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Thanks, I do have that installed, but we changed some things on our server, so it wasn't being found anymore. To add it to the matlab path for fix to run, can I simply add the path of gifti to this line in hcp_fix:

ML_PATHS="addpath('${FSL_FIXDIR}'); addpath('${FSL_MATLAB_PATH}');addpath('/home/caseylab_curate/software/gifti-1.5');"

Or better: add GIFTI_PATH=/home/caseylab_curate/software/gifti-1.5 to my own $PATH and then 

if [ -z "${GIFTI_PATH}" ]; then
        echo "GIFTI path not set for MATLAB to read CIFTI files!" >&2
        usage
fi
 
ML_PATHS="addpath('${FSL_FIXDIR}'); addpath('${FSL_MATLAB_PATH}');addpath('${GIFTI_PATH}');"

To be consistent with the rest of that script. How does that sound?

Also, I noticed that now gifti has a version 1.6. Is it worth updating from 1.5?

Thanks a lot,
Michael


________________________________________
From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Matt Glasser <[log in to unmask]>
Sent: Wednesday, January 27, 2016 12:52 PM
To: [log in to unmask]
Subject: Re: [FSL] hcp_fix

Hi Michael,

Do you have the CIFTI reader/writer matlab scripts installed?  You can get
them from here:

https://urldefense.proofpoint.com/v2/url?u=https-3A__wiki.humanconnectome.org_display_PublicData_HCP-2BUsers-2BFAQ&d=BQICAg&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg&m=0O2NTuQThZ8GqpzkvJ4SyuWP94uL10pjt1zeKSoUrKU&s=QkaqBoFvLGic-h9TJFNkIrsb3CNNn491QWJL2H0r7mw&e=

Peace,

Matt.

On 1/27/16, 9:39 AM, "FSL - FMRIB's Software Library on behalf of Michael
F.W. Dreyfuss" <[log in to unmask] on behalf of [log in to unmask]>
wrote:

>Hi,
>
>I've been trying to set up hcp_fix, but have not been getting the proper
>output. In running hcp_fix, I get the output volume file of
>${run}_hp2000.nii.gz, and the ${run}_hp2000.ica directory is produced,
>but I am not getting the files ${run}_Atlas_hp2000_clean.dtseries.nii or
>${run}_hp2000_clean.nii.gz to use in analysis. Everything seems to be
>running fine, and I cannot find where in hcp_fix of fix itself these
>files are produced, just where they are renamed and moved. May I ask if
>you have any suggestion of what may be going on here and how I can get
>the output I need? Would be very helpful.
>
>For reference, this is the output printed to the terminal:
>
>
>[mid2018@node142 Results]$ $FSL_FIXDIR/hcp_fix $run/${run}.nii.gz 2000
>processing FMRI file TGNG3 with highpass 2000
>running highpass
>running MELODIC
>running FIX
>FIX Feature extraction for Melodic output directory: TGNG3_hp2000.ica
> create edge masks
> run FAST
> registration of standard space masks
> extract features
>FIX Classifying components in Melodic directory: TGNG3_hp2000.ica using
>training file:
>/home/caseylab_curate/software/fix1.06/training_files/HCP_hp2000.RData
>and threshold 10
>FIX Applying cleanup using cleanup file:
>TGNG3_hp2000.ica/fix4melview_HCP_hp2000_thr10.txt and motion cleanup set
>to 1
>
>
>Thank you very much,
>Michael