11 Oct
2007
11 Oct
'07
2:11 p.m.
Hello,
after I figured out how to prepare the dt_recon command with the correct input (which was a long struggle to find the correct dicom input) I got now stuck as dt_recon always stops before finishing the run with the same error message: brainmask not found I attach the log file with the relevant parts. The complete log and subject dir is available upon request.
Does somebody know whats wrong? I created the complete directory tree under the subjects dir with mksubjdirs. The dicom input was created with unpacksdcmdir -src 02171336/ -targ mri -run 2 dicom dicom 002 after I copied the content of the dicom data directory from cd to disk. And thats exactly the stage where I was stuck a long time as it wasn't obvious to me to prepare dicom data with unpacksdcmdir to dicom format to satisfy dt_recon.
Thanks for any hint or help in advance
Dirk
--
Dirk Dettmering
DV-Koordinator - Klinik für Neurologie
Universitätsklinikum Gießen und Marburg GmbH,
Standort Marburg
Baldingerstraße
D-35043 Marburg
Telefon (+49) 06421 - 286 5354
Telefax (+49) 06421 - 286 5208
Pager 142 69684
E-Mail: dirk.dettmering@med.uni-marburg.de
url: http://www.med.uni-marburg.de
Aufsichtsratsvorsitzender: Wolfgang Pföhler
Geschäftsführung: Gerald Meder (Vors.), Prof. Dr. Werner Seeger (stv.
Vors.), Dr. Hans-Jürgen Hackenberg, Prof. Dr. Martin Hansis,
Dr. Peter Mein, Manfred Wiehl
Sitz der Gesellschaft: Gießen
Amtsgericht Gießen HRB 6384
dt_recon logfile
Do Okt 11 18:09:09 CEST 2007
VERSION $Id: dt_recon,v 1.6.2.2 2007/08/23 19:17:46 greve Exp $
setenv SUBJECTS_DIR /mrt-daten/dt_recon/0001_DTI_RLS2
cd /mrt-daten/dt_recon/0001_DTI_RLS2
/usr/local/freesurfer/bin/dt_recon --i mri/dicom/002/29265430 --o maps --s .
ixneurol247.med.uni-marburg.de
surfer
/usr/local/freesurfer/fsl/bin/eddy_correct
#@#-------------------------------
Converting input
Do Okt 11 18:09:09 CEST 2007
cd /mrt-daten/dt_recon/0001_DTI_RLS2
mri_convert /mrt-daten/dt_recon/0001_DTI_RLS2/mri/dicom/002/29265430 /mrt-daten/dt_recon/0001_DTI_RLS2/maps/dwi.nii
mri_convert /mrt-daten/dt_recon/0001_DTI_RLS2/mri/dicom/002/29265430 /mrt-daten/dt_recon/0001_DTI_RLS2/maps/dwi.nii
$Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $
reading from /mrt-daten/dt_recon/0001_DTI_RLS2/mri/dicom/002/29265430...
Getting Series No
INFO: Found 2103 files in /mrt-daten/dt_recon/0001_DTI_RLS2/mri/dicom/002
INFO: Scanning for Series Number 2
Scanning Directory
INFO: found 2100 files in series
INFO: loading series header info.
RunNo = 1
INFO: sorting.
INFO: (128 128 60), nframes = 35, ismosaic=0
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;
This looks like an MGH DTI volume
MGH DTI SeqPack Info
0 ep_b0#0 0.000000 0
1 ep_b0#1 0.000000 1
2 ep_b0#2 0.000000 2
3 ep_b0#3 0.000000 3
[snip]
#@#-------------------------------
Eddy/Motion Correct
Do Okt 11 18:15:26 CEST 2007
cd /mrt-daten/dt_recon/0001_DTI_RLS2/maps/ectmp
eddy_correct /mrt-daten/dt_recon/0001_DTI_RLS2/maps/dwi.nii /mrt-daten/dt_recon/0001_DTI_RLS2/maps/dwi-ec.nii 0
processing vol0000.nii
processing vol0001.nii
processing vol0002.nii
processing vol0003.nii
processing vol0004.nii
processing vol0005.nii
processing vol0006.nii
processing vol0007.nii
processing vol0008.nii
processing vol0009.nii
processing vol0010.nii
processing vol0011.nii
processing vol0012.nii
processing vol0013.nii
processing vol0014.nii
processing vol0015.nii
processing vol0016.nii
processing vol0017.nii
processing vol0018.nii
processing vol0019.nii
processing vol0020.nii
processing vol0021.nii
processing vol0022.nii
processing vol0023.nii
processing vol0024.nii
processing vol0025.nii
processing vol0026.nii
processing vol0027.nii
processing vol0028.nii
processing vol0029.nii
processing vol0030.nii
processing vol0031.nii
processing vol0032.nii
processing vol0033.nii
processing vol0034.nii
#@#-------------------------------
Fitting Tensors
Do Okt 11 18:57:54 CEST 2007
cd /mrt-daten/dt_recon/0001_DTI_RLS2
mri_glmfit --y /mrt-daten/dt_recon/0001_DTI_RLS2/maps/dwi-ec.nii --glmdir /mrt-daten/dt_recon/0001_DTI_RLS2/maps --dti /mrt-daten/dt_recon/0001_DTI_RLS2/maps/dwi-infodump.dat
$Id: mri_glmfit.c,v 1.138.2.1 2007/09/12 15:38:19 nicks Exp $
cwd /mrt-daten/dt_recon/0001_DTI_RLS2
cmdline mri_glmfit --y /mrt-daten/dt_recon/0001_DTI_RLS2/maps/dwi-ec.nii --glmdir /mrt-daten/dt_recon/0001_DTI_RLS2/maps --dti /mrt-daten/dt_recon/0001_DTI_RLS2/maps/dwi-infodump.dat
sysname Linux
hostname ixneurol247.med.uni-marburg.de
machine i686
user surfer
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y /mrt-daten/dt_recon/0001_DTI_RLS2/maps/dwi-ec.nii
logyflag 1
X /mrt-daten/dt_recon/0001_DTI_RLS2/maps/dwi-infodump.dat
usedti 1
glmdir /mrt-daten/dt_recon/0001_DTI_RLS2/maps
DoFFx 0
Creating output directory /mrt-daten/dt_recon/0001_DTI_RLS2/maps
Loading y from /mrt-daten/dt_recon/0001_DTI_RLS2/maps/dwi-ec.nii
Using DTI
bValue = 1000
nB0 = 5
nDir = 30
GradFile /usr/local/freesurfer/diffusion/mgh-dti-seqpack/gradient_mgh_dti30.gdt
Matrix condition is 27.8204
Pruning voxels by frame.
Found 972044 voxels in mask
Saving mask to /mrt-daten/dt_recon/0001_DTI_RLS2/maps/mask.nii
search space = 9.33162e+06
Computing natural log of input
DOF = 28
Starting fit and test
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
Fit completed in 1.75672 minutes
Writing results
Saving DTI Analysis
Computing fa
Computing ra
Computing vr
Computing adc
Computing ivc
Computing dwisynth
Computing dwires
Computing dwi rvar
mri_glmfit done
#@#-------------------------------
Registration
Do Okt 11 19:02:55 CEST 2007
setenv SUBJECTS_DIR /mrt-daten/dt_recon/0001_DTI_RLS2
cd /mrt-daten/dt_recon/0001_DTI_RLS2
fslregister --s . --mov /mrt-daten/dt_recon/0001_DTI_RLS2/maps/lowb.nii --reg /mrt-daten/dt_recon/0001_DTI_RLS2/maps/register.dat
Log file is /mrt-daten/dt_recon/0001_DTI_RLS2/maps/register.dat.fslregister.log
Do Okt 11 19:02:55 CEST 2007
--s . --mov /mrt-daten/dt_recon/0001_DTI_RLS2/maps/lowb.nii --reg /mrt-daten/dt_recon/0001_DTI_RLS2/maps/register.dat
$Id: fslregister,v 1.16 2007/07/26 16:52:54 greve Exp $
ixneurol247.med.uni-marburg.de
Linux ixneurol247.med.uni-marburg.de 2.6.17-1.2142_FC4smp #1 SMP Tue Jul 11 22:57:02 EDT 2006 i686 i686 i386 GNU/Linux
ERROR: /mrt-daten/dt_recon/0001_DTI_RLS2/./mri/brainmask not found