Re: [HCP-Users] Resting state networks

[Claude Bajada]

Thanks for your reply Tim, by "least pairing an LR with an RL" I assume 
you mean concatenate the time series, correct?


Claude

On 22/03/2019 19:19, Timothy Coalson wrote:

Inline replies.

Tim


On Fri, Mar 22, 2019 at 10:17 AM Claude Bajada <mailto:c.baj...@fz-juelich.de>> wrote:


Dear experts,

Could I just confirm that the data that is found in:


${SubjectFolder}/MNINinLinear/Results/rfMRI_REST?_LR/rfMRI_REST?_LR_Atlas_MSMAll_hp2000_clean.dtseries.nii

Is the resting state data using the MSMall aligned vertex coordinates


Yes.

and that these data can be used to then produce Resting state networks


Yes.

(I realize that these are available but I just want to make sure I am
understanding the data that I have). Further are the four
subfolders in
"Results" four separate runs that I can either concatenate or produce
four different RSNs?


Yes, but the LR and RL runs have different locations of signal 
dropout, so we generally recommend at least pairing an LR with an RL 
to increase the overall coverage.



Am I also correct in assuming that these data are not smoothed?


No, there is a small amount of added smoothing done (2mm FWHM) while 
putting the data into ~2mm grayordinates space - this could be done 
without any added smoothing, but for historical reasons we have kept 
it consistent with earlier releases.  Of course, this amount doesn't 
approach the smoothing done in many non-HCP analysis streams.


Regards,

Claude







Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt






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[HCP-Users] Resting state networks

[Claude Bajada]

Dear experts,

Could I just confirm that the data that is found in:

${SubjectFolder}/MNINinLinear/Results/rfMRI_REST?_LR/rfMRI_REST?_LR_Atlas_MSMAll_hp2000_clean.dtseries.nii

Is the resting state data using the MSMall aligned vertex coordinates
and that these data can be used to then produce Resting state networks
(I realize that these are available but I just want to make sure I am
understanding the data that I have). Further are the four subfolders in
"Results" four separate runs that I can either concatenate or produce
four different RSNs?

Am I also correct in assuming that these data are not smoothed?

Regards,

Claude





Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt




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Re: [HCP-Users] A few specific questions about the HCP data | MNI space dedrifting & file structure

[Claude Bajada]

Hi Tim,

Thank you very much for your detailed explanation

Regards,

Claude

On it-Tnejn, 02 ta Lul, 2018 07:35 , Timothy Coalson wrote:
On Mon, Jul 2, 2018 at 7:13 AM, Claude Bajada 
mailto:c.baj...@fz-juelich.de>> wrote:
2) from what I understand, structural qualities such as cortical
thickness etc are measured in the individual's real space. However then,
what I do not understand is the file structure of the HCP data. The
structural measures such as cortical thickness, curvature and myelin
maps etc live in the MNINonLinear/fsaverage_LR32k rather than in the
'native space' directory. Can anyone shed light on this?

It was perhaps not the best choice to put these measures inside the MNINonLinear folder, but for 
compatibility, that is where they will remain for now.  They were computed in "T1w" space 
("native volume space", not to be confused with "native mesh", which is an unrelated 
distinction).

However, the myelin measure is based on a combination of imaging contrasts, and 
is not sensitive to changes in brain size, so it doesn't quite fit in the same 
class as curvature and thickness, which are measures of the cortical 
coordinates themselves.

Tim






Forschungszentrum Juelich GmbH
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Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
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Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt




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[HCP-Users] A few specific questions about the HCP data | MNI space dedrifting & file structure

[Claude Bajada]

Dear experts,

I have a few questions:

1) I am currently working on a project using tractography and the HCP
data. I have used the HCP provided FNIRT based MNI registration in order
to register individual streamlines from "native" or diffusion space (as
per post HCP minimal processing pipeline) to MNI space. However, in
Glasser 2016 supplementary text, it states that the MNI space is drifted
relative to the mean brain size of individual brains (greatest along the
x and z axes). I've been told that it is possible to "dedrift" these
data and I wonder if anyone has experience in doing this and is able to
point me in the right direction.

2) from what I understand, structural qualities such as cortical
thickness etc are measured in the individual's real space. However then,
what I do not understand is the file structure of the HCP data. The
structural measures such as cortical thickness, curvature and myelin
maps etc live in the MNINonLinear/fsaverage_LR32k rather than in the
'native space' directory. Can anyone shed light on this?

Regards,

Claude





Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt




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Re: [HCP-Users] Problem creating scenes in wb_view

[Claude Bajada]

Thanks


On l-Erbgħa, 07 ta Mar, 2018 03:44 , Harwell, John wrote:
This error has been reported before (WB-647 in our internal bug 
tracking system).  The solution for the user that experienced this 
problem was to use the version of Workbench distributed through the 
HCP website 
(https://www.humanconnectome.org/software/get-connectome-workbench).


From some google searches, this XCB error is reported with other 
applications.  The neurodebian version of Workbench may still be using 
Qt 4 (The qt version is available in wb_view by selecting File Menu —> 
About Workbench and then clicking the More button).  Qt 5 provides 
better support for the XCB libraries.


John Harwell


On Mar 7, 2018, at 7:46 AM, Claude Bajada <c.baj...@fz-juelich.de 
<mailto:c.baj...@fz-juelich.de>> wrote:


apologies Ubuntu 16.04 LTS installed from the neurodebian repo


On l-Erbgħa, 07 ta Mar, 2018 02:44 , Glasser, Matthew wrote:

What OS is this on?

Peace,

Matt.

From: <hcp-users-boun...@humanconnectome.org 
<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Claude 
Bajada <c.baj...@fz-juelich.de <mailto:c.baj...@fz-juelich.de>>

Date: Wednesday, March 7, 2018 at 4:25 AM
To: "hcp-users@humanconnectome.org 
<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>>

Subject: [HCP-Users] Problem creating scenes in wb_view

Hi all,

I am encountering a problem when trying to create a scene with 
wb_view. As soon as I try to add my scene I get a core dump:


Anyone has a similar problem and know a solution?

Claude





Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt



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Re: [HCP-Users] Problem creating scenes in wb_view

[Claude Bajada]

apologies Ubuntu 16.04 LTS installed from the neurodebian repo


On l-Erbgħa, 07 ta Mar, 2018 02:44 , Glasser, Matthew wrote:

What OS is this on?

Peace,

Matt.

From: <hcp-users-boun...@humanconnectome.org 
<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Claude 
Bajada <c.baj...@fz-juelich.de <mailto:c.baj...@fz-juelich.de>>

Date: Wednesday, March 7, 2018 at 4:25 AM
To: "hcp-users@humanconnectome.org 
<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org 
<mailto:hcp-users@humanconnectome.org>>

Subject: [HCP-Users] Problem creating scenes in wb_view

Hi all,

I am encountering a problem when trying to create a scene with 
wb_view. As soon as I try to add my scene I get a core dump:


Anyone has a similar problem and know a solution?

Claude





Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt



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[HCP-Users] Problem creating scenes in wb_view

[Claude Bajada]

Hi all,

I am encountering a problem when trying to create a scene with wb_view. As soon 
as I try to add my scene I get a core dump:

[cid:part1.C307F21E.5B1978C7@fz-juelich.de]

Anyone has a similar problem and know a solution?

Claude




Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt




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Re: [HCP-Users] Extracting Thalamus Brainordinates

[Claude Bajada]

Thanks


On il-Ħamis, 22 ta Fra, 2018 12:41 , Glasser, Matthew wrote:

They are in ${StudyFolder}/${Subject}/MNINonLinear/xfms

Peace,

Matt.

From: <hcp-users-boun...@humanconnectome.org 
<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Claude 
Bajada <c.baj...@fz-juelich.de <mailto:c.baj...@fz-juelich.de>>

Date: Thursday, February 22, 2018 at 2:50 AM
To: Timothy Coalson <tsc...@mst.edu <mailto:tsc...@mst.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 Thalamus Brainordinates

Thanks Tim and Ely,

This is helpful.

Tim, I think I prefer your second suggestion (using the standard cifti 
MNINonLinear group definition). I need a one to one correspondence 
between every point in the thalamus across individuals and to a 
template thalamus. The reason (and perhaps I need to go into more 
detail of what I hope to do) is that I would like to perform 
tractography seeding from every voxel (independently) in the thalamus 
and then be able to project any statistics that are derived from those 
tracts back onto the thalamus itself. I would like the correspondence 
from beforehand since I would like to do all the projections directly 
onto the template thalamus in MNI space. I also do not really need 
native voxels but only a centroid coordinate for each template voxel 
in native space; since I use mrtrix for my tractography.


I am also looking for the subjects' atlas warpfields but cannot seem 
to find them could you point me in the right direction/directory?


Cheers,

Claude


On il-Ħamis, 22 ta Fra, 2018 01:07 , Timothy Coalson wrote:
It may be better to use the individual subject's "native space" 
definitions.  The files in the T1w folder are in what we refer to as 
native volume space (it is actually rigidly-aligned MNI space, but 
rigid alignment preserves shape, so it can be used as if it were 
distortion-corrected scanner coordinates, after the appropriate 
resamplings).  There are aparc*+aseg.nii.gz files in that folder, 
which should be the freesurfer segmentation/parcellation for that 
single subject, which contains a thalamus definition.


If you prefer to use our standard cifti MNINonLinear group thalamus 
definition, and work that backwards through each subject's atlas 
warpfield, you can get the entire ROI of left and right thalamus by 
using -cifti-separate with -volume THALAMUS_LEFT  -roi 
 (and similar with RIGHT) on any small full-brain cifti 
file (91282 grayordinates for 3T data), for instance the template in 
the Pipelines at 
global/templates/91282_Greyordinates/91282_Greyordinates.dscalar.nii .


Tim


On Wed, Feb 21, 2018 at 3:24 AM, Claude Bajada 
<c.baj...@fz-juelich.de <mailto:c.baj...@fz-juelich.de>> wrote:


Dear all,

I would like to perform tractography seeding from the thalamus.
So as to
ensure that I have correspondence between individuals, I would
like to
use the thalamus defined in terms of the brainordinates already
used in
each participant.

I cannot find a way to identify the brainordinates that define the
thalamus and extract their voxels / MNI coordinates. Can someone
point
me in the right direction?

Regards,

Claude







Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt






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Re: [HCP-Users] Extracting Thalamus Brainordinates

[Claude Bajada]

Thanks Tim and Ely,

This is helpful.

Tim, I think I prefer your second suggestion (using the standard cifti 
MNINonLinear group definition). I need a one to one correspondence 
between every point in the thalamus across individuals and to a template 
thalamus. The reason (and perhaps I need to go into more detail of what 
I hope to do) is that I would like to perform tractography seeding from 
every voxel (independently) in the thalamus and then be able to project 
any statistics that are derived from those tracts back onto the thalamus 
itself. I would like the correspondence from beforehand since I would 
like to do all the projections directly onto the template thalamus in 
MNI space. I also do not really need native voxels but only a centroid 
coordinate for each template voxel in native space; since I use mrtrix 
for my tractography.


I am also looking for the subjects' atlas warpfields but cannot seem to 
find them could you point me in the right direction/directory?


Cheers,

Claude


On il-Ħamis, 22 ta Fra, 2018 01:07 , Timothy Coalson wrote:
It may be better to use the individual subject's "native space" 
definitions.  The files in the T1w folder are in what we refer to as 
native volume space (it is actually rigidly-aligned MNI space, but 
rigid alignment preserves shape, so it can be used as if it were 
distortion-corrected scanner coordinates, after the appropriate 
resamplings).  There are aparc*+aseg.nii.gz files in that folder, 
which should be the freesurfer segmentation/parcellation for that 
single subject, which contains a thalamus definition.


If you prefer to use our standard cifti MNINonLinear group thalamus 
definition, and work that backwards through each subject's atlas 
warpfield, you can get the entire ROI of left and right thalamus by 
using -cifti-separate with -volume THALAMUS_LEFT  -roi 
 (and similar with RIGHT) on any small full-brain cifti 
file (91282 grayordinates for 3T data), for instance the template in 
the Pipelines at 
global/templates/91282_Greyordinates/91282_Greyordinates.dscalar.nii .


Tim


On Wed, Feb 21, 2018 at 3:24 AM, Claude Bajada <c.baj...@fz-juelich.de 
<mailto:c.baj...@fz-juelich.de>> wrote:


Dear all,

I would like to perform tractography seeding from the thalamus. So
as to
ensure that I have correspondence between individuals, I would like to
use the thalamus defined in terms of the brainordinates already
used in
each participant.

I cannot find a way to identify the brainordinates that define the
thalamus and extract their voxels / MNI coordinates. Can someone point
me in the right direction?

Regards,

Claude







Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt






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[HCP-Users] map names | wb_command

[Claude Bajada]

Dear all,

What is the wb_command syntax to label map names?

[cid:part1.24ABD659.153881EE@fz-juelich.de]

Regards,

Claude




Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt




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Re: [HCP-Users] Myelin Maps

[Claude Bajada]

Thanks very much Jenn,


Found them and downloaded them. I just have one more question. I am now 
trying to do some analysis on a subset of the individual myelin maps 
(S1200.All.MyelinMap...). I have loaded the data into matlab but this 
just gives a [vertex x participant] matrix but none of the keys



Is there a way to seprate the 4D cifti into individual files? Or 
alternatively extract the order or participant number so that I can 
index the individual maps in matlab?



Cheers,

Claude


On 25.10.2017 21:38, Elam, Jennifer wrote:


Hi Claude,

The S1200 group average myelin maps are part of the 1200 Subjects 
Group Average Data download here: 
https://db.humanconnectome.org/data/projects/HCP_1200. Individual 
subject myelin maps are also available in that dataset in the 
S1200.All.MyelinMap_BC_MSMAll.32k_fs_LR.dscalar.nii file (individual 
maps can be toggled through as Maps within the layer in Workbench. In 
fact, there's a Workbench scene in the included *.scene file that is 
already set up to look at/compare both the group average and 
individual myelin maps and a PDF Workbench tutorial for the 
whole dataset.



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 Bajada, Claude 
Julien 

*Sent:* Wednesday, October 25, 2017 2:12:52 PM
*To:* hcp-users@humanconnectome.org
*Subject:* [HCP-Users] Myelin Maps
Dear all,

Do group average myelin maps in the 32k MSMall space exist? And if so 
where can I download them?


Claude




Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt




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[HCP-Users] RSN masks for 32K surfaces?

[Claude Bajada]

Hello all,

Are there any canonical resting state network masks available for the
MSMAll 32k HCP surfaces as a gifti or cifti file? If so, where can I
obtain them?

Claude





Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt




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[HCP-Users] Question about restricted data

[Claude Bajada]

Dear all,

I have a question about some scores on the restricted data. I don't
think that I'd be divulging anything in particular but just to be safe,
is there a restricted mailing list or a specific person I can send the
question to in order to be sure not to break any terms?

Regards,

Claude





Forschungszentrum Juelich GmbH
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Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt




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Re: [HCP-Users] Gifti surface labels

[Claude Bajada]

Great, thanks!

Claude


On 18.08.2017 16:08, Glasser, Matthew wrote:
> For the 32k 2mm average spacing surfaces you can find the standard medial
> wall definitions here:
>
> https://github.com/Washington-University/Pipelines/blob/master/global/templ
> ates/91282_Greyordinates/L.atlasroi.32k_fs_LR.shape.gii
> https://github.com/Washington-University/Pipelines/blob/master/global/templ
> ates/91282_Greyordinates/R.atlasroi.32k_fs_LR.shape.gii
>
> These are the same as are used to produce the CIFTI files.  These are the
> definitions of cortex, so you will need to subtract 1 and multiply by -1
> to get a medial wall ROI with ones inside the ROI and zeros for the
> cortex.
>
> Peace,
>
> Matt.
>
> On 8/18/17, 8:55 AM, "hcp-users-boun...@humanconnectome.org on behalf of
> Claude Bajada" <hcp-users-boun...@humanconnectome.org on behalf of
> c.baj...@fz-juelich.de> wrote:
>
>> Hi all,
>>
>> I had asked a question on this forum a while ago related to medial wall
>> structures in cifti and gifti files and I have a follow-up question.
>>
>> I have been going through the gifti file format and have learned that
>> the medial wall structures are labeled as ???
>>
>> Unfortunately, it seems that most programmes do not output these vertex
>> indices easily (or at least this is my impression). I tend to use the
>> matlab gifti library by Guillaume Flandin
>> (https://www.artefact.tk/software/matlab/gifti/)
>>
>> I need to know the medial wall indices in order to exclude them from
>> some tractography seeds that I am generating.
>>
>> The way I have been retrieving these indices so far is:
>>
>> 1) locate the file ${side}.aparc.32k_fs_LR.label.gii in folder
>> MNINonLinear/fsaverage_LR32k/
>>
>> 2) load it in matlab > aparc = gifti('${side}.aparc.32k_fs_LR.label.gii');
>>
>> 3) identify the data (aparc.cdata) that are associated with label ???
>> and store the indices
>>
>> My questions are:
>>
>> a) are these vertices standard across all of the brain? eg one
>> participant has 2425 midline vertices. Should all HCP participants have
>> the same vertices or do these differ slightly across subjects?
>>
>> b) can I just map these indices onto the T1 (32k resampled) vertices, in
>> order to exclude these areas from my tractography?
>>
>> Regards,
>>
>> Claude
>>
>>
>>
>>
>>
>> --
>> --
>> --
>> --
>> Forschungszentrum Juelich GmbH
>> 52425 Juelich
>> Sitz der Gesellschaft: Juelich
>> Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
>> Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
>> Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
>> Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
>> Prof. Dr. Sebastian M. Schmidt
>> --
>> --
>> --
>> --
>>
>>
>> ___
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users

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[HCP-Users] Gifti surface labels

[Claude Bajada]

Hi all,

I had asked a question on this forum a while ago related to medial wall
structures in cifti and gifti files and I have a follow-up question.

I have been going through the gifti file format and have learned that
the medial wall structures are labeled as ???

Unfortunately, it seems that most programmes do not output these vertex
indices easily (or at least this is my impression). I tend to use the
matlab gifti library by Guillaume Flandin
(https://www.artefact.tk/software/matlab/gifti/)

I need to know the medial wall indices in order to exclude them from
some tractography seeds that I am generating.

The way I have been retrieving these indices so far is:

1) locate the file ${side}.aparc.32k_fs_LR.label.gii in folder
MNINonLinear/fsaverage_LR32k/

2) load it in matlab > aparc = gifti('${side}.aparc.32k_fs_LR.label.gii');

3) identify the data (aparc.cdata) that are associated with label ???
and store the indices

My questions are:

a) are these vertices standard across all of the brain? eg one
participant has 2425 midline vertices. Should all HCP participants have
the same vertices or do these differ slightly across subjects?

b) can I just map these indices onto the T1 (32k resampled) vertices, in
order to exclude these areas from my tractography?

Regards,

Claude







Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt




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Re: [HCP-Users] Follow-up to: Obtaining the MNI coordinates of cluster peaks in the melodic_IC.dscalar.nii ICA maps

[Claude Bajada]

Thanks for the reply Matt.

I didn't quite understand what you mean by: " I would do your mapping in 
individual subjects."


In case it was not clear, the tractography is of course performed in 
individual subject space using the MSMAll surfaces in the subject 
directory of the T1w folders. My result is data associated with those 
surfaces and I was planning on averaging the data across participants.


Claude


On 04.08.2017 00:28, Glasser, Matthew wrote:
Tractography has quite strong folding-related biases.  Using MSMAll 
might attenuate those some and focus more on the parts of tractography 
that aren’t biased by folding.  I would do your mapping in individual 
subjects.


Peace,

Matt.

From: <hcp-users-boun...@humanconnectome.org 
<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Claude 
Bajada <c.baj...@fz-juelich.de <mailto:c.baj...@fz-juelich.de>>

Date: Thursday, August 3, 2017 at 4:54 PM
To: Timothy Coalson <tsc...@mst.edu <mailto:tsc...@mst.edu>>
Cc: "hcp-users@humanconnectome.org 
<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org 
<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Follow-up to: Obtaining the MNI coordinates 
of cluster peaks in the melodic_IC.dscalar.nii ICA maps


Thanks Tim and Michael,

I am thinking about doing some work with some statistics derived from 
tractography (starting from the vertices on gray white matter 
interface and then projecting those statistics onto their respective 
vertices) My thought however, is whether the MSMAll (or functional 
registration) is the most appropriate registration for working with 
what is essentially structure. I suppose that one could argue that 
tracts should be more aligned to function than gyral anatomy but it is 
not obviously true. Would you recommend using a more "anatomical" 
group registration in this case (eg the 
${subject}.${side}.32k_fs_LR.surf.gii files over the MSMAll)?


Claude


On 03.08.2017 21:46, Timothy Coalson wrote:
On Thu, Aug 3, 2017 at 9:03 AM, Claude Bajada <c.baj...@fz-juelich.de 
<mailto:c.baj...@fz-juelich.de>> wrote:


Hi all,

I am starting a new thread because while my question is related
to the one ask, it is tangential.

Can I confirm that what you mean by not averaging surfaces is
that one should not average the vertex points across gifti
surfaces to create a so-called "average surface"

Can I ask then, is averaging the data associated with vertices
from individual subjects and plotting the result on a template
surface (eg colin or a just using an individual as a template)
also problematic?

Ah, I missed this question on my first read. You make a good point, 
that individual surfaces have some bias away from the group.  With a 
good registration, doing this could tell you interesting things about 
the subject (the relative size of a particular group-identified 
feature on this individual).  Strictly speaking, though, it will 
cause some bias in the display of group results, in terms of the size 
of features.


Displaying on group average surfaces may actually have some bias too 
- different regions will lose different amounts of folding detail 
(because of differences in variability), which also means losing 
surface area (and therefore features in high variability regions may 
*look* smaller than they should on group surfaces).  For processing 
group-average data, we compensate for this surface area loss with the 
use of vertex areas.  I'm not entirely sure whether the surface 
inflation method we use tries to keep the vertex areas relatively 
undistorted, but if so, then the group very_inflated surfaces may 
have the least bias from this effect (less folding present in the 
surfaces before averaging, so less surface area lost due to 
averaging).  Note that this bias would be only in visual size, not in 
intensity or sampling density.


Back on the single-subject template topic, as a practical matter, we 
can't yet segment individual cerebellums into surfaces reliably, so 
carefully acquired and processed single subjects such as colin are 
the best we can do at present for displaying the cerebellum as a surface.


Regards,
Claude

On 03.08.2017 02:05, Timothy Coalson wrote:

On Wed, Aug 2, 2017 at 6:02 PM, James Morrow
<james.mor...@monash.edu <mailto:james.mor...@monash.edu>> wrote:

Thanks Tim and Matt for the detailed responses.


I agree that mapping to volumes is sub-optimal. Our goal is
to identify coords to be used as targets for brain
stimulation with TMS. We need MNI coords for
neuronavigation. Given the extent of the TMS field, we have
some tolerance for imprecisions in the mapping.


I see.  We generally get asked these questions in the context of
fMRI analysis, hence our reluctance.

How does the neuronavi

Re: [HCP-Users] Follow-up to: Obtaining the MNI coordinates of cluster peaks in the melodic_IC.dscalar.nii ICA maps

[Claude Bajada]

Thanks Tim and Michael,

I am thinking about doing some work with some statistics derived from 
tractography (starting from the vertices on gray white matter interface 
and then projecting those statistics onto their respective vertices) My 
thought however, is whether the MSMAll (or functional registration) is 
the most appropriate registration for working with what is essentially 
structure. I suppose that one could argue that tracts should be more 
aligned to function than gyral anatomy but it is not obviously true. 
Would you recommend using a more "anatomical" group registration in this 
case (eg the ${subject}.${side}.32k_fs_LR.surf.gii files over the MSMAll)?


Claude


On 03.08.2017 21:46, Timothy Coalson wrote:
On Thu, Aug 3, 2017 at 9:03 AM, Claude Bajada <c.baj...@fz-juelich.de 
<mailto:c.baj...@fz-juelich.de>> wrote:


Hi all,

I am starting a new thread because while my question is related to
the one ask, it is tangential.

Can I confirm that what you mean by not averaging surfaces is that
one should not average the vertex points across gifti surfaces to
create a so-called "average surface"

Can I ask then, is averaging the data associated with vertices
from individual subjects and plotting the result on a template
surface (eg colin or a just using an individual as a template)
also problematic?

Ah, I missed this question on my first read.  You make a good point, 
that individual surfaces have some bias away from the group.  With a 
good registration, doing this could tell you interesting things about 
the subject (the relative size of a particular group-identified 
feature on this individual).  Strictly speaking, though, it will cause 
some bias in the display of group results, in terms of the size of 
features.


Displaying on group average surfaces may actually have some bias too - 
different regions will lose different amounts of folding detail 
(because of differences in variability), which also means losing 
surface area (and therefore features in high variability regions may 
*look* smaller than they should on group surfaces).  For processing 
group-average data, we compensate for this surface area loss with the 
use of vertex areas.  I'm not entirely sure whether the surface 
inflation method we use tries to keep the vertex areas relatively 
undistorted, but if so, then the group very_inflated surfaces may have 
the least bias from this effect (less folding present in the surfaces 
before averaging, so less surface area lost due to averaging).  Note 
that this bias would be only in visual size, not in intensity or 
sampling density.


Back on the single-subject template topic, as a practical matter, we 
can't yet segment individual cerebellums into surfaces reliably, so 
carefully acquired and processed single subjects such as colin are the 
best we can do at present for displaying the cerebellum as a surface.


Regards,
Claude

On 03.08.2017 02:05, Timothy Coalson wrote:

On Wed, Aug 2, 2017 at 6:02 PM, James Morrow
<james.mor...@monash.edu <mailto:james.mor...@monash.edu>> wrote:

Thanks Tim and Matt for the detailed responses.


I agree that mapping to volumes is sub-optimal. Our goal is
to identify coords to be used as targets for brain
stimulation with TMS. We need MNI coords for neuronavigation.
Given the extent of the TMS field, we have some tolerance for
imprecisions in the mapping.


I see.  We generally get asked these questions in the context of
fMRI analysis, hence our reluctance.

How does the neuronavigation go from MNI coordinates to subject
coordinates, do you happen to have a reasonable T1w MRI scan of
your subjects?  I don't know how big the TMS field is, and I
hadn't looked at the distance from subject to group average
surfaces before, but in one of the HCP subjects, I got a maximum
of 2cm distance from the group average surface (using
midthickness surfaces), which occurred in a few specific
locations, while 90% of the surface was 1cm distance or less.

Can I clarify – was the ICA run on the volumes and then later
mapped on to surfaces, or was it performed on the surface
data? If the former, are the original volumetric results for
the ICA of each subject available anywhere in .nii format?


Cheers,

James


*James Morrow*
Research assistant
Brain & Mental Health Laboratory

*Monash Institute of Cognitive and Clinical Neurosciences*
School of Psychological Sciences
Monash University
c/o MBI, 770 Blackburn Road
Clayton VIC 3800
Australia

T: 03 9902 9768
E: james.mor...@monash.edu <mailto:amy.al...@monash.edu>
www.med.monash.edu.au/psych/bmh/
<http://www.med.monash.edu.au/psych/bmh/>

<http://www.med

[HCP-Users] Follow-up to: Obtaining the MNI coordinates of cluster peaks in the melodic_IC.dscalar.nii ICA maps

[Claude Bajada]

Hi all,

I am starting a new thread because while my question is related to the one ask, 
it is tangential.

Can I confirm that what you mean by not averaging surfaces is that one should not average 
the vertex points across gifti surfaces to create a so-called "average surface"

Can I ask then, is averaging the data associated with vertices from individual 
subjects and plotting the result on a template surface (eg colin or a just 
using an individual as a template) also problematic?

Regards,
Claude

On 03.08.2017 02:05, Timothy Coalson wrote:
On Wed, Aug 2, 2017 at 6:02 PM, James Morrow 
> wrote:
Thanks Tim and Matt for the detailed responses.

I agree that mapping to volumes is sub-optimal. Our goal is to identify coords 
to be used as targets for brain stimulation with TMS. We need MNI coords for 
neuronavigation. Given the extent of the TMS field, we have some tolerance for 
imprecisions in the mapping.

I see.  We generally get asked these questions in the context of fMRI analysis, 
hence our reluctance.

How does the neuronavigation go from MNI coordinates to subject coordinates, do 
you happen to have a reasonable T1w MRI scan of your subjects?  I don't know 
how big the TMS field is, and I hadn't looked at the distance from subject to 
group average surfaces before, but in one of the HCP subjects, I got a maximum 
of 2cm distance from the group average surface (using midthickness surfaces), 
which occurred in a few specific locations, while 90% of the surface was 1cm 
distance or less.

Can I clarify – was the ICA run on the volumes and then later mapped on to 
surfaces, or was it performed on the surface data? If the former, are the 
original volumetric results for the ICA of each subject available anywhere in 
.nii format?

Cheers,
James

James Morrow
Research assistant
Brain & Mental Health Laboratory

Monash Institute of Cognitive and Clinical Neurosciences
School of Psychological Sciences
Monash University
c/o MBI, 770 Blackburn Road
Clayton VIC 3800
Australia

T: 03 9902 9768
E: james.mor...@monash.edu
www.med.monash.edu.au/psych/bmh/

[http://www.med.monash.edu.au/assets/images/psych/bmh/bannerbmh.jpg]
[http://med.monash.edu.au/psych/email-sig/miccn-email-sig.jpg]

On 3 August 2017 at 07:00, Timothy Coalson 
> wrote:
As Matt said, "MNI coordinates" of functionally-aligned cortical surface 
features don't have much meaning, similar to how T1w-aligned MNI space volumes don't have 
good cortical functional alignment (except in a few low-variability regions).  We have 
shown that group average surface coordinates do not follow the MNI cortical ribbon (see 
attached image that simply shows the average white and pial contours on top of the MNI 
nonlinear template).  The ICA maps themselves are also more informative than just the 
vertices at their peaks.

Surface group results should not be turned into volumetric files, group average 
surfaces do not have much folding left in them, and as such they do not match 
the MNI template anymore - this is due to folding incompatibilities between 
subjects, but also due to using functional surface registration instead of 
folding patterns.  Using the individual surfaces to map to the volume and then 
averaging across them would spread your data out just as badly as doing 
volume-based analysis of cortex, so this is also highly discouraged.

Despite strongly advising you not to do what you outlined, I will tell you what 
commands you would need.  The -cifti-extrema command will output a map with 1s 
and -1s at each local extrema.  The surface it uses is for neighbor information 
and distance computation - this isn't as critical as coordinates are, as it 
merely sets the maximum possible density of extrema (what you could get from a 
very noisy map).  You will need to use a threshold or other method to exclude 
local extrema that are outside the high-valued area.  We use midthickness 
surfaces for this kind of thing (and when doing some important spatial 
operation, we use corrected vertex areas to compensate for the loss of folding 
in group average surfaces, see -metric-smoothing).

You can extract the coordinates of a surface file with 
-surface-coordinates-to-metric, and you can use -cifti-separate on the 
-cifti-extrema result to get those as metric files, so that the indices will 
match, so that you can use them in matlab or some other tool for ad-hoc 
analysis (alternatively, use -cifti-create-dense-from-template to put the 
surface coordinates into a cifti file).  Since we advise not to do this with 
any group data, you are on your own here (finding the coordinates in a bunch of 
individuals and averaging those will give exactly the same bad answer, 
reflecting the fact that many/most functional areas have 

[HCP-Users] CIFTI and MATLAB

[Claude Bajada]

Dear all,

Is this post still valid re: cifti in matlab?

https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-2.HowdoyougetCIFTIfilesintoMATLAB?

Is cifti-matlab still only recommended for MEG data?

https://github.com/Washington-University/cifti-matlab

Claude





Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt




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Re: [HCP-Users] Two questions about surfaces & template spaces | MSMall & FS

[Claude Bajada]

Thanks Tim et al,

I have some follow-up questions:

 * I am performing tractography by defining an individual coordinate
   (in mm not voxels). If I use an XYZ that corresponds to one of the
   vertices on the 'white.32k' surface, that should correspond to the
   same point in the DWI data. Correct?
 * Would the rotation affect this? ("just rotated and moved to the
   usual orientation"). I was under the impression that the DWI and T1
   were also rotated into the usual orientation.

You state:

   "The surfaces in T1w are generated first, as we run freesurfer on
   the structural scans to generate them."
   I assume that these are the ones living in T1w/Native/

   "We then apply the FNIRT warpfield to them to get the MNINonLinear
   versions."
   These live in MNINonLinear/Native

   Then you downsample them to 32k... in MNINonLinear/fsaverage_LR32k

   The minimal processing pipeline publication (Glasser et al 2013)
   then states:
   "Finally, this 32k_fs_LR mesh [I'm assuming the one mentioned in the
   point above] is transformed from MNI space back to the native volume
   space"

The question is:

 * Is this now a correct interpretation?

Regards,

Claude


On 24.07.2017 22:38, Timothy Coalson wrote:
On Mon, Jul 24, 2017 at 8:40 AM, Claude Bajada <c.baj...@fz-juelich.de 
<mailto:c.baj...@fz-juelich.de>> wrote:


Dear all,

I have a two questions about the surfaces that live in the HCP
data folders:

 1. MNINonLinear/fsaverage/
 2. T1w/fsaverageLR32k/

I assume you mean the fsaverage_LR32k folder within each of those folders.

If I have understood the minimal pipeline correctly:

 1. all the surfaces in MNINonLinear/fsaverage32k/ are the
individual's surface that was warped into a template space
(either FS or MSMAll).
 2. the surfaces in T1w/fsaverageLR32k/ are the surfaces mentioned
in the above point that are warped back into the individual's
native space

Not exactly.  Volume spaces are a completely orthogonal question to 
surface registration.  Except for some special files, everything in 
the MNINonLinear folder aligns to the MNI template via FNIRT 
registration.  Everything in T1w similarly aligns to the subject's 
AC-PC rigid aligned space (original size and shape of the subject's 
structural scans, just rotated and moved to the usual orientation).


MSMAll, freesurfer, MSMSulc, or any other surface registration does 
not cause any anatomical deformations of the individual's brain.  The 
standard mesh anatomical surfaces you get after surface registration 
and resampling align with the same volumes as the original surfaces. 
There is no pre-defined anatomical coordinate template in our surface 
atlases, so we don't need to work backward from any template 
coordinate system.  Instead, we have standard spheres that define the 
standard topology (triangle relationships) - once we have the 
subject's sphere aligned to the standard sphere via template data 
(sulc for MSMSulc or FS; resting state networks, myelin, thickness, 
etc for MSMAll), we can combine the standard sphere's topology with 
the subject's anatomical coordinate data (by resampling the XYZ 
values), generating the subject's standard mesh surfaces.


The surfaces in T1w are generated first, as we run freesurfer on the 
structural scans to generate them.  We then apply the FNIRT warpfield 
to them to get the MNINonLinear versions.


As a side note, group average surfaces ARE significantly deformed from 
the individuals' brain shapes.  Most notably, they contain much less 
folding, and therefore surface area, as all the incompatible or 
non-corresponding folding patterns (when you align based on function, 
folding becomes less aligned, as function isn't always fixed with 
respect to folds) effectively smooth each other out when averaged.  
This is why we have correction methods for this when doing spatial 
operations on group average surfaces.


The two questions are:

 1. Given the above, am I right in assuming that any data that
correspond to a vertex of a surface in T1w/fsaverageLR32k/
also corresponds to the surface in MNINonLinear/fsaverageLR32k/?

 Yes.

> 2. Do you recommend that we the MSMAll surfaces over the FS ones?

Yes, they have considerably better cross subject functional 
correspondence than freesurfer.  That is, if a given vertex index is 
in area MT in one subject, MSMAll will have a considerably higher 
percentage of other subjects that also have that vertex in MT.


Regards,

Claude








Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzen

[HCP-Users] Two questions about surfaces & template spaces | MSMall & FS

[Claude Bajada]

Dear all,

I have a two questions about the surfaces that live in the HCP data folders:

 1.  MNINonLinear/fsaverage/
 2.  T1w/fsaverageLR32k/

If I have understood the minimal pipeline correctly:

 1.  all the surfaces in MNINonLinear/fsaverage32k/ are the individual's 
surface that was warped into a template space (either FS or MSMAll).
 2.  the surfaces in T1w/fsaverageLR32k/ are the surfaces mentioned in the 
above point that are warped back into the individual's native space

The two questions are:

 1.  Given the above, am I right in assuming that any data that correspond to a 
vertex of a surface in T1w/fsaverageLR32k/ also corresponds to the surface in 
MNINonLinear/fsaverageLR32k/?
 2.  Do you recommend that we the MSMAll surfaces over the FS ones?

Regards,

Claude





Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt




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Re: [HCP-Users] Flat Maps

[Claude Bajada]

Dear David,

Thank you very much for your response. A colleague has forwarded the 
mail to me. I have no idea why I am not receiving your mails, I seem to 
be receiving all the other [HCP-Users] mail. I will check my settings.

Thanks once again and regards,

Claude


>
>
>  Forwarded Message 
> Subject:  Re: [HCP-Users] Flat Maps
> Date: Thu, 13 Jul 2017 16:36:12 -0500
> From: David Van Essen <vanes...@wustl.edu>
> To:   Claude Bajada <c.baj...@fz-juelich.de>, hcp-users
> <hcp-users@humanconnectome.org>
>
>
>
> Hi Claude et al.,
>
> 1) The atlas template flatmaps surfaces are available
> at 
> https://github.com/Washington-University/Pipelines/tree/master/global/templates/standard_mesh_atlases
> 164k: colin.cerebral.L.flat.164k_fs_LR.surf.gii
> <https://github.com/Washington-University/Pipelines/blob/master/global/templates/standard_mesh_atlases/colin.cerebral.L.flat.164k_fs_LR.surf.gii>;
>  colin.cerebral.R.flat.164k_fs_LR.surf.gii
> <https://github.com/Washington-University/Pipelines/blob/master/global/templates/standard_mesh_atlases/colin.cerebral.L.flat.164k_fs_LR.surf.gii>
> 32k: colin.cerebral.L.flat.32k_fs_LR.surf.gii
> <https://github.com/Washington-University/Pipelines/blob/master/global/templates/standard_mesh_atlases/colin.cerebral.L.flat.164k_fs_LR.surf.gii>;
>  colin.cerebral.R.flat.32k_fs_LR.surf.gi
> <https://github.com/Washington-University/Pipelines/blob/master/global/templates/standard_mesh_atlases/colin.cerebral.L.flat.164k_fs_LR.surf.gii>i
>
> 2) 32k versions of the same flatmap surfaces are available (but
> named S900.L.flat.32k_fs_LR.surf.gii
> and S900.R.flat.32k_fs_LR.surf.gii) along with the group average sulc
> and other modalities are in the 900 Subjects Group Average dataset users
> can download from our BALSA database:
> https://balsa.wustl.edu/study/show/WG33
> And also here: https://db.humanconnectome.org/data/projects/HCP_1200
> Upon download, the zipped data unpacks to a folder
> named HCP_S900_GroupAvg_v1
>
> 3) Flatmaps and associated datasets for individual subjects are
> available via ConnectomeDB or Connectome-in-a-Box datasets: The 164k flat 
> maps are in {SubjectID}/MNINonLinear
> and the 32k flat maps are in {SubjectID}/MNINonLinear/fsaverage_LR32k
>
> 4) Let us know if you need help finding other reference datasets.
>
> 5) My earlier response to Claude Bajada <c.baj...@fz-juelich.de
> <mailto:c.baj...@fz-juelich.de>> failed to transmit.  If someone knows a
> different email for Claude,  please forward this email to him separately.
>
> David
>
>> On Jul 10, 2017, at 3:08 AM, Claude Bajada <c.baj...@fz-juelich.de
>> <mailto:c.baj...@fz-juelich.de>> wrote:
>>
>> Dear David,
>>
>> Thank you for your reply and apologies for the late response. It
>> appears that I did not receive the email and it was forwarded to me
>> today by a colleague of mine.
>>
>> I am assuming that I can find the atlas flatmap somewhere within the
>> HCP site?
>>
>> Kind regards,
>> Claude
>>>
>>>  Forwarded Message 
>>> Subject: Re: [HCP-Users] Flat Maps
>>> Date: Fri, 7 Jul 2017 10:16:13 -0700
>>> From: David Van Essen <vanes...@wustl.edu <mailto:vanes...@wustl.edu>>
>>> To: Claude Bajada <c.baj...@fz-juelich.de
>>> <mailto:c.baj...@fz-juelich.de>>, hcp-users
>>> <hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>>
>>>
>>> Claude et al.,
>>>
>>> The HCP pipelines include a process of registering individual-subject
>>> data to an atlas flat map (originally derived from the human PALS
>>> atlas).  This does not include a process for generating de novo flat
>>> maps.
>>> Other software (e.g., FreeSurfer and Caret) have methods for generating
>>> individual flat-maps. The Caret method is only semi-automated.
>>>
>>> David
>>>
>>>> On Jul 7, 2017, at 5:37 AM, Claude Bajada <c.baj...@fz-juelich.de
>>>> <mailto:c.baj...@fz-juelich.de>> wrote:
>>>>
>>>> Dear all,
>>>>
>>>> Are there any available scripts (preferably in matlab or python) to
>>>> generate flat maps?
>>>>
>>>> Regards,
>>>>
>>>> Claude
>>>>
>>>>
>>>>
>>>> 
>>>> 
>>>&