search

vindasna / GeoLab

Geolab : Geometric-based tractography parcellation of Superficial white matter
Apache License 2.0
3 stars 1 forks source link

Error during parcellation #3

Open cmendosanchez opened 1 year ago

cmendosanchez commented 1 year ago

Hi all! I executed the SWM parcellation on a tractogram in MNI space with 15 points per fiber, using the following command:

ProjectAtlasGeoLab -i /media/fibras/DATA/subjectHCP/3Msift_15p_sv_MNI.bundles -o /media/fibras/DATA/subjectHCP/s/ -nbPoints 15 -nbThreads 20 -v

I encountered the following error during the parcellation (copied from the terminal):

######################################################### ########### Projecting atlas bundles with SBR ########### ######################################################### Launching dipy service... Using port 5002 Number of bundles processed : [ 5 / 657 ]ERROR : could not compute centroids for /media/fibras/DATA/subjectHCP/s/tmp_neighborhood_dir/rh_PrC-PrC_4_short.bundles, got exit_code 1 ERROR WITH COMMAND : clientComputeCentroids.py -i /media/fibras/DATA/subjectHCP/s/tmp_neighborhood_dir/rh_PrC-PrC_4_short.bundles -o /media/fibras/DATA/subjectHCP/s/tmp_neighborhood_dir/rh_PrC-PrC_4_short_centroids.bundles -r Atlas/mni_icbm152_t1_tal_nlin_asym_09c_brain.nii -thr 7.1253 -nbPoints 15 -lf /media/fibras/DATA/subjectHCP/s/clientsDipyLog.txt -p 5002 -v 1 Closing dipy service...

It appears that there is an error in dipyServer.py, as reported in clientsDipyLog.txt

computeCentroids : closed connection because of timeout or error in dipyServer.py computeCentroids /media/fibras/DATA/subjectHCP/s/tmp_neighborhood_dir/rh_Cu-LO_1_short.bundles /media/fibras/DATA/subjectHCP/s/tmp_neighborhood_dir/rh_Cu-LO_1_short_centroids.bundles Atlas/mni_icbm152_t1_tal_nlin_asym_09c_brain.nii 5.85191 15 200 ConvertBundleFormat Duration : 151.55817985534668 s

Do you have any advice on how to fix this issue?

Many thanks, Cristóbal

vindasna commented 1 year ago

Hi Cristobal,

It seems that the computation of the centroids is not completing because of timeout.

I defined a timeout of 50 s but I forgot to take into account computers with limited ressources.

I will fix this bug by asking the timeout as an input to ProjectAtlasGeoLab.

In the meantime you can change the timeout manually in the file clientComputeCentroids.py (line 203) and in the file clientRegisterBundles.py (line 250) since you will probably encounter the same problem when doing the local SBR.

If the problem still persits after changing the timeout you can try to run the command with a verbose level of 2 to have more details about where the problem is coming from and post it here so I can have a look.

Cheers, Nabil