Hi Sarina - You'll have to specify the list of gradient directions (bvecfile) and b-values (bvalfile), see here for more info: http://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc
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a.y
On Wed, 11 Apr 2012, Sarina Sacco wrote:
Ciao Anastasia ho risolto il problema di FSL,ora l'installazione è corretta,però mi si presenta sempre un errore inerente al bvecs non li trova,potrebbe forse dipendere dai files DICOM che utilizzo? Questo è l'errore: sarina@thunder:/opt/freesurfer/subjects$ trac-all -prep -c $SUBJECTS_DIR/subjects_trac_all/scripts/dmrircFiles/dmrirc_Diff001_F.B. INFO: SUBJECTS_DIR is /opt/freesurfer/subjects/subjects_recon_all INFO: Diffusion root is /opt/freesurfer/subjects/subjects_trac_all Actual FREESURFER_HOME /opt/freesurfer trac-preproc -c /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./scripts/dmrirc.local -log /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./scripts/trac-all.log -cmd /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./scripts/trac-all.cmd #------------------------------------- /opt/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Wed Apr 11 18:01:15 CEST 2012 mri_convert /opt/freesurfer/subjects/subjects_trac_all//Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz mri_convert /opt/freesurfer/subjects/subjects_trac_all//Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /opt/freesurfer/subjects/subjects_trac_all//Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm... Starting DICOMRead2() dcmfile = /opt/freesurfer/subjects/subjects_trac_all//Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm dcmdir = /opt/freesurfer/subjects/subjects_trac_all//Diff001_F.B./orig Ref Series No = 7 Found 2242 files, checking for dicoms Found 2240 dicom files in series. First Sorting Computing Slice Direction Vs: 0.029 0.321 1.9739 Vs: 0.0144997 0.160497 0.98693 Second Sorting Counting frames nframes = 28 nslices = 80 ndcmfiles = 2240 PE Dir = COL (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data TR=10050.00, TE=87.10, TI=0.00, flip angle=90.00 i_ras = (-0.999859, -0.0058291, -0.0157782) j_ras = (0.00830111, -0.987041, -0.160255) k_ras = (-0.0144997, -0.160497, 0.98693) writing to /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz... mri_probedicom --i /opt/freesurfer/subjects/subjects_trac_all//Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm
/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dcminfo.dat
flip4fsl /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 2 fslswapdim /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz x -y z /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.nii.gz mv -f /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.mghdti.bvecs /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/bvecs mv: cannot stat `/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.mghdti.bvecs': No such file or directory Linux thunder 2.6.38-8-generic #42-Ubuntu SMP Mon Apr 11 03:31:24 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Wed Apr 11 18:03:33 CEST 2012
2012/3/27 Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu:
Ciao Sarina - The problem is here "fslorient: Command not found." You have to make sure that FSL is properly installed and the FSL executables are in your path, as trac-all calls a few of them.
Hope this helps, a.y
On Tue, 27 Mar 2012, Sarina Sacco wrote:
quando avvio il trac-all (relase FS5.1) mi crea questo errore:
/opt/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Tue Mar 27 11:17:27 CEST 2012 mri_convert /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm
/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz mri_convert /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm
/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm... Starting DICOMRead2() dcmfile = /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm dcmdir = /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig Ref Series No = 7 Found 2242 files, checking for dicoms Found 2240 dicom files in series. First Sorting Computing Slice Direction Vs: 0.029 0.321 1.9739 Vs: 0.0144997 0.160497 0.98693 Second Sorting Counting frames nframes = 28 nslices = 80 ndcmfiles = 2240 PE Dir = COL (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data TR=10050.00, TE=87.10, TI=0.00, flip angle=90.00 i_ras = (-0.999859, -0.0058291, -0.0157782) j_ras = (0.00830111, -0.987041, -0.160255) k_ras = (-0.0144997, -0.160497, 0.98693) writing to /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz... mri_probedicom --i
/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm
/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dcminfo.dat
flip4fsl /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz
/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 2 fslswapdim /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz x -y z /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.nii.gz fslorient -forceradiological
/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.nii.gz fslorient: Command not found. mv -f /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.mghdti.bvecs /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/bvecs mv: cannot stat
`/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.mghdti.bvecs': No such file or directory Linux thunder 2.6.38-8-generic #42-Ubuntu SMP Mon Apr 11 03:31:24 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Tue Mar 27 11:18:21 CEST 2012
Non riesco a capire perchè,da cosa può dipendere?
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Anastasia Yendiki