Re: [HCP-Users] Minimal Preprocessing Pipeline (on my own data): Flipped EPI (AP)

[Glasser, Matthew]

Can you give us more details on the data you are feeding into the pipelines and how you called fMRIVolume?  We have not experienced this issue with HCP data or the non-HCP data we have tried the pipelines with.   Peace, Matt. From: Julien Dubois <jcrdub...@gmail.com> Date: Friday, April 17, 2015 at 4:13 PM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: [HCP-Users] Minimal Preprocessing Pipeline (on my own data): Flipped EPI (AP) Dear developers I ran the minimal preprocessing pipeline on a number of my own subjects, and recently noticed that there was a rather unfortunate AP flip of the EPI during registration for ~30% of the subjects (explaining some rather odd results that I have been trying to track down for a couple of days). The first volume in which I can notice this AP flip is the "Scout_gdc_undistorted_fieldmap2str.nii.gz" in "${SUBJECT_DIR}/${RUN}/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/" (that the first first showing the incorrect AP orientation, according to `ls -lat`) . I'm having a hard time tracking down in the code (DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased.sh) where this volume is created/used, and hence how to remedy the bug. Let me know if you can help. Thanks! - Julien _______________________________________________ HCP-Users mailing list 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