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: 2.0000, 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, flip angle: 0.00 degrees
nframes: 65
PhEncDir: UNKNOWN
ras 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 1.0000
voxel-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 1.0000
On Tue, Mar 15, 2016 at 11:25 AM, Douglas N Greve <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 a dicom 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> 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 thatoccurs,
> but the files I have were directly exported from our siemensscanner
> 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 > 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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. 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
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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.ed... www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.ed...
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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_complia... . 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.