Re: [HCP-Users] Guidelines for preparing HCP-processed data for graph theory based analysis

[Glasser, Matthew]

Once you have a parcellated timeseries I would expect things to be pretty 
similar and just a matter of getting the data in the expected format for the 
software program.  I don’t have any experience with brain connectivity toolkit, 
but you can use wb_command -cifti-parcellate to generate parcellated timeseries 
and then load these into matlab with the matlab CIFTI reader/writer 
(https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-2.HowdoyougetCIFTIfilesintoMATLAB?)
 or wb_command -cifti-convert to convert CIFTI to text or a NIFTI file.

Peace,

Matt.

From: 
>
 on behalf of Yu Sun Chung >
Date: Thursday, May 24, 2018 at 10:36 AM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] Guidelines for preparing HCP-processed data for graph 
theory based analysis

Hi,

I am looking into any publications describing a step-by-step guidelines for 
preparing HCP-processed data to conduct graph theory analysis like brain 
connectivity toolkit. especially, I wonder how any data prep steps might differ 
from conventional volumetric-based processing pipelines. Anyone who can help me 
to clarify these? If any papers or guidelines are already out, would you please 
forward them to me?

Many thanks in advance!

Best,
Yu Sun

--
---
Yu Sun Chung, PhD

Postdoctoral Fellow
Clinical Neuroscience and Development Laboratory
Olin Neuropsychiatry Research Center
200 Retreat Avenue
Whitehall Building- Institute of Living
Hartford CT 06106
Phone:860-545-7144
Fax: 860-545-7797
Email: yusun.ch...@hhchealth.org

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] MMP labels and mesh modification

[Harwell, John]

There may be some confusion between annotations and labels.  Annotations are 
the text characters on the surface that identify the parcels (e.g.: “MST”).  
Labels refer to the data file overlayed on the surface that colors 
brainordinates (surface vertices) by associating a color with a name.

The annotations are contained in the scene and not in a separate data file.

If you want to disable the display of particular annotations:
* Display the features toolbox by clicking the toolbox icon on the far right 
side of the toolbar or View Menu -> Features Toolbox -> Attach to Right.
* In the Features ToolBox, click the Annot tab
* In the Main Window, click the tab for the surface that contains annotations 
that you want to hide.  A box will briefly appear around the surface when the 
tab is clicked.
* Return to the Features Toolbox.  Find the name of annotation you want to hide 
and uncheck the box next to the name.

In the features toolbox, there is a “Group” selection that allows one to 
control the display of annotations within a “Group”.  Each annotation contains 
a separate display status for each Group.  For this scene, you will see several 
annotations with the same name but each is displayed in only one group.  The 
reason is that on each surface (left, right, left flat, and right flat) the 
annotation needs a unique surface coordinate location.

To save your changes:
* Display the Scene Dialog by selecting the Clapboard icon in the Toolbar or 
Window Menu -> Scenes.
* Click the New button to create a new Scene File.
* Click the Add button to create a new scene and enter a name.
* Click the Save As button, enter the path and name for the scene file, click 
the File Dialog’s Save button to save the scene file.

For more information about annotations, select Help Menu -> Workbench Help.  In 
the Help Dialog, click on Annotations 1.3 (7th item from top in Table of 
Contents).


John Harwell


On May 24, 2018, at 2:30 AM, Amin Dadashi 
> wrote:

Thank you Tim. I could use your help to solve the second issue. However, In the 
first case, by turning the labels off their name do not disappear (the names on 
the list are even slightly different from the ones that are shown) . It seems 
to me that the ROI names are saved in a separate surface file and are shown as 
an overlay and it is not possible to remove them individually. There are so 
many files associated with this specific *.scene file and I could not figure 
out where to find the one that contains the ROIs name. I would appreciate if 
anyone could give me a hint.

On Thu, May 24, 2018, 03:37 Timothy Coalson 
> wrote:
1) Open the features toolbox (rightmost button near the top right of the 
window), select the "labels" tab, expand the list for the file in question, and 
uncheck the labels you don't want (you can use the checkbox on the file to 
start with them all turned off).

2) The command required is "wb_command -label-resample", use the 32k and 59k 
standard spheres (L.sphere... and R.sphere..., for the separate hemispheres) in 
the HCP Pipelines global/templates/standard_mesh_atlases folder.  The ideal way 
is to use ADAP_BARY_AREA, using 
global/templates/standard_mesh_atlases/resample_fsaverage/fs_LR.?.midthickness.va_avg...
 in the -area-metrics option, but since this specific case is an upsampling, 
this may only have marginal improvements over using BARYCENTRIC (which doesn't 
need vertex area data).

Tim


On Wed, May 23, 2018 at 3:45 AM, Amin Dadashi 
> wrote:
Hello,

I am using "Glasser_et_al_2016_HCP_MMP1.0_6_AllAreasMap.scene" file of 
Multimodal Parcellation to localize the connectivity pattern of my study. I am 
using the 7T(1.6mm) HCP surface fMRI dataset. Now I have the following 
questions:

1. Is there any way to modify the shown parcellation labels of the "All Areas 
Map" scene file in wb_view? I want to delete the ones which are not relevant to 
my study.

2. How can I resample the "All Areas Map" labels and borders so I can overlay 
them on my 7T connectivity maps (59k mesh surface)?

Thank you,
Amin

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] Guidelines for preparing HCP-processed data for graph theory based analysis

[Yu Sun Chung]

Hi,

I am looking into any publications describing a step-by-step guidelines for
preparing HCP-processed data to conduct graph theory analysis like brain
connectivity toolkit. especially, I wonder how any data prep steps might
differ from conventional volumetric-based processing pipelines. Anyone who
can help me to clarify these? If any papers or guidelines are already out,
would you please forward them to me?

Many thanks in advance!

Best,
Yu Sun

-- 
---
Yu Sun Chung, PhD

Postdoctoral Fellow
Clinical Neuroscience and Development Laboratory
Olin Neuropsychiatry Research Center
200 Retreat Avenue
Whitehall Building- Institute of Living
Hartford CT 06106
Phone:860-545-7144
Fax: 860-545-7797
Email: yusun.ch...@hhchealth.org 

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Downloading tutorial data

[Elam, Jennifer]

Hi Mahinda,

Can you clear the Safari browser's cache and try again? You could also try a 
different browser. Hopefully that will do the trick.


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: Mahinda Yogarajah 
Sent: Thursday, May 24, 2018 8:59:03 AM
To: Elam, Jennifer
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Downloading tutorial data

Hi,

Thanks for the quick reply. I just tried it again, but it is still hanging.

Thanks,

Mahinda

On 24 May 2018, at 14:45, Elam, Jennifer 
> wrote:

Hi Mahinda,
We had an issue with our download server that we just resolved, so please try 
your download again.

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 Mahinda Yogarajah 
>
Sent: Thursday, May 24, 2018 5:25:42 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Downloading tutorial data

Dear All,

I am having downloading the tutorial dataset from the HCP website.

I am using Safari v11.1 and I have Aspera connect installed in the browser. The 
Aspera connect is working as I can download test files from the Aspera website 
using the tool.

When I click on the tutorial data download link it takes me to the download 
resource launcher and then hangs. Clicking on the “click here” link for 
downloads taking time also does not work.

Any advice gratefully received.

Thanks,

Mahinda


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] MMP labels and mesh modification

[Amin Dadashi]

Thank you Tim. I could use your help to solve the second issue. However, In
the first case, by turning the labels off their name do not disappear (the
names on the list are even slightly different from the ones that are shown)
. It seems to me that the ROI names are saved in a separate surface file
and are shown as an overlay and it is not possible to remove them
individually. There are so many files associated with this specific *.scene
file and I could not figure out where to find the one that contains the
ROIs name. I would appreciate if anyone could give me a hint.

On Thu, May 24, 2018, 03:37 Timothy Coalson  wrote:

> 1) Open the features toolbox (rightmost button near the top right of the
> window), select the "labels" tab, expand the list for the file in question,
> and uncheck the labels you don't want (you can use the checkbox on the file
> to start with them all turned off).
>
> 2) The command required is "wb_command -label-resample", use the 32k and
> 59k standard spheres (L.sphere... and R.sphere..., for the separate
> hemispheres) in the HCP Pipelines global/templates/standard_mesh_atlases
> folder.  The ideal way is to use ADAP_BARY_AREA,
> using 
> global/templates/standard_mesh_atlases/resample_fsaverage/fs_LR.?.midthickness.va_avg...
> in the -area-metrics option, but since this specific case is an upsampling,
> this may only have marginal improvements over using BARYCENTRIC (which
> doesn't need vertex area data).
>
> Tim
>
>
> On Wed, May 23, 2018 at 3:45 AM, Amin Dadashi <
> amin.dada...@uni-tuebingen.de> wrote:
>
>> Hello,
>>
>> I am using "Glasser_et_al_2016_HCP_MMP1.0_6_AllAreasMap.scene" file of
>> Multimodal Parcellation to localize the connectivity pattern of my study. I
>> am using the 7T(1.6mm) HCP surface fMRI dataset. Now I have the following
>> questions:
>>
>> 1. Is there any way to modify the shown parcellation labels of the "All
>> Areas Map" scene file in wb_view? I want to delete the ones which are not
>> relevant to my study.
>>
>> 2. How can I resample the "All Areas Map" labels and borders so I can
>> overlay them on my 7T connectivity maps (59k mesh surface)?
>>
>> Thank you,
>> Amin
>>
>> ___
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>
>
>

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Downloading tutorial data

[Mahinda Yogarajah]

Hi, 

Thanks for the quick reply. I just tried it again, but it is still hanging.

Thanks, 

Mahinda

On 24 May 2018, at 14:45, Elam, Jennifer  wrote:

> Hi Mahinda,
> We had an issue with our download server that we just resolved, so please try 
> your download again. 
> 
> 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 Mahinda Yogarajah 
> 
> Sent: Thursday, May 24, 2018 5:25:42 AM
> To: hcp-users@humanconnectome.org
> Subject: [HCP-Users] Downloading tutorial data
>  
> Dear All, 
> 
> I am having downloading the tutorial dataset from the HCP website.
> 
> I am using Safari v11.1 and I have Aspera connect installed in the browser. 
> The Aspera connect is working as I can download test files from the Aspera 
> website using the tool.
> 
> When I click on the tutorial data download link it takes me to the download 
> resource launcher and then hangs. Clicking on the “click here” link for 
> downloads taking time also does not work.
> 
> Any advice gratefully received.
> 
> Thanks, 
> 
> Mahinda
> 
> 
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Downloading tutorial data

[Elam, Jennifer]

Hi Mahinda,
We had an issue with our download server that we just resolved, so please try 
your download again.

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 Mahinda Yogarajah 

Sent: Thursday, May 24, 2018 5:25:42 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Downloading tutorial data

Dear All,

I am having downloading the tutorial dataset from the HCP website.

I am using Safari v11.1 and I have Aspera connect installed in the browser. The 
Aspera connect is working as I can download test files from the Aspera website 
using the tool.

When I click on the tutorial data download link it takes me to the download 
resource launcher and then hangs. Clicking on the “click here” link for 
downloads taking time also does not work.

Any advice gratefully received.

Thanks,

Mahinda


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Experiencing downloading problems

[Elam, Jennifer]

Hi Mich,
We believe the issue should be resolved now,  please try the download again. 
Thanks for your patience!

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: Michel Thiebaut 
Sent: Thursday, May 24, 2018 1:39:11 AM
To: Elam, Jennifer
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Experiencing downloading problems

Hi Jenn,

Thanks for getting back to me. I tried to download a single subject this 
morning again on two different computers that I previously used to download HCP 
data, and it didn't work.
The download just doesn't start in Aspera.

Thanks for letting me know when the redeployment is done.

Kind regards

mich

Michel Thiebaut de Schotten
Associate Professor, PhD, HDR, CNRS
Sorbonne Universities, UPMC Univ Paris 06
Brain Connectivity and Behaviour Group
Frontlab, Institut du cerveau et la moelle épinière
Hôpital de la Salpêtrière - ICM
47 Bvd de l'Hôpital CS21414
75646 PARIS CEDEX 13

Skype: michel_thiebaut_de_schotten
phone: +33 7 83 50 81 60
http://www.bcblab.com
http://toolkit.bcblab.com


On Wed, May 23, 2018 at 11:10 PM, Elam, Jennifer 
> wrote:

Hi again Mich,

Go ahead and try a test download, but the developers here have found another 
issue that might be causing the problem. For their fix to go through they need 
to schedule a redeployment of ConnectomeDB, which will hopefully happen 
tomorrow. Sorry for the delay.


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 Elam, Jennifer >
Sent: Wednesday, May 23, 2018 11:32:18 AM
To: Michel Thiebaut; 
hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Experiencing downloading problems


Hi Mich,

Could you try the download again? We had an outage earlier this morning, but we 
are hoping that everything is working now. Let us know how it goes.


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 Michel Thiebaut 
>
Sent: Wednesday, May 23, 2018 4:56:46 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Experiencing downloading problems

Dear HCP team,

I've been experiencing downloading issue today.
I tried to download the 7T Resting-State fMRI FIX-Denoised (Extended), however, 
for some reason, the download doesn't start in Aspera. I also tried a single 
subject without success.
I usually have no problem.
Is it happening on your side?

Thanks a lot for letting me know
Kind regards

mich


Michel Thiebaut de Schotten
Associate Professor, PhD, HDR, CNRS
Sorbonne Universities, UPMC Univ Paris 06
Brain Connectivity and Behaviour Group
Frontlab, Institut du cerveau et la moelle épinière
Hôpital de la Salpêtrière - ICM
47 Bvd de 
l'Hôpital
 CS21414
75646 PARIS CEDEX 13

Skype: michel_thiebaut_de_schotten
phone: +33 7 83 50 81 60
http://www.bcblab.com
http://toolkit.bcblab.com


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] Downloading tutorial data

[Mahinda Yogarajah]

Dear All, 

I am having downloading the tutorial dataset from the HCP website.

I am using Safari v11.1 and I have Aspera connect installed in the browser. The 
Aspera connect is working as I can download test files from the Aspera website 
using the tool.

When I click on the tutorial data download link it takes me to the download 
resource launcher and then hangs. Clicking on the “click here” link for 
downloads taking time also does not work.

Any advice gratefully received.

Thanks, 

Mahinda


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Experiencing downloading problems

[Michel Thiebaut]

Hi Jenn,

Thanks for getting back to me. I tried to download a single subject this
morning again on two different computers that I previously used to download
HCP data, and it didn't work.
The download just doesn't start in Aspera.

Thanks for letting me know when the redeployment is done.

Kind regards

mich

*Michel Thiebaut de Schotten*
Associate Professor, PhD, HDR, CNRS
Sorbonne Universities, UPMC Univ Paris 06
Brain Connectivity and Behaviour Group
Frontlab, Institut du cerveau et la moelle épinière
Hôpital de la Salpêtrière - ICM
47 Bvd de l'Hôpital CS21414
75646 PARIS CEDEX 13

Skype: michel_thiebaut_de_schotten
phone: +33 7 83 50 81 60
http://www.bcblab.com
http://toolkit.bcblab.com 


On Wed, May 23, 2018 at 11:10 PM, Elam, Jennifer  wrote:

> Hi again Mich,
>
> Go ahead and try a test download, but the developers here have found
> another issue that might be causing the problem. For their fix to go
> through they need to schedule a redeployment of ConnectomeDB, which will
> hopefully happen tomorrow. Sorry for the delay.
>
>
> 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  humanconnectome.org> on behalf of Elam, Jennifer 
> *Sent:* Wednesday, May 23, 2018 11:32:18 AM
> *To:* Michel Thiebaut; hcp-users@humanconnectome.org
> *Subject:* Re: [HCP-Users] Experiencing downloading problems
>
>
> Hi Mich,
>
> Could you try the download again? We had an outage earlier this morning,
> but we are hoping that everything is working now. Let us know how it goes.
>
>
> 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  humanconnectome.org> on behalf of Michel Thiebaut <
> michel.thieb...@gmail.com>
> *Sent:* Wednesday, May 23, 2018 4:56:46 AM
> *To:* hcp-users@humanconnectome.org
> *Subject:* [HCP-Users] Experiencing downloading problems
>
> Dear HCP team,
>
> I've been experiencing downloading issue today.
> I tried to download the 7T Resting-State fMRI FIX-Denoised (Extended),
> however, for some reason, the download doesn't start in Aspera. I also
> tried a single subject without success.
> I usually have no problem.
> Is it happening on your side?
>
> Thanks a lot for letting me know
> Kind regards
>
> mich
>
>
> *Michel Thiebaut de Schotten*
> Associate Professor, PhD, HDR, CNRS
> Sorbonne Universities, UPMC Univ Paris 06
> Brain Connectivity and Behaviour Group
> Frontlab, Institut du cerveau et la moelle épinière
> Hôpital de la Salpêtrière - ICM
> 47 Bvd de l'Hôpital
> 
> CS21414
> 75646 PARIS CEDEX 13
>
> Skype: michel_thiebaut_de_schotten
> phone: +33 7 83 50 81 60
> http://www.bcblab.com
> http://toolkit.bcblab.com 
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users