It sounds like a problem that was specific to the centos4 build, and that
should be solved in the latest tracula update. You can download the update
from here:
http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates
VERY IMPORTANT: Use the link that says "CentOS 4 (32-bit)", so that the
update matches the freesurfer build that you have on your computer.
Best,
a.y
the On Thu, 24 Sep 2015, Karuna Subra wrote:
Yes, below is what is in the build-stamp.txt:
freesurfer-Linux-centos4-stable-pub-v5.3.0
On Thu, Sep 24, 2015 at 8:47 AM, Karuna Subra <kar...@gmail.com> wrote:
Hi Anastasia,
We're using version freesurfer 5.3.
On Thu, Sep 24, 2015 at 8:43 AM, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:
Hi Karuna - Which build of freesurfer are you using? It's written in this
file:
$FREESURFER_HOME/build-stamp.txt
a.y
On Thu, 24 Sep 2015, Karuna Subra wrote:
Dear Freesurfer experts,
I've been having issues with the trac-prep script opening the bvals
file
within the dmri folder that it
creates. Below is the full log of the current error.
When I run:
ls -l
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/bvals,
I get the below:
-rw-rw-r-- 1 karunas vapsych 376 Sep 23 15:13
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/bvals
I defined my SUBJECTS_DIR where all the freesurfer recons are
located as
shown below:
>> cd /home/karunas/Desktop/bin/freesurfer/subjects/203
>> ls
bem dlabel dmri label mri scripts src stats surf tmp
touch
trash
It seems that it has a problem with opening the bvals file within
the
dmri folder that it creates (the
values seem to be changed back to rows instead of columns) unlike
what we
created in the testbvals
file. I'm also attaching the trac-prep script and the bvals file it
creates within the dmri folder,
along with the original testbvals file that we used in our drmrirc
file.
Thanks so much! We appreciate any help you can give us with this.
Cheers,
-Karuna
INFO: SUBJECTS_DIR is /home/karunas/Desktop/bin/freesurfer/subjects
INFO: Diffusion root is
/home/karunas/Desktop/bin/freesurfer/subjects
Actual FREESURFER_HOME /home/karunas/Desktop/bin/freesurfer
trac-preproc -c
/home/karunas/Desktop/bin/freesurfer/subjects/203/scripts/dmrirc.local
-log
/home/karunas/Desktop/bin/freesurfer/subjects/203/scripts/trac-all.log
-cmd
/home/karunas/Desktop/bin/freesurfer/subjects/203/scripts/trac-all.cmd
#-------------------------------------
/home/karunas/Desktop/bin/freesurfer/bin/trac-preproc
#-------------------------------------
#@# Image corrections Wed Sep 23 18:53:13 PDT 2015
mri_convert /data/bil-mb7/fMRI/MESSI/HC2/testtrac/203/E1S16I1.dcm
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_orig.nii.gz
mri_convert /data/bil-mb7/fMRI/MESSI/HC2/testtrac/203/E1S16I1.dcm
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
reading from
/data/bil-mb7/fMRI/MESSI/HC2/testtrac/203/E1S16I1.dcm...
crypt_gkey = FSre8SL5LUSmU
Getting Series No
INFO: Found 64 files in /data/bil-mb7/fMRI/MESSI/HC2/testtrac/203
INFO: Scanning for Series Number 16
Scanning Directory
INFO: found 35 files in series
INFO: loading series header info.
RunNo = 15
WARNING: Run 1 appears to be truncated
Files Found: 35, Files Expected (lRep+1): 1
FileName
/data/bil-mb7/fMRI/MESSI/HC2/testtrac/203/E1S16I1.dcm
Identification
NumarisVer syngo MR B15
ScannerModel TrioTim
PatientName vinlab_ER_4_8_2011
Date and time
StudyDate 20110408
StudyTime 162622.453000
SeriesTime 180250.125000
AcqTime 175951.002500
Acquisition parameters
PulseSeq *ep_b0
Protocol dti_35dir
PhEncDir COL
EchoNo 1
FlipAngle 90
EchoTime 84
InversionTime -1
RepetitionTime 9000
PhEncFOV 256
ReadoutFOV 256
Image information
RunNo 15
SeriesNo 16
ImageNo 1
NImageRows 1152
NImageCols 1152
NFrames 35
SliceArraylSize 72
IsMosaic 1
ImgPos 1012.3245 1267.7782 -174.7016
VolRes 2.0000 2.0000 2.0000
VolDim 128 128 72
Vc -0.9892 -0.0962 0.1107
Vr 0.0985 -0.9950 0.0158
Vs 0.1086 0.0266 0.9937
VolCenter 0.0000 0.0000 0.0000
TransferSyntaxUID 1.2.840.10008.1.2.2
INFO: sorting.
INFO: (128 128 72), nframes = 35, ismosaic=1
Could not parse NUMARIS version string syngo MR B15
found in dicom tag 18,1020 (len = 3 != 6)
Repetition Time = 9000, TR = 9000 ms
PE Dir COL COL
AutoAlign matrix detected
AutoAlign Matrix ---------------------
0.98919 -0.12584 -0.07527 8.62242;
0.09619 0.94432 -0.31466 -12.16901;
0.11068 0.30402 0.94621 25.01079;
0.00000 0.00000 0.00000 1.00000;
FileName
/data/bil-mb7/fMRI/MESSI/HC2/testtrac/203/E1S16I1.dcm
Identification
NumarisVer syngo MR B15
ScannerModel TrioTim
PatientName vinlab_ER_4_8_2011
Date and time
StudyDate 20110408
StudyTime 162622.453000
SeriesTime 180250.125000
AcqTime 175951.002500
Acquisition parameters
PulseSeq *ep_b0
Protocol dti_35dir
PhEncDir COL
EchoNo 1
FlipAngle 90
EchoTime 84
InversionTime -1
RepetitionTime 9000
PhEncFOV 256
ReadoutFOV 256
Image information
RunNo 15
SeriesNo 16
ImageNo 1
NImageRows 1152
NImageCols 1152
NFrames 35
SliceArraylSize 72
IsMosaic 1
ImgPos 100.2677 150.4042 -45.1647
VolRes 2.0000 2.0000 2.0000
VolDim 128 128 72
Vc -0.9892 -0.0962 0.1107
Vr 0.0985 -0.9950 0.0158
Vs 0.1086 0.0266 0.9937
VolCenter -5.9201 12.6446 42.5760
TransferSyntaxUID 1.2.840.10008.1.2.2
UseSliceScaleFactor 0 (slice 0: 1)
sagrev = 0, correv =0, trarev = 0
Vs = 0.108601 0.0265576 0.993731
INFO: no Siemens slice order reversal detected (good!).
TR=9000.00, TE=84.00, TI=-1.00, flip angle=90.00
i_ras = (-0.989192, -0.0961755, 0.110675)
j_ras = (0.0985118, -0.99501, 0.0158258)
k_ras = (0.108601, 0.0265576, 0.993731)
writing to
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_orig.nii.gz...
crypt_gkey = FSre8SL5LUSmU
mri_probedicom --i
/data/bil-mb7/fMRI/MESSI/HC2/testtrac/203/E1S16I1.dcm
>
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dcminfo.dat
cp testbvecs.txt
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_orig.mghdti.bvecs
cp testbvals.txt
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_orig.mghdti.bvals
mv -f
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/bvecs.tmp
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_orig.mghdti.bvecs
mv -f
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/bvals.tmp
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_orig.mghdti.bvals
flip4fsl
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_orig.nii.gz
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_orig_flip.nii.gz
INFO: input image orientation is LPS
INFO: input image determinant is 8
> fslswapdim
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_orig.nii.gz x
-y z
>
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_orig_flip.nii.gz
> INFO: left-right orientation was flipped by fslswapdim
> fslorient -forceradiological
>
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_orig_flip.nii.gz
> INFO: found
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_orig.mghdti.bvals,
> converting to FSL format
> INFO: found
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_orig.mghdti.bvecs,
> converting to FSL format
> mv -f
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_orig_flip.mghdti.bvecs
> /home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/bvecs
> mv -f
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_orig_flip.mghdti.bvals
> /home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/bvals
> eddy_correct
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_orig_flip.nii.gz
> /home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi.nii.gz 0
> processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0000
> processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0001
> processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0002
> processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0003
> processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0004
> processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0005
> processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0006
> processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0007
> processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0008
> processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0009
> processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0010
> processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0011
> processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0012
> processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0013
> processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0014
> processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0015
> processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0016
> processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0017
> processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0018
> processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0019
> processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0020
> processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0021
> processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0022
> processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0023
> processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0024
> processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0025
> processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0026
> processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0027
> processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0028
> processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0029
> processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0030
> processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0031
> processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0032
> processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0033
> processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0034
> mv -f /home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/bvecs
> /home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/bvecs.norot
> xfmrot
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi.ecclog
> /home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/bvecs.norot
> /home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/bvecs
> ln -sf
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi.nii.gz
> /home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/data.nii.gz
> mri_convert --frame 0 1 2 3 4
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi.nii.gz
> /home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/lowb.nii.gz
> mri_convert --frame 0 1 2 3 4
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi.nii.gz
> /home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/lowb.nii.gz
> $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
> reading from
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi.nii.gz...
> crypt_gkey = FSre8SL5LUSmU
> TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-0.989192, -0.0961755, 0.110675)
> j_ras = (-0.0985118, 0.99501, -0.0158258)
> k_ras = (0.108601, 0.0265576, 0.993731)
> keeping frames 0 1 2 3 4
> writing to
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/lowb.nii.gz...
> crypt_gkey = FSre8SL5LUSmU
> mri_concat --i
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/lowb.nii.gz
--mean
--o
> /home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/lowb.nii.gz
> ninputs = 1
> Checking inputs
> nframestot = 5
> Allocing output
> Done allocing
> nframes = 5
> Computing mean across frames
> Writing to
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/lowb.nii.gz
> bet
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/lowb.nii.gz
>
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/lowb_brain.nii.gz
-m -f 0.3
> mv -f
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/lowb_brain_mask.nii.gz
> /home/karunas/Desktop/bin/freesurfer/subjects/203/dlabel/diff
> #-------------------------------------
> #@# Image quality assessment Wed Sep 23 12:44:54 PDT 2015
> /home/karunas/Desktop/bin/freesurfer/bin/dmri_motion --dwi
>
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_orig.nii.gz
--mat
> /home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi.ecclog
--bval
> /home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/bvals --out
>
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_motion.txt
>
>
> cwd /data/bil-mb7/fMRI/MESSI/HC2/testtrac/203
> cmdline /home/karunas/Desktop/bin/freesurfer/bin/dmri_motion --dwi
>
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_orig.nii.gz
--mat
> /home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi.ecclog
--bval
> /home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/bvals --out
>
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_motion.txt
> sysname Linux
> hostname manas.radiology.ucsf.edu
> machine x86_64
> user karunas
> Output motion measure file:
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_motion.txt
> Input transform file:
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi.ecclog
> Input DWI file:
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_orig.nii.gz
> Input b-value table:
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/bvals
> Low-b image intensity threshold: 100
> Nominal diffusivity: 0.001
> Loading volume-to-baseline affine transformations
> Computing between-volume head motion measures
> INFO: Processed transforms for 35 volumes
> Loading DWI volume series from
>
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_orig.nii.gz
> Loading b-value table from
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/bvals
> ERROR: Could not open
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/bvals for
reading
> Linux manas.radiology.ucsf.edu 2.6.18-406.el5 #1 SMP Fri May 1
10:37:57
EDT 2015 x86_64 x86_64
> x86_64 GNU/Linux
>
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The information in this e-mail is intended only for the person to whom it is
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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.
