app-AFQ_no-life

App to run AFQ without life

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app-afq_no-life's Issues

Not enough input arguments.

I've recompiled this app using the latest vistasoft.

I am now seeing following error message when I run it.

Not enough input arguments.

Error in nanmean (line 7)


Error in AFQ_SegmentFiberGroups (line 267)


Error in main (line 28)

@kitchell @DanNBullock Can you help me troubleshoot this?

Possible error in CST_roi2_L.nii.gz and CST_roi2_R.nii.gz

Hi, it seems to me that the ROI templates app-AFQ_no-life/templates/MNI_JHU_tracts_ROIs/CST_roi2_L.nii.gz and CST_roi2_R.nii.gz are wrong because they both include the left and right ROIs instead of just one.

Generates too many fibers

I've run this app with ensemble track output. Compared to AFQ with LiFE, it's generating a lot more fibers for each tracts than it should.

app-AFQ_no-life

Tracts,FiberCount
Left Thalamic Radiation,5019
Right Thalamic Radiation,7924
Left Corticospinal,4696
Right Corticospinal,6457
Left Cingulum Cingulate,2710
Right Cingulum Cingulate,1672
Left Cingulum Hippocampus,1561
Right Cingulum Hippocampus,1463
Callosum Forceps Major,805
Callosum Forceps Minor,6367
Left IFOF,3477
Right IFOF,1389
Left ILF,1338
Right ILF,2398
Left SLF,11485
Right SLF,17314
Left Uncinate,1266
Right Uncinate,2129
Left Arcuate,5961
Right Arcuate,1991

app-tractclassification

Tracts,FiberCount
Left Thalamic Radiation,831
Right Thalamic Radiation,1519
Left Corticospinal,910
Right Corticospinal,1067
Left Cingulum Cingulate,632
Right Cingulum Cingulate,309
Left Cingulum Hippocampus,191
Right Cingulum Hippocampus,164
Callosum Forceps Major,42
Callosum Forceps Minor,914
Left IFOF,309
Right IFOF,148
Left ILF,225
Right ILF,342
Left SLF,3047
Right SLF,3663
Left Uncinate,205
Right Uncinate,307
Left Arcuate,807
Right Arcuate,386

Maybe I shouldn't be running this app on ensemble track?

Deprecate this repo

I believe we can deprecate this app by updating https://github.com/brain-life/app-tractclassification so that it can load track.tck if "track" input is specified instead of life input.

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