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<mailto:lto...@stanford.edu> | (650) 5615738 _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ 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. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
