Re: [HCP-Users] HCP pipelines: fMRIVolume

[Glasser, Matthew]

They were hidden in 5.0.6 too, perhaps they should be unhidden in the next version.   As for the missing file, I’m a bit surprised at that, as one of the major reasons put forward for that package was to include files like that.  If you want to make your own, just copy another FreeSurfer .dat transform file and put an identity matrix in it.   Peace, Matt. From: Matthieu Vanhoutte <matthieuvanhou...@gmail.com> Date: Wednesday, September 24, 2014 at 11:34 AM To: Matt Glasser <glass...@wusm.wustl.edu> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>, Jesper Andersson <jes...@fmrib.ox.ac.uk> Subject: Re: [HCP-Users] HCP pipelines: fMRIVolume It seems that those might be some hidden options in topup, because no error from this command appeared. But it's little bit strange that these options are hidden in "topup --help" of FSL 5.0.7, how should we suppose to guess and understand these ? However, one error appeared in the bbregister step to T1w : Running FAST segmentation FLIRT pre-alignment Running BBR 0.235730 0.999994 0.001637 -0.002969 0.000000 -0.001632 0.999997 0.001602 0.000000 0.002972 -0.001597 0.999994 0.000000 -0.418826 1.188511 3.352775 1.000000 ERROR: cannot find /NAS/dumbo/matthieu/HCP/100307/T1w/100307/mri/transforms/eye.dat The file "eye.dat" doesn't exist in the "100307_3T_Structural_preproc_extended.zip" package. Best, ------------------------------------- Matthieu Vanhoutte, MSc Research Engineer - Department of Neuroradiology Regional University Hospital, Lille, France 2014-09-24 16:59 GMT+02:00 Glasser, Matthew <glass...@wusm.wustl.edu>: 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. 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