Re: [HCP-Users] "good" vs. "bad" components in ICA-FIX denoised rsfMRI data

[Harms, Michael]

Hi Steve, I’m not seeing a file by that name in the HCP FIX processing. In the 900 subject release data, there should be files in the rfMRI_REST?_{LR,RL}_hp2000.ica folders called Noise.txt and Signal.txt that contain the classifications.  But those files are created as part of a “PostFix” script, rather than the initial FIX script itself.  And, I don’t think those particular files were created as part of the 500 subject release packages. However, if you are using 500 subject release data, you can find the noise components in the rfMRI_REST?_{LR,RL}_hp2000.ica/.fix file (note that it is dot fix, so unfortunately that info is a bit hidden in the 500 subject release data).  The Signal components are then all the other components not specified in the .fix file. cheers, -MH --  Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders 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 On 3/9/16, 2:10 AM, "hcp-users-boun...@humanconnectome.org on behalf of Stephen Smith" <hcp-users-boun...@humanconnectome.org on behalf of st...@fmrib.ox.ac.uk> wrote: Hi - it's the same as in standard FIX usage - the file listing bad components is called hand_labels_noise.txt - inside the ICA output folder. Cheers On 9 Mar 2016, at 03:25, Ely, Benjamin <benjamin....@mssm.edu> wrote: Hi all, I’m interested in running some analyses (particularly smoothness estimations) on the noise components identified by ICA-FIX. I’ve looked through several subjects’ ICA folders (e.g., rfMRI_REST1_LR_hp2000.ica/filtered_func_data.ica/), which contain a number of output stats and nifti files, but I can’t find an indication of which components were classified as “good” and “bad”. Is this information available? Thanks! -Ely _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Head of Analysis,  Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK +44 (0) 1865 222726  (fax 222717) st...@fmrib.ox.ac.uk    http://www.fmrib.ox.ac.uk/~steve --------------------------------------------------------------------------- Stop the cultural destruction of Tibet _______________________________________________ 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