[Camino-users] ask for help on conmat

[Philip A Cook]

Hi,

1. You can use anything that will read in a CSV file. I've only used iGraph in R.

2. There's no replacement in Camino for the visual aspect of conmap, but we might be able to add something later.

3. I'm not familiar with Freesurfer or that label file. It should work as long as the image is in the correct space, ie a coordinate on a streamline and a coordinate in the image refer to the same place in the brain.

4. You can use images with multiple labels. One of the motivations for replacing conmap was adding more flexibility, for example your target regions no longer need to be consecutively numbered.



On May 16, 2013, at 3:18 AM, lujiao luo wrote:

> Hello experts,
> 
> I want to visualize the connectivity map and connectivity segmentation using Camino. I've read the instrution of  -conmat flag on manual list. But I still have some problems below:
> 
> (1) After finish doing the conmat, I obtained .csv files, but I couldn't figure out how to visualize the file. Should I use the camino_trackvis tool to convert the file into .trk format, and visualize it in trackvis?
> 
> (2) What flag should I use to complete the function below:
> 
> conmap -inputfile brain_track.Bdouble -roifile wm_undersampled.nii.gz 
> 
> since the conmap flag is obsolete now? I really felt that connectivity map was really a cool thing.
> 
> (3) I obtained my target volume by converting freesurfer lh.V1.label to lh.V1.nii. I am curious that if is it suitable a suitable target file which should also contain label information?
> 
> (4) Can I use lh.BA.nii which convert from freesufer lh.BA.annot and contain several labels as a target file?
> 
> Thanks so much for any help!
> 
> Yours 
> Lulu  
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