Grand mean 10000.  Find out what SPM uses and adjust your internal scale 
accordingly...

Peace,

Matt.

________________________________
From: Vadim Axelrod <axel.va...@gmail.com>
Sent: Monday, October 17, 2016 1:41:35 PM
To: Harms, Michael
Cc: Glasser, Matthew; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Extracting beta values from analyzed task-data

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<mailto: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<tel:314-747-6173>
St. Louis, MO  63110 Email: mha...@wustl.edu<mailto: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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