Hi, I am trying to combine 236 labels into one volume (for the left hemisphere). However after 233 volumes I get an 'Segmentation fault (core dumped)' which I believe is related to a memory issue. If it is relevant I am using a GIFTI image as the surface (I am using HCP data).
mri_label2vol $(cat labels_lh.txt) --temp mri/brain.nii --identity --proj frac 0 1 .1 --subject 140824 --hemi lh --surf 140824.L.sphere.reg.native.surf.gii --o vol_lh.nii 22 --label 20 --label 18 --label 16 --temp 14 --identity 13 --proj 8 --subject 6 --hemi 4 --surf 2 --o Number of labels: 236 ./labels/lh-235node-aparc.a2005s-000.label ./labels/lh-235node-aparc.a2005s-001.label ./labels/lh-235node-aparc.a2005s-002.label ./labels/lh-235node-aparc.a2005s-003.label ./labels/lh-235node-aparc.a2005s-004.label ./labels/lh-235node-aparc.a2005s-005.label ./labels/lh-235node-aparc.a2005s-006.label ........... ./labels/lh-235node-aparc.a2005s-229.label ./labels/lh-235node-aparc.a2005s-230.label ./labels/lh-235node-aparc.a2005s-231.label ./labels/lh-235node-aparc.a2005s-232.label Segmentation fault (core dumped) Additionally I have tried using less than 233 labels and encounter another error. First it is unable to find a lh.thickness file. However as I mentioned I am using a single GIFTI image. Is there another argument I should be using here? Secondly I am unable to load in more than 100 volumes. Is there a particular reason why it may be doing this? mri_label2vol $(cat label_lh_temp.txt) --temp mri/brain.nii --identity --proj frac 0 1 .1 --subject 140824 --hemi lh --surf 140824.L.sphere.reg.native.surf.gii --o vol_lh.nii Number of labels: 232 ./labels/lh-235node-aparc.a2005s-000.label ./labels/lh-235node-aparc.a2005s-001.label ./labels/lh-235node-aparc.a2005s-002.label ............ ./labels/lh-235node-aparc.a2005s-230.label ./labels/lh-235node-aparc.a2005s-231.label Annot File: (null) Template Volume: mri/brain.nii Outut Volume: vol_lh.nii Registration File: (null) Fill Threshold: 0 Label Vox Vol: 1 ProjType: frac ProjTypeId: 2 ProjStart: 0 ProjStop: 1 ProjDelta: 0.1 Subject: 140824 Hemi: lh UseNewASeg2Vol: 1 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /home/stuarto/Monash076_scratch/Stuart/HCP/dense/ subjects $Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $ Template RAS-to-Vox: -------- -0.800 0.000 0.000 72.500; -0.000 -0.000 -0.800 87.000; -0.000 0.800 -0.000 72.500; 0.000 0.000 0.000 1.000; Template Voxel Volume: 1.95312 nHits Thresh: 0 Using Identity Matrix RegMat: -------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Label RAS-to-Vox: -------- -0.800 0.000 0.000 72.500; 0.000 0.000 -0.800 87.000; 0.000 0.800 0.000 72.500; 0.000 0.000 0.000 1.000; INFO: loading surface /home/stuarto/Monash076_scratch/Stuart/HCP/dense/ subjects/140824/surf/lh.140824.L.sphere.reg.native.surf.gii nvertices = 142970 Reading thickness /home/stuarto/Monash076_scratch/Stuart/HCP/dense/ subjects/140824/surf/lh.thickness MRISreadCurvature: could not open /home/stuarto/Monash076_ scratch/Stuart/HCP/dense/subjects/140824/surf/lh.thickness No such file or directory nlabels = 232 Allocating Hit Volume (848737200) voxels Loading ./labels/lh-235node-aparc.a2005s-000.label Loading ./labels/lh-235node-aparc.a2005s-001.label Loading ./labels/lh-235node-aparc.a2005s-002.label Loading ./labels/lh-235node-aparc.a2005s-003.label ...... Loading ./labels/lh-235node-aparc.a2005s-098.label Loading ./labels/lh-235node-aparc.a2005s-099.label Loading ^A No such file or directory mri_label2vol: could not open label file ^Alabel No such file or directory ERROR reading ^A
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