[Freesurfer] Pathstat.byvoxel.txt question

2014-07-22 Thread Sarina Sacco 
Hi all freesurfer experts ,
I have a question about the command trac-all-stat-c ,what is the
interpolation that uses?
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Re: [Freesurfer] Pathstat.byvoxel.txt question

2014-07-23 Thread Sarina Sacco 
Thank you for help.
Il 23/lug/2014 10:19 "Anastasia Yendiki"  ha
scritto:

>
> Hi Sarina - It's linear interpolation.
>
> a.y
>
> On Wed, 23 Jul 2014, Sarina Sacco wrote:
>
> >
> > Hi all freesurfer experts ,
> > I have a question about the command trac-all-stat-c ,what is the
> > interpolation that uses?
> >
> >
> >
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> is
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>
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[Freesurfer] trac-all -prep error

2012-03-27 Thread Sarina Sacco 
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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[Freesurfer] trac-all -bedp error

2012-05-21 Thread Sarina Sacco 
Hi, tracula users

 I run the trac-all bedp process and resulted this error:

74 slices processed
 75 slices processed
76 slices processed
 Queuing post processing stage
80 slices processed
 For some reason the bedpostX process DOES NOT appear
 to have successfully completed. Please examine your
 results carefully.

 I look the processed data in dmri.bedpostx,but I don't identify
 the problem. help me plese.
 I run -path process and in this moment not created problem,but is not
terminated.I fear that the information is incomplete.
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