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<mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of Vadim Axelrod <axel.va...@gmail.com<mailto:axel.va...@gmail.com>>
Date: Sunday, October 16, 2016 at 7:31 AM
To: Stephen Smith <st...@fmrib.ox.ac.uk<mailto:st...@fmrib.ox.ac.uk>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto: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<mailto: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<mailto: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.humanconnectome.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
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