See lines 177-193 from the hcp_fix script. Matt.
From: Shachar Gal <gal.shac...@gmail.com<mailto:gal.shac...@gmail.com>> Date: Tuesday, December 11, 2018 at 6:33 AM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>, Ido Tavor <idota...@gmail.com<mailto:idota...@gmail.com>>, Niv Tik <niv...@gmail.com<mailto:niv...@gmail.com>> Subject: Re: [HCP-Users] HCP_FIX I'm sorry if I'm pressing the issue too much, but I still can't see how the hcp_fix solves the fact the the main FIX script expects several files that do are not available from the registration process in the hcp pipeline. Thanks for your patience, Shachar On Tue, Dec 11, 2018, 14:07 Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: You can still do training after running hcp_fix. As for not using hcp_fix initially and just running the main fix script, I haven’t tried that. You might need to ask on the main FSL list. Matt. From: Shachar Gal <gal.shac...@gmail.com<mailto:gal.shac...@gmail.com>> Date: Tuesday, December 11, 2018 at 5:21 AM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>, Ido Tavor <idota...@gmail.com<mailto:idota...@gmail.com>> Subject: Re: [HCP-Users] HCP_FIX hey Matt, I was trying to use the FIX script from the fix directory that came with this - downloadable FIX tar file<http://www.fmrib.ox.ac.uk/~steve/ftp/fix.tar.gz> tar file. I did so because I didn't see in the content of the hcp_fix script that it runs the training mode, and I needed to create the training file (as I said before, im at the stage where I have hand labelled the components of the resting state data for 10 of my subjects after running MELODIC, and I wish to train FIX using these labels). if I'm mistaken in my workflow, I would appreciate any further instructions as to the correct workflow for using the FIX pipelines. thank you On Mon, 10 Dec 2018 at 23:13, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: Did you use the hcp_fix script or some other method of running FIX on HCP data. Matt. From: Shachar Gal <gal.shac...@gmail.com<mailto:gal.shac...@gmail.com>> Date: Monday, December 10, 2018 at 7:47 AM To: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>> Cc: 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>>, Ido Tavor <idota...@gmail.com<mailto:idota...@gmail.com>> Subject: Re: [HCP-Users] HCP_FIX hey again, thanks for pointing out the relevant lines for the dual regression. I have some further questions about the workflow of running FIX. so I did hand classification for 10 of my subjects, and wished to run FIX with the -t option, in order to create the training data. but then I realized that FIX expects my .ica folder to include a /reg folder inside, which it does not include, because the input data I gave to melodic was already registered (using all of the hcp pipelines). so this brings up two questions: 1) if it still expects this kind of structure, after being tweaked to fit the hcp daa, does this mean that you run melodic with registration and all? 2) if not, then what file do you give him as the highres2example_func.mat?(the other files it expects /reg folder to include are more obvious) thanks, Shachar On Mon, 26 Nov 2018 at 19:02, Harms, Michael <mha...@wustl.edu<mailto:mha...@wustl.edu>> wrote: Hi, The cleaning of the CIFTI data is done automatically in fix_3_clean.m of the FIX distribution, which is called by the fix script itself. The only relevant aspect of hcp_fix to that process is that hcp_fix creates the following symbolic link: if [ -f ../${fmri_orig}_Atlas.dtseries.nii ] ; then $FSLDIR/bin/imln ../${fmri_orig}_Atlas.dtseries.nii Atlas.dtseries.nii fi since fix_3_clean.m is hard-coded to look for a file named Atlas.dtseries.nii 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 Shachar Gal <gal.shac...@gmail.com<mailto:gal.shac...@gmail.com>> Date: Friday, November 23, 2018 at 2:37 AM To: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] HCP_FIX hey matt, the thing is, I didn't see anything in the hip_fix script the projects the "fix cleaned" volume to surface, so when does that happen? considering that you mentioned you're currently editing these scripts, I think we would just use the original FSL FIX, and later project the fix cleaned volume to surface using your 'fMRISurface' pipeline. thanks, Shachar On Tue, 20 Nov 2018 at 04:10, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: The hcp_fix script is for enabling a few enhancements specific to HCP-Style processing. These scripts are currently being edited and tested and we will have new versions announced soon. PostFix generates the Workbench scenes for hand classification of components. Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Shachar Gal <gal.shac...@gmail.com<mailto:gal.shac...@gmail.com>> Date: Monday, November 19, 2018 at 3:30 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] HCP_FIX Dear experts, I was was looking for some documentation regarding the differences between the standard FSL FIX script, and the HCP's modified version, but could not find such. could you point me to such a documentation, if exists, or perhaps elaborate briefly on the subject? on the same subject, is there any similar documentation regarding postfix? I'm not sure what's its purpose in the cleaning and applying procedure. thanks. Shachar Gal _______________________________________________ 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. ________________________________ 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
