CPAC's SCA and FSL v6.0

[zeosmar]

Hi CPAC team,
I am writing to inform you about a problem between the way as CPAC is naming output folders and FSL v6.0. For SCA analysis, CPAC creates a different folder for each individual ROI with '.nii.gz' at the end of it, for example:

..../QC/work/resting_preproc_sub-80163_ses-1/sca_roi_0/_scan_rest1/_compcor_ncomponents_5_selector_pc10.linear1.wm1.global0.motion1.quadratic1.gm0.compcor0.csf1/_bandpass_freqs_0.01.0.1/mask_rois_2mm_mask_file..R01..wave2..ROI..rois_2mm.nii.gz/.....

Using this path name ending with .nii.gz makes the command fslmaths from FSL 6.0 crash:

Standard error:
terminate called after throwing an instance of 'NiftiException'
what(): Error: cant open file ..../QC/work/resting_preproc_sub-80163_ses-1/_scan_rest1/_compcor_ncomponents_5_selector_pc10.linear1.wm1.global0.motion1.quadratic1.gm0.compcor0.csf1/_bandpass_freqs_0.01.0.1/_bandpass_freqs_0.01.0.1/mask_rois_2mm_mask_file..R01..wave2..ROI..rois_2mm.gz/_fwhm_6/sca_roi_files_smooth_0/mapflow/_sca_roi_files_smooth_00/sca_ROI_1_maths.nii.gz
Aborted (core dumped)
Return code: 134

It seems like fslmaths misinterpret the path when it ends with .nii. This problem doesn't occur on FSL v5.0.

[sgiavasis]

Hi José,

Thanks for the report. Were you running C-PAC as part of an installation, like on a server?