This line in the pipelines deals with either case:
${FSLDIR}/bin/fslmaths ${MagnitudeInputName} -Tmean ${WD}/Magnitude
On 1/9/15, 2:17 PM, "Greg Burgess" <[email protected]> wrote:
>I think (but am not 100% certain) that the magnitude image should be a
>single volume (dim4 = 1), whereas your magnitude image appears to be two
>volumes (dim4 = 2). That could be the mismatching dimension.
>
>--Greg
>
>____________________________________________________________________
>Greg Burgess, Ph.D.
>Staff Scientist, Human Connectome Project
>Washington University School of Medicine
>Department of Anatomy and Neurobiology
>Phone: 314-362-7864
>Email: [email protected]
>
>> On Jan 9, 2015, at 1:59 PM, Glasser, Matthew <[email protected]>
>>wrote:
>>
>> Can you check that the headers of these files look okay:
>>
>>
>>${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
>>
>> We¹ve 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
>> It¹s 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. 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]
>> 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.
>>
>>
>> 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
>>
>
________________________________
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
