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
<gr...@nmr.mgh.harvard.edu <mailto:gr...@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 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 <mailto:gr...@nmr.mgh.harvard.edu>
<mailto:gr...@nmr.mgh.harvard.edu
<mailto: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>
<mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>
> <mailto:gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>
> <mailto: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>>
> <mailto:jal...@usc.edu <mailto:jal...@usc.edu>
<mailto:jal...@usc.edu <mailto:jal...@usc.edu>>>
> <mailto:jal...@usc.edu <mailto:jal...@usc.edu>
<mailto:jal...@usc.edu <mailto:jal...@usc.edu>>
> > <mailto: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>
> <mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto: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>
<mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>
> <mailto:gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>
<mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>>
> > Phone Number:617-724-2358 <tel:617-724-2358> <tel:617-724-2358
<tel:617-724-2358>>
> <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358
<tel:617-724-2358>>>
> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422
<tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422>
> <tel:617-726-7422 <tel:617-726-7422>>>
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://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=o6-ydWWvsWf-fSm5NmMZmldXpXEjEg3duz1vViy6NAc&s=JEMNVqaCWFyhIBYx595b2hHndKvujFMwSozkDcSGbIU&e=
>
> >
>
<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
<http://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=o6-ydWWvsWf-fSm5NmMZmldXpXEjEg3duz1vViy6NAc&s=0iHNzzA_YcOmdUVFE4ZkioQ3jzIzzE4UGUhUbOdZ2Vo&e=
>
> >
>
<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>
> <mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>
> <mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto: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=
> > . 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 <mailto:jal...@usc.edu> <mailto:jal...@usc.edu
<mailto:jal...@usc.edu>> <mailto: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>
> <mailto: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=Dg3E3_3nDK398YRIg5fpyFNMc_O6RObwIezN3fq92AQ&s=CqAmblGQbrSHiiR2HnmriniLIefT883nzWX7ij98H2M&e=
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
>gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
<mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>
> Phone Number: 617-724-2358 <tel:617-724-2358>
<tel:617-724-2358 <tel:617-724-2358>>
> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422
<tel:617-726-7422>>
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://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=o6-ydWWvsWf-fSm5NmMZmldXpXEjEg3duz1vViy6NAc&s=JEMNVqaCWFyhIBYx595b2hHndKvujFMwSozkDcSGbIU&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=Dg3E3_3nDK398YRIg5fpyFNMc_O6RObwIezN3fq92AQ&s=_JLzMZF53oLGA-oQwL-7Z2q1LachFF3-2TIEkkTGdcc&e=
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://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=o6-ydWWvsWf-fSm5NmMZmldXpXEjEg3duz1vViy6NAc&s=0iHNzzA_YcOmdUVFE4ZkioQ3jzIzzE4UGUhUbOdZ2Vo&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=Dg3E3_3nDK398YRIg5fpyFNMc_O6RObwIezN3fq92AQ&s=JLD-nXWKsjEKCvgUh1sKRBa_OnTn05cFSq8QsAEegp8&e=
>
> _______________________________________________
> Freesurfer mailing list
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<mailto:Freesurfer@nmr.mgh.harvard.edu>
<mailto: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=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 <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=o6-ydWWvsWf-fSm5NmMZmldXpXEjEg3duz1vViy6NAc&s=QmXOcbmhxk50ab8-qFqSUJq79Xrd-iAPmWQlf_34OVo&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
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://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=o6-ydWWvsWf-fSm5NmMZmldXpXEjEg3duz1vViy6NAc&s=bELNK7f9QHMufVuMX2ijfEBXSpDDdKM8vNr0Jsb-Y5M&e=
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Outgoing:
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Medical Biology Graduate Program
University of Southern California
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