Dear Greg, Thank you very much for your clarification.
Best, Ryota On Mon, Sep 15, 2014 at 6:42 PM, Greg Burgess <gcburg...@gmail.com> wrote: > Hello Ryota, > > Please see my comments in-line below. > > Thanks, > --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: gburg...@wustl.edu > > Ryota Tomioka wrote: >> >> Hi Greg, >> >> I was looking a bit more into other tasks and would appreciate if you >> (or others) could clarify the issues below: >> >> Language task >> I found that some times the response event starts from a time >> exceeding the number of frames in a run. For example, >> $cat 100307/MNINonLinear/Results/tfMRI_LANGUAGE_LR/EVs/response_math.txt >> 39.371 2.965 1.0 >> 51.926 2.956 1.0 >> 94.908 2.965 1.0 >> 107.703 2.959 1.0 >> 148.806 2.968 1.0 >> 161.614 2.959 1.0 >> 171.73 2.961 1.0 >> 184.138 2.966 1.0 >> 229.213 2.964 1.0 >> >> Here the number of frames is 316 (=227.52 s), whereas the last >> response event happens at 229.213 s. The RL phase encoding also had >> the same issue. > > > For LANGUAGE, the event-related EVs are actually part of the larger task > structure. In other words, each story or math trial consists of a > presentation, a question, and a response. The "dummy" math events will start > if the scan has not completed, and those events will continue for a full > trial (present, question, and response events). The scan could end somewhere > in the middle of the trial, in which case the response event might start > after the scan has completed. > > >> >> Emotion processing task >> There seem to be only fear.txt and neut.txt corresponding to the face >> blocks and shape blocks. How can I see if the face shown was an angry >> or fearful face? How about the subjects' responses? > > > If you have contrasts of interest that are not included in the EVs provided > by HCP, you can parse the TAB.txt files in each EV folder to create your own > EVs. The documentation at > http://humanconnectome.org/documentation/S500/HCP_S500_Release_Appendix_VI.pdf > will provide some additional information to help you parse those files. > > >> Also similarity to >> the language task, the last block exceeds the number of frames. Is >> this is the bug explained in the reference manual? Does this affect >> all 500 subjects? > > > Yes, this is due to the bug described in the reference manual. To maintain > consistency across participants, we have not changed the script mid-stream. > Therefore, it does affect all 500 subjects. > > >> >> >> Thanks, >> Ryota >> >> >> >> On Thu, Sep 4, 2014 at 6:42 PM, Greg Burgess<gcburg...@gmail.com> 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: burge...@pcg.wustl.edu >>> >>> On Sep 2, 2014, at 7:32 AM, Ryota Tomioka<tomi...@ttic.edu> 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 >>>> HCP-Users@humanconnectome.org >>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> >> >> >> > -- Ryota Tomioka, PhD Research Assistant Professor Toyota Technological Institute at Chicago _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
