From ayendiki@nmr.mgh.harvard.edu Thu Sep 27 14:14:24 2012
From: Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Tracula Error: bvecs and bvals don't have the same
 number of entries
Date: Thu, 27 Sep 2012 14:14:21 -0400
Message-ID: <alpine.LRH.2.00.1209271412350.18712@door.nmr.mgh.harvard.edu>
In-Reply-To:
 <CAOhfCkBjqOetd6hOdNA_44-SEvB7dEJTYmtaBVBupeYe=GZ6aQ@mail.gmail.com>
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Can you please send the original bvals and bvecs files (the ones that you=20
specify in the configuration file), and the configuration file itself?=20
Thanks!

a.y

On Thu, 27 Sep 2012, Loi wrote:

> Hello,
>
> I generate the files in Linux (using gedit) and they look normal (I
> have compared them to the files in the tutorial).
>
> So far I have tried ending both with and without .txt, transposing the
> files, changing to equal number of decimals and adding 'setenv LC_ALL
> en_US' to the .tchsrc file.
>
> The inputs I am using are dicoms, and even though I specify a path to
> the b-value files and gradient tables I make (I originally didn't
> specify these, and got the same error message), new bvecs and bvals
> are generated in the trac-all -prep process, leading to the error.
>
> Thank you,
> Joy-Loi
>
>
>
>
> On Thu, Sep 27, 2012 at 7:30 PM, Anastasia Yendiki
> <ayendiki(a)nmr.mgh.harvard.edu> wrote:
>>
>> Hi Joy - How were your bvecs and bvals files generated? In the past some
>> people have had problems with files exported from Excel b/c it generates
>> text files with Windows-specific end-of-line characters that cannot be read
>> properly on Linux. Do the files look normal when you run "more" on them on
>> the system where you ran trac-all?
>>
>> a.y
>>
>>
>> On Wed, 26 Sep 2012, Loi wrote:
>>
>>> Dear FreeSurfers,
>>>
>>> I am trying to run trac-all -prep on a single subject, and get the
>>> following error:
>>>
>>> dtifit -k
>>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id=
101/dmri/dwi.nii.gz
>>> -m
>>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id=
101/dlabel/diff/aparc+aseg_mask.flt.nii.gz
>>> -r
>>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id=
101/dmri/bvecs
>>> -b
>>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id=
101/dmri/bvals
>>> -o
>>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id=
101/dmri/dtifit
>>> Error: bvecs and bvals don't have the same number of entries
>>>
>>> I have searched the message thread, and cannot seem to find a solution
>>> applicable to my situation: it seems that the trac-all process
>>> generates transposed bvec and bval files.
>>> Therefore, I tried transposing these manually and specifying the
>>> location to these files (as explained in the tutorial:
>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula), but
>>> attempting to run trac-all again still leads to the same result: new
>>> bval and bvec files are generated, and I receive the same error
>>> message.
>>>
>>> Does anyone know how I can solve this problem?
>>>
>>> Thank you,
>>> Joy-Loi
>>>
>>>
>>> *********************
>>> My configuration file:
>>>
>>>
>>> setenv SUBJECTS_DIR
>>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_recons
>>>
>>> set dtroot =3D
>>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data
>>>
>>> set subjlist =3D id101
>>> set runlist =3D 1
>>>
>>> set dcmroot =3D
>>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data
>>> set dcmlist =3D id101/orig/1.dcm
>>>
>>> set bvalfile =3D
>>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id=
101/dmri/bvals.txt
>>>
>>> set bvecfile =3D
>>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id=
101/dmri/bvecs.txt
>>>
>>> set nb0 =3D 10
>>>
>>> set doeddy =3D 1
>>> set dorotbvecs =3D 1
>>> set thrbet =3D 0.3
>>> set doregflt =3D 1
>>> set doregbbr =3D 0
>>> set doregmni =3D 1
>>> set mnitemp =3D  /psyklab/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz
>>>
>>> #set trainfile =3D
>>>
>>> /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/su=
bj,train,difftutorial123.txt
>>>
>>> set pathlist =3D (lh.cst_AS rh.cst_AS \
>>>                  lh.ilf_AS rh.ilf_AS \
>>>                 lh.unc_AS rh.unc_AS \
>>>                  fmajor_PP fminor_PP \
>>>                  lh.atr_PP rh.atr_PP \
>>>                  lh.cab_PP rh.cab_PP \
>>>                  lh.ccg_PP rh.ccg_PP \
>>>                  lh.slfp_PP rh.slfp_PP \
>>>                  lh.slft_PP rh.slft_PP)
>>>
>>>
>>> set ncpts =3D 5
>>>
>>> set usetrunc =3D 1
>>>
>>>
>>>
>>>
>>>
>>> *********************
>>> My bvals:
>>>
>>> 0.000000
>>> 0.000000
>>> 0.000000
>>> 0.000000
>>> 0.000000
>>> 0.000000
>>> 0.000000
>>> 0.000000
>>> 0.000000
>>> 0.000000
>>> 700.000000
>>> 700.000000
>>> 700.000000
>>> 700.000000
>>> 700.000000
>>> 700.000000
>>> 700.000000
>>> 700.000000
>>> 700.000000
>>> 700.000000
>>> 700.000000
>>> 700.000000
>>> 700.000000
>>> 700.000000
>>> 700.000000
>>> 700.000000
>>> 700.000000
>>> 700.000000
>>> 700.000000
>>> 700.000000
>>> 700.000000
>>> 700.000000
>>> 700.000000
>>> 700.000000
>>> 700.000000
>>> 700.000000
>>> 700.000000
>>> 700.000000
>>> 700.000000
>>> 700.000000
>>>
>>> *********************
>>> My bvecs:
>>>
>>> 0.0000000 0.0000000 0.0000000
>>> 0.0000000 0.0000000 0.0000000
>>> 0.0000000 0.0000000 0.0000000
>>> 0.0000000 0.0000000 0.0000000
>>> 0.0000000 0.0000000 0.0000000
>>> 0.0000000 0.0000000 0.0000000
>>> 0.0000000 0.0000000 0.0000000
>>> 0.0000000 0.0000000 0.0000000
>>> 0.0000000 0.0000000 0.0000000
>>> 0.0000000 0.0000000 0.0000000
>>> -0.9998760 0.0011040 0.0157340
>>> -0.7705615 0.6320276 0.0823114
>>> -0.2461791 0.0273479 0.9688392
>>> -0.7953558 0.1076421 0.5965091
>>> 0.4620816 -0.8755928 0.1407778
>>> 0.2261090 -0.8553081 -0.4661796
>>> 0.2601186 0.4095102 -0.8744363
>>> -0.7969547 -0.5877791 0.1392076
>>> -0.5028073 -0.5104712 0.6975709
>>> -0.3073035 0.1334521 -0.9422074
>>> 0.7957742 0.1950272 -0.5733304
>>> 0.8041493 0.5924478 -0.0484727
>>> -0.1867079 -0.9528833 0.2390659
>>> 0.3898569 -0.1063898 0.9147088
>>> 0.1341999 -0.6614532 0.7378819
>>> 0.3382555 0.8823941 0.3270553
>>> -0.7688307 -0.3139264 -0.5570900
>>> -0.4086013 0.6653325 0.6248017
>>> -0.2933309 0.7581020 -0.5824408
>>> 0.7689370 -0.4282441 0.4747016
>>> 0.1800972 0.5296402 0.8288835
>>> 0.7680658 0.3158178 0.5570763
>>> -0.2214999 0.9744585 0.0370050
>>> -0.4175692 -0.8418782 -0.3418731
>>> -0.1784475 -0.4817282 -0.8579599
>>> 0.3361637 0.8554551 -0.3939400
>>> 0.7858656 -0.5091907 -0.3509137
>>> 0.4194232 -0.2589429 -0.8700761
>>> -0.7760561 0.3511497 -0.5238622
>>> 0.9987836 -0.0413076 0.0269219
>>> _______________________________________________
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>>> Freesurfer(a)nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
>>
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