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 <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
> > <gr...@nmr.mgh.harvard.edu <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 <mailto:jal...@usc.edu> <mailto:jal...@usc.edu
> > <mailto:jal...@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.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 <mailto:gr...@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.edu_fswiki_BugReporting&d=CwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=Dg3E3_3nDK398YRIg5fpyFNMc_O6RObwIezN3fq92AQ&s=GpEEtkD1BnMJzWOlXkecPjAGlZyRbfpUD2D7FRdXC7o&e=
> >
> > 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
> > <
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.nmr.mgh.harvard.edu_facility_filedrop_index.html&d=CwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=Dg3E3_3nDK398YRIg5fpyFNMc_O6RObwIezN3fq92AQ&s=hwwSX9tQxQeWZq4mK8Rpb7vYFBqUftnwxx3egrwmBdM&e=
> >
> > 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 <mailto:
> 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=
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> > but does not contain patient information, please contact the
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> >
> >
> >
> >
> > --
> > Jasmin Alves
> > Predoctoral Student
> > Medical Biology Graduate Program
> > University of Southern California
> > jal...@usc.edu <mailto: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=Dg3E3_3nDK398YRIg5fpyFNMc_O6RObwIezN3fq92AQ&s=CqAmblGQbrSHiiR2HnmriniLIefT883nzWX7ij98H2M&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=Dg3E3_3nDK398YRIg5fpyFNMc_O6RObwIezN3fq92AQ&s=_JLzMZF53oLGA-oQwL-7Z2q1LachFF3-2TIEkkTGdcc&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=Dg3E3_3nDK398YRIg5fpyFNMc_O6RObwIezN3fq92AQ&s=JLD-nXWKsjEKCvgUh1sKRBa_OnTn05cFSq8QsAEegp8&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=Dg3E3_3nDK398YRIg5fpyFNMc_O6RObwIezN3fq92AQ&s=CqAmblGQbrSHiiR2HnmriniLIefT883nzWX7ij98H2M&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=Dg3E3_3nDK398YRIg5fpyFNMc_O6RObwIezN3fq92AQ&s=8mDIOhbTFEY_zJuCIowaFDgmQ2VVcBIkkgeCv1DGyfQ&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
_______________________________________________
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The information in this e-mail is intended only for the person to whom it is
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