We have not found that is necessary. sICA+FIX worked on the HCP task data using the HCP resting state data training set.
Matt. From: Timothy Hendrickson <[email protected]<mailto:[email protected]>> Date: Friday, July 27, 2018 at 3:15 PM To: Matt Glasser <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] MSMAll I noticed on the FSL FIX FAQ page the following: Can I use FIX to clean task fMRI data? * Yes, although you will probably need to create a study-specific training dataset Can you speak to how multi run ICA+FIX gets away without needing a study-specific training dataset? -Tim Timothy Hendrickson Neuroimaging Analyst/Staff Scientist University of Minnesota Informatics Institute University of Minnesota Bioinformatics M.S. Candidate Office: 612-624-0783 Mobile: 507-259-3434 (texts okay) On Tue, Jul 24, 2018 at 3:28 PM, Timothy Hendrickson <[email protected]<mailto:[email protected]>> wrote: Sorry for the dumb question, I should have read the code further. Thanks! Timothy Hendrickson Neuroimaging Analyst/Staff Scientist University of Minnesota Informatics Institute University of Minnesota Bioinformatics M.S. Candidate Office: 612-624-0783 Mobile: 507-259-3434 (texts okay) On Tue, Jul 24, 2018 at 3:21 PM, Glasser, Matthew <[email protected]<mailto:[email protected]>> wrote: The MR+FIX pipeline automatically breaks the runs back up at the end. Matt. From: Timothy Hendrickson <[email protected]<mailto:[email protected]>> Date: Tuesday, July 24, 2018 at 3:17 PM To: Matt Glasser <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] MSMAll So once I finish with the multiICAFIX pipeline I wold have to manually separate the concatenated cleaned nifti file and then run MSMAll on those scans. Is that right? Timothy Hendrickson Neuroimaging Analyst/Staff Scientist University of Minnesota Informatics Institute University of Minnesota Bioinformatics M.S. Candidate Office: 612-624-0783 Mobile: 507-259-3434 (texts okay) On Mon, Jul 23, 2018 at 1:31 PM, Glasser, Matthew <[email protected]<mailto:[email protected]>> wrote: Give it a try, but you may find that you need to split it into two. Make sure you are using the latest released FSL for this. Matt. From: Timothy Hendrickson <[email protected]<mailto:[email protected]>> Date: Monday, July 23, 2018 at 1:26 PM To: Matt Glasser <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] MSMAll I handle processing for several studies, an upward bound for the studies I handle would be approximately 3000 frames. Timothy Hendrickson Neuroimaging Analyst/Staff Scientist University of Minnesota Informatics Institute University of Minnesota Bioinformatics M.S. Candidate Office: 612-624-0783 Mobile: 507-259-3434 (texts okay) On Mon, Jul 23, 2018 at 1:12 PM, Glasser, Matthew <[email protected]<mailto:[email protected]>> wrote: FSL 6.0 hasn’t been released but has some updates to the math library that makes melodic much faster. Also if you make too large of a merged file it will crash the old melodic because of some bugs. How many frames are you wanting to do? Peace, Matt. From: Timothy Hendrickson <[email protected]<mailto:[email protected]>> Date: Monday, July 23, 2018 at 1:02 PM To: Matt Glasser <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] MSMAll Thanks Matt. With the hcp_fix_multi_run script I notice that in the first few lines of code there is a line with software requirements which include FIX >= 1.065 and FSL 6.0 melodic version. I have FIX version = 1.066 and I have FSL 5.0.9 and melodic version 3.14. Without the FSL 6.0 release handy to me I am not sure what melodic version would be considered equivalent "FSL 6.0". Could you shed some light on this for me? -Tim Timothy Hendrickson Neuroimaging Analyst/Staff Scientist University of Minnesota Informatics Institute University of Minnesota Bioinformatics M.S. Candidate Office: 612-624-0783 Mobile: 507-259-3434 (texts okay) On Thu, Jul 19, 2018 at 6:26 PM, Glasser, Matthew <[email protected]<mailto:[email protected]>> wrote: There is a new Multi-run FIX pipeline currently available in the Git repository that you can use. I would consider it beta a this time. Matt. From: <[email protected]<mailto:[email protected]>> on behalf of Timothy Hendrickson <[email protected]<mailto:[email protected]>> Date: Thursday, July 19, 2018 at 6:24 PM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] MSMAll Hello, >From the HCP course material I noticed that that suggested format to use >MSMAll is to do so immediately after the Minimal Pre-Processing stream and >immediately before subsequent tfMRI and rfMRI processing. As MSMAll expects >the data inputted to be run through ICA-FIX I am curious what I should be >doing with tfMRI data (i.e. what mods do I have to make to hcp_fix, etc). If >you could provide me a code snippet/s that would be great! -Tim Timothy Hendrickson Neuroimaging Analyst/Staff Scientist University of Minnesota Informatics Institute University of Minnesota Bioinformatics M.S. 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