Re: [HCP-Users] Extracting beta values from analyzed task-data
Hi Micahel and all,
I am sorry to bother you again, but as a follow-up of you last remark, I
feel that
I am confused about the way the baseline is treated:
1. How contrast and beta map can be the same thing? For example, let's take
Social cognition exp. At the first (or second) level there should be 3
regressors: RANDOM, TOM and fixation. So, each one of them should have
separate beta map. So, the contrast between RANDOM and fixation is the
difference between the beta maps of RANDOM and fixation. But what I see is
that the resultant difference map is equivalent to beta map of RANDOM. To
best of my understanding, fixation is a condition as any other condition.
2. Is the baseline reflects fixation blocks? If so, in Language exp. there
is no Fixation block and in Emotional exp. there is only one fixation block
at the end. So, what does the contrast Story > baseline reflect?
3. I wanted to find beta estimate for the fixation in Social cognition
exp. The only possible pe file for the fixation is the pe file
in cope3.feat (RANDOM-TOM), because two others are the betas of the RANDOM
and TOM. However, its map almost perfectly correlates with the contrast map
of RANDOM-TOM. So, is there beta map for fixation blocks?
Thanks a lot,
Vadim
On Mon, Oct 17, 2016 at 10:30 PM, Harms, Michael <mha...@wustl.edu> wrote:
>
> And, to answer the Q in your 1st paragraph: yes.
>
> BTW: Since you want the “betas", you should use the pe1.dtseries.nii
> files. But, as an aside, note that these pe’s/cope’s are the results of
> the Level2 analysis, essentially averaging the Level 1 (individual runs).
> Because all the contrasts were defined in Level 1, and then essentially
> averaged for Level 2, I’m pretty sure that within each
> GrayordinateStats/cope{i}.feat directory, the actual grayordinate-values of
> the pe1.dtseries.nii and cope1.dtseries.nii files are identical. (i.e., we
> didn’t define any “new” contrasts specifically at Level 2, which means that
> the pe1 and cope1 will be the same within each contrast).
>
> 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: "Glasser, Matthew" <glass...@wustl.edu>
> Date: Monday, October 17, 2016 at 2:05 PM
> To: Vadim Axelrod <axel.va...@gmail.com>, Michael Harms <mha...@wustl.edu>
> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
> Subject: Re: [HCP-Users] Extracting beta values from analyzed task-data
>
> Grand mean 1. 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> 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 _tfMRI__level2_hp200_s?.dscalar.nii or
>> _tfMRI__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
>> Washingto
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> 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 _tfMRI__level2_hp200_s?.dscalar.nii or
> _tfMRI__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 an
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/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.ukhttp://www.fmrib.ox.ac.uk/~steve
>>
>> ---
>>
>> Stop the cultural destruction of Tibet <http://smithinks.net>
>>
>>
>>
>>
>>
>>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>
>
> --
>
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
> in error, please immediately notify the sender via telephone or return mail.
>
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
