Dear Greg, Thank you very much for your clarification!
Best, Ryota On Thu, Sep 4, 2014 at 6:42 PM, Greg Burgess <[email protected]> wrote: > Hi Ryota, > > Please see my comments inline below. I hope the additional info helps! > > --Greg > > ____________________________________________________________________ > Greg Burgess, Ph.D. > Staff Scientist, Human Connectome Project > Washington University School of Medicine > Department of Anatomy and Neurobiology > Phone: 314-362-7864 > Email: [email protected] > > On Sep 2, 2014, at 7:32 AM, Ryota Tomioka <[email protected]> wrote: > >> Hi all, >> >> I have been looking into the task fMRI data and comparing the timings >> saved in EVs folder with those explained Table 4 in Barch et al. >> (2013) "Function in the human connectome: Task-fMRI and individual >> differences in behavior". >> >> I am new to fMRI, so maybe I am missing something basic but the >> numbers do not seem to exactly match what I expect. I would greatly >> appreciate if some of you could l clarify this for me. >> >> 1. What is the length of a frame? >> If I use read_avw.m function provided by FSL, I get 0.72 s/frame. > > The TR is definitely 0.720 s per frame. > >> The >> numbers I get from Table 4 in Barch et al. seem to vary from a task to >> another. For example, for WM task, 5:01 / 405 frames = 0.74 s/frame. > > Our apologies for this confusion. The “run duration” values were read > directly from the Siemens syngo console. That "run duration" includes > additional preparation volumes that are present before the beginning of the > actual task scans. More specifically, the multiband fMRI sequence used in HCP > collects eight MB8 scans that are re-combined to make the SBRef image that is > necessary for registration and MB reconstruction, as well as five “dummy” > scans that are discarded to allow the MR signal to reach steady state. Those > thirteen volumes add 9.36 s of preparation time before the task scans. > > If you take the number of frames per run multiplied by 0.720 s per frame, and > add 9.36 s for the preparation volumes, your sum will be within 500 ms > (rounding error) of the run duration reported in Table 4. > > >> Actually, the numbers in this table does not add up as I would expect. >> For example, for the motor task, according to the table the run >> duration is 3:34 (min). But 10 * (12 + 3) + 3 * 15 = 3:15 (min). > > I would suggest ignoring the preparation volumes and instead accounting for > the number of frames * the TR: (284*.720) = 204.48 s for the MOTOR task. In > this example, you’ve forgotten to add the 8 s “task initiation countdown” > that occurs at the start of the run for most tasks (see last row of Table 4). > Therefore, the actual duration of the task is the sum of the task blocks, the > fixation blocks, and the initial countdown: [10 * (12 + 3)] + [3 * 15] + [8] > = 203 s. > > Because there is some variability in the timing of events in E-Prime due to > the use of the Windows OS, we have padded the end of all task runs with a > small number of additional volumes to ensure that we are acquiring BOLD > signal throughout the entire task, even if the task events were delayed due > to Windows / E-Prime. This is also the reason why precise timing is provided > for each participant, rather than using a general set of EVs across all > participants. > > >> >> 2. Does the first fMRI frame corresponds to the origin (0s) of the >> times in *.txt files in EVs folder? >> The first trial (or cue) saved in EVs folder seems to be always around >> 8s and the last trial seems to end always much earlier than the >> duration of a run. I was wondering what time the timings in *.txt >> files are measured from. > > The first fMRI frame (after the preparation volumes) corresponds to the > origin (0 s) in the .txt EV files. The first task trial occurs after an 8 s > countdown to prepare participants. Therefore, the first event in the EV files > occurs around 8s after the onset of the first fMRI frame. > >> >> 3. What is Sync.txt in EVs folder? >> It doesn't seem to be explained in the reference manual. > > The variables required to convert the E-Prime timing information in the > TAB.txt file to the timing provided in the EV files is explained in an > Appendix to the Reference Manual: > http://humanconnectome.org/documentation/S500/HCP_S500_Release_Appendix_VI.pdf > > The Sync.txt file contains the offset in ms between the start of the E-Prime > script and the onset of the first fMRI frame / countdown event. This value is > essentially subtracted from the timing in the TAB.txt files to provide the > timing relative to the onset of the first fMRI frame rather than the start of > the E-Prime script. > > >> >> Thanks, >> >> Ryota Tomioka >> _______________________________________________ >> HCP-Users mailing list >> [email protected] >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users > -- Ryota Tomioka, PhD Research Assistant Professor Toyota Technological Institute at Chicago _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
