Thanks for the reply Greg. However, I am not trying to re-establish a new GLM model. I only want to use the time-series of the WM task and specifically for the face condition in order to perform functional connectivity analyses. The file tfMRI_WM_LR.nii.gz contains the 402 frames/sec time-series. Is there a specific way to combine the results of HCP's FSF analysis with these time-series in order to spot the face task as well as the correct/error/no-response trials of this task (based on their onsets/durations from the txt files) ? I mean those 402 frames, in their current form, can be used to identify the face condition task intervals and the correct/error/no-response blocks?
2016-05-20 18:24 GMT+03:00 Burgess, Greg <[email protected]>: > > On May 18, 2016, at 1:25 PM, Manousos Klados <[email protected]> wrote: > > > > > > > > Dear HCP community, > > > > I send you a question of one of my students, because he cannot subscribe > in the mailing list. His email is the following: > > > > I am currently studying tfMRI data and especially I am interested in the > Working Memory task. However, I came up with a question regarding the > onsets of the WM condition blocks. For example, in Subject 100307 the EV > directory (path:100307/MNINonLinear/Results/tfMRI_WM_LR/ EVs) contains the > .txt files with the onsets and durations of various conditions and trials > (as already stated in the manual). Lets assume that we want to study the > 2-bk face task (2bk_faces.txt). The onset is at 79.208 sec with a duration > of 27.5 sec. > > > > The first part of my question is how to retrieve this information from > the BOLD time-series (405 frames/run)? I mean, is there a fixed way to > retrieve those frames of interest in the specific interval? > > > Traditionally, a GLM is used to estimate activation in response to each > task condition. We used FSL’s FEAT ( > http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FEAT) to estimate activation. We > have provided the parameter estimates for each subject (averaged over the > two task runs) available for download in the ConnectomeDB. > > > > The last part of my question concerns the onsets of the correct trials > in this task. More specifically, the file 2bk_cor.txt contains the onsets > of the correct trials however I would expect the onsets to be on the > interval [79.208, 79.208+27.5] since those trials are executed within the > condition block. Is there a way to match this information according to the > 2-bk face onset? > > If you want to run your own GLM using different predictors, you will need > to create those predictors and GLMs on your own. You could extract the > 2bk-face-specific correct trials from the file containing all correct 2bk > trials (i.e., 2bk_cor.txt). Or you could code your predictors in any > variety of ways by processing the information in TAB.txt files directly. > See the documentation at: > http://www.humanconnectome.org/documentation/S900/HCP_S900_Release_Appendix_VI.pdf > . > > Running a custom GLM will be a little trickier, since it will require some > custom modification to the TaskfMRIAnalysis pipeline within the HCP > Pipelines. The pipelines and some documentation is located in GitHub. > https://github.com/Washington-University/Pipelines > > An example of how these scripts might be modified was provided in > Practical #7 at last year’s HCP Course > > https://www.humanconnectome.org/courses/2015/exploring-the-human-connectome.php > > Hope this helps! > --Greg > > ____________________________________________________________________ > Greg Burgess, Ph.D. > Staff Scientist, Human Connectome Project > Washington University School of Medicine > Department of Neuroscience > Phone: 314-362-7864 > Email: [email protected] > > > > > > Best regards, > > Bill. > > Manousos Klados, PhD > > Max Planck Institute for Human Cognitive & Brain Sciences > > Research Group of Neuroanatomy and Connectivity > > Phone: +49(0)-341-9940-2507 > > Mobile: +49(0)-176-6988-1781 > > Email: [email protected] > > Website: http://www.mklados.com > > Skype: mklados | Twitter: @mklados > > Address: Stephanstraße 1a PC D-04103 Leipzig Germany > > > > Join us at our next event:SAN 2016 Conferece > > > > > > > > _______________________________________________ > > HCP-Users mailing list > > [email protected] > > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > > > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
