Hi All,
I've written a python program that does TR-wise scrubbing, code here: [
github.com]
This edits the dimensions of the output file in the time dimension, and changes the relevent fields in the header, before writing out a NIFTI file.
I've used this code in the past without much trouble, but now I am noticing that AFNI programs do not like the output of this program. When I try to do something like volume smoothing, I get these messages:
3dBlurInMask \
-prefix ${SESS}/func_volsmooth.${ID}.${NUM}.nii.gz \
-Mmask ${SESS}/anat_smoothmask.nii.gz \
-FWHM ${FWHM} \
-input ${SESS}/${INPUT}.${ID}.${NUM}.nii.gz
** WARNING: NIfTI file /projects/jdv/data/epitome/SPINS/SPN01_CMH_P001/REST/SESS01//func_scrubbed.TEST.01.nii.gz dimensions altered since AFNI extension was added
++ 3dBlurInMask: AFNI version=AFNI_2011_12_21_1014 (Sep 30 2014) [64-bit]
++ Authored by: RW Cox
++ 1 unique nonzero values in -Mmask; 43315 nonzero voxels
** WARNING: NIfTI file /projects/jdv/data/epitome/SPINS/SPN01_CMH_P001/REST/SESS01//func_scrubbed.TEST.01.nii.gz dimensions altered since AFNI extension was added
++ forcing output to be stored in float format
+ voxels in Mmask[1] = 43315
** ERROR: nifti_image_write_hdr_img: NBL does not match nim
++ Output dataset /projects/jdv/data/epitome/SPINS/SPN01_CMH_P001/REST/SESS01//func_volsmooth.TEST.01.nii.gz
and this output file "func_volsmooth.TEST.01.nii.gz" is empty.
I've uploaded the input, mask, and output files here:
[link down]
Could anyone point me in the right direction?
Thanks so much,
Joseph
[edit: updated link]
Edited 1 time(s). Last edit at 03/30/2015 08:27AM by jdviviano.
