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
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
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
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
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 $
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"
>
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.
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
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:
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:
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
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