Dear fsl experts,
We reviced the same warning message after run first_utils command. Our processing steps are as followed.
1/ DICOM converted and oriented T1 images
2/ first_run_all
3/ first_roi_slicesdir
4/ concaternate
5/ Glm model
6/ first_utils
After reading the below suggestions, we mannually check the orientation of each files in FSLView and found no mistakes.
We also tried the fslreorient2std command for orientation (but did not run robustfov) and run bet for brain extraction. While running the first_run_all command, some *_all_firstseg.nii.gz were missing and some output_name-struct_corr.nii.gz files pop out.
We are very confused now. Can anyone offer us some suggestions?
Many thanks,
Xiaoyun
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