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
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 jalves@usc.edu mailto:jalves@usc.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 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 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.ed...
-- 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...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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.
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 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 > 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.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 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 <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=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> 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= . 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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...
FileDrop:https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.ed...
www.nmr.mgh.harvard.edu/facility/filedrop/index.html <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.nmr.mgh.harvard.edu_...
Outgoing:https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.ed...
_______________________________________________ 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...
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 athttps://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.-- 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.ed...
-- 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...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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.
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 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> <mailto: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 > > 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 <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 > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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=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=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>> >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 >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.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 <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 <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=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> 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 <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 jalves@usc.edu mailto:jalves@usc.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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>>> 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 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 <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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 <https://urldefense.proofpoint.com/v2/url?u=http-3A__surfer.nmr.mgh.harvard.e...
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__surfer.nmr.mgh.harvard.e...
> > FileDrop: >https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.ed...
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.nmr.mgh.harvard.edu_...
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.nmr.mgh.harvard.edu_...
> > Outgoing: >https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.ed...
> > _______________________________________________ > 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.ed...
> > > 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. > > > > > -- > 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...
FileDrop:https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.ed...
www.nmr.mgh.harvard.edu/facility/filedrop/index.html <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.nmr.mgh.harvard.edu_...
Outgoing:https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.ed...
_______________________________________________ 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...
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 athttps://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.-- 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.ed...
-- 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...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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.
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 mailto: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 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 <mailto:greve@nmr.mgh.harvard.edu> <mailto: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 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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto: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 > > > 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>>> > <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 <mailto:jalves@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 > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 > >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 <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 >greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 > 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= > > > 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 >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.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 greve@nmr.mgh.harvard.edu <mailto:greve@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: 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=o6-ydWWvsWf-fSm5NmMZmldXpXEjEg3duz1vViy6NAc&s=-5VhrwXWwPpKox8-jmZl_1_Ucv9MQtpYXaGlDDWtkoo&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=o6-ydWWvsWf-fSm5NmMZmldXpXEjEg3duz1vViy6NAc&s=QmXOcbmhxk50ab8-qFqSUJq79Xrd-iAPmWQlf_34OVo&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=o6-ydWWvsWf-fSm5NmMZmldXpXEjEg3duz1vViy6NAc&s=OD8AVSmvHiAKa7hyRNMRoHXcW7kar7LqwI4rHhtPjSo&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 jalves@usc.edu mailto:jalves@usc.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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<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> <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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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 athttps://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.-- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jalves@usc.edu mailto:jalves@usc.edu
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-- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jalves@usc.edujalves@usc.edu
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No, I mean that when the command is run, it will print a lot of text to the screen. I want to know what that text is. You can run the following command and send me the dng.log file
dt_recon --debug --i DTI.nii.gz --s 40 --o /Users/jasminalves/Desktop/data/FREESURFER/40 |& tee dng.log
On 03/16/2016 11:35 AM, Jasmin Alves wrote:
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 mailto: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 <mailto: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 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 <mailto:greve@nmr.mgh.harvard.edu> <mailto: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 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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto: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 > > > 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>>> > <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 <mailto:jalves@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 > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 <https://urldefense.proofpoint.com/v2/url?u=http-3A__surfer.nmr.mgh.harvard.edu_fswiki_BugReporting&d=CwMD-g&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=kUuMsvGkF90j7MrnR1WzFM-p2ZBt4XLVQjd46fokEaU&s=MK31sF-RJdk6uPRbA3WqaZvEnAO7Om7G1iX60nDdKDU&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=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 <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.nmr.mgh.harvard.edu_facility_filedrop_index.html&d=CwMD-g&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=kUuMsvGkF90j7MrnR1WzFM-p2ZBt4XLVQjd46fokEaU&s=RSVB1NkchYqjnISeOuHCIb2NZhwZCjamwvm14kpP5TE&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=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 > >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 <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 >greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 <https://urldefense.proofpoint.com/v2/url?u=http-3A__surfer.nmr.mgh.harvard.edu_fswiki_BugReporting&d=CwMD-g&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=kUuMsvGkF90j7MrnR1WzFM-p2ZBt4XLVQjd46fokEaU&s=MK31sF-RJdk6uPRbA3WqaZvEnAO7Om7G1iX60nDdKDU&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=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 <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.nmr.mgh.harvard.edu_facility_filedrop_index.html&d=CwMD-g&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=kUuMsvGkF90j7MrnR1WzFM-p2ZBt4XLVQjd46fokEaU&s=RSVB1NkchYqjnISeOuHCIb2NZhwZCjamwvm14kpP5TE&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=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 > 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= > > > 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 >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.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 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.edu_fswiki_BugReporting&d=CwMD-g&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=kUuMsvGkF90j7MrnR1WzFM-p2ZBt4XLVQjd46fokEaU&s=MK31sF-RJdk6uPRbA3WqaZvEnAO7Om7G1iX60nDdKDU&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=o6-ydWWvsWf-fSm5NmMZmldXpXEjEg3duz1vViy6NAc&s=bELNK7f9QHMufVuMX2ijfEBXSpDDdKM8vNr0Jsb-Y5M&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=CwMD-g&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=kUuMsvGkF90j7MrnR1WzFM-p2ZBt4XLVQjd46fokEaU&s=RSVB1NkchYqjnISeOuHCIb2NZhwZCjamwvm14kpP5TE&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=o6-ydWWvsWf-fSm5NmMZmldXpXEjEg3duz1vViy6NAc&s=-5VhrwXWwPpKox8-jmZl_1_Ucv9MQtpYXaGlDDWtkoo&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=o6-ydWWvsWf-fSm5NmMZmldXpXEjEg3duz1vViy6NAc&s=QmXOcbmhxk50ab8-qFqSUJq79Xrd-iAPmWQlf_34OVo&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=o6-ydWWvsWf-fSm5NmMZmldXpXEjEg3duz1vViy6NAc&s=OD8AVSmvHiAKa7hyRNMRoHXcW7kar7LqwI4rHhtPjSo&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 jalves@usc.edu <mailto:jalves@usc.edu> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=CwMD-g&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=kUuMsvGkF90j7MrnR1WzFM-p2ZBt4XLVQjd46fokEaU&s=H6NI99x-WlflQb2NzJ70ZN24kUzdOMoat4qJM9yvJPU&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=kUuMsvGkF90j7MrnR1WzFM-p2ZBt4XLVQjd46fokEaU&s=H6NI99x-WlflQb2NzJ70ZN24kUzdOMoat4qJM9yvJPU&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=kUuMsvGkF90j7MrnR1WzFM-p2ZBt4XLVQjd46fokEaU&s=oYACqI7QKb5b2LHkR1y0vPH0gSrswPwceqLzKoaNa5g&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 jalves@usc.edu mailto:jalves@usc.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 5 != 0 )
set flag = $argv[1] ; shift ;
set flag = --i
shift
switch ( $flag )
switch ( --i )
if ( $#argv < 1 ) goto arg1err ;
if ( 4 < 1 ) goto arg1err
set InputVol = "$argv[1]" ; shift ;
set InputVol = DTI.nii.gz
shift
if ( ! -e "$InputVol" ) then
if ( ! -e DTI.nii.gz ) then
if ( ! -r "$InputVol" ) then
if ( ! -r DTI.nii.gz ) then
set InVolDir = `dirname "$InputVol"` ;
set InVolDir = `dirname "$InputVol"`
dirname DTI.nii.gz
set InVolBase = `basename "$InputVol"` ;
set InVolBase = `basename "$InputVol"`
basename DTI.nii.gz
pushd $InVolDir > /dev/null
pushd .
set InVolDir = `pwd` ;
set InVolDir = `pwd`
pwd
popd > /dev/null
popd
set InputVol = "$InVolDir/$InVolBase" ;
set InputVol = /Users/jasminalves/Desktop/data/40/DTI.nii.gz
set DoConvertInput = 1 ;
set DoConvertInput = 1
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 3 != 0 )
set flag = $argv[1] ; shift ;
set flag = --s
shift
switch ( $flag )
switch ( --s )
if ( $#argv < 1 ) goto arg1err ;
if ( 2 < 1 ) goto arg1err
set subject = $argv[1] ; shift ;
set subject = 40
shift
set subject = `basename $subject` ;
set subject = `basename $subject`
basename 40
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 1 != 0 )
set flag = $argv[1] ; shift ;
set flag = --o
shift
switch ( $flag )
switch ( --o )
if ( $#argv < 1 ) goto arg1err ;
if ( 0 < 1 ) goto arg1err
goto arg1err
echo "ERROR: flag $flag requires one argument"
echo ERROR: flag --o requires one argument
ERROR: flag --o requires one argument
exit 1
exit 1
The second part of the command "/Users/jasminalves/Desktop/data/FREESURFER/40 |& tee dng.log" won't work, but I sent you the output from the first part.
On Wed, Mar 16, 2016 at 8:50 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
No, I mean that when the command is run, it will print a lot of text to the screen. I want to know what that text is. You can run the following command and send me the dng.log file
dt_recon --debug --i DTI.nii.gz --s 40 --o /Users/jasminalves/Desktop/data/FREESURFER/40 |& tee dng.log
On 03/16/2016 11:35 AM, Jasmin Alves wrote:
Do you mean, what ends up happening? I have attached a screen shot of what files are made.
On Wed, Mar 16, 2016 at 7:31 AM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Can you send me what dt_recon prints to the screen when your run the command below? On 3/15/16 11:40 PM, Jasmin Alves wrote:Jasmins-MacBook-Pro:40 jasminalves$ 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 <mailto: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 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 <mailto:greve@nmr.mgh.harvard.edu> <mailto: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 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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto: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 > > > 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>>> > <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 <mailto:jalves@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.ed...
> > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 <https://urldefense.proofpoint.com/v2/url?u=http-3A__surfer.nmr.mgh.harvard.e...
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__surfer.nmr.mgh.harvard.e...
> > > > <https://urldefense.proofpoint.com/v2/url?u=http-3A__surfer.nmr.mgh.harvard.e...
> > > > FileDrop: > > >https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.ed...
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.nmr.mgh.harvard.edu_...
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.nmr.mgh.harvard.edu_...
> > > > <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.nmr.mgh.harvard.edu_...
> > > > Outgoing: > > >https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.ed...
> > > > _______________________________________________ > > 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.ed...
> > > > > > 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. > > > > > > > > > > -- > > 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 <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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 <https://urldefense.proofpoint.com/v2/url?u=http-3A__surfer.nmr.mgh.harvard.e...
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__surfer.nmr.mgh.harvard.e...
> > FileDrop: >https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.ed...
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.nmr.mgh.harvard.edu_...
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.nmr.mgh.harvard.edu_...
> > Outgoing: >https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.ed...
> > _______________________________________________ > 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.ed...
> > > 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. > > > > > -- > 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...
FileDrop:https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.ed...
www.nmr.mgh.harvard.edu/facility/filedrop/index.html <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.nmr.mgh.harvard.edu_...
Outgoing:https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.ed...
_______________________________________________ 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...
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 athttps://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. -- 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 <mailto:Freesurfer@nmr.mgh.harvard.edu>https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
<https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
_______________________________________________ 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...
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 athttps://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.-- 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.ed...
-- 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...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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.
the command must be the entire line and all on one line
dt_recon --debug --i DTI.nii.gz --s 40 --o /Users/jasminalves/Desktop/data/FREESURFER/40 |& tee dng.log
On 03/16/2016 11:56 AM, Jasmin Alves wrote:
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 5 != 0 )
set flag = $argv[1] ; shift ;
set flag = --i
shift
switch ( $flag )
switch ( --i )
if ( $#argv < 1 ) goto arg1err ;
if ( 4 < 1 ) goto arg1err
set InputVol = "$argv[1]" ; shift ;
set InputVol = DTI.nii.gz
shift
if ( ! -e "$InputVol" ) then
if ( ! -e DTI.nii.gz ) then
if ( ! -r "$InputVol" ) then
if ( ! -r DTI.nii.gz ) then
set InVolDir = `dirname "$InputVol"` ;
set InVolDir = `dirname "$InputVol"`
dirname DTI.nii.gz
set InVolBase = `basename "$InputVol"` ;
set InVolBase = `basename "$InputVol"`
basename DTI.nii.gz
pushd $InVolDir > /dev/null
pushd .
set InVolDir = `pwd` ;
set InVolDir = `pwd`
pwd
popd > /dev/null
popd
set InputVol = "$InVolDir/$InVolBase" ;
set InputVol = /Users/jasminalves/Desktop/data/40/DTI.nii.gz
set DoConvertInput = 1 ;
set DoConvertInput = 1
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 3 != 0 )
set flag = $argv[1] ; shift ;
set flag = --s
shift
switch ( $flag )
switch ( --s )
if ( $#argv < 1 ) goto arg1err ;
if ( 2 < 1 ) goto arg1err
set subject = $argv[1] ; shift ;
set subject = 40
shift
set subject = `basename $subject` ;
set subject = `basename $subject`
basename 40
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 1 != 0 )
set flag = $argv[1] ; shift ;
set flag = --o
shift
switch ( $flag )
switch ( --o )
if ( $#argv < 1 ) goto arg1err ;
if ( 0 < 1 ) goto arg1err
goto arg1err
echo "ERROR: flag $flag requires one argument"
echo ERROR: flag --o requires one argument
ERROR: flag --o requires one argument
exit 1
exit 1
The second part of the command "/Users/jasminalves/Desktop/data/FREESURFER/40 |& tee dng.log" won't work, but I sent you the output from the first part.
On Wed, Mar 16, 2016 at 8:50 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
No, I mean that when the command is run, it will print a lot of text to the screen. I want to know what that text is. You can run the following command and send me the dng.log file dt_recon --debug --i DTI.nii.gz --s 40 --o /Users/jasminalves/Desktop/data/FREESURFER/40 |& tee dng.log On 03/16/2016 11:35 AM, Jasmin Alves wrote: > Do you mean, what ends up happening? I have attached a screen shot of > what files are made. > > > > On Wed, Mar 16, 2016 at 7:31 AM, Douglas Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > Can you send me what dt_recon prints to the screen when your run > the command below? > > > On 3/15/16 11:40 PM, Jasmin Alves wrote: >> >> Jasmins-MacBook-Pro:40 jasminalves$ 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 <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto: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 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 <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> >> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> <mailto: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 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> >> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> >> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> >> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> >> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> <mailto: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 >> > > > 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>>> >> > <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 <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> <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 <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 <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> >> <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 >> > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> >> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> >> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> >> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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>>> >> > <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 <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>>> <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=CwMD-g&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=kUuMsvGkF90j7MrnR1WzFM-p2ZBt4XLVQjd46fokEaU&s=MK31sF-RJdk6uPRbA3WqaZvEnAO7Om7G1iX60nDdKDU&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=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=CwMD-g&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=kUuMsvGkF90j7MrnR1WzFM-p2ZBt4XLVQjd46fokEaU&s=RSVB1NkchYqjnISeOuHCIb2NZhwZCjamwvm14kpP5TE&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=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>>> >> > <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 <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 >> > >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>>> <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 <mailto:jalves@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=Dg3E3_3nDK398YRIg5fpyFNMc_O6RObwIezN3fq92AQ&s=CqAmblGQbrSHiiR2HnmriniLIefT883nzWX7ij98H2M&e= >> > >> > -- >> > Douglas N. Greve, Ph.D. >> > MGH-NMR Center >> >greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> >> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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=CwMD-g&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=kUuMsvGkF90j7MrnR1WzFM-p2ZBt4XLVQjd46fokEaU&s=MK31sF-RJdk6uPRbA3WqaZvEnAO7Om7G1iX60nDdKDU&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=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=CwMD-g&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=kUuMsvGkF90j7MrnR1WzFM-p2ZBt4XLVQjd46fokEaU&s=RSVB1NkchYqjnISeOuHCIb2NZhwZCjamwvm14kpP5TE&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=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 >> > 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=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 >> >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 <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 >>greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto: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 <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=CwMD-g&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=kUuMsvGkF90j7MrnR1WzFM-p2ZBt4XLVQjd46fokEaU&s=MK31sF-RJdk6uPRbA3WqaZvEnAO7Om7G1iX60nDdKDU&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=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> >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.nmr.mgh.harvard.edu_facility_filedrop_index.html&d=CwMD-g&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=kUuMsvGkF90j7MrnR1WzFM-p2ZBt4XLVQjd46fokEaU&s=RSVB1NkchYqjnISeOuHCIb2NZhwZCjamwvm14kpP5TE&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=o6-ydWWvsWf-fSm5NmMZmldXpXEjEg3duz1vViy6NAc&s=-5VhrwXWwPpKox8-jmZl_1_Ucv9MQtpYXaGlDDWtkoo&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>> >>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= >> >> >> 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=o6-ydWWvsWf-fSm5NmMZmldXpXEjEg3duz1vViy6NAc&s=OD8AVSmvHiAKa7hyRNMRoHXcW7kar7LqwI4rHhtPjSo&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 >> 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 <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=eQSHoAP4pcZSGqmfMdw3jfhexMmXoooSK-cfBt8beRE&s=WEokhaVpleyEtgA0ype9S_NQHSWEthfIMwRUAuZCo6I&e= >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=CwMD-g&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=kUuMsvGkF90j7MrnR1WzFM-p2ZBt4XLVQjd46fokEaU&s=H6NI99x-WlflQb2NzJ70ZN24kUzdOMoat4qJM9yvJPU&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>> >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=kUuMsvGkF90j7MrnR1WzFM-p2ZBt4XLVQjd46fokEaU&s=H6NI99x-WlflQb2NzJ70ZN24kUzdOMoat4qJM9yvJPU&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=kUuMsvGkF90j7MrnR1WzFM-p2ZBt4XLVQjd46fokEaU&s=oYACqI7QKb5b2LHkR1y0vPH0gSrswPwceqLzKoaNa5g&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 >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.edu_mailman_listinfo_freesurfer&d=CwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=eQSHoAP4pcZSGqmfMdw3jfhexMmXoooSK-cfBt8beRE&s=WEokhaVpleyEtgA0ype9S_NQHSWEthfIMwRUAuZCo6I&e= -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@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=eQSHoAP4pcZSGqmfMdw3jfhexMmXoooSK-cfBt8beRE&s=Z1nenseuAM5wjRh9HMu9FeoRXpa35orzmi8KuW1TXf0&e= www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://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=eQSHoAP4pcZSGqmfMdw3jfhexMmXoooSK-cfBt8beRE&s=2GGcaDEb5zAEtp67KypSO-P1xMhDwF4wDdWRpcMQCUU&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=eQSHoAP4pcZSGqmfMdw3jfhexMmXoooSK-cfBt8beRE&s=WEokhaVpleyEtgA0ype9S_NQHSWEthfIMwRUAuZCo6I&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=eQSHoAP4pcZSGqmfMdw3jfhexMmXoooSK-cfBt8beRE&s=bUrO7CND84PblHfZqBfj2_UaWRaUNkqD1DM3MbOeS94&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 jalves@usc.edu mailto:jalves@usc.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
This is the result when it is all in one line.
Jasmins-MacBook-Pro:~ jasminalves$ dt_recon --debug --i DTI.nii.gz --s 40 -o /Users/jasminalves/Desktop/data/FREESURFER/40 |& tee dng.log
-bash: syntax error near unexpected token `&'
On Wed, Mar 16, 2016 at 9:02 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
the command must be the entire line and all on one line
dt_recon --debug --i DTI.nii.gz --s 40 --o /Users/jasminalves/Desktop/data/FREESURFER/40 |& tee dng.log
On 03/16/2016 11:56 AM, Jasmin Alves wrote:
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 5 != 0 )
set flag = $argv[1] ; shift ;
set flag = --i
shift
switch ( $flag )
switch ( --i )
if ( $#argv < 1 ) goto arg1err ;
if ( 4 < 1 ) goto arg1err
set InputVol = "$argv[1]" ; shift ;
set InputVol = DTI.nii.gz
shift
if ( ! -e "$InputVol" ) then
if ( ! -e DTI.nii.gz ) then
if ( ! -r "$InputVol" ) then
if ( ! -r DTI.nii.gz ) then
set InVolDir = `dirname "$InputVol"` ;
set InVolDir = `dirname "$InputVol"`
dirname DTI.nii.gz
set InVolBase = `basename "$InputVol"` ;
set InVolBase = `basename "$InputVol"`
basename DTI.nii.gz
pushd $InVolDir > /dev/null
pushd .
set InVolDir = `pwd` ;
set InVolDir = `pwd`
pwd
popd > /dev/null
popd
set InputVol = "$InVolDir/$InVolBase" ;
set InputVol = /Users/jasminalves/Desktop/data/40/DTI.nii.gz
set DoConvertInput = 1 ;
set DoConvertInput = 1
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 3 != 0 )
set flag = $argv[1] ; shift ;
set flag = --s
shift
switch ( $flag )
switch ( --s )
if ( $#argv < 1 ) goto arg1err ;
if ( 2 < 1 ) goto arg1err
set subject = $argv[1] ; shift ;
set subject = 40
shift
set subject = `basename $subject` ;
set subject = `basename $subject`
basename 40
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 1 != 0 )
set flag = $argv[1] ; shift ;
set flag = --o
shift
switch ( $flag )
switch ( --o )
if ( $#argv < 1 ) goto arg1err ;
if ( 0 < 1 ) goto arg1err
goto arg1err
echo "ERROR: flag $flag requires one argument"
echo ERROR: flag --o requires one argument
ERROR: flag --o requires one argument
exit 1
exit 1
The second part of the command "/Users/jasminalves/Desktop/data/FREESURFER/40 |& tee dng.log" won't work, but I sent you the output from the first part.
On Wed, Mar 16, 2016 at 8:50 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
No, I mean that when the command is run, it will print a lot of text to the screen. I want to know what that text is. You can run the following command and send me the dng.log file dt_recon --debug --i DTI.nii.gz --s 40 --o /Users/jasminalves/Desktop/data/FREESURFER/40 |& tee dng.log On 03/16/2016 11:35 AM, Jasmin Alves wrote: > Do you mean, what ends up happening? I have attached a screen shot of > what files are made. > > > > On Wed, Mar 16, 2016 at 7:31 AM, Douglas Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > Can you send me what dt_recon prints to the screen when yourrun
> the command below? > > > On 3/15/16 11:40 PM, Jasmin Alves wrote: >> >> Jasmins-MacBook-Pro:40 jasminalves$ 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 <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto: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 convertedfrom
>> 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 <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> <mailto: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 beenstripped
>> 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> >> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> >> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> >> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> >> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> <mailto: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 >> > > > 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>>> >> > <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 <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> <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 <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 <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> >> <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.ed...
>> > > >> > > -- >> > > Douglas N. Greve, Ph.D. >> > > MGH-NMR Center >> > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> >> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> >> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> >> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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>>> >> > <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 <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>>> <tel:617-726-7422 >> <tel:617-726-7422> >> > <tel: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...
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__surfer.nmr.mgh.harvard.e...
>> > >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__surfer.nmr.mgh.harvard.e...
>> > >> > > >> > >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__surfer.nmr.mgh.harvard.e...
>> > > >> > > FileDrop: >> > > >> > >>https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.ed...
>> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.nmr.mgh.harvard.edu_...
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.nmr.mgh.harvard.edu_...
>> > >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.nmr.mgh.harvard.edu_...
>> > >> > > >> > >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.nmr.mgh.harvard.edu_...
>> > > >> > > Outgoing: >> > > >> > >>https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.ed...
>> > > >> > > _______________________________________________ >> > > 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>>> >> > <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 <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> >> > >> >https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
>> > > >> > > >> > > The information in this e-mail is intendedonly
>> 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. >> > > >> > > >> > > >> > > >> > > -- >> > > 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>>> <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 <mailto:jalves@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.ed...
>> > >> > -- >> > Douglas N. Greve, Ph.D. >> > MGH-NMR Center >> >greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 <https://urldefense.proofpoint.com/v2/url?u=http-3A__surfer.nmr.mgh.harvard.e...
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__surfer.nmr.mgh.harvard.e...
>> > >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__surfer.nmr.mgh.harvard.e...
>> > >> > FileDrop: >> > >>https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.ed...
>> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.nmr.mgh.harvard.edu_...
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.nmr.mgh.harvard.edu_...
>> > >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.nmr.mgh.harvard.edu_...
>> > >> > Outgoing: >> > >>https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.ed...
>> > >> > _______________________________________________ >> > 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.ed...
>> > >> > >> > 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 toyou
>> 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. >> > >> > >> > >> > >> > -- >> > 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 <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> <mailto: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...
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__surfer.nmr.mgh.harvard.e...
>> FileDrop: >>https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.ed...
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.nmr.mgh.harvard.edu_...
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.nmr.mgh.harvard.edu_...
>> Outgoing: >>https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.ed...
>> >> _______________________________________________ >> 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.ed...
>> >> >> 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. >> >> >> >> >> -- >> 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> >> <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.ed...
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
> > > _______________________________________________ > 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.ed...
> > > 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. > > > > > -- > 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 Fax: 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...
FileDrop:https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.ed...
www.nmr.mgh.harvard.edu/facility/filedrop/index.html <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.nmr.mgh.harvard.edu_...
Outgoing:https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.ed...
_______________________________________________ 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...
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 athttps://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.-- 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.ed...
-- 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...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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.
freesurfer@nmr.mgh.harvard.edu
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Douglas Greve -
Douglas N Greve
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Jasmin Alves