Dear all,
I am very new to using TRACULA and Freesurfer. I am trying to apply tracula on the provided tutorial data. When I ran the command trac-all -prep -c dmrirc.tutorial, after eddy current correction, I get this error:
mv -f /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/bvecs /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/bvecs.norot xfmrot /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/dwi.ecclog /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/bvecs.norot /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/bvecs R: Subscript out of range. R: Subscript out of range. R: Subscript out of range.
n -sf /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/dwi.nii.gz /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/data.nii.gz mri_convert --frame 0 /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/dwi.nii.gz /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/dwi_frame0.nii.gz mri_convert --frame 0 /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/dwi.nii.gz /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/dwi_frame0.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999278, -0.0375823, -0.00564044) j_ras = (-0.0367492, 0.917788, 0.395367) k_ras = (0.00968205, -0.395289, 0.918506) keeping frame 0 writing to /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/dwi_frame0.nii.gz... mri_concat --i /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/dwi_frame0.nii.gz --mean --o /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/lowb.nii.gz ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Computing mean across frames Writing to /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/lowb.nii.gz bet /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/lowb.nii.gz /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/lowb_brain.nii.gz -m -f 0.3 mv -f /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/lowb_brain_mask.nii.gz /data_augus t/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dlabel/diff #------------------------------------- #@# Inter-subject registration Mon Nov 2 15:39:02 CET 2015 flirt -in /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/lowb_brain.nii.gz -ref /data_RAID/Kathrin/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/lowb_brain_mni.nii.gz -omat /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/xfms/diff2mni.mat -cost corratio convert_xfm -omat /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/xfms/mni2diff.mat -inverse /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/xfms/diff2mni.mat #------------------------------------- #@# Masks Mon Nov 2 15:39:20 CET 2015 flirt -in /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dlabel/diff/lowb_brain_mask.nii.gz -ref /data_RAID/Kathrin/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dlabel/mni/lowb_brain_mask.bbr.nii.gz -applyxfm -init /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/xfms/diff2mni.bbr.mat -interp nearestneighbour flirt -in /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dlabel/diff/lowb_brain_mask.nii.gz -ref /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/brain_anat_orig.nii.gz -out /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz -applyxfm -init /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/xfms/diff2anatorig.bbr.mat -interp nearestneighbour ln -sf /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dlabel/diff/aparc+aseg_mask.bbr.nii.gz /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/nodif_brain_mask.nii.gz #------------------------------------- #@# Tensor fit Mon Nov 2 15:39:23 CET 2015 dtifit -k /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/dwi.nii.gz -m /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -r /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/bvecs -b /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/bvals -o /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/dtifit 0 128 0 128 0 64 terminate called after throwing an instance of 'NEWMAT::IndexException' Abort Linux slow.mri.tu-muenchen.de 3.7.10-1.40-desktop #1 SMP PREEMPT Thu Jul 10 11:22:12 UTC 2014 (9b06319) x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Mon Nov 2 15:39:23 CET 2015
My config file is as simple as possible. I only defined the data path, output path, subject list and dcmlist.
The problem seems to be related to bvecs file, I looked at it, and it seems to have 0.0000 in the beginning. Could this create a problem?
Thank you. Best,