If you run fslhd on the SBRef and SE fieldmap images, are they different? Ideally these are matched exactly on the scanner.
Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Bourguignon, Nicolas" <nicolas.bourguig...@uconn.edu<mailto:nicolas.bourguig...@uconn.edu>> Date: Wednesday, April 10, 2019 at 3:40 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] Query: Error: Spin echo fieldmap has different dimensions than scout image, this requires a manual fix Hi HCP people, Still a newbie on the use of HCP pipelines, please excuse me if my question/comment is trivial. I'm currently attempting to run a fMRIVolume pipeline on an fMRI dataset using spin echo field maps (AP - PA). This pipeline worked fine the very first time I ran it, but now it stops running when calling for the TopupPreprocessingAll.sh, with the following error: Error: Spin echo fieldmap has different dimensions than scout image, this requires a manual fix. A more complete version of the report is: Wed Apr 10 15:44:04 EDT 2019 - MotionCorrection.sh: Change names of all matrices in OutputMotionMatrixFolder Wed Apr 10 15:44:07 EDT 2019 - MotionCorrection.sh: Run the Derive function to generate appropriate regressors from the par file Wed Apr 10 15:44:30 EDT 2019 - MotionCorrection.sh: END Wed Apr 10 15:44:30 EDT 2019 - GenericfMRIVolumeProcessingPipeline.sh: EPI Distortion Correction and EPI to T1w Registration Wed Apr 10 15:44:30 EDT 2019 - GenericfMRIVolumeProcessingPipeline.sh: mkdir -p /Users/nib19005/Desktop/2019/TMS/BIDS/TMS_BIDS3/Bids/01/MotorLoc_AP/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased Wed Apr 10 15:44:32 EDT 2019 - DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased.sh: START Wed Apr 10 15:44:32 EDT 2019 - TopupPreprocessingAll.sh: START: Topup Field Map Generation and Gradient Unwarping Wed Apr 10 15:44:32 EDT 2019 - TopupPreprocessingAll.sh: Error: Spin echo fieldmap has different dimensions than scout image, this requires a manual fix Been looking up for similar issues in the past but couldn't find any. I have run the PreFreeSurfer, FreeSurfer and PostFresurfer pipelines before on the structural images. Been thinking about changing the field map size myself, but still wonder why things worked in the past and not anymore. I'm willing to share whatever bit of code/data might be helpful to figure out the issue, but I prefer to wait until you tell me what you need exactly. Thanks! Nicolas _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> 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 HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
