It's probably best to post these kinds of questions to the HCP Users list for faster support. Is this happening on clean runs of the latest version of the HCP Pipelines? If so, perhaps posting the output of fslhd on the various input images would reveal the problem.
Peace, Matt. From: Sung Yu <s...@mprc.umaryland.edu<mailto:s...@mprc.umaryland.edu>> Date: Monday, September 19, 2016 at 2:39 PM To: Peter Kochunov <pkochu...@gmail.com<mailto:pkochu...@gmail.com>>, Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Subject: Re: hcp pipeline problem hi Matt, we recently had MRI upgrade and HCP script is not working anymore. here is the error message from PreFreeSurferPipeline.sh. ******************** WARNING:: Inconsistent orientations for individual images when attempting to merge. Merge will use voxel-based orientation which is probably incorrect - *PLEASE CHECK*! Error in size-match along non-concatenated dimension for input file: /home/tomcat/Library/Data/HCP//ACP1086/T2w/T2wToT1wDistortionCorrectAndReg/FieldMap/PhaseTwo_gdc ********************* and i get this message when i try to run FreeSurferPipeline.sh Image Exception : #22 :: ERROR: Could not open image /home/tomcat/Library/Data/HCP//ACP1086/T1w/T1w_acpc_dc_restore_brain do you know how we can fix this problem? thanks, Sung >>> Peter Kochunov <pkochu...@gmail.com<mailto:pkochu...@gmail.com>> 9/19/2016 >>> 3:26 PM >>> Can you send an email to Matt Glassier? On Mon, Sep 19, 2016 at 3:06 PM, Sung Yu <s...@mprc.umaryland.edu<mailto:s...@mprc.umaryland.edu>> wrote: hi Peter, the hcp scripts i ran actually created Diffusion/eddy directory so i didn't notice until today but it looks like there is error in pre-freesurfer and skip to diffusion script without running freesurfer and post-freesurfer. this is the error message. ******************** WARNING:: Inconsistent orientations for individual images when attempting to merge. Merge will use voxel-based orientation which is probably incorrect - *PLEASE CHECK*! Error in size-match along non-concatenated dimension for input file: /home/tomcat/Library/Data/HCP//ACP1086/T2w/T2wToT1wDistortionCorrectAndReg/FieldMap/PhaseTwo_gdc Image Exception : #22 :: ERROR: Could not open image /home/tomcat/Library/Data/HCP//ACP1086/T1w/T1w_acpc_dc_restore_brain ******************** it supposes to create a file "T1w_acpc_dc_restore_brain". looks like all the subject has same problem since the MRI upgrade and i am not sure how to fix this. thanks, Sung ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
