Point it to the folder where those functions are. Matt.
From: Leonardo Tozzi <lto...@stanford.edu<mailto:lto...@stanford.edu>> Date: Tuesday, January 8, 2019 at 5:50 PM To: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>>, Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] Identifying noise components in group MELODIC on ciftis Dear Michael, The hcp_fix in the master works with fix1.067 up to the last step. It does compute and I think classify the components, but it throws an error when it should clean up the data: FIX Applying cleanup using cleanup file: rfMRI_REST1_PA_hp2000.ica/fix4melview_HCP_hp2000_thr10.txt and motion cleanup set to 0 Could not find a supported file with prefix "rfMRI_REST1_PA_hp2000.ica/filtered_func_data_clean" Could not find a supported file with prefix "rfMRI_REST1_PA_hp2000.ica/filtered_func_data_clean_vn" I found a thread on the mailing list related to this problem here: https://www.mail-archive.com/hcp-users@humanconnectome.org/msg07077.html Timothy Coalson answered saying: .”fix.log says that the specified path for the cifti matlab functions is wrong (nonexistent directory).”. Indeed my .fix.log file says: [Warning: Name is nonexistent or not a directory: /vols/Data/HCP/workbench/CIFTIMatlabReaderWriter] I think this comes from the file: fix1.067/settings.sh. Inside it, it says: # Set this to CIFTI Matlab Reader/Writer for use within HCP pipelines FSL_FIX_CIFTIRW='/vols/Data/HCP/workbench/CIFTIMatlabReaderWriter'; I am unsure what is meant here and where I should point this variable: I am using the ciftiopen and ciftisave functions to open and read cifti files. Would you have any suggestion on what the FSL_FIX_CIFTIRW variable should be so that I can write the cleaned timeseries? 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 From: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>> Date: Tuesday, January 8, 2019 at 1:58 PM To: Leonardo Tozzi <lto...@stanford.edu<mailto:lto...@stanford.edu>>, "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>> Subject: Re: [HCP-Users] Identifying noise components in group MELODIC on ciftis We run a group ICA following FIX (ICA) cleanup all the time. BTW: The whole HCP FIX suite is getting a thorough updating. I’m not sure if the ‘hcp_fix’ currently in the github master even works or not. Hopefully we’ll have GitHub updated within a week. The main issue then with MR-FIX will be the need for a new FSL release (which is pending as well). 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: Leonardo Tozzi <lto...@stanford.edu<mailto:lto...@stanford.edu>> Date: Tuesday, January 8, 2019 at 3:49 PM To: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>>, "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] Identifying noise components in group MELODIC on ciftis Dear Matthew and Michael, Thank you very much for your suggestions! I will then wait for your release of the multi-run fix, in the meantime I will try to run it on the individual tasks/resting state sessions. Just a follow-up question: would it make sense to you to first run FIX to remove artifacts, then run MELODIC ICA on the cleaned data at the group level to get some group components and then get the individual components with double regression? Or is there some problem you see in running an ICA after an ICA? 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 From: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>> Date: Tuesday, January 8, 2019 at 1:40 PM To: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>>, Leonardo Tozzi <lto...@stanford.edu<mailto:lto...@stanford.edu>> Subject: Re: [HCP-Users] Identifying noise components in group MELODIC on ciftis Hi Leonardo, Note that we’re in the middle of a rather large set of modifications related to “multi-run” FIX, and it isn’t quite ready for easy public use. Hopefully soon. 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 "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>> Date: Tuesday, January 8, 2019 at 3:20 PM 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] Identifying noise components in group MELODIC on ciftis I would recommend running the multi-run FIX pipeline for that on all the fMRI data together. That works on the volume data and then also cleans the CIFTI data at the same time. 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: Tuesday, January 8, 2019 at 11:35 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] Identifying noise components in group MELODIC on ciftis Dear experts, I have preprocessed with the minimal preprocessing pipeline some data which includes resting state and 3 fMRI tasks. I have then ran MELODIC group ICA on the resulting dtseries.nii files (for each task separately). My question is this: I have only greyordinate data in the outputs, so how can I optimally identify the noise components since I have no data for example from the CSF or white matter? I am also wondering if running the ICA on the greyordinate data is already somehow excluding the noise components that are predominantly in the CSF and white matter. I was thinking one way I could proceed is to use the statistics produced from MELODIC of the comparison between the components and the “background noise” (although I am unsure about how this is defined) and/or enter the GLMs of my tasks in MELODIC and see if I find components that correlate with the design (but then I would not know what to do with resting state). Another possibility would be to use the FIX pipeline, but I am not sure if it’s implemented for tasks and if it can be used at the group level. In any case, I wanted to make sure that the processing is the same for resting state and task data. Also, I would probably need to retrain the classifier, since we are conducting our experiment at a different site and on a GE magnet, correct? I would appreciate any pointers on how to best proceed with this matter. 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<mailto: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<mailto: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. ________________________________ 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. ________________________________ 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
