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
>
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