra setting in SPM. I have this error:
Failed 'Segment'
Error using sqrtm (line 35)
Expected input to be finite.
In file "C:\Program Files\MATLAB\R2017a\toolbox\matlab\matfun\sqrtm.m" (???), function "sqrtm" at line 35.
In file "C:\Users\PC4\Desktop\spm12-Copy\spm_preproc8.m" (v7172), function "spm_preproc8" at line 673.
In file "C:\Users\PC4\Desktop\spm12-Copy\spm_preproc_run.m" (v6365), function "run_job" at line 131.
In file "C:\Users\PC4\Desktop\spm12-Copy\spm_preproc_run.m" (v6365), function "spm_preproc_run" at line 41.
In file "C:\Users\PC4\Desktop\spm12-Copy\config\spm_cfg_preproc8.m" (v6952), function "spm_local_preproc_run" at line 450.

The following modules did not run:
Failed: Segment

I attach my dataset and if you have time it is really of your kind to guide me. 
Again thanks and wish you best
Vania