Re: [HCP-Users] ICA FIX output missing

[Leonardo Tozzi]

Dear Michael,

Thank you very much for all the consideration on the use of FIX for the task 
data.

I have tried the addition you suggest. I think the command is detected, but I 
get the following error in tfMRI_EMOTION_RL_hp2000.ica/.fix.log:


{^HUndefined function or variable 'gifti'.

Error in ciftiopen (line 31)
cifti = gifti([tmpfile '.gii']);

Error in fix_3_clean (line 46)
  BO=ciftiopen('Atlas.dtseries.nii',WBC);
}^H




Would you have any thoughts on this?
Thank you,


Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Fellow
Stanford University | 401 Quarry Rd
lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738


From: "Harms, Michael" <mha...@wustl.edu>
Date: Tuesday, February 26, 2019 at 7:37 AM
To: "Glasser, Matthew" <glass...@wustl.edu>, Leonardo Tozzi 
<lto...@stanford.edu>, "hcp-users@humanconnectome.org" 
<hcp-users@humanconnectome.org>
Cc: "Burgess, Gregory" <gburg...@wustl.edu>
Subject: Re: [HCP-Users] ICA FIX output missing


Hi Leonardo,
Couple things:

1)  In the context of FIX, things get a little convoluted, since the FIX 
distribution has its own settings.sh file that needs to be set appropriately.  
If you’ve hard-coded the FSL_FIX_WBC variable in that settings.sh file, then 
the location to wb_command in the Examples/Scripts/SetUpHCPPipeline.sh isn’t 
necessarily relevant.  In the settings.sh file for FIX on our cluster, we use 
the following construction:

if [ -x "$(command -v wb_command)" ]; then
    FSL_FIX_WBC=$(command -v wb_command)
else
    echo "ERROR in $0: wb_command (Workbench) must be in your path"
    exit 1
fi
so that FIX does actually respect that location of wb_command that is already 
in your path.

2) Regarding MR-FIX and the TaskfMRIAnalysis scripts, while they may run after 
MR-FIX, there are two issues that need to be addressed yet:
a) The temporal filter, which was presumably already applied during MR-FIX, 
gets applied again with TaskfMRILevel1.sh.  This script needs to be modified to 
be smarter regarding the temporal filtering (i.e., provide an option to NOT 
reapply the temporal filter).
b) The space spanned by the noise regressors from FIX is not regressed out of 
the task regressor prior to the GLM, which means that variance removed during 
FIX can be reintroduced during the task GLM fitting (depending on the extent to 
which the space spanned by the noise regressors overlaps with the task GLM).

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: "Glasser, Matthew" <glass...@wustl.edu>
Date: Monday, February 25, 2019 at 6:53 PM
To: Leonardo Tozzi <lto...@stanford.edu>, "Harms, Michael" <mha...@wustl.edu>, 
"hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] ICA FIX output missing

You’ll want to be using wb_command 1.3.2.  I am not aware of any modifications 
that are necessary to use the TaskfMRIAnalysis scripts on MR+FIX data and have 
analyzed hundreds of subjects after MR+FIX.

As for this issue, is wb_command set properly here: 
https://github.com/Washington-University/HCPpipelines/blob/master/Examples/Scripts/SetUpHCPPipeline.sh

What about on your ${PATH}?

As for MR+FIX itself, we are only waiting on an FSL 6.0.1 release as testing 
has concluded successfully.

Matt.

From: 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Leonardo Tozzi <lto...@stanford.edu<mailto:lto...@stanford.edu>>
Date: Monday, February 25, 2019 at 5:09 PM
To: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>>, 
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] ICA FIX output missing

Dear Michael,

Thank you for pointing me to the logfiles.

It seems like the script is not finding the directory where wb_command is. In 
my case, I am loading it as a module in my HPC cluster. I have also put its 
path in ICAFIX/fix1.067/settings.sh as follows:


# Set this to the location of the HCP Workbench command for your platform
FSL_FIX_WBC='/share/software/user/open/workbench/1.3.1/bin/wb_command';



However, the script does not seem to “see” this path and instead uses the 
setting I was using on my local machine. In the logfile 
tfMRI_EMOTION_RL_hp2000.ica/.fix.log, I get the following error:


/bin/bash: /Applications/workbench/bin_macosx64/wb_command: No such file or 
directory


Is there another place in the scripts that is overriding my settings.sh?
Concerning the length or the runs, I will look into the multirun 
implementation, but indeed my intention was of using the TaskfMRIAnalysis 
scripts to get my “activations”.
Thank you,

Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Fellow
Stanford University | 401 Quarry Rd
lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738


From: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>>
Date: Monday, February 25, 2019 at 9:59 AM
To: Leonardo Tozzi <lto...@stanford.edu<mailto:lto...@stanford.edu>>, 
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] ICA FIX output missing


Hi,
The log files for ICA FIX are a bit scattered.
In the .ica directory check: .fix_2b_predict.log (from the prediction – i.e,. R 
code) and .fix.log (from the cleaning stage).
And in the .ica/fix directory, check logMatlab.txt (I believe that is from the 
feature extraction stage).

Note that our recommendation is to use “multi-run” FIX on the task data, due to 
its shorter run length.  We hope to have an announcement on that in the near 
future.  In that regard, you would implement your desired filtering as part of 
the MR-FIX cleaning (and there is a new “polynomial detrend” option, for faster 
execution), although I believe that we haven’t quite gotten around to adapting 
the TaskfMRIAnalysis scripts to work on data from MR-FIX.

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<mailto:mha...@wustl.edu>

From: 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Leonardo Tozzi <lto...@stanford.edu<mailto:lto...@stanford.edu>>
Date: Monday, February 25, 2019 at 11:42 AM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] ICA FIX output missing

Dear Experts,

I have been trying to use ICA FIX to denoise task data of a large number of 
subjects from the HYA release.

I have managed to make it run with no errors on our local HPC cluster, but I 
still have one problem. In the vast majority of subjects, even if FIX works and 
produces a file (“fix4melview_HCP_hp2000_thr10.txt”) which shows which 
components are noise, I don’t get the final output, for example 
“tfMRI_EMOTION_RL_Atlas_hp2000_clean.dtseries.nii”. This is especially puzzling 
since it does seem to work for a minority of subjects. The matlab log also 
shows no errors.

A related question I would have is what filter you would recommend for task 
data. My intention is to use a GLM on the cleaned data, so is 2000 (linear 
detrending) ok, since then a lower high-pass will be applied in the GLM step?

Thank you very much,



Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Fellow
Stanford University | 401 Quarry Rd
lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738


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The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.

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