Hi Michele,
Yes, tracula would have complained at the very first call, if the dwi
data was not there.
So here is the problem, you write:
setenv
/Users/michele/Desktop/tracula/sages_diff_test_tracula/SD000040_1/FSout_P00000401_e20130813_s002_Cor7minMDEFT_T1_b
in the very first line in your config file, it should read
setenv SUBJECTS_DIR
/Users/michele/Desktop/tracula/sages_diff_test_tracula/SD000040_1/FSout_P00000401_e20130813_s002_Cor7minMDEFT_T1_b
The problem was that recon-all files were not found (because the path
was never set to the right environment variable SUBJECTS_DIR.
Try now.
Best,
Barbara
On 03/09/2014 18:04, Michele Cavallari wrote:
Hi Barbara,
I checked the path. The folder with the trac-all output is is the very
same folder of the dwi dicoms.
Attached is the dmrirc file I am using, with all the specs.
Thanks
On Wed, Sep 3, 2014 at 12:59 PM, Barbara Kreilkamp
<bakk....@googlemail.com <mailto:bakk....@googlemail.com>> wrote:
Hi Michele,
You would have to make sure that the files are written to the same
folder for both commands (recon-all and trac-all)
Right now it seems you wrote the output of recon-all to
/PHShome/my738/FSout/FSout_P00000401_e20130813_s002_Cor7minMDEFT_T1_b/
and trac-all output to
/Users/michele/Desktop/tracula/sages_diff_test_tracula/SD000040_1/
This is what the code was looking for but did not find:
Location of aparc+aseg's relative to base:
dlabel/mni/aparc+aseg.nii.gz
What path did you specify for the T1 segmentations (by recon-all)
in your configuration file?
Hope it helps,
All the best,
Barbara
On 03.09.14 17:31, Michele Cavallari wrote:
Hi Barbara,
thanks again for your help.
I checked the bvecs file using the 'more' command, and (as you
pointed out) there was some extra text. This was likely due to
MS-excel formatting, which I have used to reshape the bvecs file
from row to column configuration. Such extra text was not part of
the original bvecs file organized in rows though, but tracula was
not giving errors as well.
So, take home message#1
It is not true that FreeSurfer 5.3 allows both rows and columns
configuration of the bvecs (as stated in the wiki page). Or at
least that's not true for all the scanners. I'd recommend a
column configuration of the bvecs, even with FreeSurfer 5.3.
Also - take home message#2
verify that there's no extra text due to excel formatting in the
reshaped bvecs file.
That said, now this lead me to the next error!
It seems that there's a problem with the recon-all output that
I'm using (?). However, both the log file and the output of the
recon-all processing seem fine to me.
Here is the detail of the error message I am getting
ERROR: fio_pushd: path/to/dlabel/mni
And attached are the log files of both tracula pre-processing
(with errors) and recon-all (apparently without errors).
Any help/suggestions?
Thanks.
On Mon, Sep 1, 2014 at 5:51 AM, Barbara Kreilkamp
<bakk....@googlemail.com <mailto:bakk....@googlemail.com>> wrote:
Hi Michele,
This might be the solution - try the command 'more' in unix
on your column bvec and bval, they should each have one
(bval) and three (bvec) columns and no strange symbols. But
you have these symbols in the bvec-file (probably because you
have extra formatting information, that is not needed and an
obstacle to Tracula).
more original_columns.bval
0
0
0
0
0
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
1000
NEURO-222:tracula_help NEURO-222$ more original_columns.bvec
0 0 0
0 0 0 ^M0 0 0 ^M0 0 0 ^M0 0 0 ^M-1 0 0 ^M-0.166 0.986 0
^M0.11 0.664 0.74 ^M-0.901 -0.419 -0.11 ^M0.169 -0.601 0.781
^M0.815 -0.386 0.433 ^M-0.656 0.366 0.66 ^M^M-0.582 0.8 0.143
^M-0.9 0.259 0.35 ^M-0.693 -0.698 0.178 ^M-0.357 -0.924 -0.14
^M-0.543 -0.488 -0.683 ^M0.525 -0.396 0.753 ^M0.639 0.689
0.341 ^M0.33 -0.013 -0.944 ^M0.524 -0.783 0.335 ^M-0.609
-0.065 -0.791 ^M-0.22 -0.233 -0.947 ^M0.004 -0.91 -0.415
^M0.511 0.627 -0.589 ^M-0.414 0.737 0.535 ^M0.679 0.139
-0.721 ^M-0.884 -0.296 0.362 ^M-0.262 0.432 0.863 ^M-0.088
0.185 -0.979 ^M-0.294 -0.907 0.302 ^M-0.887 -0.089 -0.453
^M-0.257 -0.443 0.859 ^M-0.086 0.867 -0.491 ^M-0.863 0.504
-0.025
You are ending up with multiple columns in the second row,
please make sure they are 3 columns.
Good luck,
Barbara
On Mon, Sep 1, 2014 at 10:36 AM, Barbara Kreilkamp
<bakk....@googlemail.com <mailto:bakk....@googlemail.com>> wrote:
Hi Michele,
Do you use the dicoms or the nifti files as input to TRACULA?
Also, I think the complete trac-all.log could be even
more helpful.
I am a newbie myself but I am having a similar problem,
so I am trying to find a solution as well :).
Best,
Barbara
On Fri, Aug 29, 2014 at 4:48 PM, Michele Cavallari
<mic...@bwh.harvard.edu <mailto:mic...@bwh.harvard.edu>>
wrote:
Hi Barbara,
thanks for your reply. I checked the dwi series on a
viewer and it looks
fine: I have 1960 dicoms, corresponding to 56 slices
x 35 directions
specified in the bval/bvec. Also, I was able to
obtain the FA and MD maps
through fsl using the very same dicoms and bval/bvec.
Any suggestion?
Thanks
On Thu, Aug 28, 2014 at 7:30 PM, Barbara Kreilkamp
<bakk....@googlemail.com
<mailto:bakk....@googlemail.com>> wrote:
Dear Michele,
I cannot find anything wrong with your bvec and bval
files.
Seeing as you had an errormessage related to the dwi
(the one about the
dwi_frame.nii.gz): Did you check that your dwi data
have the same amount of
volumes as entries in bvec and bval?
Good luck,
Barbara
On 28/08/2014 22:47, Michele Cavallari wrote:
Hi,
I'm having some problems with the first command of
the tracula pipeline.
I am using FreeSurfer 5.3 on a mac (OS 10.9).
The problem seems to be related to the bvecs file. I
received the following
error message:
niiRead(): error opening file
/path/to/dmri/dwi_frame.nii.gz
I read some threads available on your website, but
couldn't figured out a
solution yet. I tried to organize the bvecs in
columns, as opposed to the
original configuration in rows. By doing that and
re-launching the
pre-processing command I obtained a differente error
message:
Error: bvecs and bvals don't have the same number of
entries
The original bvals and bvecs files seem to have the
same numbers of entries
to me. But the bvecs file produced by the processing
- both the bvecs.norot
and the bvecs files in the dmri folder - don't have
all the information of
the vectors.
I am enclosing a zip folder with attachments:
1) original bvecs and bvals files organized in rows
and columns
2) bvecs and bvals files generated by tracula
3) error logs
Let me know if you need any other information.
Thanks in advance for your help.
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Magnetic Resonance and Image Analysis Research Center
University of Liverpool
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