Hi Liliana - It looks like you are using a very old FreeSurfer build (from 2016) and an old TRACULA configuration file. You should update to the latest version of FreeSurfer and follow the instructions on the wiki for how to set up TRACULA. We have many more tracts now and the naming has changed. To reconstruct the subset of tracts you want with the new version, you just need this in the config file:
set pathlist = (lh.cst rh.cst lh.uf rh.uf lh.cbd rh.cbd lh.cbv rh.cbv)
Anastasia. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Liliana Wu liliana.wu@mail.utoronto.ca Sent: Friday, August 19, 2022 1:43 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] TRACULA - preprocessing error
External Email - Use Caution
Here is the error log information:
INFO: SUBJECTS_DIR is /home/lwu/Desktop/OIRM02/trc INFO: Diffusion root is /home/lwu/Desktop/OIRM02/trc/output Actual FREESURFER_HOME /usr/local/freesurfer trac-preproc -c /home/lwu/Desktop/OIRM02/trc/output/OIRM02/scripts/dmrirc.local -log /home/lwu/Desktop/OIRM02/trc/output/OIRM02/scripts/trac-all.log -cmd /home/lwu/Desktop/OIRM02/trc/output/OIRM02/scripts/trac-all.cmd #------------------------------------- /usr/local/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Fri Aug 19 13:27:09 EDT 2022 mri_convert --bvec-voxel /home/lwu/Desktop/OIRM02/trc/OIRM02/OIRM02_DTI.nii.gz /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.nii.gz mri_convert.bin --bvec-voxel /home/lwu/Desktop/OIRM02/trc/OIRM02/OIRM02_DTI.nii.gz /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /home/lwu/Desktop/OIRM02/trc/OIRM02/OIRM02_DTI.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999551, 0.00440173, 0.0296355) j_ras = (-0.0024424, 0.973885, -0.227028) k_ras = (0.0298609, 0.226998, 0.973437) writing to /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.nii.gz... cp /home/lwu/Desktop/OIRM02/trc/OIRM02/bvecs_path.txt /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.bvecs cp /home/lwu/Desktop/OIRM02/trc/OIRM02/bvals_path.txt /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.bvals mv -f /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/bvecs.tmp /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.bvecs mv -f /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/bvals.tmp /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.bvals orientLAS /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.nii.gz /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig_las.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -8 mri_convert -oni 122 -onj 122 -onk 70 -oid -0.999551 0.00440173 0.0296355 -ojd -0.0024424 0.973885 -0.227028 -okd 0.0298609 0.226998 0.973437 -oc -0.949776 14.1753 25.1557 -rt nearest /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.nii.gz /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig_las.nii.gz mri_convert.bin -oni 122 -onj 122 -onk 70 -oid -0.999551 0.00440173 0.0296355 -ojd -0.0024424 0.973885 -0.227028 -okd 0.0298609 0.226998 0.973437 -oc -0.949776 14.1753 25.1557 -rt nearest /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.nii.gz /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig_las.nii.gz normalizing out_i_direction: (-0.999551, 0.00440173, 0.0296355) -> (-0.999551, 0.00440173, 0.0296355) normalizing out_j_direction: (-0.0024424, 0.973885, -0.227028) -> (-0.0024424, 0.973885, -0.227028) normalizing out_k_direction: (0.0298609, 0.226998, 0.973437) -> (0.0298609, 0.226998, 0.973437) $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999551, 0.00440173, 0.0296355) j_ras = (-0.0024424, 0.973885, -0.227028) k_ras = (0.0298609, 0.226998, 0.973437) Reslicing using nearest writing to /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig_las.nii.gz... INFO: found /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.bvals, copying INFO: found /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.bvecs, converting to LAS mv -f /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig_las.bvecs /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/bvecs mv -f /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig_las.bvals /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/bvals eddy_correct /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig_las.nii.gz /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi.nii.gz 0 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0000 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0001 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0002 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0003 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0004 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0005 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0006 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0007 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0008 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0009 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0010 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0011 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0012 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0013 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0014 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0015 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0016 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0017 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0018 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0019 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0020 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0021 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0022 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0023 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0024 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0025 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0026 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0027 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0028 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0029 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0030 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0031 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0032 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0033 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processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0104 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0105 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0106 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0107 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0108 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0109 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0110 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0111 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0112 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0113 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0114 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0115 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0116 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0117 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0118 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0119 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0120 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0121 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0122 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0123 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0124 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0125 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0126 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0127 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0128 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0129 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0130 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0131 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0132 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0133 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0134 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0135 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0136 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0137 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0138 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0139 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0140 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0141 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0142 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0143 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0144 processing /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_tmp0145 mv -f /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/bvecs /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/bvecs.norot xfmrot /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi.ecclog /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/bvecs.norot /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/bvecs ln -sf /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi.nii.gz /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/data.nii.gz mri_convert --frame 6 13 20 27 34 45 56 67 79 90 100 111 122 133 145 /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi.nii.gz /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/lowb.nii.gz mri_convert.bin --frame 6 13 20 27 34 45 56 67 79 90 100 111 122 133 145 /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi.nii.gz /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/lowb.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999551, 0.00440173, 0.0296355) j_ras = (-0.0024424, 0.973885, -0.227028) k_ras = (0.0298609, 0.226998, 0.973437) keeping frames 6 13 20 27 34 45 56 67 79 90 100 111 122 133 145 writing to /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/lowb.nii.gz... mri_concat --i /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/lowb.nii.gz --mean --o /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/lowb.nii.gz ninputs = 1 Checking inputs nframestot = 15 Allocing output Done allocing nframes = 15 Computing mean across frames Writing to /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/lowb.nii.gz bet /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/lowb.nii.gz /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/lowb_brain.nii.gz -m -f 0.3 mv -f /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/lowb_brain_mask.nii.gz /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dlabel/diff #------------------------------------- #@# Image quality assessment Fri Aug 19 13:42:27 EDT 2022 /usr/local/freesurfer/bin/dmri_motion --dwi /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.nii.gz --mat /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi.ecclog --bval /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/bvals --T 227.122620 --out /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_motion.txt
cwd /home/lwu/Desktop/OIRM02/trc cmdline /usr/local/freesurfer/bin/dmri_motion --dwi /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.nii.gz --mat /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi.ecclog --bval /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/bvals --T 227.122620 --out /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_motion.txt sysname Linux hostname il-isotropic machine x86_64 user lwu Output motion measure file: /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_motion.txt Input transform file: /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi.ecclog Input DWI file: /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.nii.gz Input b-value table: /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/bvals Low-b image intensity threshold: 227.123 Nominal diffusivity: 0.001 Loading volume-to-baseline affine transformations Computing between-volume head motion measures INFO: Processed transforms for 146 volumes Loading DWI volume series from /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi_orig.nii.gz Loading b-value table from /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/bvals Computing within-volume head motion measures Done in 6.688 sec. dmri_motion done #------------------------------------- #@# Inter-subject registration Fri Aug 19 13:42:34 EDT 2022 flirt -in /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/lowb_brain.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/lowb_brain_mni.nii.gz -omat /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/xfms/diff2mni.mat -cost corratio convert_xfm -omat /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/xfms/mni2diff.mat -inverse /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/xfms/diff2mni.mat #------------------------------------- #@# Masks Fri Aug 19 13:42:43 EDT 2022 WARN: Could not find /home/lwu/Desktop/OIRM02/trc/OIRM02/mri/aparc+aseg.mgz WARN: You will not be able to complete TRACULA processing without it ln -sf /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dlabel/diff/lowb_brain_mask.nii.gz /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/nodif_brain_mask.nii.gz #------------------------------------- #@# Tensor fit Fri Aug 19 13:42:43 EDT 2022 dtifit -k /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dwi.nii.gz -m /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dlabel/diff/lowb_brain_mask.nii.gz -r /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/bvecs -b /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/bvals -o /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dtifit 0 122 0 122 0 70 0 slices processed 1 slices processed 2 slices processed 3 slices processed 4 slices processed 5 slices processed 6 slices processed 7 slices processed 8 slices processed 9 slices processed 10 slices processed 11 slices processed 12 slices processed 13 slices processed 14 slices processed 15 slices processed 16 slices processed 17 slices processed 18 slices processed 19 slices processed 20 slices processed 21 slices processed 22 slices processed 23 slices processed 24 slices processed 25 slices processed 26 slices processed 27 slices processed 28 slices processed 29 slices processed 30 slices processed 31 slices processed 32 slices processed 33 slices processed 34 slices processed 35 slices processed 36 slices processed 37 slices processed 38 slices processed 39 slices processed 40 slices processed 41 slices processed 42 slices processed 43 slices processed 44 slices processed 45 slices processed 46 slices processed 47 slices processed 48 slices processed 49 slices processed 50 slices processed 51 slices processed 52 slices processed 53 slices processed 54 slices processed 55 slices processed 56 slices processed 57 slices processed 58 slices processed 59 slices processed 60 slices processed 61 slices processed 62 slices processed 63 slices processed 64 slices processed 65 slices processed 66 slices processed 67 slices processed 68 slices processed 69 slices processed #------------------------------------- #@# Priors Fri Aug 19 13:42:49 EDT 2022 /usr/local/freesurfer/bin/dmri_train --outdir /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dlabel/mni --out lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr --slist /tmp/subj33.OIRM02.18847.txt --trk dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz --bmask /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dlabel/mni/lowb_brain_mask.bbr.nii.gz --fa /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dtifit_FA.nii.gz --cptdir /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dlabel/diff --reg /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/xfms/mni2diff.bbr.mat --ncpts 6 6 5 5 5 5 4 4 --trunc ERROR: fio_pushd: /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dlabel/mni
cwd /home/lwu/Desktop/OIRM02/trc cmdline /usr/local/freesurfer/bin/dmri_train --outdir /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dlabel/mni --out lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr --slist /tmp/subj33.OIRM02.18847.txt --trk dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz --bmask /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dlabel/mni/lowb_brain_mask.bbr.nii.gz --fa /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/dtifit_FA.nii.gz --cptdir /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dlabel/diff --reg /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dmri/xfms/mni2diff.bbr.mat --ncpts 6 6 5 5 5 5 4 4 --trunc sysname Linux hostname il-isotropic machine x86_64 user lwu Output directory: /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dlabel/mni Output directory in test subject's space: /home/lwu/Desktop/OIRM02/trc/output/OIRM02/dlabel/diff Output base: lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr Training subject directory list: /tmp/subj33.OIRM02.18847.txt Location of streamline files relative to base: dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk Location of start ROI files relative to base: dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz Location of end ROI files relative to base: dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz Location of cortex masks relative to base: dlabel/mni/cortex+2mm.nii.gz Label ID's from aparc+aseg to add to cortex mask: 16 16 0 0 0 0 0 0 Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz Brain mask for output subject: Segmentation fault (core dumped) Linux il-isotropic 5.4.0-122-generic #138~18.04.1-Ubuntu SMP Fri Jun 24 14:14:03 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Fri Aug 19 13:42:49 EDT 2022
________________________________ From: Liliana Wu liliana.wu@mail.utoronto.ca Sent: August 19, 2022 12:44 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: TRACULA - preprocessing error
Hi,
I ran the preprocessing command trac-all -prep -c $SUBJECTS_DIR/script and I am getting the following error
ERROR: fio_pushd: /home/lwu/Desktop/OIRM02/trc/OIRM02/dlabel/mni
I don’t see the mni folder created in my files… I am trying to only reconstruct the following pathways.
set pathlist = ( lh.cst_JL rh.cst_JL \
lh.unc_JL rh.unc_JL \
lh.ccg_PP rh.ccg_PP \
lh.cab_PP rh.cab_PP)
set ncpts = (6 6 5 5 5 5 4 4)
I appreciate any help,
Thank you
Liliana