Alan - Where is the location that has plenty of space? You should set your
SUBJECTS_DIR to that location, e.g.,
setenv SUBJECTS_DIR
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons
On Wed, 14 Aug 2013, Alan Francis wrote:
Hi Anastasia/ FreeSurfers
I did not use the conventional path usr/local/freesurfer. since there is very
little disc space in this location.
Alternately I set the environment at a location where is plenty of disc space
and then sourced it.
For the SUBJECTS_DIR I set the environment without using the dollar sign $.
The Freesurfer recons and Tracula ran without problem and saved the processed
data to this location. So the
FReeSurfer recons and tracula data are in the same location.
Now I am trying to use the dollar sign, so that I can extract the trac data,
but I keep getting the error message.
csh::alanf@cerebro
[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons]
: setenv
SUBJECTS_DIR $FreeSurfer_Data/diffusion_recons
FreeSurfer_Data: Undefined variable.
thanks,
Alan
On Wed, Aug 14, 2013 at 1:08 PM, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:
Where did you get this command line? You should set the SUBJECTS_DIR to
the location on disk where your
freesurfer recons are.
On Wed, 14 Aug 2013, Alan Francis wrote:
Hi Anastasia:
I fixed that problem - thank you. However, I have another question. i am
trying extract trac data
but when I set
environment, I get an error message:
csh::alanf@cerebro
[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons]
: setenv
SUBJECTS_DIR $FreeSurfer_Data/diffusion_recons
FreeSurfer_Data: Undefined variable.
How do I solve this?
Thanks again,
Alan
On Wed, Aug 14, 2013 at 11:06 AM, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:
Hi Alan - I'm not sure where the output from the one subject ends
the the other starts. For
future
reference, it's best to attach the entire trac-all.log files
instead of copying and pasting
parts of them
into your message.
I see two error messages here:
1. "ERROR: must specify as many DWI dicoms as subjects"
This is as it says. Check your configuration file and see if the
numbers of entries in
subjlist and
dcmlist are the same.
2. "ERROR: reading
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_frame.nii.gz"
I'm guessing the problem is in the b-value table. How many entries
are there that correspond
to low-b
images?
a.y
On Tue, 13 Aug 2013, Alan Francis wrote:
Hi Anastasia:
Thanks to your advice most of the data have been processed using
Tracula. Two brains gave me
error
messages that are
as follows:
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-124
ERROR: must specify as many DWI dicoms as subjects
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-118
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//118/scripts/dmrirc.local
-log
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/scripts/trac-all.log
-cmd
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/scripts/trac-all.cmd
#-------------------------------------
/usr/local/freesurfer/stable5_3_0//bin/trac-preproc
#-------------------------------------
#@# Image corrections Mon Aug 12 17:11:05 EDT 2013
mri_convert/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/Diffusion_Recons/200
90224_14110
2DIFFUSIONHighRess016a001.nii
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.nii.gz
mri_convert/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/Diffusion_Recons/200
90224_14110
2DIFFUSIONHighRess016a001.nii
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
readingfrom/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/Diffusion_Recons/200
90224_1
4110
2DIFFUSIONHighRess016a001.nii...
TR=7640.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.997762, -0.0667414, -0.00403802)
j_ras = (-0.0662713, 0.979101, 0.192276)
k_ras = (0.00887916, -0.192114, 0.981333)
writing to
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.nii.gz...
cp
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/118/Diffusion_Recons/118.bvecs
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.mghdti.bvecs
cp
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/118/Diffusion_Recons/118.bvals
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.mghdti.bvals
flip4fsl
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig.nii.gz
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/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//118/dmri/dwi_orig.nii.gz
x y z
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig_flip.nii.gz
fslorient -forceradiological
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig_flip.nii.gz
INFO: found
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/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//118/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//118/dmri/dwi_orig_flip.mghdti.b
ve
cs
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/bvecs
mv-f/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig_flip.mghdti.b
va
ls
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/bvals
eddy_correct
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_orig_flip.nii.gz
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi.nii.gz
0
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0000
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0001
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0002
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0003
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0004
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0005
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0006
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0007
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0008
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0009
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0010
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0011
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0012
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0013
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0014
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0015
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0016
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0017
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0018
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0019
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0020
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0021
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0022
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0023
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0024
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0025
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0026
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0027
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0028
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0029
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0030
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0031
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0032
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0033
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0034
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0035
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0036
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0037
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0038
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0039
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0040
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0041
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0042
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0043
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0044
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0045
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0046
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0047
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0048
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0049
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0050
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0051
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0052
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0053
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0054
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0055
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0056
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0057
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0058
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0059
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0060
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0061
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0062
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0063
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0064
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0065
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0066
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0067
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0068
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_tmp0069
mv -f
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/bvecs
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/bvecs.norot
xfmrot
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi.ecclog
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/bvecs.norot
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/bvecs
ln -sf
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi.nii.gz
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/data.nii.gz
awk: cmd. line:1: fatal: cannot open file `0' for reading (No such file or
directory)
mri_concat --i
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/dwi_frame.nii.gz
--mean --o
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/dmri/lowb.nii.gz
niiRead(): error opening file
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//118/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//118/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 Mon Aug 12 17:30:05 EDT 2013
As always - thanks for your help,
best,
Alan
Martinos Center.
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