The argument of --s should be the freesurfer subject (ie, the same as when you run recon-all -s ). If you don't have one, you can use fsaverage.
doug
Dirk Dettmering wrote:
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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer