Re: [Freesurfer] tracula: bvec-error

Anastasia Yendiki Mon, 25 Aug 2014 10:53:02 -0700

Hi Robby - Which version of tracula are you using? In general it's hard toguess what's going on just by seeing the error message. Please attach theentire log file (scripts/trac-all.log).


a.y

On Mon, 25 Aug 2014, Robby De Pauw wrote:

Hi Anastasia

Thanks for your quick reply. I’ve changed the command and I got one step 
further. Now I get another error:

mv -f 
/Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig_flip.mghdti.bvecs
/Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/bvecs
mv: rename 
/Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig_flip.mghdti.bvecs
 to
/Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/bvecs: No such file 
or directory
Darwin ge24p176.ugent.be 13.3.0 Darwin Kernel Version 13.3.0: Tue Jun  3 
21:27:35 PDT 2014; root:xnu-2422.110.17~1/RELEASE_X86_64 x86_64

trac-preproc exited with ERRORS at Mon Aug 25 14:23:03 CEST 2014

Somehow the folder bvecs was not created? 

Regards,

Robby



Hi Robby - It looks like in your config file "setbveclist" is one word, instead of 
"set bveclist". This may be why you're getting the
"Badly placed ()'s." error at the very beginning of your trac-all output. And 
it would explain why it can't find the files.

Hope this helps,
a.y

On Thu, 21 Aug 2014, Robby De Pauw wrote:

Dear FreeSurfer,

When I try to use TRACULA I keep getting the following error:

mv -f/Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig_flip.mghdti.bvecs

 /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/bvecs

mv: rename/Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig_flip.mghdti.bvecsto /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/bvecs: No suchfile or directory


after entering the following command:

$ trac-all -prep -c dmrirc.preproc

I tried to specify my bval and bvec in the config file, but that doesn’t seemto help.

My data was assessed using a Siemens-scanner. Attached you can find theconfig-file.


Thank you in advance,

Best regards,

Robby

—————————————

the complete output can be found here:

~/Desktop/SUBJECTS_FS $ trac-all -prep -c dmrirc.preproc
Badly placed ()'s.
INFO: SUBJECTS_DIR is /Users/rdpauw/Desktop/SUBJECTS_FS/T1
INFO: Diffusion root is /Users/rdpauw/Desktop/SUBJECTS_FS/T1
Actual FREESURFER_HOME /Applications/freesurfer
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
INFO: current FREESURFER_HOME does not match that of previous processing.
   Current: /Applications/freesurfer
   Previous: /apps/gent/SL6/sandybridge/software/FreeSurfer/5.3.0-centos4_x86_64

trac-preproc -c/Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/scripts/dmrirc.local -log/Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/scripts/trac-all.log -cmd/Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/scripts/trac-all.cmd

#-------------------------------------
/Applications/freesurfer/bin/trac-preproc
#-------------------------------------
#@# Image corrections Thu Aug 21 15:59:52 CEST 2014

mri_convert /Users/rdpauw/Desktop/SUBJECTS_FS/Diffusion/INP_080_LISA_V_1/1.IMA/Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig.nii.gzmri_convert /Users/rdpauw/Desktop/SUBJECTS_FS/Diffusion/INP_080_LISA_V_1/1.IMA/Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig.nii.gz

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading from/Users/rdpauw/Desktop/SUBJECTS_FS/Diffusion/INP_080_LISA_V_1/1.IMA...INFO: this looks like a dicom, not an old Siemens .ima file, so I'm going tounpack it as a dicom.

If this fails, run mri_convert with -it dicom
Getting Series No

INFO: Found 71 files in/Users/rdpauw/Desktop/SUBJECTS_FS/Diffusion/INP_080_LISA_V_1

INFO: Scanning for Series Number 5
Scanning Directory
INFO: found 65 files in series
INFO: loading series header info.

RunNo = 4
WARNING: Run 1 appears to be truncated
 Files Found: 65, Files Expected (lRep+1): 1

FileName/Users/rdpauw/Desktop/SUBJECTS_FS/Diffusion/INP_080_LISA_V_1/1.IMA

Identification
        NumarisVer        syngo MR B17
        ScannerModel      TrioTim
        PatientName       Sabbe^Linde
Date and time
        StudyDate         20140422
        StudyTime         164616.578000
        SeriesTime        171854.765000
        AcqTime           171832.007500
Acquisition parameters
        PulseSeq          *ep_b0
        Protocol          DTI64dir_1av_b1200_2.5x2.5x2.5_sfs
        PhEncDir          COL
        EchoNo            1
        FlipAngle         90
        EchoTime          83
        InversionTime     -1
        RepetitionTime    10800
        PhEncFOV          240
        ReadoutFOV        240
Image information
        RunNo             4
        SeriesNo          5
        ImageNo           1
        NImageRows        768
        NImageCols        768
        NFrames           65
        SliceArraylSize   60
        IsMosaic          1
        ImgPos            961.3685 959.9193 107.7635
        VolRes              2.5000   2.5000   2.5000
        VolDim             96       96       60
        Vc                 -1.0000  -0.0011   0.0062
        Vr                  0.0000  -0.9841  -0.1774
        Vs                  0.0063  -0.1774   0.9841
        VolCenter           0.0000   0.0000   0.0000
        TransferSyntaxUID 1.2.840.10008.1.2.1
INFO: sorting.
INFO: ( 96  96  60), nframes = 65, ismosaic=1
Could not parse NUMARIS version string syngo MR B17
found in dicom tag 18,1020 (len = 3 != 6)
Repetition Time = 10800, TR = 10800 ms
PE Dir COL COL
AutoAlign matrix detected
AutoAlign Matrix ---------------------
1.000   0.000   0.000   0.000;
0.000   1.000   0.000   0.000;
0.000   0.000   1.000   0.000;
0.000   0.000   0.000   1.000;

FileName/Users/rdpauw/Desktop/SUBJECTS_FS/Diffusion/INP_080_LISA_V_1/1.IMA

Identification
        NumarisVer        syngo MR B17
        ScannerModel      TrioTim
        PatientName       Sabbe^Linde
Date and time
        StudyDate         20140422
        StudyTime         164616.578000
        SeriesTime        171854.765000
        AcqTime           171832.007500
Acquisition parameters
        PulseSeq          *ep_b0
        Protocol          DTI64dir_1av_b1200_2.5x2.5x2.5_sfs
        PhEncDir          COL
        EchoNo            1
        FlipAngle         90
        EchoTime          83
        InversionTime     -1
        RepetitionTime    10800
        PhEncFOV          240
        ReadoutFOV        240
Image information
        RunNo             4
        SeriesNo          5
        ImageNo           1
        NImageRows        768
        NImageCols        768
        NFrames           65
        SliceArraylSize   60
        IsMosaic          1
        ImgPos            121.3850 132.3092 -36.0742
        VolRes              2.5000   2.5000   2.5000
        VolDim             96       96       60
        Vc                 -1.0000  -0.0011   0.0062
        Vr                  0.0000  -0.9841  -0.1774
        Vs                  0.0063  -0.1774   0.9841
        VolCenter           1.8567   0.7748  17.1866
        TransferSyntaxUID 1.2.840.10008.1.2.1
UseSliceScaleFactor 0 (slice 0: 1)
sagrev = 0, correv =0, trarev = 0
Vs = 0.0062587 -0.177391 0.98412
INFO: no Siemens slice order reversal detected (good!).
TR=10800.00, TE=83.00, TI=-1.00, flip angle=90.00
i_ras = (-0.99998, -0.00111026, 0.00615943)
j_ras = (3.52518e-09, -0.98414, -0.177395)
k_ras = (0.0062587, -0.177391, 0.98412)

writing to/Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig.nii.gz...flip4fsl/Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig.nii.gz/Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig_flip.nii.gz

INFO: input image orientation is LPS
INFO: input image determinant is 15.625

fslswapdim/Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig.nii.gz x -yz/Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig_flip.nii.gz

INFO: left-right orientation was flipped by fslswapdim

fslorient -forceradiological/Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig_flip.nii.gzmv -f/Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig_flip.mghdti.bvecs

 /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/bvecs

mv: rename/Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig_flip.mghdti.bvecsto /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/bvecs: No suchfile or directoryDarwin ge24p176.ugent.be 13.3.0 Darwin Kernel Version 13.3.0: Tue Jun 321:27:35 PDT 2014; root:xnu-2422.110.17~1/RELEASE_X86_64 x86_64


trac-preproc exited with ERRORS at Thu Aug 21 16:00:45 CEST 2014

Robby De Pauw, dra.
Ghent University
Department of Physiotherapy and Rehabilitation Sciences
3B3
De Pintelaan 185
B-9000 Ghent

robby.dep...@ugent.be





____________________________________

Robby De Pauw, dra.
Ghent University
Department of Physiotherapy and Rehabilitation Sciences
3B3
De Pintelaan 185
B-9000 Ghent

robby.dep...@ugent.be

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Re: [Freesurfer] tracula: bvec-error

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