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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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
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PhD Candidate
Magnetic Resonance and Image Analysis Research Center
University of Liverpool
b.kreilk...@liverpool.ac.uk
http://www.liverpool.ac.uk
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