That is saying that you don't have the matlab gifti library installed (or
it isn't on your matlab path).
Tim
On Tue, Feb 26, 2019 at 6:09 PM Leonardo Tozzi <lto...@stanford.edu> wrote:
> 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 | (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> on behalf of Leonardo
> Tozzi <lto...@stanford.edu>
> *Date: *Monday, February 25, 2019 at 5:09 PM
> *To: *"Harms, Michael" <mha...@wustl.edu>, "hcp-users@humanconnectome.org"
> <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 | (650) 5615738
>
>
>
>
>
> *From: *"Harms, Michael" <mha...@wustl.edu>
> *Date: *Monday, February 25, 2019 at 9:59 AM
> *To: *Leonardo Tozzi <lto...@stanford.edu>, "hcp-users@humanconnectome.org"
> <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
>
>
>
> *From: *<hcp-users-boun...@humanconnectome.org> on behalf of Leonardo
> Tozzi <lto...@stanford.edu>
> *Date: *Monday, February 25, 2019 at 11:42 AM
> *To: *"hcp-users@humanconnectome.org" <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 | (650) 5615738
>
>
>
> _______________________________________________
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>
>
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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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