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Dear Freesurfer team, I am a user of freesurfer. The tool mri_info provides me useful information from nifti files. As part of my project, I am using VTK to programmatically extract information like direction matrix, size, origin etc from a nifti file. However, I am unable to extract --cras information from a nifti file. Could you please throw some light on how I can extract the CRAS values from a NIFTI file using matlab or vtk or itk ot nibabel? If the CRAS values are computed, I would like to know how they are computed. Basically, I am trying to understand how I can get the CRAS values without using mri_info tool. Thanks in advance!
Regards, Sherin Sugathan
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They are computed from the s-form/q-form in the NIFTI header. You can see how it's done in the FreeSurfer source code, which is available on github here: https://github.com/freesurfer/freesurfer
It won't be done in 3 minutes, but I did it in R and it's doable.
Tim
On June 25, 2020 at 12:22 AM Sherin Sugathan Sherin.Sugathan@uib.no wrote:
External Email - Use CautionDear Freesurfer team, I am a user of freesurfer. The tool mri_info provides me useful information from nifti files. As part of my project, I am using VTK to programmatically extract information like direction matrix, size, origin etc from a nifti file. However, I am unable to extract --cras information from a nifti file. Could you please throw some light on how I can extract the CRAS values from a NIFTI file using matlab or vtk or itk ot nibabel? If the CRAS values are computed, I would like to know how they are computed. Basically, I am trying to understand how I can get the CRAS values without using mri_info tool. Thanks in advance!
Regards, Sherin Sugathan
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Sherin Sugathan -
Tim Schäfer