Re: [HCP-Users] How can I convert subcortical nifti files to dlabel files?

2017-08-10 Thread Xavier Guell Paradis
Dear Tim and Matt,
Thank you very much for your help, now it works! I had my clusters registered 
to the S900_Average_T1w_restore.nii file, but they had to be registered to the 
MNI152_T1_2mm.nii.gz file.
Thank you very much,
Xavier.

From: Timothy Coalson [tsc...@mst.edu]
Sent: Wednesday, August 09, 2017 6:55 PM
To: Xavier Guell Paradis
Cc: Glasser, Matthew; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] How can I convert subcortical nifti files to dlabel 
files?

If your "mycluster.nii" is in a different volume space than 222 MNI RPI space, 
then it may not let you use it that way.  Compare the nifti header against this 
file in the HCP pipelines, using fslhd or wb_command -nifti-information 
-print-header:

global/templates/MNI152_T1_2mm.nii.gz

If it is different, then you will need to resample your label volume.

Tim


On Wed, Aug 9, 2017 at 4:38 PM, Xavier Guell Paradis 
<xavie...@mit.edu<mailto:xavie...@mit.edu>> wrote:
Dear Tim,
Thank you for your reply
I have made sure that I have the group .dconn file opened, and I can see that 
it is correctly opened because I can see connectivity when I click on any 
structure.
However, I still have the same problem: I do not see the option of "Show Cifti 
Connectivity" when I right-click the cluster of the dlabel file I have created 
(however, I can see the dlabel file in the "Labels" list of the "Features 
Toolbox").

These are the steps I followed to create the dlabel file; I imagine I did 
something wrong in these steps but I cannot figure out what:
My original nifti file with the right cerebellum cluster is called 
"mycluster.nii".
I created the file "textforvolumelabelimport.txt" with the following text:
CEREBELLUM_RIGHT
1 1 1 1
Then I did the following:
wb_command -volume-label-import mycluster.nii textforvolumelabelimport.txt 
mycluster_label.nii
wb_command -cifti-create-label 
mycluster_labelStep2.dlabel.ni<http://mycluster_labelStep2.dlabel.ni>i -volume 
mycluster_label.nii mycluster_label.nii
The resulting dlabel file is "mycluster_labelStep2.dlabel.nii"

Thank you very much,
Xavier.


From: Timothy Coalson [tsc...@mst.edu<mailto:tsc...@mst.edu>]
Sent: Wednesday, August 09, 2017 4:57 PM
To: Xavier Guell Paradis
Cc: Glasser, Matthew; 
hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>

Subject: Re: [HCP-Users] How can I convert subcortical nifti files to dlabel 
files?

You need to have a dtseries (or dconn) file open before you can see any kind of 
connectivity.  If you only have the labels/rois open, how do you expect it to 
figure out connectivity information?

Note that we only have options for averaging things inside a label, the ROI 
file will not be useful in the GUI for this purpose.

Tim


On Wed, Aug 9, 2017 at 3:42 PM, Xavier Guell Paradis 
<xavie...@mit.edu<mailto:xavie...@mit.edu>> wrote:
Dear Matt,
Thank you for your reply. I have realized that a very curious thing happens:
- If I open the dlabel file and right-click the cluster in wb_view, I do not 
see any option
- If I open the dscalar file and right-click the cluster in wb_view, I do not 
see any option
- If I open the dlabel file AND the dscalar file and right-click the cluster in 
wb_view (note that the cluster is now present twice: in the dlabel file and in 
the dscalar file), I see the "Show Data/Time Series Graph" but not the "Show 
Cifti Connectivity" option.

I opened wb_view multiple times to make sure that this is true: I only see the 
"Show Data/Time Series Graph" once I have opened both files; but I still do not 
see the "Show Cifti Connectivity" option.

This is a strange pattern, but perhaps it is a clue to find out what I am doing 
wrong.

An extra piece of information that might be useful: when I open the dlabel 
file, I can see it listed in the "Labels" list of the "Features ToolBox".

Thank you very much,
Xavier.

From: Glasser, Matthew [glass...@wustl.edu<mailto:glass...@wustl.edu>]
Sent: Wednesday, August 09, 2017 2:13 PM
To: Xavier Guell Paradis; NEUROSCIENCE tim

Cc: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] How can I convert subcortical nifti files to dlabel 
files?

It should work if you skip the last step and use the dlabel file.

Peace,

Matt.

From: Xavier Guell Paradis <xavie...@mit.edu<mailto:xavie...@mit.edu>>
Date: Wednesday, August 9, 2017 at 9:43 AM
To: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>, Matt Glasser 
<glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: RE: [HCP-Users] Ho

Re: [HCP-Users] How can I convert subcortical nifti files to dlabel files?

2017-08-09 Thread Timothy Coalson
If your "mycluster.nii" is in a different volume space than 222 MNI RPI
space, then it may not let you use it that way.  Compare the nifti header
against this file in the HCP pipelines, using fslhd or wb_command
-nifti-information -print-header:

global/templates/MNI152_T1_2mm.nii.gz

If it is different, then you will need to resample your label volume.

Tim


On Wed, Aug 9, 2017 at 4:38 PM, Xavier Guell Paradis <xavie...@mit.edu>
wrote:

> Dear Tim,
> Thank you for your reply
> I have made sure that I have the group .dconn file opened, and I can see
> that it is correctly opened because I can see connectivity when I click on
> any structure.
> However, I still have the same problem: I do not see the option of "Show
> Cifti Connectivity" when I right-click the cluster of the dlabel file I
> have created (however, I can see the dlabel file in the "Labels" list of
> the "Features Toolbox").
>
> These are the steps I followed to create the dlabel file; I imagine I did
> something wrong in these steps but I cannot figure out what:
> My original nifti file with the right cerebellum cluster is called
> "mycluster.nii".
>
> I created the file "textforvolumelabelimport.txt" with the following text:
>
> CEREBELLUM_RIGHT
>
> 1 1 1 1
>
> Then I did the following:
>
> wb_command -volume-label-import mycluster.nii textforvolumelabelimport.txt
> mycluster_label.nii
>
> wb_command -cifti-create-label mycluster_labelStep2.dlabel.nii -volume
> mycluster_label.nii mycluster_label.nii
> The resulting dlabel file is "mycluster_labelStep2.dlabel.nii"
>
> Thank you very much,
> Xavier.
>
> --
> *From:* Timothy Coalson [tsc...@mst.edu]
> *Sent:* Wednesday, August 09, 2017 4:57 PM
> *To:* Xavier Guell Paradis
> *Cc:* Glasser, Matthew; hcp-users@humanconnectome.org
>
> *Subject:* Re: [HCP-Users] How can I convert subcortical nifti files to
> dlabel files?
>
> You need to have a dtseries (or dconn) file open before you can see any
> kind of connectivity.  If you only have the labels/rois open, how do you
> expect it to figure out connectivity information?
>
> Note that we only have options for averaging things inside a label, the
> ROI file will not be useful in the GUI for this purpose.
>
> Tim
>
>
> On Wed, Aug 9, 2017 at 3:42 PM, Xavier Guell Paradis <xavie...@mit.edu>
> wrote:
>
>> Dear Matt,
>> Thank you for your reply. I have realized that a very curious thing
>> happens:
>> - If I open the dlabel file and right-click the cluster in wb_view, I do
>> not see any option
>> - If I open the dscalar file and right-click the cluster in wb_view, I do
>> not see any option
>> - If I open the dlabel file *AND* the dscalar file and right-click the
>> cluster in wb_view (note that the cluster is now present twice: in the
>> dlabel file and in the dscalar file), I see the "Show Data/Time Series
>> Graph" but not the "Show Cifti Connectivity" option.
>>
>> I opened wb_view multiple times to make sure that this is true: I only
>> see the "Show Data/Time Series Graph" once I have opened both files; but
>> I still do not see the "Show Cifti Connectivity" option.
>>
>> This is a strange pattern, but perhaps it is a clue to find out what I am
>> doing wrong.
>>
>> An extra piece of information that might be useful: when I open the
>> dlabel file, I can see it listed in the "Labels" list of the "Features
>> ToolBox".
>>
>> Thank you very much,
>> Xavier.
>> --
>> *From:* Glasser, Matthew [glass...@wustl.edu]
>> *Sent:* Wednesday, August 09, 2017 2:13 PM
>> *To:* Xavier Guell Paradis; NEUROSCIENCE tim
>>
>> *Cc:* hcp-users@humanconnectome.org
>> *Subject:* Re: [HCP-Users] How can I convert subcortical nifti files to
>> dlabel files?
>>
>> It should work if you skip the last step and use the dlabel file.
>>
>> Peace,
>>
>> Matt.
>>
>> From: Xavier Guell Paradis <xavie...@mit.edu>
>> Date: Wednesday, August 9, 2017 at 9:43 AM
>> To: Timothy Coalson <tsc...@mst.edu>, Matt Glasser <glass...@wustl.edu>
>> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>> Subject: RE: [HCP-Users] How can I convert subcortical nifti files to
>> dlabel files?
>>
>> Dear Tim and Matt,
>> Thank you very much for your reply.
>>
>> I tried -volume-label-import, followed by -cifti-create-label, followed
>> by -cifti-all-labels-to-rois.
>> After this,

Re: [HCP-Users] How can I convert subcortical nifti files to dlabel files?

2017-08-09 Thread Xavier Guell Paradis
Dear Tim,
Thank you for your reply
I have made sure that I have the group .dconn file opened, and I can see that 
it is correctly opened because I can see connectivity when I click on any 
structure.
However, I still have the same problem: I do not see the option of "Show Cifti 
Connectivity" when I right-click the cluster of the dlabel file I have created 
(however, I can see the dlabel file in the "Labels" list of the "Features 
Toolbox").

These are the steps I followed to create the dlabel file; I imagine I did 
something wrong in these steps but I cannot figure out what:
My original nifti file with the right cerebellum cluster is called 
"mycluster.nii".
I created the file "textforvolumelabelimport.txt" with the following text:
CEREBELLUM_RIGHT
1 1 1 1
Then I did the following:
wb_command -volume-label-import mycluster.nii textforvolumelabelimport.txt 
mycluster_label.nii
wb_command -cifti-create-label mycluster_labelStep2.dlabel.nii -volume 
mycluster_label.nii mycluster_label.nii
The resulting dlabel file is "mycluster_labelStep2.dlabel.nii"

Thank you very much,
Xavier.


From: Timothy Coalson [tsc...@mst.edu]
Sent: Wednesday, August 09, 2017 4:57 PM
To: Xavier Guell Paradis
Cc: Glasser, Matthew; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] How can I convert subcortical nifti files to dlabel 
files?

You need to have a dtseries (or dconn) file open before you can see any kind of 
connectivity.  If you only have the labels/rois open, how do you expect it to 
figure out connectivity information?

Note that we only have options for averaging things inside a label, the ROI 
file will not be useful in the GUI for this purpose.

Tim


On Wed, Aug 9, 2017 at 3:42 PM, Xavier Guell Paradis 
<xavie...@mit.edu<mailto:xavie...@mit.edu>> wrote:
Dear Matt,
Thank you for your reply. I have realized that a very curious thing happens:
- If I open the dlabel file and right-click the cluster in wb_view, I do not 
see any option
- If I open the dscalar file and right-click the cluster in wb_view, I do not 
see any option
- If I open the dlabel file AND the dscalar file and right-click the cluster in 
wb_view (note that the cluster is now present twice: in the dlabel file and in 
the dscalar file), I see the "Show Data/Time Series Graph" but not the "Show 
Cifti Connectivity" option.

I opened wb_view multiple times to make sure that this is true: I only see the 
"Show Data/Time Series Graph" once I have opened both files; but I still do not 
see the "Show Cifti Connectivity" option.

This is a strange pattern, but perhaps it is a clue to find out what I am doing 
wrong.

An extra piece of information that might be useful: when I open the dlabel 
file, I can see it listed in the "Labels" list of the "Features ToolBox".

Thank you very much,
Xavier.

From: Glasser, Matthew [glass...@wustl.edu<mailto:glass...@wustl.edu>]
Sent: Wednesday, August 09, 2017 2:13 PM
To: Xavier Guell Paradis; NEUROSCIENCE tim

Cc: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] How can I convert subcortical nifti files to dlabel 
files?

It should work if you skip the last step and use the dlabel file.

Peace,

Matt.

From: Xavier Guell Paradis <xavie...@mit.edu<mailto:xavie...@mit.edu>>
Date: Wednesday, August 9, 2017 at 9:43 AM
To: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>, Matt Glasser 
<glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: RE: [HCP-Users] How can I convert subcortical nifti files to dlabel 
files?

Dear Tim and Matt,
Thank you very much for your reply.

I tried -volume-label-import, followed by -cifti-create-label, followed by 
-cifti-all-labels-to-rois.
After this, when I right-click the cluster in wb_view, I see the option "Show 
Data/Time Series Graph For Parcel [my cluster]" but I do not see the option 
"Show Cifti Connectivity For Parcel [my cluster]" (even though I can see this 
option for other parcels, such as the Yeo map).
I have been trying different things but cannot figure it out.

Some extra information in case it is useful:

My clusters are a group average registered to the HCP 
"S900_Average_T1w_restore.nii", so at this point I am not concerned about 
comparison across subjects. I would like to calculate functional connectivity 
from each of my subcortical clusters using your S900 .dconn file.
My original nifti file with the right cerebellum cluster is called 
"mycluster.nii".
I created the file "textforvolumelabelimport.txt" with the following text:
CEREBELLUM_RIGHT
1 1 1 1
Then

Re: [HCP-Users] How can I convert subcortical nifti files to dlabel files?

2017-08-09 Thread Timothy Coalson
You need to have a dtseries (or dconn) file open before you can see any
kind of connectivity.  If you only have the labels/rois open, how do you
expect it to figure out connectivity information?

Note that we only have options for averaging things inside a label, the ROI
file will not be useful in the GUI for this purpose.

Tim


On Wed, Aug 9, 2017 at 3:42 PM, Xavier Guell Paradis <xavie...@mit.edu>
wrote:

> Dear Matt,
> Thank you for your reply. I have realized that a very curious thing
> happens:
> - If I open the dlabel file and right-click the cluster in wb_view, I do
> not see any option
> - If I open the dscalar file and right-click the cluster in wb_view, I do
> not see any option
> - If I open the dlabel file *AND* the dscalar file and right-click the
> cluster in wb_view (note that the cluster is now present twice: in the
> dlabel file and in the dscalar file), I see the "Show Data/Time Series
> Graph" but not the "Show Cifti Connectivity" option.
>
> I opened wb_view multiple times to make sure that this is true: I only see
> the "Show Data/Time Series Graph" once I have opened both files; but I
> still do not see the "Show Cifti Connectivity" option.
>
> This is a strange pattern, but perhaps it is a clue to find out what I am
> doing wrong.
>
> An extra piece of information that might be useful: when I open the dlabel
> file, I can see it listed in the "Labels" list of the "Features ToolBox".
>
> Thank you very much,
> Xavier.
> --
> *From:* Glasser, Matthew [glass...@wustl.edu]
> *Sent:* Wednesday, August 09, 2017 2:13 PM
> *To:* Xavier Guell Paradis; NEUROSCIENCE tim
>
> *Cc:* hcp-users@humanconnectome.org
> *Subject:* Re: [HCP-Users] How can I convert subcortical nifti files to
> dlabel files?
>
> It should work if you skip the last step and use the dlabel file.
>
> Peace,
>
> Matt.
>
> From: Xavier Guell Paradis <xavie...@mit.edu>
> Date: Wednesday, August 9, 2017 at 9:43 AM
> To: Timothy Coalson <tsc...@mst.edu>, Matt Glasser <glass...@wustl.edu>
> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
> Subject: RE: [HCP-Users] How can I convert subcortical nifti files to
> dlabel files?
>
> Dear Tim and Matt,
> Thank you very much for your reply.
>
> I tried -volume-label-import, followed by -cifti-create-label, followed by
> -cifti-all-labels-to-rois.
> After this, when I right-click the cluster in wb_view, I see the option
> "Show Data/Time Series Graph For Parcel [my cluster]" *but I do not see
> the option "Show Cifti Connectivity* For Parcel [my cluster]" (even
> though I can see this option for other parcels, such as the Yeo map).
> I have been trying different things but cannot figure it out.
>
> Some extra information in case it is useful:
>
> My clusters are a group average registered to the HCP
> "S900_Average_T1w_restore.nii", so at this point I am not concerned about
> comparison across subjects. I would like to calculate functional
> connectivity from each of my subcortical clusters using your S900 .dconn
> file.
> My original nifti file with the right cerebellum cluster is called
> "mycluster.nii".
>
> I created the file "textforvolumelabelimport.txt" with the following text:
>
> CEREBELLUM_RIGHT
>
> 1 1 1 1
>
> Then I did the following:
>
> wb_command -volume-label-import mycluster.nii textforvolumelabelimport.txt
> mycluster_label.nii
>
> wb_command -cifti-create-label mycluster_labelStep2.dlabel.nii -volume
> mycluster_label.nii mycluster_label.nii
>
> wb_command -cifti-all-labels-to-rois mycluster_labelStep2.dlabel.nii 1
> mycluster_labelStep3.dscalar.nii
>
> When I right-click "mycluster_labelStep3.dscalar.nii" in wb_view, I can
> see the option of "Show Data/Time Series Graph" *but not the option of
> "Show Cifti Connectivity*".
>
> Thank you very much,
> Xavier.
>
> --
> *From:* Timothy Coalson [tsc...@mst.edu]
> *Sent:* Tuesday, August 08, 2017 4:39 PM
> *To:* Xavier Guell Paradis
> *Cc:* hcp-users@humanconnectome.org
> *Subject:* Re: [HCP-Users] How can I convert subcortical nifti files to
> dlabel files?
>
> I'm assuming you want them to match a standard grayordinate space, so that
> they can be compared across subjects.
>
> The simple way that doesn't account for residual subject differences in
> subcortical locations is to first resample the data to the appropriate
> resolution/orientation MNI space (222 for the 91k grayordinates), then use
> -cifti-create-dense-from-template with the -volume-all optio

Re: [HCP-Users] How can I convert subcortical nifti files to dlabel files?

2017-08-09 Thread Xavier Guell Paradis
Dear Matt,
Thank you for your reply. I have realized that a very curious thing happens:
- If I open the dlabel file and right-click the cluster in wb_view, I do not 
see any option
- If I open the dscalar file and right-click the cluster in wb_view, I do not 
see any option
- If I open the dlabel file AND the dscalar file and right-click the cluster in 
wb_view (note that the cluster is now present twice: in the dlabel file and in 
the dscalar file), I see the "Show Data/Time Series Graph" but not the "Show 
Cifti Connectivity" option.

I opened wb_view multiple times to make sure that this is true: I only see the 
"Show Data/Time Series Graph" once I have opened both files; but I still do not 
see the "Show Cifti Connectivity" option.

This is a strange pattern, but perhaps it is a clue to find out what I am doing 
wrong.

An extra piece of information that might be useful: when I open the dlabel 
file, I can see it listed in the "Labels" list of the "Features ToolBox".

Thank you very much,
Xavier.

From: Glasser, Matthew [glass...@wustl.edu]
Sent: Wednesday, August 09, 2017 2:13 PM
To: Xavier Guell Paradis; NEUROSCIENCE tim
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] How can I convert subcortical nifti files to dlabel 
files?

It should work if you skip the last step and use the dlabel file.

Peace,

Matt.

From: Xavier Guell Paradis <xavie...@mit.edu<mailto:xavie...@mit.edu>>
Date: Wednesday, August 9, 2017 at 9:43 AM
To: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>, Matt Glasser 
<glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: RE: [HCP-Users] How can I convert subcortical nifti files to dlabel 
files?

Dear Tim and Matt,
Thank you very much for your reply.

I tried -volume-label-import, followed by -cifti-create-label, followed by 
-cifti-all-labels-to-rois.
After this, when I right-click the cluster in wb_view, I see the option "Show 
Data/Time Series Graph For Parcel [my cluster]" but I do not see the option 
"Show Cifti Connectivity For Parcel [my cluster]" (even though I can see this 
option for other parcels, such as the Yeo map).
I have been trying different things but cannot figure it out.

Some extra information in case it is useful:

My clusters are a group average registered to the HCP 
"S900_Average_T1w_restore.nii", so at this point I am not concerned about 
comparison across subjects. I would like to calculate functional connectivity 
from each of my subcortical clusters using your S900 .dconn file.
My original nifti file with the right cerebellum cluster is called 
"mycluster.nii".
I created the file "textforvolumelabelimport.txt" with the following text:
CEREBELLUM_RIGHT
1 1 1 1
Then I did the following:
wb_command -volume-label-import mycluster.nii textforvolumelabelimport.txt 
mycluster_label.nii
wb_command -cifti-create-label mycluster_labelStep2.dlabel.nii -volume 
mycluster_label.nii mycluster_label.nii
wb_command -cifti-all-labels-to-rois mycluster_labelStep2.dlabel.nii 1 
mycluster_labelStep3.dscalar.nii

When I right-click "mycluster_labelStep3.dscalar.nii" in wb_view, I can see the 
option of "Show Data/Time Series Graph" but not the option of "Show Cifti 
Connectivity".

Thank you very much,
Xavier.


From: Timothy Coalson [tsc...@mst.edu<mailto:tsc...@mst.edu>]
Sent: Tuesday, August 08, 2017 4:39 PM
To: Xavier Guell Paradis
Cc: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] How can I convert subcortical nifti files to dlabel 
files?

I'm assuming you want them to match a standard grayordinate space, so that they 
can be compared across subjects.

The simple way that doesn't account for residual subject differences in 
subcortical locations is to first resample the data to the appropriate 
resolution/orientation MNI space (222 for the 91k grayordinates), then use 
-cifti-create-dense-from-template with the -volume-all option.

The better but more involved way is to take the subject's subcortical structure 
labels from freesurfer, import them to workbench format with the names that 
-cifti-create-label specifies, use -cifti-create-label to make a 
subject-specific cifti file (you will also need to provide some dummy surface 
data for the next step to work), and then use -cifti-resample to use only the 
same-structure-overlap information, and dilate to fill in any holes if desired.

We use this second method for fMRI data in the pipelines, see here:

https://github.com/Washington-University/Pipelines/blob/master/fMRISurface/scripts/SubcorticalProcessing.sh#L40

Though t

Re: [HCP-Users] How can I convert subcortical nifti files to dlabel files?

2017-08-09 Thread Glasser, Matthew
It should work if you skip the last step and use the dlabel file.

Peace,

Matt.

From: Xavier Guell Paradis <xavie...@mit.edu<mailto:xavie...@mit.edu>>
Date: Wednesday, August 9, 2017 at 9:43 AM
To: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>, Matt Glasser 
<glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: RE: [HCP-Users] How can I convert subcortical nifti files to dlabel 
files?

Dear Tim and Matt,
Thank you very much for your reply.

I tried -volume-label-import, followed by -cifti-create-label, followed by 
-cifti-all-labels-to-rois.
After this, when I right-click the cluster in wb_view, I see the option "Show 
Data/Time Series Graph For Parcel [my cluster]" but I do not see the option 
"Show Cifti Connectivity For Parcel [my cluster]" (even though I can see this 
option for other parcels, such as the Yeo map).
I have been trying different things but cannot figure it out.

Some extra information in case it is useful:

My clusters are a group average registered to the HCP 
"S900_Average_T1w_restore.nii", so at this point I am not concerned about 
comparison across subjects. I would like to calculate functional connectivity 
from each of my subcortical clusters using your S900 .dconn file.
My original nifti file with the right cerebellum cluster is called 
"mycluster.nii".
I created the file "textforvolumelabelimport.txt" with the following text:
CEREBELLUM_RIGHT
1 1 1 1
Then I did the following:
wb_command -volume-label-import mycluster.nii textforvolumelabelimport.txt 
mycluster_label.nii
wb_command -cifti-create-label mycluster_labelStep2.dlabel.nii -volume 
mycluster_label.nii mycluster_label.nii
wb_command -cifti-all-labels-to-rois mycluster_labelStep2.dlabel.nii 1 
mycluster_labelStep3.dscalar.nii

When I right-click "mycluster_labelStep3.dscalar.nii" in wb_view, I can see the 
option of "Show Data/Time Series Graph" but not the option of "Show Cifti 
Connectivity".

Thank you very much,
Xavier.


From: Timothy Coalson [tsc...@mst.edu<mailto:tsc...@mst.edu>]
Sent: Tuesday, August 08, 2017 4:39 PM
To: Xavier Guell Paradis
Cc: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] How can I convert subcortical nifti files to dlabel 
files?

I'm assuming you want them to match a standard grayordinate space, so that they 
can be compared across subjects.

The simple way that doesn't account for residual subject differences in 
subcortical locations is to first resample the data to the appropriate 
resolution/orientation MNI space (222 for the 91k grayordinates), then use 
-cifti-create-dense-from-template with the -volume-all option.

The better but more involved way is to take the subject's subcortical structure 
labels from freesurfer, import them to workbench format with the names that 
-cifti-create-label specifies, use -cifti-create-label to make a 
subject-specific cifti file (you will also need to provide some dummy surface 
data for the next step to work), and then use -cifti-resample to use only the 
same-structure-overlap information, and dilate to fill in any holes if desired.

We use this second method for fMRI data in the pipelines, see here:

https://github.com/Washington-University/Pipelines/blob/master/fMRISurface/scripts/SubcorticalProcessing.sh#L40

Though that script actually only outputs a volume file, and therefore it 
doesn't bother with having surface data in those temporary cifti files.

Tim


On Tue, Aug 8, 2017 at 3:19 PM, Xavier Guell Paradis 
<xavie...@mit.edu<mailto:xavie...@mit.edu>> wrote:
Dear HCP experts,
I have several subcortical nifti files, each containing one cluster. I would 
like to convert them to dlabel files, so that then I can use wb_view to see the 
functional connectivity from each of these clusters (using your group .dconn 
file).

How can I convert subcortical nifti files to dlabel files?
I have been exploring several wb_commands but I cannot figure it out.

Thank you very much,
Xavier.

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Re: [HCP-Users] How can I convert subcortical nifti files to dlabel files?

2017-08-09 Thread Xavier Guell Paradis
Dear Tim and Matt,
Thank you very much for your reply.

I tried -volume-label-import, followed by -cifti-create-label, followed by 
-cifti-all-labels-to-rois.
After this, when I right-click the cluster in wb_view, I see the option "Show 
Data/Time Series Graph For Parcel [my cluster]" but I do not see the option 
"Show Cifti Connectivity For Parcel [my cluster]" (even though I can see this 
option for other parcels, such as the Yeo map).
I have been trying different things but cannot figure it out.

Some extra information in case it is useful:

My clusters are a group average registered to the HCP 
"S900_Average_T1w_restore.nii", so at this point I am not concerned about 
comparison across subjects. I would like to calculate functional connectivity 
from each of my subcortical clusters using your S900 .dconn file.
My original nifti file with the right cerebellum cluster is called 
"mycluster.nii".
I created the file "textforvolumelabelimport.txt" with the following text:
CEREBELLUM_RIGHT
1 1 1 1
Then I did the following:
wb_command -volume-label-import mycluster.nii textforvolumelabelimport.txt 
mycluster_label.nii
wb_command -cifti-create-label mycluster_labelStep2.dlabel.nii -volume 
mycluster_label.nii mycluster_label.nii
wb_command -cifti-all-labels-to-rois mycluster_labelStep2.dlabel.nii 1 
mycluster_labelStep3.dscalar.nii

When I right-click "mycluster_labelStep3.dscalar.nii" in wb_view, I can see the 
option of "Show Data/Time Series Graph" but not the option of "Show Cifti 
Connectivity".

Thank you very much,
Xavier.


From: Timothy Coalson [tsc...@mst.edu]
Sent: Tuesday, August 08, 2017 4:39 PM
To: Xavier Guell Paradis
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] How can I convert subcortical nifti files to dlabel 
files?

I'm assuming you want them to match a standard grayordinate space, so that they 
can be compared across subjects.

The simple way that doesn't account for residual subject differences in 
subcortical locations is to first resample the data to the appropriate 
resolution/orientation MNI space (222 for the 91k grayordinates), then use 
-cifti-create-dense-from-template with the -volume-all option.

The better but more involved way is to take the subject's subcortical structure 
labels from freesurfer, import them to workbench format with the names that 
-cifti-create-label specifies, use -cifti-create-label to make a 
subject-specific cifti file (you will also need to provide some dummy surface 
data for the next step to work), and then use -cifti-resample to use only the 
same-structure-overlap information, and dilate to fill in any holes if desired.

We use this second method for fMRI data in the pipelines, see here:

https://github.com/Washington-University/Pipelines/blob/master/fMRISurface/scripts/SubcorticalProcessing.sh#L40

Though that script actually only outputs a volume file, and therefore it 
doesn't bother with having surface data in those temporary cifti files.

Tim


On Tue, Aug 8, 2017 at 3:19 PM, Xavier Guell Paradis 
<xavie...@mit.edu<mailto:xavie...@mit.edu>> wrote:
Dear HCP experts,
I have several subcortical nifti files, each containing one cluster. I would 
like to convert them to dlabel files, so that then I can use wb_view to see the 
functional connectivity from each of these clusters (using your group .dconn 
file).

How can I convert subcortical nifti files to dlabel files?
I have been exploring several wb_commands but I cannot figure it out.

Thank you very much,
Xavier.

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


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Re: [HCP-Users] How can I convert subcortical nifti files to dlabel files?

2017-08-08 Thread Timothy Coalson
I'm assuming you want them to match a standard grayordinate space, so that
they can be compared across subjects.

The simple way that doesn't account for residual subject differences in
subcortical locations is to first resample the data to the appropriate
resolution/orientation MNI space (222 for the 91k grayordinates), then use
-cifti-create-dense-from-template with the -volume-all option.

The better but more involved way is to take the subject's subcortical
structure labels from freesurfer, import them to workbench format with the
names that -cifti-create-label specifies, use -cifti-create-label to make a
subject-specific cifti file (you will also need to provide some dummy
surface data for the next step to work), and then use -cifti-resample to
use only the same-structure-overlap information, and dilate to fill in any
holes if desired.

We use this second method for fMRI data in the pipelines, see here:

https://github.com/Washington-University/Pipelines/blob/master/fMRISurface/scripts/SubcorticalProcessing.sh#L40

Though that script actually only outputs a volume file, and therefore it
doesn't bother with having surface data in those temporary cifti files.

Tim


On Tue, Aug 8, 2017 at 3:19 PM, Xavier Guell Paradis 
wrote:

> Dear HCP experts,
> I have several subcortical nifti files, each containing one cluster. I
> would like to convert them to dlabel files, so that then I can use wb_view
> to see the functional connectivity from each of these clusters (using your
> group .dconn file).
>
> How can I convert subcortical nifti files to dlabel files?
> I have been exploring several wb_commands but I cannot figure it out.
>
> Thank you very much,
> Xavier.
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>

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Re: [HCP-Users] How can I convert subcortical nifti files to dlabel files?

2017-08-08 Thread Glasser, Matthew
wb_command -cifti-create-dense-scalar and then wb_command -cifti-label-import 
with an appropriate label tabel.  Alternatively, wb_command 
-volume-label-import and wb_command -cifti-create-label.

Peace,

Matt.

From: 
>
 on behalf of Xavier Guell Paradis >
Date: Tuesday, August 8, 2017 at 3:19 PM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] How can I convert subcortical nifti files to dlabel files?

Dear HCP experts,
I have several subcortical nifti files, each containing one cluster. I would 
like to convert them to dlabel files, so that then I can use wb_view to see the 
functional connectivity from each of these clusters (using your group .dconn 
file).

How can I convert subcortical nifti files to dlabel files?
I have been exploring several wb_commands but I cannot figure it out.

Thank you very much,
Xavier.

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HCP-Users@humanconnectome.org
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