hey Matt,
I was trying to use the FIX script from the fix directory that came with
this - downloadable FIX tar file
<http://www.fmrib.ox.ac.uk/~steve/ftp/fix.tar.gz> tar file.
I did so because I didn't see in the content of the hcp_fix script that it
runs the training mode, and I needed to create the training file (as I said
before, im at the stage where I have hand labelled the components of the
resting state data for 10 of my subjects after running MELODIC, and I wish
to train FIX using these labels).
if I'm mistaken in my workflow, I would appreciate any further instructions
as to the correct workflow for using the FIX pipelines.
thank you
On Mon, 10 Dec 2018 at 23:13, Glasser, Matthew <glass...@wustl.edu> wrote:
> Did you use the hcp_fix script or some other method of running FIX on HCP
> data.
>
> Matt.
>
> From: Shachar Gal <gal.shac...@gmail.com>
> Date: Monday, December 10, 2018 at 7:47 AM
> To: "Harms, Michael" <mha...@wustl.edu>
> Cc: Matt Glasser <glass...@wustl.edu>, "hcp-users@humanconnectome.org" <
> hcp-users@humanconnectome.org>, Ido Tavor <idota...@gmail.com>
> Subject: Re: [HCP-Users] HCP_FIX
>
> hey again,
>
> thanks for pointing out the relevant lines for the dual regression.
>
> I have some further questions about the workflow of running FIX.
> so I did hand classification for 10 of my subjects, and wished to run FIX
> with the -t option, in order to create the training data.
> but then I realized that FIX expects my .ica folder to include a /reg
> folder inside, which it does not include, because the input data I gave to
> melodic was *already registered* (using all of the hcp pipelines).
> so this brings up two questions:
> 1) if it still expects this kind of structure, after being tweaked to fit
> the hcp daa, does this mean that you run melodic with registration and all?
> 2) if not, then what file do you give him as the highres2example_func.mat?(the
> other files it expects /reg folder to include are more obvious)
>
> thanks,
> Shachar
>
>
>
> On Mon, 26 Nov 2018 at 19:02, Harms, Michael <mha...@wustl.edu> wrote:
>
>>
>>
>> Hi,
>>
>> The cleaning of the CIFTI data is done automatically in fix_3_clean.m of
>> the FIX distribution, which is called by the fix script itself.
>>
>>
>>
>> The only relevant aspect of hcp_fix to that process is that hcp_fix
>> creates the following symbolic link:
>>
>>
>>
>> if [ -f ../${fmri_orig}_Atlas.dtseries.nii ] ; then
>>
>> $FSLDIR/bin/imln ../${fmri_orig}_Atlas.dtseries.nii Atlas.dtseries.nii
>>
>> fi
>>
>>
>>
>> since fix_3_clean.m is hard-coded to look for a file named
>> Atlas.dtseries.nii
>>
>>
>>
>> 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 Shachar Gal
>> <gal.shac...@gmail.com>
>> *Date: *Friday, November 23, 2018 at 2:37 AM
>> *To: *"Glasser, Matthew" <glass...@wustl.edu>
>> *Cc: *"hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>> *Subject: *Re: [HCP-Users] HCP_FIX
>>
>>
>>
>> hey matt,
>>
>> the thing is, I didn't see anything in the hip_fix script the projects
>> the "fix cleaned" volume to surface, so when does that happen?
>>
>> considering that you mentioned you're currently editing these scripts, I
>> think we would just use the original FSL FIX, and later project the fix
>> cleaned volume to surface using your 'fMRISurface' pipeline.
>>
>>
>>
>> thanks,
>>
>> Shachar
>>
>>
>>
>>
>>
>> On Tue, 20 Nov 2018 at 04:10, Glasser, Matthew <glass...@wustl.edu>
>> wrote:
>>
>> The hcp_fix script is for enabling a few enhancements specific to
>> HCP-Style processing. These scripts are currently being edited and tested
>> and we will have new versions announced soon. PostFix generates the
>> Workbench scenes for hand classification of components.
>>
>>
>>
>> Matt.
>>
>>
>>
>> *From: *<hcp-users-boun...@humanconnectome.org> on behalf of Shachar Gal
>> <gal.shac...@gmail.com>
>> *Date: *Monday, November 19, 2018 at 3:30 AM
>> *To: *"hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>> *Subject: *[HCP-Users] HCP_FIX
>>
>>
>>
>> Dear experts,
>>
>> I was was looking for some documentation regarding the differences
>> between the standard FSL FIX script, and the HCP's modified version, but
>> could not find such.
>>
>> could you point me to such a documentation, if exists, or perhaps
>> elaborate briefly on the subject?
>>
>> on the same subject, is there any similar documentation regarding
>> postfix? I'm not sure what's its purpose in the cleaning and applying
>> procedure.
>>
>>
>>
>> thanks.
>>
>> Shachar Gal
>>
>>
>>
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