Hi Juan - I suspect that there was no freesurfer recon found for this subject under SUBJECTS_DIR.

On a separate note, that is not related to this error, I highly recommend using the version of TRACULA that's included in freesurfer 6.0, not 5.3. Even if you processed your T1 scans using recon-all from 5.3, that does not matter.

a.y ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Juan Rivas jcrn12@gmail.com Sent: Friday, October 18, 2019 8:08 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Tracula

External Email - Use Caution

Hi, I am trying to run tracula, but I have this error:

[shiraz:sub-esq-01-en] (nmr-stable53-env) trac-all -prep -c dmrirc-sub-esq-01-en

INFO: SUBJECTS_DIR is /autofs/cluster/neuromod/rivas/imagenes/processing

INFO: Diffusion root is /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en

Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0

INFO: FreeSurfer build stamps do not match

Subject Stamp: freesurfer-Linux-centos7_x86_64-stable-v6-20161229-80ac5eb

Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

INFO: current FREESURFER_HOME does not match that of previous processing.

Current: /usr/local/freesurfer/stable5_3_0

Previous: /usr/local/freesurfer/stable6

trac-preproc -c /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/scripts/dmrirc.local -log /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/scripts/trac-all.log -cmd /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/scripts/trac-all.cmd

#-------------------------------------

/usr/local/freesurfer/stable5_3_0/bin/trac-preproc

#-------------------------------------

#@# Image corrections Fri Oct 18 09:29:48 EDT 2019

mri_convert /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/esq-01-en_dwi.nii.gz /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_orig.nii.gz

mri_convert /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/esq-01-en_dwi.nii.gz /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_orig.nii.gz

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading from /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/esq-01-en_dwi.nii.gz...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-0.978979, -0.0979427, -0.178907)

j_ras = (-0.0632554, 0.979704, -0.190207)

k_ras = (-0.193905, 0.174892, 0.965305)

writing to /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_orig.nii.gz...

cp /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/38567200_bvecs /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_orig.mghdti.bvecs

cp /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/38567200_bvals /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_orig.mghdti.bvals

flip4fsl /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_orig.nii.gz /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_orig_flip.nii.gz

INFO: input image orientation is LAS

INFO: input image determinant is -10.3297

fslswapdim /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_orig.nii.gz x y z /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_orig_flip.nii.gz

fslorient -forceradiological /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_orig_flip.nii.gz

INFO: found /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_orig.mghdti.bvals, converting to FSL format

INFO: found /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_orig.mghdti.bvecs, converting to FSL format

mv -f /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_orig_flip.mghdti.bvecs /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/bvecs

mv -f /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_orig_flip.mghdti.bvals /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/bvals

eddy_correct /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_orig_flip.nii.gz /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi.nii.gz 0

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0000

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0001

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0002

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0003

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0004

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0005

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0006

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0007

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0008

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0009

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0010

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0011

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0012

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0013

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0014

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0015

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0016

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0017

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0018

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0019

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0020

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0021

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0022

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0023

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0024

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0025

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0026

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0027

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0028

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0029

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0030

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0031

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0032

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0033

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0034

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0035

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0036

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0037

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0038

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0039

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0040

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0041

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0042

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0043

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0044

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0045

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0046

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0047

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0048

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0049

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0050

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0051

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0052

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0053

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0054

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0055

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0056

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0057

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0058

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0059

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0060

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0061

processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0062

mv -f /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/bvecs /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/bvecs.norot

xfmrot /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi.ecclog /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/bvecs.norot /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/bvecs

ln -sf /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi.nii.gz /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/data.nii.gz

mri_convert --frame 0 /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi.nii.gz /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_frame0.nii.gz

mri_convert --frame 0 /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi.nii.gz /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_frame0.nii.gz

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading from /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi.nii.gz...

TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-0.978979, -0.0979427, -0.178907)

j_ras = (-0.0632554, 0.979704, -0.190207)

k_ras = (-0.193905, 0.174892, 0.965305)

keeping frame 0

writing to /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_frame0.nii.gz...

mri_convert --frame 1 /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi.nii.gz /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_frame1.nii.gz

mri_convert --frame 1 /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi.nii.gz /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_frame1.nii.gz

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading from /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi.nii.gz...

TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-0.978979, -0.0979427, -0.178907)

j_ras = (-0.0632554, 0.979704, -0.190207)

k_ras = (-0.193905, 0.174892, 0.965305)

keeping frame 1

writing to /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_frame1.nii.gz...

mri_convert --frame 2 /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi.nii.gz /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_frame2.nii.gz

mri_convert --frame 2 /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi.nii.gz /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_frame2.nii.gz

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading from /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi.nii.gz...

TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-0.978979, -0.0979427, -0.178907)

j_ras = (-0.0632554, 0.979704, -0.190207)

k_ras = (-0.193905, 0.174892, 0.965305)

keeping frame 2

writing to /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_frame2.nii.gz...

mri_convert --frame 3 /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi.nii.gz /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_frame3.nii.gz

mri_convert --frame 3 /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi.nii.gz /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_frame3.nii.gz

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading from /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi.nii.gz...

TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-0.978979, -0.0979427, -0.178907)

j_ras = (-0.0632554, 0.979704, -0.190207)

k_ras = (-0.193905, 0.174892, 0.965305)

keeping frame 3

writing to /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_frame3.nii.gz...

mri_concat --i /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_frame0.nii.gz /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_frame1.nii.gz /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_frame2.nii.gz /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_frame3.nii.gz --mean --o /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/lowb.nii.gz

ninputs = 4

Checking inputs

nframestot = 4

Allocing output

Done allocing

nframes = 4

Computing mean across frames

Writing to /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/lowb.nii.gz

bet /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/lowb.nii.gz /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/lowb_brain.nii.gz -m -f 0.5

mv -f /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/lowb_brain_mask.nii.gz /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dlabel/diff

#-------------------------------------

#@# Inter-subject registration Fri Oct 18 09:57:04 EDT 2019

flirt -in /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/lowb_brain.nii.gz -ref /usr/pubsw/packages/fsl/5.0.0/data/standard/MNI152_T1_1mm_brain.nii.gz -out /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/lowb_brain_mni.nii.gz -omat /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/xfms/diff2mni.mat -cost corratio

convert_xfm -omat /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/xfms/mni2diff.mat -inverse /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/xfms/diff2mni.mat

#-------------------------------------

#@# Masks Fri Oct 18 09:57:39 EDT 2019

ln -sf /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dlabel/diff/lowb_brain_mask.nii.gz /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/nodif_brain_mask.nii.gz

#-------------------------------------

#@# Tensor fit Fri Oct 18 09:57:39 EDT 2019

dtifit -k /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi.nii.gz -m /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dlabel/diff/lowb_brain_mask.nii.gz -r /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/bvecs -b /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/bvals -o /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dtifit

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#-------------------------------------

#@# Priors Fri Oct 18 09:57:50 EDT 2019

/usr/local/freesurfer/stable5_3_0/bin/dmri_train --outdir /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/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.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr --slist /tmp/subj33.sub-esq-01-en.4921.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.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_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 10 49 0 0 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.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_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 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.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz --bmask /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dlabel/mni/lowb_brain_mask.bbr.nii.gz --fa /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dtifit_FA.nii.gz --cptdir /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dlabel/diff --reg /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/xfms/mni2diff.bbr.mat --ncpts 6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5 --trunc

ERROR: fio_pushd: /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dlabel/mni

cwd /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en

cmdline /usr/local/freesurfer/stable5_3_0/bin/dmri_train --outdir /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/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.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr --slist /tmp/subj33.sub-esq-01-en.4921.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.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_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 10 49 0 0 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.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_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 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.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz --bmask /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dlabel/mni/lowb_brain_mask.bbr.nii.gz --fa /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dtifit_FA.nii.gz --cptdir /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dlabel/diff --reg /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/xfms/mni2diff.bbr.mat --ncpts 6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5 --trunc

sysname Linux

hostname shiraz.nmr.mgh.harvard.eduhttp://shiraz.nmr.mgh.harvard.edu/

machine x86_64

user ji733

Output directory: /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dlabel/mni

Output directory in test subject's space: /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/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.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr

Training subject directory list: /tmp/subj33.sub-esq-01-en.4921.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.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_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.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_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.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_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.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_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.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_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 10 49 0 0 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 shiraz.nmr.mgh.harvard.eduhttp://shiraz.nmr.mgh.harvard.edu/ 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Fri Oct 18 09:57:50 EDT 2019

Ihave dlabel/mni folder. Could you please gimme some light about it?

Thanks,

JC