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.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://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>
>     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
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>     . If the e-mail was sent to you in error
>     but does not contain patient information, please contact the
>     sender and properly
>     dispose of the e-mail.
>
>
>
>
> --
> Jasmin Alves
> Predoctoral Student
> Medical Biology Graduate Program
> University of Southern California
> jalves@usc.edu <mailto:jalves@usc.edu>
>
>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_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