[Prabhjot Kaur]

Hello Matt,

We are using workbench to process our  restFMRI data. We are using Cole anticevic atlas for parcellations. 

When trying to generate connectivity maps using wb-view, we are not getting connectivity matrix. What we can understand with our limited experience is that the label names are not been carried forward by parcels when applying  cifti-correlation command after cifti-parcellate. When checked using file info, the generated pconn.nii file is showing 'Maps with labelTable as false'. 

We have tried it with v2.1.0 also along with v1.4.2. 

Please guide with step-by-step process on how to go about this.

Prabhjot Kaur

PhD Scholar (IIT, Delhi) 

Senior Technical Officer (DRDO, Ministry of Defence, Govt of India)

91-9810904950

[Glasser, Matthew]

Maybe you should start with showing the commands you have used (with the latest version of Connectome Workbench).

Matt.

--
You received this message because you are subscribed to the Google Groups "HCP-Users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to hcp-users+...@humanconnectome.org.
To view this discussion visit https://groups.google.com/a/humanconnectome.org/d/msgid/hcp-users/CANTmu3kMVQ6KM0AimgBmYrCHOJ3CW4Qnr0oUdq6qx1ht_YqPvQ%40mail.gmail.com.

 

---

The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

[Prabhjot Kaur]

Dear Mathew, 

I am using the following command line for generating pconn.nii file.

wb_command -cifti-parcellate sub-H002_bold.ptseries.nii \
           CortexSubcortex_ColeAnticevic_NetPartition_wSubcorGSR_parcels_LR.dlabel.nii \
           COLUMN sub-H002_bold_parcellated.ptseries.nii - method MEAN

wb_command -cifti-correlation sub-H002_bold_parcellated.ptseries.nii \
           sub-H002_bold.pconn.nii -fisher-z
The .pconn.nii file is created successfully and contains the correlation matrix, but the label tables from the atlas are missing (label table shows as false in Workbench).

Prabhjot Kaur

Delhi

To view this discussion visit https://groups.google.com/a/humanconnectome.org/d/msgid/hcp-users/4D46B2A6-E241-4E48-962A-9066852CE4DF%40wustl.edu.

[Glasser, Matthew]

That is expected behavior.  Label tables are found only in label files.

To view this discussion visit https://groups.google.com/a/humanconnectome.org/d/msgid/hcp-users/CANTmu3m%3D9a4Xx7xQJTTPAgX%3DX6%3D%3DbU4y6JHU1ui2oks4E8Zqfg%40mail.gmail.com.

[Tim Coalson]

To elaborate, -cifti-parcellate uses the information from the label table to make the parcel definitions, but the vertices and voxels that participate in a parcel are encoded directly into the cifti XML, without using the table of "label colors, names, and keys" (which is only needed for displaying the extent of the labels when there isn't any associated area-averaged data in the file).  ptseries, pscalar, and pconn, etc. all contain parcel-summarized data values that can be colored with continuous palettes, so they don't need to know about label colors.

Tim

To view this discussion visit https://groups.google.com/a/humanconnectome.org/d/msgid/hcp-users/EA55B79A-D49A-4505-9545-9AFB31892AF6%40wustl.edu.

[Prabhjot Kaur]

Hello Tim,

Understood that Pconn or ptseries is not supposed to retain those labels. But when I am trying to open this pconn.nii file in wb_view to generate connectome, it is not showing the connectivity matrix. As per my understanding, when I click on any voxel, it should show its connections in the form of connectivity matrix. Guide me to generate those connectivity maps or heatmaps.

Thanks

Prabhjot Kaur

Delhi

To view this discussion visit https://groups.google.com/a/humanconnectome.org/d/msgid/hcp-users/CANm3QU5CeCC7h0hbDx0B%3DhyutoAOCbFMNJ%3DiTiuHSasJvmeO4g%40mail.gmail.com.

[Tim Coalson]

You need to click on a vertex or voxel that is actually used by a parcel for the pconn layer to show anything, even when enabled.  Also make sure that both "load" and "layer" checkboxes in the connectivity tab are enabled (I think they should be by default).  You can load your dlabel file in another layer to show you where clicking will do something, and either turn the label layer off or change it to outline mode so you can see the pconn data through it.

Tim

To view this discussion visit https://groups.google.com/a/humanconnectome.org/d/msgid/hcp-users/CANTmu3%3DFqLH1vmAD3O9g_dh5xUiq00oX2AcJ%2BT6Gv-nWfDDEGQ%40mail.gmail.com.

[Prabhjot Kaur]

Hello Tim

Thanks for providing some clarity. As I can see, on adding pconn.nii files and dlabel.nii files, my layers box is not checked and is disabled in the connectivity tab.

But when I loaded dtseries.nii instead of pconn.nii, it generated an empty dynconn.nii file with both load and layer boxes checked in the connectivity tab.

Please guide.

Regards

Prabhjot Kaur

Delhi, India

To view this discussion visit https://groups.google.com/a/humanconnectome.org/d/msgid/hcp-users/CANm3QU77Pxw_rE3Yk-sO9y_1SC8k-JOQZYLDBnb%3DJPDYdSAhtA%40mail.gmail.com.

[Tim Coalson]

For files that already contain a connectivity matrix, they are already available as a layer, so that checkbox wouldn't do anything, so we disable it, but disabling it may prevent it from appearing to be checked, so that is fine.  Make sure the load checkbox is checked.  Then, make sure the pconn layer in the overlays tab is also enabled, click inside one of your parcel labels in the 3D view, and turn off any layers above the pconn to see the connectivity data. 

The "layer" checkbox is basically for disabling the dynconn feature per-file when you don't want to do correlations in wb_view, in order to make the list of files in the overlay selection shorter and easier to work with. 

Tim

To view this discussion visit https://groups.google.com/a/humanconnectome.org/d/msgid/hcp-users/CANTmu3kV0pfK%2B0D6Y3FMctucPFWQpYQarC_r%2BrSidcEx01WMPQ%40mail.gmail.com.

[Prabhjot Kaur]

Hello tim

I am still struggling with the issue.... 

I am hereby sharing the snippet of the wb_view window that is opening with pconn.nii and dlabel.nii files. Please have a look and guide as we are not getting an option to open 3d view.

Prabhjot Kaur

Delhi

To view this discussion visit https://groups.google.com/a/humanconnectome.org/d/msgid/hcp-users/CANm3QU7we4QmL6tHeCmR8-t_enyfmDMQ-5nYNDk_ffRok3%3Dz-A%40mail.gmail.com.

[Glasser, Matthew]

You also need to open some surface files (.surf.gii) to view things on surface models.

To view this discussion visit https://groups.google.com/a/humanconnectome.org/d/msgid/hcp-users/CANTmu3nXQ3ZCJ3T-QtDHgKGZfHXwOqp7Ndf%2BjiBxUx7dWq1nTQ%40mail.gmail.com.