subject:"Re\: \[Freesurfer\] error while running dt\-recon all"

Re: [Freesurfer] error while running dt-recon all

2016-03-20 Thread Jasmin Alves

breaksw

breaksw

end

end

while ( $#argv != 0 )

while ( 5 != 0 )

set flag = $argv[1] ; shift ;

set flag = --i

shift

switch ( $flag )

switch ( --i )

if ( $#argv < 1 ) goto arg1err ;

if ( 4 < 1 ) goto arg1err

set InputVol = "$argv[1]" ; shift ;

set InputVol = DTI.nii.gz

shift

if ( ! -e "$InputVol" ) then

if ( ! -e DTI.nii.gz ) then

if ( ! -r "$InputVol" ) then

if ( ! -r DTI.nii.gz ) then

set InVolDir = `dirname  "$InputVol"` ;

set InVolDir = `dirname  "$InputVol"`

dirname DTI.nii.gz

set InVolBase = `basename "$InputVol"` ;

set InVolBase = `basename "$InputVol"`

basename DTI.nii.gz

pushd $InVolDir > /dev/null

pushd .

set InVolDir = `pwd` ;

set InVolDir = `pwd`

pwd

popd > /dev/null

popd

set InputVol = "$InVolDir/$InVolBase" ;

set InputVol = /Users/jasminalves/Desktop/data/40/DTI.nii.gz

set DoConvertInput = 1 ;

set DoConvertInput = 1

breaksw

breaksw

end

end

while ( $#argv != 0 )

while ( 3 != 0 )

set flag = $argv[1] ; shift ;

set flag = --s

shift

switch ( $flag )

switch ( --s )

if ( $#argv < 1 ) goto arg1err ;

if ( 2 < 1 ) goto arg1err

set subject = $argv[1] ; shift ;

set subject = 40

shift

set subject = `basename $subject` ;

set subject = `basename $subject`

basename 40

breaksw

breaksw

end

end

while ( $#argv != 0 )

while ( 1 != 0 )

set flag = $argv[1] ; shift ;

set flag = --o

shift

switch ( $flag )

switch ( --o )

if ( $#argv < 1 ) goto arg1err ;

if ( 0 < 1 ) goto arg1err

goto arg1err

echo "ERROR: flag $flag requires one argument"

echo ERROR: flag --o requires one argument

ERROR: flag --o requires one argument

exit 1

exit 1


The second part of the command "/Users/jasminalves/Desktop/data/FREESURFER/40
|& tee dng.log" won't work, but I sent you the output from the first part.

On Wed, Mar 16, 2016 at 8:50 AM, Douglas N Greve 
wrote:

>
> No, I mean that when the command is run, it will print a lot of text to
> the screen. I want to know what that text is. You can run the following
> command and send me the dng.log file
>
> dt_recon --debug --i DTI.nii.gz --s 40 --o
> /Users/jasminalves/Desktop/data/FREESURFER/40 |& tee dng.log
>
>
>
>
>
> On 03/16/2016 11:35 AM, Jasmin Alves wrote:
> > Do you mean, what ends up happening? I have attached a screen shot of
> > what files are made.
> >
> >
> >
> > On Wed, Mar 16, 2016 at 7:31 AM, Douglas Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> > Can you send me what dt_recon prints to the screen when your run
> > the command below?
> >
> >
> > On 3/15/16 11:40 PM, Jasmin Alves wrote:
> >>
> >> Jasmins-MacBook-Pro:40 jasminalves$ dt_recon --i DTI.nii.gz --s
> >> 40 --o /Users/jasminalves/Desktop/data/FREESURFER/40
> >>
> >> INFO: SUBJECTS_DIR is /Users/jasminalves/Desktop/data/FREESURFER/
> >>
> >> dt_recon logfile
> >>
> >> Tue Mar 15 20:37:35 PDT 2016
> >>
> >> VERSION $Id: dt_recon,v 1.15 2011/01/25 21:53:04 greve Exp $
> >>
> >> setenv SUBJECTS_DIR /Users/jasminalves/Desktop/data/FREESURFER/
> >>
> >> cd /Users/jasminalves/Desktop/data/40
> >>
> >> /Applications/freesurfer/bin/dt_recon --i DTI.nii.gz --s 40 --o
> >> /Users/jasminalves/Desktop/data/FREESURFER/40
> >>
> >> Jasmins-MacBook-Pro.local
> >>
> >> jasminalves
> >>
> >> /Applications/Utilities/fsl/bin/eddy_correct
> >>
> >> ECRefTP 0
> >>
> >> #@#---
> >>
> >> Converting input
> >>
> >> Tue Mar 15 20:37:35 PDT 2016
> >>
> >> cd /Users/jasminalves/Desktop/data/40
> >>
> >> mri_convert /Users/jasminalves/Desktop/data/40/DTI.nii.gz
> >> /Users/jasminalves/Desktop/data/FREESURFER/40/dwi.nii
> >>
> >> mri_convert /Users/jasminalves/Desktop/data/40/DTI.nii.gz
> >> /Users/jasminalves/Desktop/data/FREESURFER/40/dwi.nii
> >>
> >> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> >>
> >> reading from /Users/jasminalves/Desktop/data/40/DTI.nii.gz...
> >>
> >> TR=8100.00, TE=0.00, TI=0.00, flip angle=0.00
> >>
> >> i_ras = (-0.29, 0.0116015, -0.00282784)
> >>
> >> j_ras = (0.0115984, 0.32, 0.00109136)
> >>
> >> k_ras = (-0.00284031, -0.00105848, 0.95)
> >>
> >> writing to /Users/jasminalves/Desktop/data/FREESURFER/40/dwi.nii...
> >>
> >> cd /Users/jasminalves/Desktop/data/40
> >>
> >> mri_probedicom --i /Users/jasminalves/Desktop/data/40/DTI.nii.gz
> >>
> >> Jasmins-MacBook-Pro:40 jasminalves$
> >>
> >>
> >>
> >> On Tue, Mar 15, 2016 at 12:34 PM, Douglas N Greve
> >> mailto:gr...@nmr.mgh.harvard.edu>>
> wrote:
> >>
> >> Can you send the full terminal output from when you run
> >> dt_recon with
> >> the nifti as input?
> >>
> >> On 03/15/2016 03:07 PM, Jasmin Alves wrote:
> >> > How was DTI.nii.gz created? DTI.nii.gz was converted from
> >> the raw
> >> > dicom data using dcm2nii.
> >> >
> >> > Response for: "What happens if you run mri_info DTI.nii.gz"
> >> >
> >>

Re: [Freesurfer] error while running dt-recon all

2016-03-19 Thread Douglas N Greve


the command must be the entire line and all on one line

dt_recon --debug --i DTI.nii.gz --s 40 --o 
/Users/jasminalves/Desktop/data/FREESURFER/40 |& tee dng.log



On 03/16/2016 11:56 AM, Jasmin Alves wrote:
>
> breaksw
>
> breaksw
>
> end
>
> end
>
> while ( $#argv != 0 )
>
> while ( 5 != 0 )
>
> set flag = $argv[1] ; shift ;
>
> set flag = --i
>
> shift
>
> switch ( $flag )
>
> switch ( --i )
>
> if ( $#argv < 1 ) goto arg1err ;
>
> if ( 4 < 1 ) goto arg1err
>
> set InputVol = "$argv[1]" ; shift ;
>
> set InputVol = DTI.nii.gz
>
> shift
>
> if ( ! -e "$InputVol" ) then
>
> if ( ! -e DTI.nii.gz ) then
>
> if ( ! -r "$InputVol" ) then
>
> if ( ! -r DTI.nii.gz ) then
>
> set InVolDir = `dirname  "$InputVol"` ;
>
> set InVolDir = `dirname  "$InputVol"`
>
> dirname DTI.nii.gz
>
> set InVolBase = `basename "$InputVol"` ;
>
> set InVolBase = `basename "$InputVol"`
>
> basename DTI.nii.gz
>
> pushd $InVolDir > /dev/null
>
> pushd .
>
> set InVolDir = `pwd` ;
>
> set InVolDir = `pwd`
>
> pwd
>
> popd > /dev/null
>
> popd
>
> set InputVol = "$InVolDir/$InVolBase" ;
>
> set InputVol = /Users/jasminalves/Desktop/data/40/DTI.nii.gz
>
> set DoConvertInput = 1 ;
>
> set DoConvertInput = 1
>
> breaksw
>
> breaksw
>
> end
>
> end
>
> while ( $#argv != 0 )
>
> while ( 3 != 0 )
>
> set flag = $argv[1] ; shift ;
>
> set flag = --s
>
> shift
>
> switch ( $flag )
>
> switch ( --s )
>
> if ( $#argv < 1 ) goto arg1err ;
>
> if ( 2 < 1 ) goto arg1err
>
> set subject = $argv[1] ; shift ;
>
> set subject = 40
>
> shift
>
> set subject = `basename $subject` ;
>
> set subject = `basename $subject`
>
> basename 40
>
> breaksw
>
> breaksw
>
> end
>
> end
>
> while ( $#argv != 0 )
>
> while ( 1 != 0 )
>
> set flag = $argv[1] ; shift ;
>
> set flag = --o
>
> shift
>
> switch ( $flag )
>
> switch ( --o )
>
> if ( $#argv < 1 ) goto arg1err ;
>
> if ( 0 < 1 ) goto arg1err
>
> goto arg1err
>
> echo "ERROR: flag $flag requires one argument"
>
> echo ERROR: flag --o requires one argument
>
> ERROR: flag --o requires one argument
>
> exit 1
>
> exit 1
>
>
> The second part of the command 
> "/Users/jasminalves/Desktop/data/FREESURFER/40 |& tee dng.log" won't 
> work, but I sent you the output from the first part.
>
>
> On Wed, Mar 16, 2016 at 8:50 AM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
> No, I mean that when the command is run, it will print a lot of
> text to
> the screen. I want to know what that text is. You can run the
> following
> command and send me the dng.log file
>
> dt_recon --debug --i DTI.nii.gz --s 40 --o
> /Users/jasminalves/Desktop/data/FREESURFER/40 |& tee dng.log
>
>
>
>
>
> On 03/16/2016 11:35 AM, Jasmin Alves wrote:
> > Do you mean, what ends up happening? I have attached a screen
> shot of
> > what files are made.
> >
> >
> >
> > On Wed, Mar 16, 2016 at 7:31 AM, Douglas Greve
> > mailto:gr...@nmr.mgh.harvard.edu>
>  >> wrote:
> >
> > Can you send me what dt_recon prints to the screen when your run
> > the command below?
> >
> >
> > On 3/15/16 11:40 PM, Jasmin Alves wrote:
> >>
> >> Jasmins-MacBook-Pro:40 jasminalves$ dt_recon --i DTI.nii.gz --s
> >> 40 --o /Users/jasminalves/Desktop/data/FREESURFER/40
> >>
> >> INFO: SUBJECTS_DIR is
> /Users/jasminalves/Desktop/data/FREESURFER/
> >>
> >> dt_recon logfile
> >>
> >> Tue Mar 15 20:37:35 PDT 2016
> >>
> >> VERSION $Id: dt_recon,v 1.15 2011/01/25 21:53:04 greve Exp $
> >>
> >> setenv SUBJECTS_DIR /Users/jasminalves/Desktop/data/FREESURFER/
> >>
> >> cd /Users/jasminalves/Desktop/data/40
> >>
> >> /Applications/freesurfer/bin/dt_recon --i DTI.nii.gz --s 40 --o
> >>  /Users/jasminalves/Desktop/data/FREESURFER/40
> >>
> >> Jasmins-MacBook-Pro.local
> >>
> >> jasminalves
> >>
> >>  /Applications/Utilities/fsl/bin/eddy_correct
> >>
> >> ECRefTP 0
> >>
> >> #@#---
> >>
> >> Converting input
> >>
> >> Tue Mar 15 20:37:35 PDT 2016
> >>
> >> cd /Users/jasminalves/Desktop/data/40
> >>
> >> mri_convert /Users/jasminalves/Desktop/data/40/DTI.nii.gz
> >>  /Users/jasminalves/Desktop/data/FREESURFER/40/dwi.nii
> >>
> >> mri_convert /Users/jasminalves/Desktop/data/40/DTI.nii.gz
> >>  /Users/jasminalves/Desktop/data/FREESURFER/40/dwi.nii
> >>
> >> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter
> Exp $
> >>
> >> reading from /Users/jasminalves/Desktop/data/40/DTI.nii.gz...
> >>
> >> TR=8100.00, TE=0.00, TI=0.00, flip angle=0.00
> >>
> >> i_ras = (-0.29, 0.0116015, -0.00282784)
> >>
> >> j_ras = (0.0115984, 0.32, 0.00109136)
> >>
> >> k_r

Re: [Freesurfer] error while running dt-recon all

2016-03-19 Thread Jasmin Alves

Do you mean, what ends up happening? I have attached a screen shot of what
files are made.



On Wed, Mar 16, 2016 at 7:31 AM, Douglas Greve 
wrote:

> Can you send me what dt_recon prints to the screen when your run the
> command below?
>
>
> On 3/15/16 11:40 PM, Jasmin Alves wrote:
>
> Jasmins-MacBook-Pro:40 jasminalves$ dt_recon --i DTI.nii.gz --s 40 --o
> /Users/jasminalves/Desktop/data/FREESURFER/40
>
> INFO: SUBJECTS_DIR is /Users/jasminalves/Desktop/data/FREESURFER/
>
> dt_recon logfile
>
> Tue Mar 15 20:37:35 PDT 2016
>
> VERSION $Id: dt_recon,v 1.15 2011/01/25 21:53:04 greve Exp $
>
> setenv SUBJECTS_DIR /Users/jasminalves/Desktop/data/FREESURFER/
>
> cd /Users/jasminalves/Desktop/data/40
>
> /Applications/freesurfer/bin/dt_recon --i DTI.nii.gz --s 40 --o
> /Users/jasminalves/Desktop/data/FREESURFER/40
>
> Jasmins-MacBook-Pro.local
>
> jasminalves
>
> /Applications/Utilities/fsl/bin/eddy_correct
>
> ECRefTP 0
>
> #@#---
>
> Converting input
>
> Tue Mar 15 20:37:35 PDT 2016
>
> cd /Users/jasminalves/Desktop/data/40
>
> mri_convert /Users/jasminalves/Desktop/data/40/DTI.nii.gz
> /Users/jasminalves/Desktop/data/FREESURFER/40/dwi.nii
>
> mri_convert /Users/jasminalves/Desktop/data/40/DTI.nii.gz
> /Users/jasminalves/Desktop/data/FREESURFER/40/dwi.nii
>
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>
> reading from /Users/jasminalves/Desktop/data/40/DTI.nii.gz...
>
> TR=8100.00, TE=0.00, TI=0.00, flip angle=0.00
>
> i_ras = (-0.29, 0.0116015, -0.00282784)
>
> j_ras = (0.0115984, 0.32, 0.00109136)
>
> k_ras = (-0.00284031, -0.00105848, 0.95)
>
> writing to /Users/jasminalves/Desktop/data/FREESURFER/40/dwi.nii...
>
> cd /Users/jasminalves/Desktop/data/40
>
> mri_probedicom --i /Users/jasminalves/Desktop/data/40/DTI.nii.gz
>
> Jasmins-MacBook-Pro:40 jasminalves$
>
>
>
> On Tue, Mar 15, 2016 at 12:34 PM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>> Can you send the full terminal output from when you run dt_recon with
>> the nifti as input?
>>
>> On 03/15/2016 03:07 PM, Jasmin Alves wrote:
>> > How was DTI.nii.gz created? DTI.nii.gz was converted from the raw
>> > dicom data using dcm2nii.
>> >
>> > Response for: "What happens if you run mri_info DTI.nii.gz"
>> >
>> > Volume information for DTI.nii.gz
>> >
>> >   type: nii
>> >
>> > dimensions: 128 x 128 x 70 x 65
>> >
>> >voxel sizes: 2., 2., 2.
>> >
>> >   type: FLOAT (3)
>> >
>> >fov: 256.000
>> >
>> >dof: 0
>> >
>> > xstart: -128.0, xend: 128.0
>> >
>> > ystart: -128.0, yend: 128.0
>> >
>> > zstart: -70.0, zend: 70.0
>> >
>> > TR: 8100.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip
>> > angle: 0.00 degrees
>> >
>> >nframes: 65
>> >
>> >PhEncDir: UNKNOWN
>> >
>> > ras xform present
>> >
>> > xform info: x_r =  -0., y_r =   0.0116, z_r =  -0.0028, c_r =
>> >   -0.4290
>> >
>> >   : x_a =   0.0116, y_a =   0., z_a =  -0.0011, c_a =
>> > 4.1548
>> >
>> >   : x_s =  -0.0028, y_s =   0.0011, z_s =   1., c_s =
>> >   30.9622
>> >
>> > Orientation   : LAS
>> >
>> > Primary Slice Direction: axial
>> >
>> > voxel to ras transform:
>> >
>> >-1.   0.0232 -0.0057   126.2761
>> >
>> > 0.0232   1. -0.0021  -125.2474
>> >
>> >-0.0057   0.0022 2.   -38.8153
>> >
>> > 0.   0. 0. 1.
>> >
>> > voxel-to-ras determinant -8
>> >
>> > ras to voxel transform:
>> >
>> >-0.5000   0.0058 -0.001463.8052
>> >
>> > 0.0058   0.5000 0.000561.9083
>> >
>> >-0.0014  -0.0005 0.500019.5206
>> >
>> > 0.   0. 0. 1.
>> >
>> >
>> > On Tue, Mar 15, 2016 at 11:25 AM, Douglas N Greve
>> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>> >
>> >
>> > How was DTI.nii.gz created? What happens if you run
>> > mri_info DTI.nii.gz
>> >
>> > If the DICOM is a siemens dicom but has been stripped of special
>> > siemens
>> > info, then we cannot unpack it
>> >
>> >
>> > On 03/15/2016 02:02 PM, Jasmin Alves wrote:
>> > >
>> > > Still get the same error:
>> > >
>> > > WARNING: file /Users/jasminalves/Desktop/data/40/00010001 does not
>> > > contain a Siemens ASCII header
>> > >
>> > > has this file been anonymized?
>> > >
>> > > ERROR: cannot unpack mosiacs without ASCII header
>> > >
>> > >
>> > > The error I get when running in nifti format is actually found
>> > in the
>> > > log file.
>> > >
>> > >  ERROR: /Users/jasminalves/Desktop/data/40/DTI.nii.gz is not a
>> dicom
>> > > file or some other problem
>> > >
>> > >
>> > >
>> > >
>> > > On Tue, Mar 15, 2016 at 9:01 AM, Douglas N Greve
>> > > mailto:gr...@nmr.mgh.harvard.edu>
>> > > > gr...@n

Re: [Freesurfer] error while running dt-recon all

2016-03-19 Thread Douglas Greve

Can you send me what dt_recon prints to the screen when your run the 
command below?


On 3/15/16 11:40 PM, Jasmin Alves wrote:


Jasmins-MacBook-Pro:40 jasminalves$ dt_recon --i DTI.nii.gz --s 40 --o 
/Users/jasminalves/Desktop/data/FREESURFER/40


INFO: SUBJECTS_DIR is /Users/jasminalves/Desktop/data/FREESURFER/

dt_recon logfile

Tue Mar 15 20:37:35 PDT 2016

VERSION $Id: dt_recon,v 1.15 2011/01/25 21:53:04 greve Exp $

setenv SUBJECTS_DIR /Users/jasminalves/Desktop/data/FREESURFER/

cd /Users/jasminalves/Desktop/data/40

/Applications/freesurfer/bin/dt_recon --i DTI.nii.gz --s 40 --o 
/Users/jasminalves/Desktop/data/FREESURFER/40


Jasmins-MacBook-Pro.local

jasminalves

/Applications/Utilities/fsl/bin/eddy_correct

ECRefTP 0

#@#---

Converting input

Tue Mar 15 20:37:35 PDT 2016

cd /Users/jasminalves/Desktop/data/40

mri_convert /Users/jasminalves/Desktop/data/40/DTI.nii.gz 
/Users/jasminalves/Desktop/data/FREESURFER/40/dwi.nii


mri_convert /Users/jasminalves/Desktop/data/40/DTI.nii.gz 
/Users/jasminalves/Desktop/data/FREESURFER/40/dwi.nii


$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading from /Users/jasminalves/Desktop/data/40/DTI.nii.gz...

TR=8100.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-0.29, 0.0116015, -0.00282784)

j_ras = (0.0115984, 0.32, 0.00109136)

k_ras = (-0.00284031, -0.00105848, 0.95)

writing to /Users/jasminalves/Desktop/data/FREESURFER/40/dwi.nii...

cd /Users/jasminalves/Desktop/data/40

mri_probedicom --i /Users/jasminalves/Desktop/data/40/DTI.nii.gz

Jasmins-MacBook-Pro:40 jasminalves$



On Tue, Mar 15, 2016 at 12:34 PM, Douglas N Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:


Can you send the full terminal output from when you run dt_recon with
the nifti as input?

On 03/15/2016 03:07 PM, Jasmin Alves wrote:
> How was DTI.nii.gz created? DTI.nii.gz was converted from the raw
> dicom data using dcm2nii.
>
> Response for: "What happens if you run mri_info DTI.nii.gz"
>
> Volume information for DTI.nii.gz
>
>   type: nii
>
> dimensions: 128 x 128 x 70 x 65
>
>voxel sizes: 2., 2., 2.
>
>   type: FLOAT (3)
>
>fov: 256.000
>
>dof: 0
>
> xstart: -128.0, xend: 128.0
>
> ystart: -128.0, yend: 128.0
>
> zstart: -70.0, zend: 70.0
>
> TR: 8100.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip
> angle: 0.00 degrees
>
>nframes: 65
>
>PhEncDir: UNKNOWN
>
> ras xform present
>
> xform info: x_r =  -0., y_r =   0.0116, z_r =  -0.0028,
c_r =
>   -0.4290
>
>   : x_a =   0.0116, y_a =   0., z_a =  -0.0011,
c_a =
> 4.1548
>
>   : x_s =  -0.0028, y_s =   0.0011, z_s =   1.,
c_s =
>   30.9622
>
> Orientation   : LAS
>
> Primary Slice Direction: axial
>
> voxel to ras transform:
>
>-1.   0.0232 -0.0057   126.2761
>
> 0.0232   1. -0.0021  -125.2474
>
>-0.0057   0.0022 2.   -38.8153
>
> 0.   0. 0. 1.
>
> voxel-to-ras determinant -8
>
> ras to voxel transform:
>
>-0.5000   0.0058 -0.001463.8052
>
> 0.0058   0.5000 0.000561.9083
>
>-0.0014  -0.0005 0.500019.5206
>
> 0.   0. 0. 1.
>
>
> On Tue, Mar 15, 2016 at 11:25 AM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>
>> wrote:
>
>
> How was DTI.nii.gz created? What happens if you run
> mri_info DTI.nii.gz
>
> If the DICOM is a siemens dicom but has been stripped of special
> siemens
> info, then we cannot unpack it
>
>
> On 03/15/2016 02:02 PM, Jasmin Alves wrote:
> >
> > Still get the same error:
> >
> > WARNING: file /Users/jasminalves/Desktop/data/40/00010001
does not
> > contain a Siemens ASCII header
> >
> > has this file been anonymized?
> >
> > ERROR: cannot unpack mosiacs without ASCII header
> >
> >
> > The error I get when running in nifti format is actually found
> in the
> > log file.
> >
> >  ERROR: /Users/jasminalves/Desktop/data/40/DTI.nii.gz is
not a dicom
> > file or some other problem
> >
> >
> >
> >
> > On Tue, Mar 15, 2016 at 9:01 AM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>
>
>

Re: [Freesurfer] error while running dt-recon all

2016-03-19 Thread Douglas N Greve


No, I mean that when the command is run, it will print a lot of text to 
the screen. I want to know what that text is. You can run the following 
command and send me the dng.log file

dt_recon --debug --i DTI.nii.gz --s 40 --o 
/Users/jasminalves/Desktop/data/FREESURFER/40 |& tee dng.log





On 03/16/2016 11:35 AM, Jasmin Alves wrote:
> Do you mean, what ends up happening? I have attached a screen shot of 
> what files are made.
>
>
>
> On Wed, Mar 16, 2016 at 7:31 AM, Douglas Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> Can you send me what dt_recon prints to the screen when your run
> the command below?
>
>
> On 3/15/16 11:40 PM, Jasmin Alves wrote:
>>
>> Jasmins-MacBook-Pro:40 jasminalves$ dt_recon --i DTI.nii.gz --s
>> 40 --o /Users/jasminalves/Desktop/data/FREESURFER/40
>>
>> INFO: SUBJECTS_DIR is /Users/jasminalves/Desktop/data/FREESURFER/
>>
>> dt_recon logfile
>>
>> Tue Mar 15 20:37:35 PDT 2016
>>
>> VERSION $Id: dt_recon,v 1.15 2011/01/25 21:53:04 greve Exp $
>>
>> setenv SUBJECTS_DIR /Users/jasminalves/Desktop/data/FREESURFER/
>>
>> cd /Users/jasminalves/Desktop/data/40
>>
>> /Applications/freesurfer/bin/dt_recon --i DTI.nii.gz --s 40 --o
>> /Users/jasminalves/Desktop/data/FREESURFER/40
>>
>> Jasmins-MacBook-Pro.local
>>
>> jasminalves
>>
>> /Applications/Utilities/fsl/bin/eddy_correct
>>
>> ECRefTP 0
>>
>> #@#---
>>
>> Converting input
>>
>> Tue Mar 15 20:37:35 PDT 2016
>>
>> cd /Users/jasminalves/Desktop/data/40
>>
>> mri_convert /Users/jasminalves/Desktop/data/40/DTI.nii.gz
>> /Users/jasminalves/Desktop/data/FREESURFER/40/dwi.nii
>>
>> mri_convert /Users/jasminalves/Desktop/data/40/DTI.nii.gz
>> /Users/jasminalves/Desktop/data/FREESURFER/40/dwi.nii
>>
>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>>
>> reading from /Users/jasminalves/Desktop/data/40/DTI.nii.gz...
>>
>> TR=8100.00, TE=0.00, TI=0.00, flip angle=0.00
>>
>> i_ras = (-0.29, 0.0116015, -0.00282784)
>>
>> j_ras = (0.0115984, 0.32, 0.00109136)
>>
>> k_ras = (-0.00284031, -0.00105848, 0.95)
>>
>> writing to /Users/jasminalves/Desktop/data/FREESURFER/40/dwi.nii...
>>
>> cd /Users/jasminalves/Desktop/data/40
>>
>> mri_probedicom --i /Users/jasminalves/Desktop/data/40/DTI.nii.gz
>>
>> Jasmins-MacBook-Pro:40 jasminalves$
>>
>>
>>
>> On Tue, Mar 15, 2016 at 12:34 PM, Douglas N Greve
>> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>>
>> Can you send the full terminal output from when you run
>> dt_recon with
>> the nifti as input?
>>
>> On 03/15/2016 03:07 PM, Jasmin Alves wrote:
>> > How was DTI.nii.gz created? DTI.nii.gz was converted from
>> the raw
>> > dicom data using dcm2nii.
>> >
>> > Response for: "What happens if you run mri_info DTI.nii.gz"
>> >
>> > Volume information for DTI.nii.gz
>> >
>> >   type: nii
>> >
>> > dimensions: 128 x 128 x 70 x 65
>> >
>> >voxel sizes: 2., 2., 2.
>> >
>> >   type: FLOAT (3)
>> >
>> >fov: 256.000
>> >
>> >dof: 0
>> >
>> > xstart: -128.0, xend: 128.0
>> >
>> > ystart: -128.0, yend: 128.0
>> >
>> > zstart: -70.0, zend: 70.0
>> >
>> > TR: 8100.00 msec, TE: 0.00 msec, TI: 0.00 msec,
>> flip
>> > angle: 0.00 degrees
>> >
>> >nframes: 65
>> >
>> >PhEncDir: UNKNOWN
>> >
>> > ras xform present
>> >
>> > xform info: x_r =  -0., y_r =   0.0116, z_r = 
>> -0.0028, c_r =
>> >   -0.4290
>> >
>> >   : x_a =   0.0116, y_a =   0., z_a = 
>> -0.0011, c_a =
>> > 4.1548
>> >
>> >   : x_s =  -0.0028, y_s =   0.0011, z_s = 
>>  1., c_s =
>> >   30.9622
>> >
>> > Orientation   : LAS
>> >
>> > Primary Slice Direction: axial
>> >
>> > voxel to ras transform:
>> >
>> >-1.   0.0232 -0.0057   126.2761
>> >
>> > 0.0232   1. -0.0021  -125.2474
>> >
>> >-0.0057   0.0022 2.   -38.8153
>> >
>> > 0.   0. 0. 1.
>> >
>> > voxel-to-ras determinant -8
>> >
>> > ras to voxel transform:
>> >
>> >-0.5000   0.0058 -0.001463.8052
>> >
>> > 0.0058   0.5000 0.000561.9083
>> >
>> >-0.0014  -0.0005 0.500019.5206
>> >
>>

Re: [Freesurfer] error while running dt-recon all

2016-03-15 Thread Jasmin Alves

Jasmins-MacBook-Pro:40 jasminalves$ dt_recon --i DTI.nii.gz --s 40 --o
/Users/jasminalves/Desktop/data/FREESURFER/40

INFO: SUBJECTS_DIR is /Users/jasminalves/Desktop/data/FREESURFER/

dt_recon logfile

Tue Mar 15 20:37:35 PDT 2016

VERSION $Id: dt_recon,v 1.15 2011/01/25 21:53:04 greve Exp $

setenv SUBJECTS_DIR /Users/jasminalves/Desktop/data/FREESURFER/

cd /Users/jasminalves/Desktop/data/40

/Applications/freesurfer/bin/dt_recon --i DTI.nii.gz --s 40 --o
/Users/jasminalves/Desktop/data/FREESURFER/40

Jasmins-MacBook-Pro.local

jasminalves

/Applications/Utilities/fsl/bin/eddy_correct

ECRefTP 0

#@#---

Converting input

Tue Mar 15 20:37:35 PDT 2016

cd /Users/jasminalves/Desktop/data/40

mri_convert /Users/jasminalves/Desktop/data/40/DTI.nii.gz
/Users/jasminalves/Desktop/data/FREESURFER/40/dwi.nii

mri_convert /Users/jasminalves/Desktop/data/40/DTI.nii.gz
/Users/jasminalves/Desktop/data/FREESURFER/40/dwi.nii

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading from /Users/jasminalves/Desktop/data/40/DTI.nii.gz...

TR=8100.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-0.29, 0.0116015, -0.00282784)

j_ras = (0.0115984, 0.32, 0.00109136)

k_ras = (-0.00284031, -0.00105848, 0.95)

writing to /Users/jasminalves/Desktop/data/FREESURFER/40/dwi.nii...

cd /Users/jasminalves/Desktop/data/40

mri_probedicom --i /Users/jasminalves/Desktop/data/40/DTI.nii.gz

Jasmins-MacBook-Pro:40 jasminalves$



On Tue, Mar 15, 2016 at 12:34 PM, Douglas N Greve  wrote:

> Can you send the full terminal output from when you run dt_recon with
> the nifti as input?
>
> On 03/15/2016 03:07 PM, Jasmin Alves wrote:
> > How was DTI.nii.gz created? DTI.nii.gz was converted from the raw
> > dicom data using dcm2nii.
> >
> > Response for: "What happens if you run mri_info DTI.nii.gz"
> >
> > Volume information for DTI.nii.gz
> >
> >   type: nii
> >
> > dimensions: 128 x 128 x 70 x 65
> >
> >voxel sizes: 2., 2., 2.
> >
> >   type: FLOAT (3)
> >
> >fov: 256.000
> >
> >dof: 0
> >
> > xstart: -128.0, xend: 128.0
> >
> > ystart: -128.0, yend: 128.0
> >
> > zstart: -70.0, zend: 70.0
> >
> > TR: 8100.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip
> > angle: 0.00 degrees
> >
> >nframes: 65
> >
> >PhEncDir: UNKNOWN
> >
> > ras xform present
> >
> > xform info: x_r =  -0., y_r =   0.0116, z_r =  -0.0028, c_r =
> >   -0.4290
> >
> >   : x_a =   0.0116, y_a =   0., z_a =  -0.0011, c_a =
> > 4.1548
> >
> >   : x_s =  -0.0028, y_s =   0.0011, z_s =   1., c_s =
> >   30.9622
> >
> > Orientation   : LAS
> >
> > Primary Slice Direction: axial
> >
> > voxel to ras transform:
> >
> >-1.   0.0232 -0.0057   126.2761
> >
> > 0.0232   1. -0.0021  -125.2474
> >
> >-0.0057   0.0022 2.   -38.8153
> >
> > 0.   0. 0. 1.
> >
> > voxel-to-ras determinant -8
> >
> > ras to voxel transform:
> >
> >-0.5000   0.0058 -0.001463.8052
> >
> > 0.0058   0.5000 0.000561.9083
> >
> >-0.0014  -0.0005 0.500019.5206
> >
> > 0.   0. 0. 1.
> >
> >
> > On Tue, Mar 15, 2016 at 11:25 AM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> >
> > How was DTI.nii.gz created? What happens if you run
> > mri_info DTI.nii.gz
> >
> > If the DICOM is a siemens dicom but has been stripped of special
> > siemens
> > info, then we cannot unpack it
> >
> >
> > On 03/15/2016 02:02 PM, Jasmin Alves wrote:
> > >
> > > Still get the same error:
> > >
> > > WARNING: file /Users/jasminalves/Desktop/data/40/00010001 does not
> > > contain a Siemens ASCII header
> > >
> > > has this file been anonymized?
> > >
> > > ERROR: cannot unpack mosiacs without ASCII header
> > >
> > >
> > > The error I get when running in nifti format is actually found
> > in the
> > > log file.
> > >
> > >  ERROR: /Users/jasminalves/Desktop/data/40/DTI.nii.gz is not a
> dicom
> > > file or some other problem
> > >
> > >
> > >
> > >
> > > On Tue, Mar 15, 2016 at 9:01 AM, Douglas N Greve
> > > mailto:gr...@nmr.mgh.harvard.edu>
> >  > >> wrote:
> > >
> > > if you run
> > > mri_convert 00010001 deleteme.nii
> > > what happens?
> > >
> > > what is the error when running with nifti?
> > >
> > >
> > > On 03/14/2016 05:59 PM, Jasmin Alves wrote:
> > > >
> > > > Dear Freesurfer experts,
> > > >
> > > > FREESURFER_HOME: /Applications/freesurfer
> > > >
> > > > Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
> > > >
>

Re: [Freesurfer] error while running dt-recon all

2016-03-15 Thread Douglas N Greve

Can you send the full terminal output from when you run dt_recon with 
the nifti as input?

On 03/15/2016 03:07 PM, Jasmin Alves wrote:
> How was DTI.nii.gz created? DTI.nii.gz was converted from the raw 
> dicom data using dcm2nii.
>
> Response for: "What happens if you run mri_info DTI.nii.gz"
>
> Volume information for DTI.nii.gz
>
>   type: nii
>
> dimensions: 128 x 128 x 70 x 65
>
>voxel sizes: 2., 2., 2.
>
>   type: FLOAT (3)
>
>fov: 256.000
>
>dof: 0
>
> xstart: -128.0, xend: 128.0
>
> ystart: -128.0, yend: 128.0
>
> zstart: -70.0, zend: 70.0
>
> TR: 8100.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip 
> angle: 0.00 degrees
>
>nframes: 65
>
>PhEncDir: UNKNOWN
>
> ras xform present
>
> xform info: x_r =  -0., y_r =   0.0116, z_r =  -0.0028, c_r =  
>   -0.4290
>
>   : x_a =   0.0116, y_a =   0., z_a =  -0.0011, c_a = 
> 4.1548
>
>   : x_s =  -0.0028, y_s =   0.0011, z_s =   1., c_s =  
>   30.9622
>
> Orientation   : LAS
>
> Primary Slice Direction: axial
>
> voxel to ras transform:
>
>-1.   0.0232 -0.0057   126.2761
>
> 0.0232   1. -0.0021  -125.2474
>
>-0.0057   0.0022 2.   -38.8153
>
> 0.   0. 0. 1.
>
> voxel-to-ras determinant -8
>
> ras to voxel transform:
>
>-0.5000   0.0058 -0.001463.8052
>
> 0.0058   0.5000 0.000561.9083
>
>-0.0014  -0.0005 0.500019.5206
>
> 0.   0. 0. 1.
>
>
> On Tue, Mar 15, 2016 at 11:25 AM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
> How was DTI.nii.gz created? What happens if you run
> mri_info DTI.nii.gz
>
> If the DICOM is a siemens dicom but has been stripped of special
> siemens
> info, then we cannot unpack it
>
>
> On 03/15/2016 02:02 PM, Jasmin Alves wrote:
> >
> > Still get the same error:
> >
> > WARNING: file /Users/jasminalves/Desktop/data/40/00010001 does not
> > contain a Siemens ASCII header
> >
> > has this file been anonymized?
> >
> > ERROR: cannot unpack mosiacs without ASCII header
> >
> >
> > The error I get when running in nifti format is actually found
> in the
> > log file.
> >
> >  ERROR: /Users/jasminalves/Desktop/data/40/DTI.nii.gz is not a dicom
> > file or some other problem
> >
> >
> >
> >
> > On Tue, Mar 15, 2016 at 9:01 AM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>
>  >> wrote:
> >
> > if you run
> > mri_convert 00010001 deleteme.nii
> > what happens?
> >
> > what is the error when running with nifti?
> >
> >
> > On 03/14/2016 05:59 PM, Jasmin Alves wrote:
> > >
> > > Dear Freesurfer experts,
> > >
> > > FREESURFER_HOME: /Applications/freesurfer
> > >
> > > Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
> > >
> > > Kernel info: Darwin 14.5.0 x86_64
> > >
> > >
> > > I received the following error while running the dt_recon --i
> > 00010001
> > > --s 40 --o /Users/jasminalves/Desktop/data/FREESURFER/40.
> > >
> > > The participant is 40.
> > >
> > > And I received the following error:
> > >
> > > WARNING: file /Users/jasminalves/Desktop/data/40/00010001
> does not
> > > contain a Siemens ASCII header has this file been anonymized?
> > >
> > > ERROR: cannot unpack mosiacs without ASCII header
> > >
> > >
> > > I did notice on previous threads this is a common error
> that occurs,
> > > but the files I have were directly exported from our
> siemens scanner
> > > via Osirix. I also tried running dt_recon using nifti
> format but
> > that
> > > resulted in an error as well. Is there anything else I can do?
> > >
> > > Thanks,
> > >
> > > Jasmin
> > >
> > >
> > > --
> > > Jasmin Alves
> > > Predoctoral Student
> > > Medical Biology Graduate Program
> > > University of Southern California
> > > jal...@usc.edu 
> >
> 
> > >>
> > >
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> 
> >

Re: [Freesurfer] error while running dt-recon all

2016-03-15 Thread Jasmin Alves

 How was DTI.nii.gz created? DTI.nii.gz was converted from the raw dicom
data using dcm2nii.

Response for: "What happens if you run mri_info DTI.nii.gz"

Volume information for DTI.nii.gz

  type: nii

dimensions: 128 x 128 x 70 x 65

   voxel sizes: 2., 2., 2.

  type: FLOAT (3)

   fov: 256.000

   dof: 0

xstart: -128.0, xend: 128.0

ystart: -128.0, yend: 128.0

zstart: -70.0, zend: 70.0

TR: 8100.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle:
0.00 degrees

   nframes: 65

   PhEncDir: UNKNOWN

ras xform present

xform info: x_r =  -0., y_r =   0.0116, z_r =  -0.0028, c_r =
-0.4290

  : x_a =   0.0116, y_a =   0., z_a =  -0.0011, c_a =
4.1548

  : x_s =  -0.0028, y_s =   0.0011, z_s =   1., c_s =
30.9622

Orientation   : LAS

Primary Slice Direction: axial

voxel to ras transform:

   -1.   0.0232  -0.0057   126.2761

0.0232   1.  -0.0021  -125.2474

   -0.0057   0.0022   2.   -38.8153

0.   0.   0. 1.

voxel-to-ras determinant -8

ras to voxel transform:

   -0.5000   0.0058  -0.001463.8052

0.0058   0.5000   0.000561.9083

   -0.0014  -0.0005   0.500019.5206

0.   0.   0. 1.

On Tue, Mar 15, 2016 at 11:25 AM, Douglas N Greve  wrote:

>
> How was DTI.nii.gz created? What happens if you run
> mri_info DTI.nii.gz
>
> If the DICOM is a siemens dicom but has been stripped of special siemens
> info, then we cannot unpack it
>
>
> On 03/15/2016 02:02 PM, Jasmin Alves wrote:
> >
> > Still get the same error:
> >
> > WARNING: file /Users/jasminalves/Desktop/data/40/00010001 does not
> > contain a Siemens ASCII header
> >
> > has this file been anonymized?
> >
> > ERROR: cannot unpack mosiacs without ASCII header
> >
> >
> > The error I get when running in nifti format is actually found in the
> > log file.
> >
> >  ERROR: /Users/jasminalves/Desktop/data/40/DTI.nii.gz is not a dicom
> > file or some other problem
> >
> >
> >
> >
> > On Tue, Mar 15, 2016 at 9:01 AM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> > if you run
> > mri_convert 00010001 deleteme.nii
> > what happens?
> >
> > what is the error when running with nifti?
> >
> >
> > On 03/14/2016 05:59 PM, Jasmin Alves wrote:
> > >
> > > Dear Freesurfer experts,
> > >
> > > FREESURFER_HOME: /Applications/freesurfer
> > >
> > > Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
> > >
> > > Kernel info: Darwin 14.5.0 x86_64
> > >
> > >
> > > I received the following error while running the dt_recon --i
> > 00010001
> > > --s 40 --o /Users/jasminalves/Desktop/data/FREESURFER/40.
> > >
> > > The participant is 40.
> > >
> > > And I received the following error:
> > >
> > > WARNING: file /Users/jasminalves/Desktop/data/40/00010001 does not
> > > contain a Siemens ASCII header has this file been anonymized?
> > >
> > > ERROR: cannot unpack mosiacs without ASCII header
> > >
> > >
> > > I did notice on previous threads this is a common error that
> occurs,
> > > but the files I have were directly exported from our siemens
> scanner
> > > via Osirix. I also tried running dt_recon using nifti format but
> > that
> > > resulted in an error as well. Is there anything else I can do?
> > >
> > > Thanks,
> > >
> > > Jasmin
> > >
> > >
> > > --
> > > Jasmin Alves
> > > Predoctoral Student
> > > Medical Biology Graduate Program
> > > University of Southern California
> > > jal...@usc.edu   > >
> > >
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > 
> > >
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=CwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=v9tFPBwUhooWQdua1MFl4G-WkZdqs5b-a3SFZRYSRDs&s=369GPCb6aThxDDKHEPitpYUvNATIrFBISf_vC_ldmDs&e=
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu 
> > Phone Number: 617-724-2358 
> > Fax: 617-726-7422 
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > <
> https://urldefense.proofpoint.com/v2/url?u=http-3A__surfer.nmr.mgh.harvard.edu_fswiki_BugReporting&d=CwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=Dg3E3_3nDK398YRIg5fpyFNMc_O6RObwIezN3fq92AQ&s=GpEEtkD1BnMJzWOlXkecPjAGlZyRbfpUD2D7FRdXC7o&e=
> >
> > FileDrop:
> >
> https://urldefense.proof

Re: [Freesurfer] error while running dt-recon all

2016-03-15 Thread Douglas N Greve


How was DTI.nii.gz created? What happens if you run
mri_info DTI.nii.gz

If the DICOM is a siemens dicom but has been stripped of special siemens 
info, then we cannot unpack it


On 03/15/2016 02:02 PM, Jasmin Alves wrote:
>
> Still get the same error:
>
> WARNING: file /Users/jasminalves/Desktop/data/40/00010001 does not 
> contain a Siemens ASCII header
>
> has this file been anonymized?
>
> ERROR: cannot unpack mosiacs without ASCII header
>
>
> The error I get when running in nifti format is actually found in the 
> log file.
>
>  ERROR: /Users/jasminalves/Desktop/data/40/DTI.nii.gz is not a dicom 
> file or some other problem
>
>
>
>
> On Tue, Mar 15, 2016 at 9:01 AM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> if you run
> mri_convert 00010001 deleteme.nii
> what happens?
>
> what is the error when running with nifti?
>
>
> On 03/14/2016 05:59 PM, Jasmin Alves wrote:
> >
> > Dear Freesurfer experts,
> >
> > FREESURFER_HOME: /Applications/freesurfer
> >
> > Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
> >
> > Kernel info: Darwin 14.5.0 x86_64
> >
> >
> > I received the following error while running the dt_recon --i
> 00010001
> > --s 40 --o /Users/jasminalves/Desktop/data/FREESURFER/40.
> >
> > The participant is 40.
> >
> > And I received the following error:
> >
> > WARNING: file /Users/jasminalves/Desktop/data/40/00010001 does not
> > contain a Siemens ASCII header has this file been anonymized?
> >
> > ERROR: cannot unpack mosiacs without ASCII header
> >
> >
> > I did notice on previous threads this is a common error that occurs,
> > but the files I have were directly exported from our siemens scanner
> > via Osirix. I also tried running dt_recon using nifti format but
> that
> > resulted in an error as well. Is there anything else I can do?
> >
> > Thanks,
> >
> > Jasmin
> >
> >
> > --
> > Jasmin Alves
> > Predoctoral Student
> > Medical Biology Graduate Program
> > University of Southern California
> > jal...@usc.edu   >
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> >
> 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=CwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=v9tFPBwUhooWQdua1MFl4G-WkZdqs5b-a3SFZRYSRDs&s=369GPCb6aThxDDKHEPitpYUvNATIrFBISf_vC_ldmDs&e=
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358 
> Fax: 617-726-7422 
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> FileDrop:
> 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.edu_filedrop2&d=CwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=v9tFPBwUhooWQdua1MFl4G-WkZdqs5b-a3SFZRYSRDs&s=K5-xLMTkmvO4akwQ1yNQhCyFkQ3yeGkg4bIrAd6xArI&e=
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> Outgoing:
> 
> https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.edu_transfer_outgoing_flat_greve_&d=CwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=v9tFPBwUhooWQdua1MFl4G-WkZdqs5b-a3SFZRYSRDs&s=XP0Fok4OAHAC7DYzCOyUrPu9PLDR_RULGfbnE8c0hNs&e=
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=CwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=v9tFPBwUhooWQdua1MFl4G-WkZdqs5b-a3SFZRYSRDs&s=369GPCb6aThxDDKHEPitpYUvNATIrFBISf_vC_ldmDs&e=
>
>
> The information in this e-mail is intended only for the person to
> whom it is
> addressed. If you believe this e-mail was sent to you in error and
> the e-mail
> contains patient information, please contact the Partners
> Compliance HelpLine at
> 
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline&d=CwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=v9tFPBwUhooWQdua1MFl4G-WkZdqs5b-a3SFZRYSRDs&s=kr8DioqB8ZA30rJ-OJWi601znNchJg-CCjnpQKvHYhI&e=
> . If the e-mail was sent to you in error
> but does not contain patient information, please contact the
> sender and properly
> dispose of the e-mail.
>
>
>
>
> -- 
> Jasmin Alves
> Predoctoral Stud

Re: [Freesurfer] error while running dt-recon all

2016-03-15 Thread Jasmin Alves

Still get the same error:

WARNING: file /Users/jasminalves/Desktop/data/40/00010001 does not contain
a Siemens ASCII header

has this file been anonymized?

ERROR: cannot unpack mosiacs without ASCII header


The error I get when running in nifti format is actually found in the log
file.

 ERROR: /Users/jasminalves/Desktop/data/40/DTI.nii.gz is not a dicom file
or some other problem




On Tue, Mar 15, 2016 at 9:01 AM, Douglas N Greve 
wrote:

> if you run
> mri_convert 00010001 deleteme.nii
> what happens?
>
> what is the error when running with nifti?
>
>
> On 03/14/2016 05:59 PM, Jasmin Alves wrote:
> >
> > Dear Freesurfer experts,
> >
> > FREESURFER_HOME: /Applications/freesurfer
> >
> > Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
> >
> > Kernel info: Darwin 14.5.0 x86_64
> >
> >
> > I received the following error while running the dt_recon --i 00010001
> > --s 40 --o /Users/jasminalves/Desktop/data/FREESURFER/40.
> >
> > The participant is 40.
> >
> > And I received the following error:
> >
> > WARNING: file /Users/jasminalves/Desktop/data/40/00010001 does not
> > contain a Siemens ASCII header has this file been anonymized?
> >
> > ERROR: cannot unpack mosiacs without ASCII header
> >
> >
> > I did notice on previous threads this is a common error that occurs,
> > but the files I have were directly exported from our siemens scanner
> > via Osirix. I also tried running dt_recon using nifti format but that
> > resulted in an error as well. Is there anything else I can do?
> >
> > Thanks,
> >
> > Jasmin
> >
> >
> > --
> > Jasmin Alves
> > Predoctoral Student
> > Medical Biology Graduate Program
> > University of Southern California
> > jal...@usc.edu 
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=CwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=v9tFPBwUhooWQdua1MFl4G-WkZdqs5b-a3SFZRYSRDs&s=369GPCb6aThxDDKHEPitpYUvNATIrFBISf_vC_ldmDs&e=
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.edu_filedrop2&d=CwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=v9tFPBwUhooWQdua1MFl4G-WkZdqs5b-a3SFZRYSRDs&s=K5-xLMTkmvO4akwQ1yNQhCyFkQ3yeGkg4bIrAd6xArI&e=
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing:
> https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.edu_transfer_outgoing_flat_greve_&d=CwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=v9tFPBwUhooWQdua1MFl4G-WkZdqs5b-a3SFZRYSRDs&s=XP0Fok4OAHAC7DYzCOyUrPu9PLDR_RULGfbnE8c0hNs&e=
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=CwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=v9tFPBwUhooWQdua1MFl4G-WkZdqs5b-a3SFZRYSRDs&s=369GPCb6aThxDDKHEPitpYUvNATIrFBISf_vC_ldmDs&e=
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
>
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline&d=CwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=v9tFPBwUhooWQdua1MFl4G-WkZdqs5b-a3SFZRYSRDs&s=kr8DioqB8ZA30rJ-OJWi601znNchJg-CCjnpQKvHYhI&e=
> . If the e-mail was sent to you in error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>


-- 
Jasmin Alves
Predoctoral Student
Medical Biology Graduate Program
University of Southern California
jal...@usc.edu
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] error while running dt-recon all

2016-03-15 Thread Douglas N Greve

if you run
mri_convert 00010001 deleteme.nii
what happens?

what is the error when running with nifti?


On 03/14/2016 05:59 PM, Jasmin Alves wrote:
>
> Dear Freesurfer experts,
>
> FREESURFER_HOME: /Applications/freesurfer
>
> Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
>
> Kernel info: Darwin 14.5.0 x86_64
>
>
> I received the following error while running the dt_recon --i 00010001 
> --s 40 --o /Users/jasminalves/Desktop/data/FREESURFER/40.
>
> The participant is 40.
>
> And I received the following error:
>
> WARNING: file /Users/jasminalves/Desktop/data/40/00010001 does not 
> contain a Siemens ASCII header has this file been anonymized?
>
> ERROR: cannot unpack mosiacs without ASCII header
>
>
> I did notice on previous threads this is a common error that occurs, 
> but the files I have were directly exported from our siemens scanner 
> via Osirix. I also tried running dt_recon using nifti format but that 
> resulted in an error as well. Is there anything else I can do?
>
> Thanks,
>
> Jasmin
>
>
> -- 
> Jasmin Alves
> Predoctoral Student
> Medical Biology Graduate Program
> University of Southern California
> jal...@usc.edu 
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] error while running dt-recon all

Re: [Freesurfer] error while running dt-recon all

Re: [Freesurfer] error while running dt-recon all

Re: [Freesurfer] error while running dt-recon all

Re: [Freesurfer] error while running dt-recon all

Re: [Freesurfer] error while running dt-recon all

Re: [Freesurfer] error while running dt-recon all

Re: [Freesurfer] error while running dt-recon all

Re: [Freesurfer] error while running dt-recon all

Re: [Freesurfer] error while running dt-recon all

Re: [Freesurfer] error while running dt-recon all

11 matches

Site Navigation

Mail list logo

Footer information