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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
