Hello everyone,

I was trying out FS-FAST tutorial with my set of images (converted to NIFTI from AFNI BRIK format using 3dAFNItoNIFTI). However, I get this error 'nifti1Read(): unsupported slice timing pattern 5 in … '.

Looking at NIFTI.h, this value (#define NIFTI_SLICE_ALT_INC2 5) is added to cater for acquisition schemes in some siemens scanners (ours is siemens). Why doesn't Freesurfer like this?

I looked through the Freesurfer mailing list, but didn't quite find a solution yet. I am new to whole fMRI analysis, so apologies if I am missing something obvious.

Many thanks, Mariam.

Hi Doug,

Thank you for your reply. I was using AFNI's 3dAFNItoNIFTI program to convert BRIK to NIFTI. This writes out files in NIFTI-1.1 format. Freesurfer programs such as mri_info etc was not happy with the NIFTI files generated above. After reading your mail, I tried mri_convert. That works.

Mariam.

On 18 Jun 2013, at 07:42, Douglas Greve greve@nmr.mgh.harvard.edu wrote:

Hi Mariam, I don't know why it does not read this particular code. I can modify it when I get back from HBM and send you a new version of mri_convert. Or you might be able to change the way you convert from BRIK to use a different slice code. doug

On 6/17/13 4:13 PM, Mariam Sood wrote:

...

Hello everyone,

I was trying out FS-FAST tutorial with my set of images (converted to NIFTI from AFNI BRIK format using 3dAFNItoNIFTI). However, I get this error 'nifti1Read(): unsupported slice timing pattern 5 in … '.

Looking at NIFTI.h, this value (#define NIFTI_SLICE_ALT_INC2 5) is added to cater for acquisition schemes in some siemens scanners (ours is siemens). Why doesn't Freesurfer like this?

I looked through the Freesurfer mailing list, but didn't quite find a solution yet. I am new to whole fMRI analysis, so apologies if I am missing something obvious.

Many thanks, Mariam. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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