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 greve@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 = (-0.999929, 0.0116015, -0.00282784)
j_ras = (0.0115984, 0.999932, 0.00109136)
k_ras = (-0.00284031, -0.00105848, 0.999995)
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 < greve@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 65voxel sizes: 2.0000, 2.0000, 2.0000
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, flipangle: 0.00 degrees
nframes: 65 PhEncDir: UNKNOWNras xform present
xform info: x_r = -0.9999, y_r = 0.0116, z_r = -0.0028, c_r =-0.4290
: x_a = 0.0116, y_a = 0.9999, z_a = -0.0011, c_a = 4.1548 : x_s = -0.0028, y_s = 0.0011, z_s = 1.0000, c_s =30.9622
Orientation : LAS
Primary Slice Direction: axial
voxel to ras transform:
-1.9999 0.0232 -0.0057 126.2761 0.0232 1.9999 -0.0021 -125.2474 -0.0057 0.0022 2.0000 -38.8153 0.0000 0.0000 0.0000 1.0000voxel-to-ras determinant -8
ras to voxel transform:
-0.5000 0.0058 -0.0014 63.8052 0.0058 0.5000 0.0005 61.9083 -0.0014 -0.0005 0.5000 19.5206 0.0000 0.0000 0.0000 1.0000On Tue, Mar 15, 2016 at 11:25 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@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 adicom
> file or some other problem > > > > > On Tue, Mar 15, 2016 at 9:01 AM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto: <greve@nmr.mgh.harvard.edu>greve@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 beenanonymized?
> > > > 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 cando?
> > > > Thanks, > > > > Jasmin > > > > > > -- > > Jasmin Alves > > Predoctoral Student > > Medical Biology Graduate Program > > University of Southern California > > jalves@usc.edu <mailto:jalves@usc.edu> <mailto:jalves@usc.edu <mailto:jalves@usc.edu>> <mailto:jalves@usc.edu <mailto:jalves@usc.edu> > <mailto:jalves@usc.edu <mailto:jalves@usc.edu>>> > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: <Freesurfer@nmr.mgh.harvard.edu>Freesurfer@nmr.mgh.harvard.edu
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> . 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 >jalves@usc.edu <mailto:jalves@usc.edu> <mailto:jalves@usc.edu <mailto:jalves@usc.edu>> > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting<https://urldefense.proofpoint.com/v2/url?u=http-3A__surfer.nmr.mgh.harvard.e...
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