I think (but am not 100% certain) that the magnitude image should be a single volume (dim4 = 1), whereas your magnitude image appears to be two volumes (dim4 = 2). That could be the mismatching dimension.
--Greg ____________________________________________________________________ Greg Burgess, Ph.D. Staff Scientist, Human Connectome Project Washington University School of Medicine Department of Anatomy and Neurobiology Phone: 314-362-7864 Email: [email protected] > On Jan 9, 2015, at 1:59 PM, Glasser, Matthew <[email protected]> wrote: > > 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 ${DeltaTE} > > Peace, > > Matt. > > From: <Book>, Gregory <[email protected]> > Date: Friday, January 9, 2015 at 1:26 PM > To: Matt Glasser <[email protected]>, "[email protected]" > <[email protected]> > Subject: RE: [HCP-Users] fieldmap processing error > > Digging deeper into it, I think the fieldmap voxel sizes may be changed or > misreported inside the HCP script. > > In the analysis/unprocessed directory, the headers look like this: > [Gbook@compute31 T1w_MPR1]$ 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:[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]> > Date: Thursday, January 8, 2015 at 12:18 PM > To: "[email protected]" <[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] > 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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