Reply To: Connectivity

Forums Forums BrainSuite Diffusion Pipeline (BDP) Connectivity Reply To: Connectivity

#337
iidaka
Participant

Hi, experts.

Thank you for response.
I installed TRACTCONNECT module and tried to extract MD value from fibers.
To do so, I computed the tract and (File -> Save Fiber Tracks -> Save All Fiber Tracks)
saved it as fibers.dft.

Which of all or filtered tarcks should be saved?

Then on the command line, I entered
tractconnect (‘fibers.dft’, ‘–label’, ‘name.svreg.label.nii.gz’, ‘–allROI’, ‘–data’, ‘name.dwi.RAS.correct.MD.T1_coord.nii.gz’, ‘–desc’, ‘brainsuite_labeldescription.xml’, ‘–pvc’, ‘name.pvc.frac.nii.gz’);

Is this corerct?
Particularly, are RAS and reoriented… same meaning?

Then memory error occurred but it was fixed.

The computation lasted 9 hours!! and following message appeared.
Does message “Exception….” indicate error?

*******************************
Load tract file successfully
Load arguments succesfully
Calculating connectivity
Calculation done and saved succesfully
Time is 118846.479214 sec
Exception in thread “Timer-36505” java.lang.OutOfMemoryError: GC overhead limit exceeded
at com.mathworks.mlwidgets.explorer.model.FileDecorationModel.<init>(FileDecorationModel.java:59)
at com.mathworks.mlwidgets.explorer.util.FileSystemUtils.getDecorationSynchronously(FileSystemUtils.java:113)
at com.mathworks.mlwidgets.explorer.model.table.FileSystemExpansionProvider.getDecoration(FileSystemExpansionProvider.java:124)
at com.mathworks.mlwidgets.explorer.model.table.FileSystemExpansionProvider.getDecoration(FileSystemExpansionProvider.java:131)
at com.mathworks.mlwidgets.explorer.model.table.PathAffordance.shouldEverShowAffordance(PathAffordance.java:330)
at com.mathworks.mlwidgets.e
*****************************

I found results.csv that appeared to have tract MD values , but it contained so many
data, 60000 rows! Are these connectivity between voxels, but not ROIs?

One row is shown below.
612 and 2163 126 914 0.000499 0.000785 0.000717 0.001763 0.000205

Is this corerct value for MD of particular fiber?

I expected to have connectivity between ROIs as defined by Surface Registration,
but not between each voxels

Your help is veyy much appreciated.

tetsuya