vindasna / geolab Goto Github PK

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