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#2verify 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 gettingERROR: 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.hbg@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.hbg@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 <miches@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.hbg@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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Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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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
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.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
-- Barbara Kreilkamp PhD Candidate Magnetic Resonance and Image Analysis Research Center University of Liverpool B.Kreilkamp@Liverpool.ac.uk http://www.liverpool.ac.uk