Hi Freesurfer People,

The aim is get ROI masks for my functional images and to achieve that for each of the subjects in my data, I am:

1. Running freesurfer for segmentation of structural scan,

2. Running feat analysis that would give me transformation matrices including structural2functional and then,

3. I am transforming my masks from step 1 to functional space using flirt.

The first step requires me to use the actual structural image and the second step won't produce good results if I don't do brain extraction on the structural image.

Now the problem is, for structural image of one of the subjects, I cannot get good brain extraction unless I use fslroi to crop the neck out first. And if I do that, the transformation matrices that I get using resulting bet image won't be usable with the freesurfer masks that I have obtained using the uncropped structural image.

And if I try to use fslroi-cropped-structural-image with freesurfer, the nii2mnc command would produce this error:

$ nii2mnc output_better.nii.gz
** ERROR: nifti_image_read(output_better.nii.gz): bad dim[0]
Segmentation fault (core dumped)

I don't know how am I supposed to fix this issue.

Thanks,

Usman Ayub Sh