Re: [HCP-Users] HCP Pipeline BIDS app - fMRI processing with reversed phase-encode file in "fmap" directory?
Indeed we are unable to offer BIDS support, but are happy to support running the HCP Pipelines from our GitHub repository. Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>> Date: Friday, April 6, 2018 at 12:05 PM To: Scott Burwell <burw...@umn.edu<mailto:burw...@umn.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] HCP Pipeline BIDS app - fMRI processing with reversed phase-encode file in "fmap" directory? Hi, We didn’t create the HCP Pipeline BIDS app, and have no experience using it. Users should be aware that the current BIDS App “hides” various choices that one would normally have to make when running the HCP Pipelines, and I’m not sure what particular choices it has implemented. In that regard, starting with the BID App, rather than the HCP Pipeline scripts themselves, may abstract the pipelines in a manner that is not conducive to you understanding what they are doing with your data. Additionally, last time I checked (which was many months ago) there was no simple process for getting HCP-style acquired data into the BID directory structure. More fundamentally, the “PEpolar” method for correcting the distortions expects that spin-echo acquisitions with both polarities were collected, so that you avoid susceptibility dropout and can estimate the field properly throughout the entire brain. The HCP Pipelines are not constructed to correct for distortions using gradient-echo acquisitions to estimate the field maps, and thus I rather doubt that the BIDS app is equipped to handle that situation either, since the BIDS app is simply a “wrapper” into the HCP Pipeline scripts. Cheers, -MH -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu<mailto:mha...@wustl.edu> From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Scott Burwell <burw...@umn.edu<mailto:burw...@umn.edu>> Date: Friday, April 6, 2018 at 10:35 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] HCP Pipeline BIDS app - fMRI processing with reversed phase-encode file in "fmap" directory? I want to use the HCP Pipeline BIDS app to preprocess T1w, T2w, and BOLD data collected at the CMRR. The BOLD data were acquired to apply the "PEpolar" method, whereby one short (TR=1.5s, 10 reps) set of EPI data were collected with AP phase-encoding, and one long (TR=1.5s, 400 reps) set of EPI data were collected with PA phase-encoding. Per BIDS specifications and others' suggestions (e.g., https://neurostars.org/t/fmriprep-docker-fieldmap-correction/623 ), I have stored the short acquisition AP data in the "fmap" directory and the long acquisition PA data in the "func" directory; the JSON sidecar for the "fmap" file points to the appropriate BOLD series via the "IntendedFor" key (see directory contents below). I know that the HCP Pipeline BIDS app expects a fieldmap in order for the functional data to be preprocessed. However, based on documentation, I suspect the BIDS app in its current version does not support when the "fmap" is a paired reverse-phase encode image? I.e., the BIDS app does not sense that FSL's TOPUP should be used (rather than FUGUE or whatever program is currently used for this distortion correction). Has anyone else encountered this dilemma? Are there plans to add this functionality to the BIDS app? Any information would be greatly appreciated. Thank you in advance. Best, Scott ##bids subject session directory contents: ./func/sub-7536262_ses-00_task-rest_run-01_bold.nii.gz ./func/sub-7536262_ses-00_task-rest_run-01_bold.json ./func/sub-7536262_ses-00_task-rest_run-01_events.tsv - ./fmap/sub-7536262_ses-00_acq-rest_dir-AP_run-01_epi.nii.gz ./fmap/sub-7536262_ses-00_acq-rest_dir-AP_run-01_epi.json - cat ./fmap/sub-7536262_ses-00_acq-rest_dir-AP_run-01_epi.json "PhaseEncodingDirection": "j-", "IntendedFor": "func/sub-7536262_ses-00_task-rest_run-01_bold.nii.gz", "TotalReadoutTime": 0.0527996, -- Scott J. Burwell, PhD Postdoctoral Research Fellow Department of Psychiatry University of Minnesota, Minneapolis, MN burw...@umn.edu<mailto
Re: [HCP-Users] HCP Pipeline BIDS app - fMRI processing with reversed phase-encode file in "fmap" directory?
Hi, We didn’t create the HCP Pipeline BIDS app, and have no experience using it. Users should be aware that the current BIDS App “hides” various choices that one would normally have to make when running the HCP Pipelines, and I’m not sure what particular choices it has implemented. In that regard, starting with the BID App, rather than the HCP Pipeline scripts themselves, may abstract the pipelines in a manner that is not conducive to you understanding what they are doing with your data. Additionally, last time I checked (which was many months ago) there was no simple process for getting HCP-style acquired data into the BID directory structure. More fundamentally, the “PEpolar” method for correcting the distortions expects that spin-echo acquisitions with both polarities were collected, so that you avoid susceptibility dropout and can estimate the field properly throughout the entire brain. The HCP Pipelines are not constructed to correct for distortions using gradient-echo acquisitions to estimate the field maps, and thus I rather doubt that the BIDS app is equipped to handle that situation either, since the BIDS app is simply a “wrapper” into the HCP Pipeline scripts. Cheers, -MH -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: <hcp-users-boun...@humanconnectome.org> on behalf of Scott Burwell <burw...@umn.edu> Date: Friday, April 6, 2018 at 10:35 AM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: [HCP-Users] HCP Pipeline BIDS app - fMRI processing with reversed phase-encode file in "fmap" directory? I want to use the HCP Pipeline BIDS app to preprocess T1w, T2w, and BOLD data collected at the CMRR. The BOLD data were acquired to apply the "PEpolar" method, whereby one short (TR=1.5s, 10 reps) set of EPI data were collected with AP phase-encoding, and one long (TR=1.5s, 400 reps) set of EPI data were collected with PA phase-encoding. Per BIDS specifications and others' suggestions (e.g., https://neurostars.org/t/fmriprep-docker-fieldmap-correction/623 ), I have stored the short acquisition AP data in the "fmap" directory and the long acquisition PA data in the "func" directory; the JSON sidecar for the "fmap" file points to the appropriate BOLD series via the "IntendedFor" key (see directory contents below). I know that the HCP Pipeline BIDS app expects a fieldmap in order for the functional data to be preprocessed. However, based on documentation, I suspect the BIDS app in its current version does not support when the "fmap" is a paired reverse-phase encode image? I.e., the BIDS app does not sense that FSL's TOPUP should be used (rather than FUGUE or whatever program is currently used for this distortion correction). Has anyone else encountered this dilemma? Are there plans to add this functionality to the BIDS app? Any information would be greatly appreciated. Thank you in advance. Best, Scott ##bids subject session directory contents: ./func/sub-7536262_ses-00_task-rest_run-01_bold.nii.gz ./func/sub-7536262_ses-00_task-rest_run-01_bold.json ./func/sub-7536262_ses-00_task-rest_run-01_events.tsv - ./fmap/sub-7536262_ses-00_acq-rest_dir-AP_run-01_epi.nii.gz ./fmap/sub-7536262_ses-00_acq-rest_dir-AP_run-01_epi.json - cat ./fmap/sub-7536262_ses-00_acq-rest_dir-AP_run-01_epi.json "PhaseEncodingDirection": "j-", "IntendedFor": "func/sub-7536262_ses-00_task-rest_run-01_bold.nii.gz", "TotalReadoutTime": 0.0527996, -- Scott J. Burwell, PhD Postdoctoral Research Fellow Department of Psychiatry University of Minnesota, Minneapolis, MN burw...@umn.edu<mailto:burw...@umn.edu> ___ 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
[HCP-Users] HCP Pipeline BIDS app - fMRI processing with reversed phase-encode file in "fmap" directory?
I want to use the HCP Pipeline BIDS app to preprocess T1w, T2w, and BOLD data collected at the CMRR. The BOLD data were acquired to apply the "PEpolar" method, whereby one short (TR=1.5s, 10 reps) set of EPI data were collected with AP phase-encoding, and one long (TR=1.5s, 400 reps) set of EPI data were collected with PA phase-encoding. Per BIDS specifications and others' suggestions (e.g., https://neurostars.org/t/fmriprep-docker-fieldmap-correction/623 ), I have stored the short acquisition AP data in the "fmap" directory and the long acquisition PA data in the "func" directory; the JSON sidecar for the "fmap" file points to the appropriate BOLD series via the "IntendedFor" key (see directory contents below). I know that the HCP Pipeline BIDS app expects a fieldmap in order for the functional data to be preprocessed. However, based on documentation, I suspect the BIDS app in its current version does not support when the "fmap" is a paired reverse-phase encode image? I.e., the BIDS app does not sense that FSL's TOPUP should be used (rather than FUGUE or whatever program is currently used for this distortion correction). Has anyone else encountered this dilemma? Are there plans to add this functionality to the BIDS app? Any information would be greatly appreciated. Thank you in advance. Best, Scott *##bids subject session directory contents:* *./func/sub-7536262_ses-00_task-rest_run-01_bold.nii.gz* *./func/sub-7536262_ses-00_task-rest_run-01_bold.json* *./func/sub-7536262_ses-00_task-rest_run-01_events.tsv* *-* *./fmap/sub-7536262_ses-00_acq-rest_dir-AP_run-01_epi.nii.gz* *./fmap/sub-7536262_ses-00_acq-rest_dir-AP_run-01_epi.json* *-* *cat ./fmap/sub-7536262_ses-00_acq-rest_dir-AP_run-01_epi.json* *"PhaseEncodingDirection": "j-", * *"IntendedFor": "func/sub-7536262_ses-00_task-rest_run-01_bold.nii.gz", * *"TotalReadoutTime": 0.0527996, * -- Scott J. Burwell, PhD Postdoctoral Research Fellow Department of Psychiatry University of Minnesota, Minneapolis, MN burw...@umn.edu ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
