Hi there,
the reason for having certain options hidden (eddy has for example many more
hidden options than it has exposed options) is either i) because an option
increases the risk of users making mistakes or ii) I am not really sure yet if
it is a good idea or not but I want to have the possibility to reveal them to
selected users who can help me test them.
The —dfout and —rbmout options fall in the former category and for that reason
I don’t want to expose them.
Is that a problem for you as long as the HCP scripts work as intended?
Jesper
On 24 Sep 2014, at 18:02, Glasser, Matthew <glass...@wusm.wustl.edu> wrote:
> 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
>>>
>>>
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>>
>>
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>
>
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> not the intended recipient, be advised that any unauthorized use, disclosure,
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