Thank you for the help! So, if I want to get a beta estimate for the condition, I should take pe image in the cope#.feat folder, where this condition is compared vs. fixation. For example, in the Language task, for the Math beta I should take pe image in cope1.feat (MATH-fixation) and the Story betas are stored in cope2.feat (STORY-fixation contrast). Correct?
One more question: I noticed that betas might have high values (e.g., 50). I am used to work with SPM, and their the beta estimates are order of magnitude smaller. Is there some scaling here? Harms, Michael <[email protected]> wrote: > > No, in the updated pipeline, we simply have some code to merge the > copes/betas from the different contrasts into a single file for each task > (as we did for the zstat maps, which perhaps somewhat confusingly, are the > files named as <subject>_tfMRI_<task>_level2_hp200_s?.dscalar.nii or > <subject>_tfMRI_<task>_level2_hp200_s?_MSMAll.dscalar.nii — i.e., “zstat” > is not part of the file name). > > There is no need to re-run the pipelines. You can just use the > appropriate “merge” command in wb_shortcuts to merge the copes/betas into a > similar single file. As Matt pointed out, those copes/betas are in the > GrayordinateStats/cope{i}.feat/{pe1,cope1}.dtseries.nii files — “pe1” for > the betas; “cope1” for the contrasts). > > 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: [email protected] > > From: <[email protected]> on behalf of Vadim Axelrod < > [email protected]> > Date: Monday, October 17, 2016 at 8:28 AM > To: "Glasser, Matthew" <[email protected]> > > Cc: "[email protected]" <[email protected]> > Subject: Re: [HCP-Users] Extracting beta values from analyzed task-data > > Thank you, Matt. > So, you mean that in the updated pipeline cope1.dtseries.nii contains > multiple beta maps (two or more, depending on a contrast)? Practically, do > you think in the foreseeable future there will be an update of task data > for the download, that will include the betas? If not, then I should > probably run the pipeline myself. Can you please advice the efficient way > of doing this (see my original post). > > Many thanks! > > On Mon, Oct 17, 2016 at 4:02 PM, Glasser, Matthew <[email protected]> > wrote: > >> It looks like the released HCP task fMRI data were produced using an >> older version of the Task analysis pipeline that does not automatically >> collate the beta maps into a labeled and easy to use dscalar file. The >> beta maps will be in these files: >> >> ${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/$ >> {fMRIName}_hp200_s2_level2_MSMAll.feat/GrayordinatesStats >> /cope${i}.feat/cope1.dtseries.nii where ${i} = 1 to N contrasts >> >> Peace, >> >> Matt. >> >> From: <[email protected]> on behalf of Vadim Axelrod >> <[email protected]> >> Date: Sunday, October 16, 2016 at 7:31 AM >> To: Stephen Smith <[email protected]> >> Cc: "[email protected]" <[email protected]> >> Subject: Re: [HCP-Users] Extracting beta values from analyzed task-data >> >> Thank you Stephen for the prompt reply. >> But why there is only one pe1 file with only one volume in it? For the >> contrast like, story > math I would expect to find two beta images, one >> for the "story" and one for the "math". In addition, the pe1.dtseries.nii >> maps are very correlated with tstat1.dtseries.nii (R>0.85) and there is >> similar correlation for all contrasts of the same task/subject. >> >> On Sun, Oct 16, 2016 at 2:09 PM, Stephen Smith <[email protected]> >> wrote: >> >>> HI - "pe" are the beta files and "cope" are contrasts of these. >>> Cheers. >>> >>> >>> On 16 Oct 2016, at 12:03, Vadim Axelrod <[email protected]> wrote: >>> >>> Dear list, >>> >>> I downloaded the analyzed 3T HCP fMRI task-data. In the cope* subfolders >>> I can find the outputs of the contrast calculation, >>> e.g., Zstat1.dtseries.nii. However, I do not see beta estimates for each >>> regressor. Do I miss something or they are just not included in the >>> analyzed archive. If the latter is correct, should I download non-analyzed >>> data and run the analysis myself? What is the simplest way to to that? The >>> only instructions that I found are from the last year course, and I am not >>> sure how valid they are: https://www.humanconnecto >>> me.org/courses/2015/exploring-the-human-connectome.php >>> https://wustl.box.com/shared/static/0vcsqc0yg3ncqmirryyxpgs >>> iqhxww659.pdf >>> >>> Probably someone can post more recent instructions from the last month >>> course. >>> >>> Many thanks for the help, >>> Vadim >>> >>> _______________________________________________ >>> HCP-Users mailing list >>> [email protected] >>> 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) >>> [email protected] http://www.fmrib.ox.ac.uk/~steve >>> ------------------------------------------------------------ >>> --------------- >>> >>> Stop the cultural destruction of Tibet <http://smithinks.net> >>> >>> >>> >>> >>> >>> >> _______________________________________________ >> HCP-Users mailing list >> [email protected] >> 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 > [email protected] > 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 [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
