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
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
> > jalves@usc.edu <mailto:jalves@usc.edu> <mailto:jalves@usc.edu> <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 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
> <mailto:jalves@usc.edu>>
> >
> >
> >
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>
> --
> 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>
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>
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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
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>
>
> --
> Jasmin Alves
> Predoctoral Student
> Medical Biology Graduate Program
> University of Southern California
> jalves@usc.edu <mailto:jalves@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=Dg3E3_3nDK398YRIg5fpyFNMc_O6RObwIezN3fq92AQ&s=CqAmblGQbrSHiiR2HnmriniLIefT883nzWX7ij98H2M&e=
--
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.edu_filedrop2&d=CwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=Dg3E3_3nDK398YRIg5fpyFNMc_O6RObwIezN3fq92AQ&s=_JLzMZF53oLGA-oQwL-7Z2q1LachFF3-2TIEkkTGdcc&e=
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