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
Please send email to the freesurfer list and not to me directly. Emails
sent to the freesurfer list are saved in a searchable archive so that
other users can benefit from these pearls of wisdom.
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/
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 <ayend...@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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