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…v5 (and Mac25Cyno.
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Please see my above comments.
Co-authored-by: Tim Coalson <coalsont@users.noreply.github.com>
| RegName="" | ||
| MatlabMode=1 | ||
| RunLocal=0 | ||
| QUEUE="matlabparallelhigh.q@brainmappers-desktop3" |
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For your testing purposes, please make a copy of the batch rather than pushing your settings (and paths), even to a branch.
I'm not sure we have any other batch scripts that submit a job that is expected to go highly parallel on each job (the non-longitudinal tICA batch examples are configured to run locally).
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Yeah the batch script needs to be still needs to be overhauled.. It should probably use HCP_YA task data like fMRIStats does.
…ROFUMO input dtseries ciftis to cifti v1 to work around weird PROFUMO file loading bug where it thinks the files aren't the same size.
| # Validate required PROFUMO parameters | ||
| if [[ "$ProfumoConfig" == "" ]] | ||
| then | ||
| log_Err_Abort "PROFUMO config file must be specified with --profumo-config" |
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It would appear that the user has to write the config file, which must contain the list of subjects (among other things), since it doesn't appear to get passed to profumo in another way. How complicated (or version-dependent) is the config format, and should we consider having the pipeline script generate it?
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It's written by the batch script, which I think offers a little more flexibility for the user than putting it directly in the pipeline script. but I can see the argument for moving it into the pipeline script.
…, to avoid SIMD buffer alignment issue in PROFUMO if files were written with an older version of cifti-matlab with 8-byte instead of 16-byte alignment.
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Pipeline for PROFUMO decomposition. I started from Andrea's Yang's PFMs code, and finished generalizing it in the HCP Pipelines style. I tested in on Mac25Rhesus and Mac25Cyno, and it is working there.
Known issues:
(1) This PR does not include the ./PFM/profumo_v2.sif singularity container, because it is 6.6G.
(2) The full run example script uses Mac25Rhesus rather than something more standard like HCP1071 and has local paths in it.
(3) The matlab needs to be compiled