Digging deeper into it, I think the fieldmap voxel sizes may be changed or misreported inside the HCP script.
In the analysis/unprocessed directory, the headers look like this: [Gbook@compute31 T1w_MPR1]$ fslinfo analysis_3T_FieldMap_Magnitude.nii.gz data_type INT16 dim1 80 dim2 80 dim3 48 dim4 2 datatype 4 pixdim1 3.000000 pixdim2 3.000000 pixdim3 3.000000 pixdim4 0.731000 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+ [Gbook@compute31 T1w_MPR1]$ fslinfo analysis_3T_FieldMap_Phase.nii.gz data_type INT16 dim1 80 dim2 80 dim3 48 dim4 1 datatype 4 pixdim1 3.000000 pixdim2 3.000000 pixdim3 3.000000 pixdim4 0.731000 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+ Then, when running the HCP pipeline, it reports this error (found through grep): ./S6024ZVW/2/HCPfMRI-MID/pipeline/step48.log:Phase and Magnitude images must have the same number of voxels and voxel dimensions ./S6024ZVW/2/HCPfMRI-MID/pipeline/step48.log-Current dimensions are: ./S6024ZVW/2/HCPfMRI-MID/pipeline/step48.log- Phase image: 80 x 80 x 48 with dims of 3.000000 x 3.000000 x 3.000001 mm ./S6024ZVW/2/HCPfMRI-MID/pipeline/step48.log- Magnitude image: 80 x 80 x 48 with dims of 3.000000 x 3.000000 x 3.000000 mm ./S6024ZVW/2/HCPfMRI-MID/pipeline/step48.log-Fix this (probably in reconstruction stage) before re-running this script From: Glasser, Matthew [mailto:[email protected]] Sent: Thursday, January 08, 2015 2:07 PM To: Book, Gregory; [email protected] Subject: Re: [HCP-Users] fieldmap processing error Probably the easiest thing to do would be to fix the outlying image dimension by editing the NIFTI header. What program are you using to convert from scanner format to NIFTI? We use dcm2nii in the HCP. Peace, Matt. From: <Book>, Gregory <[email protected]<mailto:[email protected]>> Date: Thursday, January 8, 2015 at 12:18 PM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] fieldmap processing error We've noticed an error while processing some fMRI data through the HCP pipeline. Several series are failing with the following message: Phase and Magnitude images must have the same number of voxels and voxel dimensions Current dimensions are: Phase image: 80 x 80 x 48 with dims of 3.000000 x 3.000000 x 3.000000 mm Magnitude image: 80 x 80 x 48 with dims of 3.000000 x 3.000000 x 3.000001 mm Fix this (probably in reconstruction stage) before re-running this script Is there any way we can bypass this error? The voxel sizes are only off by 0.000001 mm It's also weird, because the pipeline contains 5 runs of the same task, and all use the same fieldmap files. The first task processes fine, but the next 4 fail with this error message. -G _________________________________________________ Gregory Book Senior Technology Manager Olin Neuropsychiatry Research Center, Institute of Living, Hartford Hospital 200 Retreat Avenue Hartford, CT 06106 Tel: 860-545-7267 Fax: 860-545-7797 [email protected]<mailto:[email protected]> http://nidb.sourceforge.net This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure, or distribution is prohibited. If you are not the intended recipient, or an employee or agent responsible for delivering the message to the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message, including any attachments. _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ 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 [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
