Re: [HCP-Users] Subcortical atlas of S900_AverageT1w_restore.nii.gz?

[Timothy Coalson]

Using -cifti-separate will get you the 2mm definitions of these structures,
in particular using "-volume-all  -label ", but the same
information is already available in the pipellines repository:

https://github.com/Washington-University/Pipelines/raw/master/global/templates/91282_Greyordinates/Atlas_ROIs.2.nii.gz

There is also the 1.6mm definition:

https://github.com/Washington-University/Pipelines/raw/master/global/templates/170494_Greyordinates/Atlas_ROIs.1.60.nii.gz

However, if you want these at 0.7mm resolution, you would be better off
generating them from the freesurfer outputs, because upsampling of binary
classifications results in rough edges.

Tim


On Wed, Nov 22, 2017 at 9:00 AM, Xavier Guell Paradis 
wrote:

> Dear Michael and Matt,
> Thank you very much for your reply.
> As for Michael's question - yes, I am looking for a dlabel file that
> includes volumes such as caudate and putamen as separate structures.
> Perhaps there is a workbench command that would allow to isolate these
> structures in a random MNINonLinear dscalar file?
> I have been exploring -cifti-restrict-dense-map and
> -cifti-create-dense-scalar but have not figured it out. I have also tried
> using python's nibabel and numpy tools to isolate the rows corresponding to
> each structure, but this seems to be a much more complicated route.
>
> Thank you very much for your help,
> Xavier.
>
> --
> *From:* Harms, Michael [mha...@wustl.edu]
> *Sent:* Tuesday, November 21, 2017 7:29 PM
> *To:* Xavier Guell Paradis; hcp-users@humanconnectome.org
> *Subject:* Re: [HCP-Users] Subcortical atlas of
> S900_AverageT1w_restore.nii.gz?
>
>
>
> Hi,
>
>
>
> The subcortical structures are already defined in the standard CIFTI
> space.  Are you just looking for a dlabel file that includes those
> subcortical labels?
>
>
>
> 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 <(314)%20747-6173>
>
> St. Louis, MO  63110  Email:
> mha...@wustl.edu
>
>
>
> *From: * on behalf of Xavier Guell
> Paradis 
> *Date: *Tuesday, November 21, 2017 at 5:23 PM
> *To: *"hcp-users@humanconnectome.org" 
> *Subject: *[HCP-Users] Subcortical atlas of S900_AverageT1w_restore.nii.
> gz?
>
>
>
> Dear HCP experts,
> I was wondering if there is a publicly available, basic subcortical
> parcellation (deliniating structures such as caudate and putamen) of the
> standard volume structural file of HCP (such as S900_AverageT1w_restore.nii.
> gz).
> Restated, is there a parcellation that deliniates structures such as
> caudate and putamen in S900_AverageT1w_restore.nii.gz?
> Thank you very much,
> Xavier.
>
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> 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
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Re: [HCP-Users] FreeSurfer brain volume question

[Chao Zhang]

Thanks, Jennifer and Michael.

Best,
Chao

On Wed, Nov 22, 2017 at 3:38 PM, Harms, Michael  wrote:

>
>
> Hi,
>
> In FS, “Intracranial volume”, renamed to “EstimatedTotalIntraCranialVol”
> (aka “eTIV”) in more recent FS versions, is solely based on the determinant
> of a talairach transform that is internal to FS.  That particular transform
> does not necessarily need to be accurate for FS to generate accurate
> surfaces/segmentations, so we did not QC it.  For that reason, I do not
> recommend using it.
>
>
>
> 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 <(314)%20747-6173>
>
> St. Louis, MO  63110  Email:
> mha...@wustl.edu
>
>
>
> *From: * on behalf of Chao Zhang <
> cha...@gmail.com>
> *Date: *Wednesday, November 22, 2017 at 2:25 PM
> *To: *"hcp-users@humanconnectome.org" 
> *Subject: *[HCP-Users] FreeSurfer brain volume question
>
>
>
> Hi
>
>
>
> We were checking the FS brain volumes and found that out of the 1113
> subjects for 14 subjects the FS_BrainSeg_Vol is larger than the
> FS_IntraCranial_Vol (so that the column FS_BrainSegVol_eTIV_Ratio is larger
> than 1). We wonder if this is due to some error in calculating either of
> the two columns (FS_BrainSeg_Vol, FS_IntraCranial_Vol)? Thanks!
>
>
>
> Best,
>
> Chao
>
>
>
>
>
>
>
>
>
>
>
>
>
> ___
> 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.
>

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Re: [HCP-Users] FreeSurfer brain volume question

[Harms, Michael]

Hi,
In FS, “Intracranial volume”, renamed to “EstimatedTotalIntraCranialVol” (aka 
“eTIV”) in more recent FS versions, is solely based on the determinant of a 
talairach transform that is internal to FS.  That particular transform does not 
necessarily need to be accurate for FS to generate accurate 
surfaces/segmentations, so we did not QC it.  For that reason, I do not 
recommend using it.

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:  on behalf of Chao Zhang 

Date: Wednesday, November 22, 2017 at 2:25 PM
To: "hcp-users@humanconnectome.org" 
Subject: [HCP-Users] FreeSurfer brain volume question

Hi

We were checking the FS brain volumes and found that out of the 1113 subjects 
for 14 subjects the FS_BrainSeg_Vol is larger than the FS_IntraCranial_Vol (so 
that the column FS_BrainSegVol_eTIV_Ratio is larger than 1). We wonder if this 
is due to some error in calculating either of the two columns (FS_BrainSeg_Vol, 
FS_IntraCranial_Vol)? Thanks!

Best,
Chao







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Re: [HCP-Users] FreeSurfer brain volume question

[Elam, Jennifer]

Hi Chao,

See this earlier list thread: 
https://www.mail-archive.com/hcp-users@humanconnectome.org/msg05148.html


As is stated in that thread, we don't recommend using the the IntraCranial 
volume estimate.


Best,

Jenn

Jennifer Elam, Ph.D.
Scientific Outreach, Human Connectome Project
Washington University School of Medicine
Department of Neuroscience, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
e...@wustl.edu
www.humanconnectome.org



From: hcp-users-boun...@humanconnectome.org 
 on behalf of Chao Zhang 

Sent: Wednesday, November 22, 2017 2:25:32 PM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] FreeSurfer brain volume question

Hi

We were checking the FS brain volumes and found that out of the 1113 subjects 
for 14 subjects the FS_BrainSeg_Vol is larger than the FS_IntraCranial_Vol (so 
that the column FS_BrainSegVol_eTIV_Ratio is larger than 1). We wonder if this 
is due to some error in calculating either of the two columns (FS_BrainSeg_Vol, 
FS_IntraCranial_Vol)? Thanks!

Best,
Chao







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[HCP-Users] FreeSurfer brain volume question

[Chao Zhang]

Hi

We were checking the FS brain volumes and found that out of the 1113
subjects for 14 subjects the FS_BrainSeg_Vol is larger than the
FS_IntraCranial_Vol (so that the column FS_BrainSegVol_eTIV_Ratio is larger
than 1). We wonder if this is due to some error in calculating either of
the two columns (FS_BrainSeg_Vol, FS_IntraCranial_Vol)? Thanks!

Best,
Chao

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Re: [HCP-Users] R: MEG resting state

[A Nunes]

Hi Georgios and Francesco

Thanks for your help and the script! My doubts are solved.

Cheers,
Adoney

On Mon, Nov 20, 2017 at 10:22 AM, Georgios Michalareas 
wrote:

> Hi Adoney (and Francesco),
>
> Francesco is right. The ICA was done independently per session. But this
> should not cause a problem to your analysis if you are using the
> preprocessed resting state data i.e.
>
> 177746_MEG_3-Restin_rmegpreproc.mat
>
> 177746_MEG_4-Restin_rmegpreproc.mat
>
> 177746_MEG_5-Restin_rmegpreproc.mat
> Because in these files only the independent components corresponding to
> eye movements and heart artifacts have been removed. This artifacts have
> quite standard topology, quite similar across the different scans.
> So under the assumption that there are small head movements between scans
> , if you concatanate the datasets and then you do ICA then you should be
> able to capture the same brain Independent components across all three
> scans. The effect of the removed eye and heart artifacts from each scan
> separately on the ICA on the concatenated data should be negligible as long
> as the head movement is small.
>
> I hope this helps
> Best
> Giorgos
>
>
> On 11/20/2017 2:09 PM, Francesco Di Pompeo wrote:
>
> Hi,
>
>
>
> ICA has been performed on the three sessions separately so I think it’s
> better to use a different strategy.
>
>
>
> Best,
>
> Francesco
>
>
>
> *Da:* hcp-users-boun...@humanconnectome.org [mailto:hcp-users-bounces@
> humanconnectome.org ] *Per conto
> di *Michalareas, Georgios
> *Inviato:* venerdì 17 novembre 2017 14:15
> *A:* A Nunes  ;
> HCP-Users@humanconnectome.org
> *Oggetto:* Re: [HCP-Users] MEG resting state
>
>
>
> Hi Adoney,
>
> The released data has been only 7.5 mm maximum movement within scan.
>
> So the sensor positions should be quite close in all three resting state
> scans.
>
> ICA was done with all three sessions concatenated together.
>
> So I believe it should be one to concatenate them for your analysis too
> and assume sensors are more or less on same location.
>
> If you want to treat each different scan separately then you have to
> follow different strategies like:
>
> -Perform beamforming for each session separately and project each session
> separately into source space and then concatenate data in source space and
> do further analysis there.
>
> -Make a virtual gradiometer array as the mean of the three gradiometer
> positions in the three scans and then interpolate the data of each session
> to this virtual MEG sensors using Fieltrip’s function ft_megrealign and
> then combine all data in this virtual sensor space. Keep in mind that this
> projects the data into source space and projects it back to the virtual
> sensor space.
>
>
>
> I hope this helps
>
> Best
>
> Giorgos
>
>
>
> *From: * on behalf of A Nunes <
> adonay.s.nu...@gmail.com>
> *Date: *Thursday, 16. November 2017 at 21:56
> *To: *"hcp-users@humanconnectome.org" 
> *Subject: *[HCP-Users] MEG resting state
>
>
>
> Hi,
>
>
>
> The MEG resting state data is split in three sessions, is it possible to
> append the data before computing the covariance matrix?
>
> I have some doubts because the sensor position might change between the
> recordings and if ICA was done separately, then the rank would change
> between sessions and I don't know how would this affect beamforming.
>
>
>
> Any suggestions?
>
>
>
> Thanks
>
> Adonay
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>
> ___
> HCP-Users mailing list
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> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>
>
> 
>  Virus-free.
> www.avg.com
> 
> <#m_-6511468309016046648_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>
>
> --
> 
> Dr. Georgios Michalareas
> Neuroscience Department
> Max Planck Institute for Empirical Aesthetics
>
> email: g...@aesthetics.mpg.de
> phone: +49 69 8300479-325 <+49%2069%208300479325>
> 
>
>

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Re: [HCP-Users] Accessing full SSAGA HCP-Wu-Min1200 data

[Elam, Jennifer]

Hi James,

We used a version of SSAGA for HCP in which some items were omitted. We did ask 
about medications used for anxiety and depression, and drugs used in 
combination with alcohol or illicit drugs, but the other categories were 
omitted.


In order to get access to the HCP SSAGA data as collected:

  1.  You (and every researcher in your group who will use the data) need to be 
approved for HCP Restricted access (see application: 
http://humanconnectome.org/storage/app/media/data_use_terms/DataUseTerms_HCP_RestrictedAccess_26Jan2016.pdf)
  2.  You need to get IRB approval for a study of HCP Data Analysis -- the IRB 
approval can not be only an IRB waiver/exemption that assumes deidentified data 
because, in combination with other restricted data available, the SSAGA 
responses could be identifying.

If you already have restricted access, please send me your ConnectomeDB 
username. When you get IRB approval, please send me your approval letter and I 
can send you the data.

Best,
Jenn

Jennifer Elam, Ph.D.
Scientific Outreach, Human Connectome Project
Washington University School of Medicine
Department of Neuroscience, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
e...@wustl.edu
www.humanconnectome.org



From: hcp-users-boun...@humanconnectome.org 
 on behalf of James Condon 

Sent: Wednesday, November 22, 2017 12:47:28 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Accessing full SSAGA HCP-Wu-Min1200 data

Hi,

I'm a researcher from Australia hoping to use the HCP-Wu-Min n1200 data.

1. How can I access full SSAGA (semi-structured assessment for the genetics of 
alcoholism) data?
Exploring the connectomedb site, can only get CSV column stating SSAGA is 
complete, rather than the details within it.

2. I'm hoping to access each subjects medication history (which should be 
included in the SSAGA).

3. What format is the full SSAGA data in? Is medication history available in a 
CSV file?

Thanks for your fantastic work!

Kind regards,

Dr. James Condon
0411688811


Resident Medical Officer

Royal Adelaide Hospital – Mobile via main switchboard: +618 7074 

North Terrace, Adelaide, South Australia, 5000


Subeditor

Radiopaedia.org

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[HCP-Users] Accessing full SSAGA HCP-Wu-Min1200 data

[James Condon]

Hi,

I'm a researcher from Australia hoping to use the HCP-Wu-Min n1200 data.

1. How can I access full SSAGA (semi-structured assessment for the genetics
of alcoholism) data?
Exploring the connectomedb site, can only get CSV column stating SSAGA is
complete, rather than the details within it.

2. I'm hoping to access each subjects medication history (which should be
included in the SSAGA).

3. What format is the full SSAGA data in? Is medication history available
in a CSV file?

Thanks for your fantastic work!

Kind regards,

Dr. James Condon
0411688811

Resident Medical Officer

Royal Adelaide Hospital – Mobile via main switchboard: +618 7074 

North Terrace, Adelaide, South Australia, 5000


Subeditor

Radiopaedia.org
---
This email may contain confidential information, which also may be legally
privileged. Only the intended recipient(s) may access, use, distribute or
copy this email. If this email is received in error, please inform the
sender by return email and delete the original. If there are doubts about
the validity of this message, please contact the sender by telephone. It is
the recipient’s responsibility to check the email and any attached files
for viruses.

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Re: [HCP-Users] How does the HCP calculate the Cohen d effect in S1200 GroupAvg results?

[Harms, Michael]

Hi,
It’s a standard Cohen’s d calculation -- mean of the individual subject (lev2) 
copes, divided by the std of the individual subject copes

In terms of FSL code, if $mergedcope is the 4D file containing all the 
individual subject cope estimates, the code is just:
  fslmaths $mergedcope -Tmean ${mergedcope}_mean
  fslmaths $mergedcope -Tstd -div ${mergedcope}_mean -recip cohensd

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:  on behalf of 王潇潇 

Date: Tuesday, November 21, 2017 at 7:50 PM
To: hcp-users 
Subject: [HCP-Users] How does the HCP calculate the Cohen d effect in S1200 
GroupAvg results?

Dear HCP users
I've downloaded the S1200 GroupAvg results from the HCP website, and looked up 
the 7-task Cohen d effect results.
Could anyone tell me how the Cohen d effect was calculated?
Was it calculated by Cohen t-test d effect size of the beta value of GLM to 
each task?
Thanks, ~^_^~

--
Wang, Xiaoxiao
Biomedical Engineering Center
University of Science & Technology of China
Hefei, Anhui 230027, P.R.China
Email: wang...@mail.ustc.edu.cn


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Re: [HCP-Users] A question about brain registration matrix

[Glasser, Matthew]

You can compute the displacement of vertices on the spherical surface by 
comparing the registered spheres to the original or MSMSulc spheres.

Peace,

Matt.

From: Timothy Coalson >
Date: Tuesday, November 21, 2017 at 11:17 PM
To: Aaron C >
Cc: Matt Glasser >, 
"hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] A question about brain registration matrix

"How much deformation" is a tricky subject, and we may very well mean something 
different than you do when you say it.

The short version: surface registration does not cause anatomical deformation.  
Any registered, resampled anatomical surface will still line up perfectly with 
the volume it started from.  There is nothing like a volumetric warpfield for 
surface-based registration.

However, we do in fact apply the FNIRT volumetric MNI registration warp to our 
surfaces, and we provide these surfaces in both subject structural space (in 
the T1w folder), and in MNI space (in the MNINonLinear folder).  Because this 
is a volumetric registration, it does in fact cause anatomical deformation.  
You can measure this volume-registration-induced distortion on the surface, if 
you want, by comparing the anatomical surfaces (midthickness, etc) from the T1w 
and MNINonLinear folders to each other.

The "spherical deformation" that we regularize during the surface registration 
(and which is captured by the MSMAll sphere surfaces) is really an artifact of 
keeping the registration from doing something silly - specifically, it is to 
prevent the registration from creating drastic changes in triangle density of 
the surface (which would lead to having too few datapoints in some locations, 
causing loss of detail).  It is only a modification of the spherical 
coordinates, which are conceptually unrelated to the anatomical coordinates - 
the only purpose of the spherical coordinates is to make the surface-based 
registration easier to do.

Tim


On Tue, Nov 21, 2017 at 10:49 PM, Aaron C 
> wrote:
Hi Matt,

Thank you for your reply. I am looking for the file which provides me with the 
information to calculate how much deformation was done for some subjects. Will 
it possible for me to compute the displacements of vertices for the MSM-All 
registration using this file "${Subject}.L.sphere.MSMAll.native.surf.gii"? 
Thank you.

Aaron

From: Glasser, Matthew >
Sent: Sunday, November 19, 2017 10:47 PM
To: Aaron C; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] A question about brain registration matrix

This is a deformed spherical surface, not a warpfield or affine matrix as you 
might be used to using, however, we do provide this:

${StudyFolder}/${Subject}/MNINonLinear/Native/${Subject}.L.sphere.MSMAll.native.surf.gii
${StudyFolder}/${Subject}/MNINonLinear/Native/${Subject}.R.sphere.MSMAll.native.surf.gii

What is it specifically that you need to do?

Peace,

Matt.

From: 
>
 on behalf of Aaron C >
Date: Sunday, November 19, 2017 at 9:38 PM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] A question about brain registration matrix


Dear HCP experts,

I have a question about the transformation matrix aligning the raw data to the 
MSM-All registered data. Could I find the file of this matrix in the 
preprocessed data? Thank you.


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Re: [HCP-Users] Subcortical atlas of S900_AverageT1w_restore.nii.gz?

[Xavier Guell Paradis]

Dear Michael and Matt,
Thank you very much for your reply.
As for Michael's question - yes, I am looking for a dlabel file that includes 
volumes such as caudate and putamen as separate structures. Perhaps there is a 
workbench command that would allow to isolate these structures in a random 
MNINonLinear dscalar file?
I have been exploring -cifti-restrict-dense-map and -cifti-create-dense-scalar 
but have not figured it out. I have also tried using python's nibabel and numpy 
tools to isolate the rows corresponding to each structure, but this seems to be 
a much more complicated route.

Thank you very much for your help,
Xavier.


From: Harms, Michael [mha...@wustl.edu]
Sent: Tuesday, November 21, 2017 7:29 PM
To: Xavier Guell Paradis; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Subcortical atlas of S900_AverageT1w_restore.nii.gz?


Hi,

The subcortical structures are already defined in the standard CIFTI space.  
Are you just looking for a dlabel file that includes those subcortical labels?

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:  on behalf of Xavier Guell Paradis 

Date: Tuesday, November 21, 2017 at 5:23 PM
To: "hcp-users@humanconnectome.org" 
Subject: [HCP-Users] Subcortical atlas of S900_AverageT1w_restore.nii.gz?

Dear HCP experts,
I was wondering if there is a publicly available, basic subcortical 
parcellation (deliniating structures such as caudate and putamen) of the 
standard volume structural file of HCP (such as S900_AverageT1w_restore.nii.gz).
Restated, is there a parcellation that deliniates structures such as caudate 
and putamen in S900_AverageT1w_restore.nii.gz?
Thank you very much,
Xavier.

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