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<mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of Vadim Axelrod <axel.va...@gmail.com<mailto:axel.va...@gmail.com>>
Date: Monday, October 17, 2016 at 8:28 AM
To: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>>
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, 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<mailto: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<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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