Re: [HCP-Users] A minor question regarding HCP 7T movie data
Hi, It isn’t surprising that data will be missing in some subjects, due either to problems at the scanner, or problems during processing. 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: on behalf of Reza Rajimehr Date: Friday, June 7, 2019 at 11:00 AM To: Keith Jamison , hcp-users Subject: Re: [HCP-Users] A minor question regarding HCP 7T movie data Thanks Keith! I am currently working with the Movie Task fMRI 2mm/32k FIX-Denoised (Compact) dataset, and I noticed the issues below: 1) Two subjects (126931 and 74) do not have MSMAll-registered time-series data. 2) Five subjects (181636, 473952, 536647, 552241, and 973770) have two runs (MOVIE1 and MOVIE2). 3) One subject (585256) has three runs (MOVIE1, MOVIE3, and MOVIE4). Best, Reza On Mon, Jun 3, 2019 at 8:33 PM Keith Jamison mailto:kjami...@umn.edu>> wrote: Hi Reza, Your interpretation of the timing is correct. The validation segment in each movie scan was shifted by 40-200ms for the "v2" version. This was done in order to make that final 83 second clip begin precisely at the start of the next TR for all 4 movie sessions. Given HRF variability, ignoring this change will probably not adversely impact most analyses. -Keith On Fri, May 31, 2019 at 9:05 PM Reza Rajimehr mailto:rajim...@gmail.com>> wrote: Hi, The HCP S1200 Reference Manual says that there are two versions of 4 movie files. Some subjects have been scanned with one version, and the remaining subjects have been scanned with another version. Version 2 includes these changes: 7T_MOVIE1_CC1_v2 remains unchanged. 7T_ MOVIE2_HO1_v2 removed 1 frame of rest before the validation clip. 7T_MOVIE3_CC2_v2 removed 5 frames of rest before the validation clip. 7T_MOVIE4_HO2_v2 added 4 frames of rest before the validation clip. Here *frame* is a frame of the movie, right? Assuming that the movies are ~25 frames per second, the deviations are between 0 and ~200 ms in each movie file. Considering the TR of one second and the slow hemodynamic BOLD responses, these deviations are negligible, and we can possibly ignore them when concatenating time-series data across all subjects. Would you agree? Thanks, Reza ___ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ___ 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
Re: [HCP-Users] A minor question regarding HCP 7T movie data
Thanks Keith! I am currently working with the Movie Task fMRI 2mm/32k FIX-Denoised (Compact) dataset, and I noticed the issues below: 1) Two subjects (126931 and 74) do not have MSMAll-registered time-series data. 2) Five subjects (181636, 473952, 536647, 552241, and 973770) have two runs (MOVIE1 and MOVIE2). 3) One subject (585256) has three runs (MOVIE1, MOVIE3, and MOVIE4). Best, Reza On Mon, Jun 3, 2019 at 8:33 PM Keith Jamison wrote: > Hi Reza, > > Your interpretation of the timing is correct. The validation segment in > each movie scan was shifted by 40-200ms for the "v2" version. This was done > in order to make that final 83 second clip begin precisely at the start of > the next TR for all 4 movie sessions. > > Given HRF variability, ignoring this change will probably not adversely > impact most analyses. > > -Keith > > > On Fri, May 31, 2019 at 9:05 PM Reza Rajimehr wrote: > >> Hi, >> >> The HCP S1200 Reference Manual says that there are two versions of 4 >> movie files. Some subjects have been scanned with one version, and the >> remaining subjects have been scanned with another version. Version 2 >> includes these changes: >> >> 7T_MOVIE1_CC1_v2 remains unchanged. >> >> 7T_ MOVIE2_HO1_v2 removed 1 frame of rest before the validation clip. >> >> 7T_MOVIE3_CC2_v2 removed 5 frames of rest before the validation clip. >> >> 7T_MOVIE4_HO2_v2 added 4 frames of rest before the validation clip. >> >> Here *frame* is a frame of the movie, right? >> >> Assuming that the movies are ~25 frames per second, the deviations are >> between 0 and ~200 ms in each movie file. Considering the TR of one second >> and the slow hemodynamic BOLD responses, these deviations are negligible, >> and we can possibly ignore them when concatenating time-series data across >> all subjects. Would you agree? >> >> Thanks, >> Reza >> >> ___ >> HCP-Users mailing list >> HCP-Users@humanconnectome.org >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] A minor question regarding HCP 7T movie data
Hi Reza, Your interpretation of the timing is correct. The validation segment in each movie scan was shifted by 40-200ms for the "v2" version. This was done in order to make that final 83 second clip begin precisely at the start of the next TR for all 4 movie sessions. Given HRF variability, ignoring this change will probably not adversely impact most analyses. -Keith On Fri, May 31, 2019 at 9:05 PM Reza Rajimehr wrote: > Hi, > > The HCP S1200 Reference Manual says that there are two versions of 4 movie > files. Some subjects have been scanned with one version, and the remaining > subjects have been scanned with another version. Version 2 includes these > changes: > > 7T_MOVIE1_CC1_v2 remains unchanged. > > 7T_ MOVIE2_HO1_v2 removed 1 frame of rest before the validation clip. > > 7T_MOVIE3_CC2_v2 removed 5 frames of rest before the validation clip. > > 7T_MOVIE4_HO2_v2 added 4 frames of rest before the validation clip. > > Here *frame* is a frame of the movie, right? > > Assuming that the movies are ~25 frames per second, the deviations are > between 0 and ~200 ms in each movie file. Considering the TR of one second > and the slow hemodynamic BOLD responses, these deviations are negligible, > and we can possibly ignore them when concatenating time-series data across > all subjects. Would you agree? > > Thanks, > Reza > > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
