and if I can be more specific on what we don't really understand regarding the procedure-
the procedure when using FSL's FIX is as follows: we run melodic -> then we hand-classify the components and create the label files -> the we train the FIX algorithm -> the we use it to clean all of our data. but in the hcp_fix script, i saw it calls melodic by itself, so im a bit confused about the parallel step-by-step procedure, that includes the hcp_fix script and the PostFix script. hope this clears things up. thanks, Shachar On Thu, 22 Nov 2018 at 17:43, Shachar Gal <gal.shac...@gmail.com> wrote: > Hi Michael, > the context is that we are currently in the last stages of planning our > new research, after finishing a pilot experiment, and we want to be sure we > understand each processing and analysis step we take along the way. > we have some experience in the lab with using FSL's FIX, and after > implementing the HCP's surface based analysis and processing on all the > other stages of analysing our data, we wanted to understand the differences > between the two approaches of Ica-cleaning (volume and surface), and the > way your FIX pipeline works. > > Cheers, > Shachar > > On Thu, 22 Nov 2018 at 16:49, Harms, Michael <mha...@wustl.edu> wrote: > >> >> >> Hi, >> >> What is the overall context of this inquiry? Are you getting errors with >> running the version of hcp_fix in ICAFIX/hcp_fix? If so, simply revert to >> using the version of hcp_fix supplied with the FIX distribution itself. >> That doesn’t include some of the enhancements that Matt mentioned are being >> worked on, but it works. >> >> >> >> 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 "Glasser, >> Matthew" <glass...@wustl.edu> >> *Date: *Thursday, November 22, 2018 at 8:29 AM >> *To: *Shachar Gal <gal.shac...@gmail.com> >> *Cc: *"hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >> *Subject: *Re: [HCP-Users] HCP_FIX >> >> >> >> hcp_fix cleans both the volume and CIFTI data in parallel. If you >> regress the spatial ICA timecourses from the volume-based ICA into the >> CIFTI data, you produce CIFTI spatial maps. >> >> >> >> Matt. >> >> >> >> *From: *Shachar Gal <gal.shac...@gmail.com> >> *Date: *Thursday, November 22, 2018 at 6:10 AM >> *To: *Matt Glasser <glass...@wustl.edu> >> *Cc: *"hcp-users@humanconnectome.org" <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> >> 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> on behalf of Shachar Gal >> <gal.shac...@gmail.com> >> *Date: *Monday, November 19, 2018 at 3:30 AM >> *To: *"hcp-users@humanconnectome.org" <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 >> 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. >> >> _______________________________________________ >> 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
