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 <mha...@wustl.edu> 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: mha...@wustl.edu
>
> From: <hcp-users-boun...@humanconnectome.org> on behalf of Vadim Axelrod <
> axel.va...@gmail.com>
> Date: Monday, October 17, 2016 at 8:28 AM
> To: "Glasser, Matthew" <glass...@wustl.edu>
>
> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
> 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 <glass...@wustl.edu>
> 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: <hcp-users-boun...@humanconnectome.org> on behalf of Vadim Axelrod
>> <axel.va...@gmail.com>
>> Date: Sunday, October 16, 2016 at 7:31 AM
>> To: Stephen Smith <st...@fmrib.ox.ac.uk>
>> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>> 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 <st...@fmrib.ox.ac.uk>
>> wrote:
>>
>>> HI - "pe" are the beta files and "cope" are contrasts of these.
>>> Cheers.
>>>
>>>
>>> On 16 Oct 2016, at 12:03, Vadim Axelrod <axel.va...@gmail.com> 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
>>> HCP-Users@humanconnectome.org
>>> 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)
>>> st...@fmrib.ox.ac.uk    http://www.fmrib.ox.ac.uk/~steve
>>> ------------------------------------------------------------
>>> ---------------
>>>
>>> Stop the cultural destruction of Tibet <http://smithinks.net>
>>>
>>>
>>>
>>>
>>>
>>>
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>>
>>
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