Re: [HCP-Users] phase encoding and group ICA

[Harms, Michael]

As a brief follow-up to this:  As you see from Steve's pasted code, the order of the time series in the PTN is based solely on the file name in ConnectomeDB.  Importantly, nothing in the REST{1,2}_{LR,RL} naming tells you whether the LR run came first, or vice-versa.  All you know for sure is that REST1 runs came before REST2.  (Most typically, a day beforehand, but a minority of subjects have multiple days between their REST1 and REST2 sessions).  While there is a prototypical temporal ordering of the runs, which would hold for the vast majority of subjects, on infrequent occasions that ordering might have been violated -- e.g., if a scan had to be reacquired.   So, if you are investigating something that explicitly and critically depends on knowing the exact order in which the LR/RL runs were acquired for each and every subject, then you will have to pull the series acquisition times from the database.  There is a previous post to the list with details on how to do that.  Off the top of my head, I can't remember if that post included a mechanism to also get the number of days between the REST1 and REST2 sessions.  We've talked about making those sort of details more readily available, but it hasn't been a priority. 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 From: Stephen Smith <st...@fmrib.ox.ac.uk> Date: Wednesday, November 25, 2015 1:18 AM To: Mary Beth <m...@jhmi.edu> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] phase encoding and group ICA Hi -  Wrt group-ICA, it makes no difference what order the data was fed into the MIGP group-PCA. Wrt the 4 chunks combined into the node timeseries in the 500-subject PTN release:  the order is always the following, so you will need to take into account the information you pasted below if you want to know about how this interacts with session orderings. ff{1}=sprintf('%s/%d/RESOURCES/rfMRI_REST1_LR_FIX/rfMRI_REST1_LR/rfMRI_REST1_LR_Atlas_hp2000_clean.dtseries.nii',SUBJECTS,subID); ff{2}=sprintf('%s/%d/RESOURCES/rfMRI_REST1_RL_FIX/rfMRI_REST1_RL/rfMRI_REST1_RL_Atlas_hp2000_clean.dtseries.nii',SUBJECTS,subID); ff{3}=sprintf('%s/%d/RESOURCES/rfMRI_REST2_LR_FIX/rfMRI_REST2_LR/rfMRI_REST2_LR_Atlas_hp2000_clean.dtseries.nii',SUBJECTS,subID); ff{4}=sprintf('%s/%d/RESOURCES/rfMRI_REST2_RL_FIX/rfMRI_REST2_RL/rfMRI_REST2_RL_Atlas_hp2000_clean.dtseries.nii',SUBJECTS,subID); Cheers, Steve. ps - for the 900 PTN release we will be releasing the code used to generate it. On 25 Nov 2015, at 01:17, Mary Beth <m...@jhmi.edu> wrote: The subject-specific parcel timeseries were provided in a single text file for each model order with 4800 time points each. I am trying to figure out if time points 2401-3600 from those text files always correspond to the LR session from Day 2, or if they correspond to the RL session from Day 2 for the handful of subjects collected before  1 October 2012 and the LR session from Day 2 for everyone else. I just want to make sure that I label everything correctly. I hope this clarifies my question. Thanks again for your help. -mb On Tue, Nov 24, 2015, 19:29 Glasser, Matthew <glass...@wustl.edu> wrote: I’m still not following why it matters. Peace, Matt. From: Mary Beth <m...@jhmi.edu> Date: Tuesday, November 24, 2015 at 6:18 PM To: Matt Glasser <glass...@wustl.edu>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] phase encoding and group ICA I just want to make sure I'm comparing apples to apples when I use the subject-specific timeseries.  best, mb On Tue, Nov 24, 2015 at 7:11 PM Glasser, Matthew <glass...@wustl.edu> wrote: Why does the order of the individual subject sessions matter for group ICA or PTNs? Peace, Matt. From: <hcp-users-boun...@humanconnectome.org> on behalf of Mary Beth <m...@jhmi.edu> Date: Tuesday, November 24, 2015 at 5:59 PM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: [HCP-Users] phase encoding and group ICA Hi all, According to this page http://www.humanconnectome.org/documentation/Q1/data-in-this-release.html, prior to 1 October 2012, the first resting state session of each visit was acquired with RL phase encoding, and the second session was acquired with LR phase encoding (RL/LR).  After this date, the first visit continued to be acquired in the RL/LR order, but the second visit was acquired in the opposite order, with the LR acquisition followed by the RL acquisition (LR/RL). Here's my question: prior to group ICA and the generation of subject-specific sets of node timeseries in the August, 2014 “HCP500-PTN” (Parcellation+Timeseries+Netmats) data release, were the sessions for subjects acquired before 1 October 2012 reordered to match the order of sessions for subjects acquired after 1 October 2012? Thanks in advance, Mary Beth _______________________________________________ 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 --------------------------------------------------------------------------- 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