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/0vcsqc0yg3ncqmirryyxpgsiqhxww659.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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