Hi Anastasia:

Here is the trac-all log. Thanks so much:


csh::alanf@cerebro [/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/106/Diffusion_Recons] : trac-all -prep -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-106
INFO: SUBJECTS_DIR is /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons
INFO: Diffusion root is /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/
Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0
trac-preproc -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/scripts/dmrirc.local -log /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/scripts/trac-all.log -cmd /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/scripts/trac-all.cmd
#-------------------------------------
/usr/local/freesurfer/stable5_3_0//bin/trac-preproc
#-------------------------------------
#@# Image corrections Wed Aug  7 13:16:17 EDT 2013
mri_convert /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/Diffusion_Recons/20080928_121245216000-000021-000001DIFFUSIONHighResValeraBI106s021a001.nii /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig.nii.gz
mri_convert /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/Diffusion_Recons/20080928_121245216000-000021-000001DIFFUSIONHighResValeraBI106s021a001.nii /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/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/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/Diffusion_Recons/20080928_121245216000-000021-000001DIFFUSIONHighResValeraBI106s021a001.nii...
TR=7570.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 1.63925e-05, 3.62902e-06)
j_ras = (1.67894e-05, 0.976296, 0.21644)
k_ras = (0, -0.21644, 0.976296)
writing to /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig.nii.gz...
cp /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/106/Diffusion_Recons/bvecs /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig.mghdti.bvecs
cp /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/106/Diffusion_Recons/bvecs /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig.mghdti.bvals
flip4fsl /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig_flip.nii.gz
INFO: input image orientation is LAS
INFO: input image determinant is -6.8719
fslswapdim /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig.nii.gz x y z /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig_flip.nii.gz
fslorient -forceradiological /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig_flip.nii.gz
INFO: found /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig.mghdti.bvals, converting to FSL format
INFO: found /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig.mghdti.bvecs, converting to FSL format
mv -f /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig_flip.mghdti.bvecs /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/bvecs
mv -f /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig_flip.mghdti.bvals /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/bvals
eddy_correct /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig_flip.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi.nii.gz 0
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0000
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0001
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0002
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0003
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0004
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0005
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0006
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0007
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0008
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0009
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0010
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0011
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0012
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0013
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0014
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0015
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0016
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0017
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0018
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0019
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0020
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0021
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0022
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0023
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0024
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0025
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0026
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0027
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0028
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0029
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0030
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0031
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0032
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0033
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0034
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0035
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0036
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0037
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0038
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0039
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0040
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0041
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0042
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0043
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0044
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0045
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0046
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0047
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0048
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0049
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0050
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0051
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0052
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0053
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0054
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0055
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0056
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0057
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0058
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0059
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0060
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0061
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0062
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0063
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0064
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0065
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0066
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0067
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0068
processing /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0069
mv -f /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/bvecs /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/bvecs.norot
xfmrot /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi.ecclog /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/bvecs.norot /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/bvecs
ln -sf /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi.nii.gz /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/data.nii.gz
Usage: awk [POSIX or GNU style options] -f progfile [--] file ...
Usage: awk [POSIX or GNU style options] [--] 'program' file ...
POSIX options:        GNU long options:
    -f progfile        --file=progfile
    -F fs            --field-separator=fs
    -v var=val        --assign=var=val
    -m[fr] val
    -O            --optimize
    -W compat        --compat
    -W copyleft        --copyleft
    -W copyright        --copyright
    -W dump-variables[=file]    --dump-variables[=file]
    -W exec=file        --exec=file
    -W gen-po        --gen-po
    -W help            --help
    -W lint[=fatal]        --lint[=fatal]
    -W lint-old        --lint-old
    -W non-decimal-data    --non-decimal-data
    -W profile[=file]    --profile[=file]
    -W posix        --posix
    -W re-interval        --re-interval
    -W source=program-text    --source=program-text
    -W traditional        --traditional
    -W usage        --usage
    -W use-lc-numeric    --use-lc-numeric
    -W version        --version

To report bugs, see node `Bugs' in `gawk.info', which is
section `Reporting Problems and Bugs' in the printed version.

gawk is a pattern scanning and processing language.
By default it reads standard input and writes standard output.

Examples:
    gawk '{ sum += $1 }; END { print sum }' file
    gawk -F: '{ print $1 }' /etc/passwd
mri_concat --i /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_frame.nii.gz --mean --o /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/lowb.nii.gz
niiRead(): error opening file /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_frame.nii.gz
ninputs = 1
Checking inputs
ERROR: reading /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_frame.nii.gz
Linux cerebro 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Wed Aug  7 13:34:45 EDT 2013



On Wed, Aug 7, 2013 at 1:20 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote:

Please attach the file trac-all.log. I can't tell what's going on just by looking at the end of it.


On Wed, 7 Aug 2013, Alan Francis wrote:

Thank you Anastasia. Another brain had a different problem: Here is the trac-all log:

mri_concat --i
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_frame.nii.gz --mean --o
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/lowb.nii.gz
niiRead(): error opening file
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_frame.nii.gz
ninputs = 1
Checking inputs
ERROR: reading
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_frame.nii.gz
Linux cerebro 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Wed Aug  7 13:01:21 EDT 2013

thanks so much,

Alan


On Wed, Aug 7, 2013 at 1:11 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote:

      Hi Alan - Try removing the "\" character from the end of the dcmlist definition. That's a change of line
      character.

      a.y

      On Wed, 7 Aug 2013, Alan Francis wrote:

            Hi Anastasia:

            Here is the trac-all log. Please find attached the dmrirc file.

            csh::alanf@cerebro
            [/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : trac-all
            -prep
            -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-107

            Too many ('s.
            ERROR: must specify as many DWI dicoms as subjects

            Thank you so much.

            Alan


            On Wed, Aug 7, 2013 at 12:32 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote:

                  Yes, please attach the dmrirc and trac-all.log. Thanks!

                  a.y

                  On Wed, 7 Aug 2013, Alan Francis wrote:

                        Hi Anastasia:

                        For one brain I got this error message :

                        csh::alanf@cerebro
                        [/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons]
            : trac-all
                        -prep
                        -c
            /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-107

                        Too many ('s.
                        ERROR: must specify as many DWI dicoms as subjects

                        I tried specifying the exact number of DWI dicoms but it is not working. Should I
            send you my
                        dmrirc for this brain?

                        thanks,

                        Alan




            The information in this e-mail is intended only for the person to whom it is
            addressed. If you believe this e-mail was sent to you in error and the e-mail
            contains patient information, please contact the Partners Compliance HelpLine at
            http://www.partners.org/complianceline . If the e-mail was sent to you in error
            but does not contain patient information, please contact the sender and properly
            dispose of the e-mail.