date:20170919

Re: [HCP-Users] about surface template and writing matrix to.dlabel cifti file

2017-09-19 Thread Timothy Coalson

We do have a version of the 7 networks labels as the first map in this file:

https://balsa.wustl.edu/file/show/Q2xn

It currently does not use a medial wall mask, so extra steps may be needed
for using it with HCP data.

I don't know if either current matlab method of cifti file IO has much
support for label-type data.  One way to do this with the
ciftiopen/ciftisave functions we are more familiar with is to save the
integer label data as a .dscalar.nii file by first reading in another small
cifti file with ciftiopen, replacing the data matrix in the object, and
saving it (with ciftisavereset if needed), then using wb_command
-cifti-label-import to turn it into a dlabel file.

Tim


On Tue, Sep 19, 2017 at 3:26 AM, 罗 <963619...@qq.com> wrote:

> Dear professors:
> I have two questions. The first one is that do you have a surface template
> of 32k cifti file of Yeo_2011 7networks or just contain four lobes?
> The second one is that, how can I write a matrix into a .dlabel.nii file?
> It seems that ft_write_cifti (filename, source, 'dlabel') is wrong.
> Thanks and best wishes!
>
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> Content preview:  Dear professors: I have two questions. The first one is
> that
>do you have a surface template of 32k cifti file of Yeo_2011 7networks
> or
>just contain four lobes? The second one is that, how can I write a
> matrix
>into a .dlabel.nii file? It seems that ft_write_cifti (filename, source,
>   'dlabel') is wrong. Thanks and best wishes! [...]
>
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> Content preview:  Dear professors: I have two questions. The first one is
> that
>do you have a surface template of 32k cifti file of Yeo_2011 7networks
> or
>just contain four lobes? The second one is that, how can I write a
> matrix
>into a .dlabel.nii file? It seems that ft_write_cifti (filename, source,
>   'dlabel') is wrong. Thanks and best wishes! [...]
>
> Content analysis details:   (6.4 points, 5.0 required)
>
>  pts rule name  description
>  -- --
> 
>  2.8 FROM_STARTS_WITH_NUMS  From: starts with many numbers
>  3.2 CHARSET_FARAWAY_HEADER A foreign language charset used in headers
>  0.0 HTML_MESSAGE   BODY: HTML included in message
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Re: [HCP-Users] Correlation matrices

2017-09-19 Thread Timothy Coalson

The -cifti-create-dense-* commands are indeed involved in manually making
cifti versions of your data, though you would also need things like
-volume-to-surface-mapping, as well as FreeSurfer to generate the subject
surfaces - the HCP pipelines are designed for automating these steps for
HCP and similar data - as Matt said, the easiest way is to start from the
CIFTI files we already made by running these pipelines.

For how the cifti format works, start with FAQ #1 here:

https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-1.Whatare*dtseries.nii,*.dconn.nii,*dlabel.nii,*.dscalar.niifiles
?

In particular it (now) links to some additional explanation provided in
"wb_command -cifti-help":

https://www.humanconnectome.org/software/workbench-command/-cifti-help

If you want the painful low-level details, the pdfs on NITRC that both
places refer to contain the info you would need to make another cifti
library.

Tim


On Tue, Sep 19, 2017 at 2:32 AM, Carole Guedj  wrote:

> Hi Matt,
>
> Thank for getting back to me.
> I am not familiar at all with the CIFTI format. I made all my
> preprocessing using NIFTI volume files, so the preprocessing output is in
> NIFTI format. I guess that I couldn’t use the -cifti-cross-correlation command
> with a NIFTI format.
> Could I create the CIFTI files needed using the command
> -cifti-create-dense-timeseries ? How does it works to keep both cortical
> and subcortical gray matter?
>
> Thank you again,
> Carole
>
>
>
> Le 18 sept. 2017 à 17:08, Glasser, Matthew  a écrit :
>
> This should be possible with wb_command -cifti-cross-correlation.  You
> would create a CIFTI dense timeseries file of the subcortical region of
> interest and a CIFTI parcellated timeseries using the parcellation of your
> choice.  You could then visualize the results in wb_view (depending on the
> order in which you specify the arguments, either you can visualize the
> connectivity in the space of the subcortical ROI or as parcellation.  You
> would click in the other space to see the results.
>
> Peace,
>
> Matt.
>
> From:  on behalf of Carole Guedj <
> carole.gu...@unige.ch>
> Date: Monday, September 18, 2017 at 3:58 AM
> To: "hcp-users@humanconnectome.org" 
> Subject: [HCP-Users] Correlation matrices
>
> Dear HCP experts,
>
> I’m using HCP resting-state fMRI data for functional connectivity
> analyses. I have actually two question about that:
>
> 1/ After preprocessed the data, I would like to compute a functional
> connectivity matrix between all voxels of a defined subcortical
> region-of-interest with the rest of the brain (using a GM mask) to obtain
> an NxM correlation matrix. Could I do that with wb_command?
>
> 2/ To reduce the size of this correlation matrix, is it possible to resample
> the M dimension using an atlas?
>
> Thanks in advance for any help!
>
> Carole
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>
>
> ___
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>

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Re: [HCP-Users] Cerebellum surface

2017-09-19 Thread Dierker, Donna

Maybe also have a look at Joern Diedrichsen’s page:

http://www.diedrichsenlab.org/imaging/propatlas.htm



> On Sep 19, 2017, at 9:42 AM, Glasser, Matthew  wrote:
>
> This is built into the CIFTI format for the future, however we do not yet 
> have an algorithm for making individual subject cerebellar surfaces.  I 
> believe a “Colin” individual surface is available somewhere and perhaps David 
> knows the details.
>
> Peace,
>
> Matt.
>
> From:  on behalf of Avital Hahamy 
> 
> Reply-To: "avitalhah...@gmail.com" 
> Date: Tuesday, September 19, 2017 at 2:37 AM
> To: "hcp-users@humanconnectome.org" 
> Subject: [HCP-Users] Cerebellum surface
>
> Dear experts,
>
> I was wondering whether workbench enables projecting cerebellum group data 
> onto an available surface, and if so, where I could find the relevant surface?
>
> Kind regards,
> Avital
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Re: [HCP-Users] CIFTI files do not contain volume data

2017-09-19 Thread Sang-Young Kim

Dear Matt:

Thanks for your reply. Now I can run PALM for testing myelin map difference 
between groups. 

Best regards,

Sang-Young


> On Sep 18, 2017, at 4:22 PM, Glasser, Matthew  wrote:
> 
> Myelin maps are only for the cortex so you can omit the -volume-all 
> data_sub.nii portion of the command.
> 
> Peace,
> 
> Matt.
> 
> From:  > on behalf of Sang-Young Kim 
> mailto:sykim...@gmail.com>>
> Date: Monday, September 18, 2017 at 3:13 PM
> To: "HCP-Users@humanconnectome.org " 
> mailto:HCP-Users@humanconnectome.org>>
> Subject: [HCP-Users] CIFTI files do not contain volume data
> 
> Dear HCP experts:
> 
> I’m trying to compare myelin map between two groups using FSL Palm. I 
> generated each subject’s myelin map using the HCP pipelines scripts (e.g., 
> PreFreeSurfer, FreeSurfer, and PostFreeSurfer pipeline). Before running FSL 
> Palm, I have merged each subject myelin map using following command: 
> wb_command -cifti-merge. 
> 
> Then, to separate a CIFTI file into GIFTI and NIFTI, I ran the following 
> command:
> wb_command -cifti-separate data.dscalar.nii COLUMN -volume-all data_sub.nii 
> -metric CORTEX_LEFT data_L.func.gii -metric CORTEX_RIGHT data_R.func.gii
> 
> When I run above command, I get error message as below:
> ERROR: specified file and direction does not contain any volume data
> 
> So I checked the information of both merged myelin map data and each subject 
> data using wb_command -file-information. 
> I found that the CIFTI file really does not contain any volume data (Please 
> see below).
> 
> Name: data.dscalar.nii
> Type: Connectivity - Dense Scalar
> Structure:CortexLeft CortexRight 
> Data Size:4.28 Megabytes
> Maps to Surface:  true
> Maps to Volume:   false
> Maps with LabelTable: false
> Maps with Palette:true
> All Map Palettes Equal:   true
> Map Interval Units:   NIFTI_UNITS_UNKNOWN
> Number of Maps:   18
> Number of Rows:   59412
> Number of Columns:18
> Volume Dim[0]:0
> Volume Dim[1]:0
> Volume Dim[2]:0
> Palette Type: Map (Unique for each map)
> CIFTI Dim[0]: 18
> CIFTI Dim[1]: 59412
> ALONG_ROW map type:   SCALARS
> ALONG_COLUMN map type:BRAIN_MODELS
> Has Volume Data:  false
> CortexLeft:   29696 out of 32492 vertices
> CortexRight:  29716 out of 32492 vertices
> 
> Could anyone please explain what’s wrong with data processing?
> Since I didn't see any error messages when I ran the HCP pipeline, I have no 
> idea why CIFTI file does not contain volume data. 
> 
> Thanks in advance. 
> 
> Sang-Young Kim
> 
> Postdoctoral Research Fellow
> Department of Radiology, University of Pittsburgh 
>   
> 
> 
> 
> 
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Re: [HCP-Users] Cerebellum surface

2017-09-19 Thread Glasser, Matthew

This is built into the CIFTI format for the future, however we do not yet have 
an algorithm for making individual subject cerebellar surfaces.  I believe a 
“Colin” individual surface is available somewhere and perhaps David knows the 
details.

Peace,

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Avital Hahamy 
mailto:avitalhah...@gmail.com>>
Reply-To: "avitalhah...@gmail.com" 
mailto:avitalhah...@gmail.com>>
Date: Tuesday, September 19, 2017 at 2:37 AM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Cerebellum surface

Dear experts,

I was wondering whether workbench enables projecting cerebellum group data onto 
an available surface, and if so, where I could find the relevant surface?

Kind regards,
Avital

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[HCP-Users] Cerebellum surface

2017-09-19 Thread Avital Hahamy

Dear experts,

I was wondering whether workbench enables projecting cerebellum group data
onto an available surface, and if so, where I could find the relevant
surface?

Kind regards,
Avital

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Re: [HCP-Users] Correlation matrices

2017-09-19 Thread Glasser, Matthew

I’d recommend using the MSMAll aligned, cleaned CIFTI data provided by the HCP.

Peace,

Matt.

From: Carole Guedj mailto:carole.gu...@unige.ch>>
Date: Tuesday, September 19, 2017 at 2:32 AM
To: Matt Glasser mailto:glass...@wustl.edu>>, 
"hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Correlation matrices

Hi Matt,

Thank for getting back to me.
I am not familiar at all with the CIFTI format. I made all my preprocessing 
using NIFTI volume files, so the preprocessing output is in NIFTI format. I 
guess that I couldn’t use the -cifti-cross-correlation command with a NIFTI 
format.
Could I create the CIFTI files needed using the command 
-cifti-create-dense-timeseries ? How does it works to keep both cortical and 
subcortical gray matter?

Thank you again,
Carole

Le 18 sept. 2017 à 17:08, Glasser, Matthew 
mailto:glass...@wustl.edu>> a écrit :

This should be possible with wb_command -cifti-cross-correlation.  You would 
create a CIFTI dense timeseries file of the subcortical region of interest and 
a CIFTI parcellated timeseries using the parcellation of your choice.  You 
could then visualize the results in wb_view (depending on the order in which 
you specify the arguments, either you can visualize the connectivity in the 
space of the subcortical ROI or as parcellation.  You would click in the other 
space to see the results.

Peace,

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Carole Guedj mailto:carole.gu...@unige.ch>>
Date: Monday, September 18, 2017 at 3:58 AM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Correlation matrices

Dear HCP experts,

I’m using HCP resting-state fMRI data for functional connectivity analyses. I 
have actually two question about that:

1/ After preprocessed the data, I would like to compute a functional 
connectivity matrix between all voxels of a defined subcortical 
region-of-interest with the rest of the brain (using a GM mask) to obtain an 
NxM correlation matrix. Could I do that with wb_command?

2/ To reduce the size of this correlation matrix, is it possible to resample 
the M dimension using an atlas?

Thanks in advance for any help!

Carole

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Re: [HCP-Users] Correlation matrices

2017-09-19 Thread Carole Guedj

Hi Matt,

Thank for getting back to me.
I am not familiar at all with the CIFTI format. I made all my preprocessing 
using NIFTI volume files, so the preprocessing output is in NIFTI format. I 
guess that I couldn’t use the -cifti-cross-correlation command with a NIFTI 
format.
Could I create the CIFTI files needed using the command 
-cifti-create-dense-timeseries ? How does it works to keep both cortical and 
subcortical gray matter?

Thank you again,
Carole


Le 18 sept. 2017 à 17:08, Glasser, Matthew 
mailto:glass...@wustl.edu>> a écrit :

This should be possible with wb_command -cifti-cross-correlation.  You would 
create a CIFTI dense timeseries file of the subcortical region of interest and 
a CIFTI parcellated timeseries using the parcellation of your choice.  You 
could then visualize the results in wb_view (depending on the order in which 
you specify the arguments, either you can visualize the connectivity in the 
space of the subcortical ROI or as parcellation.  You would click in the other 
space to see the results.

Peace,

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Carole Guedj mailto:carole.gu...@unige.ch>>
Date: Monday, September 18, 2017 at 3:58 AM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Correlation matrices

Dear HCP experts,

I’m using HCP resting-state fMRI data for functional connectivity analyses. I 
have actually two question about that:

1/ After preprocessed the data, I would like to compute a functional 
connectivity matrix between all voxels of a defined subcortical 
region-of-interest with the rest of the brain (using a GM mask) to obtain an 
NxM correlation matrix. Could I do that with wb_command?

2/ To reduce the size of this correlation matrix, is it possible to resample 
the M dimension using an atlas?

Thanks in advance for any help!

Carole

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Re: [HCP-Users] about surface template and writing matrix to.dlabel cifti file

Re: [HCP-Users] Correlation matrices

Re: [HCP-Users] Cerebellum surface

Re: [HCP-Users] CIFTI files do not contain volume data

Re: [HCP-Users] Cerebellum surface

[HCP-Users] Cerebellum surface

Re: [HCP-Users] Correlation matrices

Re: [HCP-Users] Correlation matrices

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