Re: [HCP-Users] HCP pipelines: fMRIVolume

[Glasser, Matthew]

Did it actually throw an error when you ran it?  I think those might just be hidden options in topup.  I would really hope these options didn’t get removed in a later version, as they are quite useful.   Peace, Matt. From: Matthieu Vanhoutte <matthieuvanhou...@gmail.com> Date: Wednesday, September 24, 2014 at 9:55 AM To: Matt Glasser <glass...@wusm.wustl.edu> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] HCP pipelines: fMRIVolume Dear HCP experts, According to Matt advices, I use FSL 5.0.7 for fMRIVolume prepocessed pipeline "GenericfMRIVolumeProcessingPipeline.sh". However, in EPI distorsion correction "TopupPreprocessingAll.sh", the topup command from FSL 5.0.6 is unique and used : # RUN TOPUP # Needs FSL (version 5.0.6) ${FSLDIR}/bin/topup --imain=${WD}/BothPhases --datain=$txtfname --config=${TopupConfig} --out=${WD}/Coefficents --iout=${WD}/Magnitudes --fout=${WD}/TopupField --dfout=${WD}/WarpField --rbmout=${WD}/MotionMatrix --jacout=${WD}/Jacobian -v The three respective options : --dfout=${WD}/WarpField --rbmout=${WD}/MotionMatrix --jacout=${WD}/Jacobian exist only in FSL 5.0.6 and the three options outputs are used in the rest of the "TopupPreprocessingAll.sh" script... How could I patch this script and is it possible ? In the other case, how could I install FSL 5.0.6 on Ubuntu 14.04 ? Thank in advance for any help ! Best, ------------------------------------- Matthieu Vanhoutte, MSc Research Engineer - Department of Neuroradiology Regional University Hospital, Lille, France 2014-09-19 17:37 GMT+02:00 Glasser, Matthew <glass...@wusm.wustl.edu>: Except for the task analysis pipeline, it should be fine to run the others (like fMRIVolume) with FSL 5.0.7.  The task analysis pipeline needs a patch for FSL 5.0.7, because that release changed some core functionality of fslmaths (temporal filtering). Peace, Matt. From: Matthieu Vanhoutte <matthieuvanhou...@gmail.com> Date: Friday, September 19, 2014 at 10:34 AM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: [HCP-Users] HCP pipelines: fMRIVolume Dear HCP's experts, I'm trying to follow fMRI Volume pipeline from "The minimal preprocessing pipelines for the Human Connectome Project" (NeuroImage, 2013) on HCP data. One has suggested me to follow the released HCP pipelines : http://www.humanconnectome.org/documentation/HCP-pipelines/. However, it seems that we have to install very precise versions of FSL and Freesurfer. Once we get fsl-5.0.6 package (http://fsl.fmrib.ox.ac.uk/fsldownloads/oldversions/), how to install this one on ubuntu 12.10 or 14.04 ? Thanks ! Cheers, ------------------------------------- Matthieu Vanhoutte, MSc Research Engineer - Department of Neuroradiology Regional University Hospital, Lille, France _______________________________________________ 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.   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