Hi Francesco - Please attach your trac-all.log file. There may be an error
at an earlier stage that's causing this error.
Thanks,
a.y
On Thu, 13 Feb 2014, Francesco Baldacchini wrote:
Hi Anastasia,
Thank you for the help, finally I discovered the cause of the problem. The
language of the system was set to Italian which
use the comma as a decimal separator instead of the dot. So I was able to run
the trac-all but I encountered another
problem. The error I'm getting is the following:
#@# Priors Thu Feb 13 17:33:25 CET 2014
/usr/local/freesurfer/bin/dmri_train --outdir
/media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dlabel/mni --out
lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr
rh.ilf_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr
rh.unc_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.Beal.2838.txt --trk
dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk
dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk
dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_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.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/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/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
/media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dlabel/mni/lowb_brain_mask.bbr.nii.gz
--fa
/media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dtifit_FA.nii.gz --cptdir
/media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dlabel/diff --reg
/media/opbg/dati/Baldacchini/Beal00/Beal/Beal/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: /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dlabel/mni
cwd /home/opbg
cmdline /usr/local/freesurfer/bin/dmri_train --outdir
/media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dlabel/mni --out
lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr
rh.ilf_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr
rh.unc_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.Beal.2838.txt --trk
dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk
dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk
dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_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.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/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/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
/media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dlabel/mni/lowb_brain_mask.bbr.nii.gz
--fa
/media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dtifit_FA.nii.gz --cptdir
/media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dlabel/diff --reg
/media/opbg/dati/Baldacchini/Beal00/Beal/Beal/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 opbg
machine x86_64
user opbg
Output directory: /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dlabel/mni
Output directory in test subject's space:
/media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dlabel/diff
Output base: lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr
lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr
lh.unc_AS_avg33_mni_bbr rh.unc_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.Beal.2838.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.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk
dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_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.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_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/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.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_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/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 opbg 3.11.0-17-generic #31-Ubuntu SMP Mon Feb 3 21:52:43 UTC 2014 x86_64
x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Thu Feb 13 17:33:25 CET 2014
So it seems that TRACULA is not finding this "aparc+aseg.nii.gz" file. Maybe
this error is due to the fact that I didn't
run RECON ALL to my .nii file but I did directly the TRAC-ALL -PREP. If it
isn't so I would like to know why am I getting
this problem.
What can I do? Shall I use for trac all the same subjdir as in recon all so
that it can find the file aparc+aseg.nii.gz in
one of the subfolder structure? But then I come with the second question: why
the folders created by TRAC-ALL are called
dlabel and dmri and not just label and mri like the ones I get when I run recon
all?
Still thank you so much for the great help you gave me.
Francesco Baldacchini
2014-02-13 2:07 GMT+01:00 Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>:
Hi Francesco - The decimal separator should be dot, not comma. Can you
send me the bvecs/bvals that you get
after you change from row to column format? (Both the ones that you feed
into trac-all and the ones that get
created under dmri/.)
Thanks,
a.y
On Tue, 11 Feb 2014, Francesco Baldacchini wrote:
Hi again Anastasia,
I tried also to convert my three row bvecs file in a three column
one but I still got the same
"bvecs and bvals don't have
the same number of entries" error. I then tried also to change the
dot to comma as the decimal
separator but still nothing
Francesco Baldacchini
2014-02-11 15:06 GMT+01:00 Francesco Baldacchini
<frankb...@gmail.com>:
Ciao Anastasia, I checked and I'm using the latest version of
Freesurfer, version 5.3.0. It
seems like that
the command trac-all path while working on the bvecs table
and doing the corrections makes
some errors and you
can see it from the bvecs file I found in the dmri directory
which is only 4 rows long.
2014-02-06 1:18 GMT+01:00 Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu>:
Hi Francesco - Which version of tracula are you running? To
be able to use bvecs files that
are in 3
rows instead of 3 columns, you need to make sure that you
have the latest update to tracula,
see here:
http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula/#Updates
This option was not available in the previous releases of
tracula.
Hope this helps,
a.y
On Mon, 20 Jan 2014, Francesco Baldacchini wrote:
Hi,
Sorry Anastasia, I'm seeing that my question was not so
clear. The files I sent you in
the first mail are the bvecs and bvals saved by
trac-all -prep in the dmri directory.
The original files are in attachment in this mail,
Francesco Baldacchini
2014/1/13 Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu>
Hi Francesco - The bvecs file that you're
attaching has only 3 vectors,
while the bvals file has 65 b-values. Are these
your original files, or the
ones saved by trac-all in the dmri/ directory?
a.y
On Mon, 13 Jan 2014, Francesco Baldacchini wrote:
Hi everybody,
I'm trying to run the trac all -prep
command but after some
times I get this
error "bvecs and bvals don't have the same
number of entries".
I've checked
my bvals and bvecs, which are in attach,
but they seems to be
formatted in
the right way. What can I do? Thanks,
Francesco Baldacchini
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