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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