Re: [HCP-Users] fieldmap processing error

[Glasser, Matthew]

Can you check that the headers of these files look okay: ${StudyFolder}/${Subject}/${fMRIName}/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/FieldMap/Phase.nii.gz ${StudyFolder}/${Subject}/${fMRIName}/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/FieldMap/Magnitude_brain  The first file is directly copied from the input location  ${FSLDIR}/bin/imcp ${PhaseInputName} ${WD}/Phase And the second one has had the following done to it (initial fslmaths command reads from input location): ${FSLDIR}/bin/fslmaths ${MagnitudeInputName} -Tmean ${WD}/Magnitude ${FSLDIR}/bin/bet ${WD}/Magnitude ${WD}/Magnitude_brain -f 0.35 -m #Brain extract the magnitude image If all those files look okay, then the issue is with the fsl_prepare_fieldmap script, which is a part of the FSL distribution and is supported by the FSL team: ${FSLDIR}/bin/fsl_prepare_fieldmap SIEMENS ${WD}/Phase ${WD}/Magnitude_brain ${WD}/FieldMap ${DeltaTE} Peace, Matt. From: <Book>, Gregory <gregory.b...@hhchealth.org> Date: Friday, January 9, 2015 at 1:26 PM To: Matt Glasser <glass...@wusm.wustl.edu>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: RE: [HCP-Users] fieldmap processing error Digging deeper into it, I think the fieldmap voxel sizes may be changed or misreported inside the HCP script.   In the analysis/unprocessed directory, the headers look like this: [Gbook@compute31 T1w_MPR1]$ 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:glass...@wusm.wustl.edu] Sent: Thursday, January 08, 2015 2:07 PM To: Book, Gregory; hcp-users@humanconnectome.org 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 <gregory.b...@hhchealth.org> Date: Thursday, January 8, 2015 at 12:18 PM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> 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 gregory.b...@hhchealth.org 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. 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