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] 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.ni<http://mycluster_labelStep2.dlabel.ni>i -volume 
mycluster_label.nii mycluster_label.nii
wb_command -cifti-all-labels-to-rois 
mycluster_labelStep2.dlabel.ni<http://mycluster_labelStep2.dlabel.ni>i 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.

_______________________________________________
HCP-Users mailing list
HCP-Users@humanconnectome.org<mailto: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

Reply via email to