you can only give it one dicom file from the series, it will find the rest.
On 2/14/19 4:11 PM, Daniel Callow wrote:
External Email - Use Caution
As you can see the folder has 65 DICOM images labeled images000001.dcm-images000065.dcm.
I tried
dt_recon --i /Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/*.dcm --s ${subj}.${cond} --o /Volumes/DANIEL/tutorial_data/dtrecon
and got this error.
./dt_recon.sh
subj =AES101 , cond =Ex
ERROR: Flag /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000002.dcm unrecognized.
--i /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000002.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000003.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000004.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000005.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000006.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000007.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000008.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000009.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000010.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000011.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000012.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000013.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000014.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000015.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000016.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000017.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000018.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000019.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000020.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000021.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000022.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000023.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000024.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000025.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000026.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000027.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000028.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000029.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000030.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000031.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000032.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000033.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000034.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000035.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000036.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000037.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000038.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000039.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000040.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000041.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000042.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000043.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000044.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000045.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000046.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000047.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000048.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000049.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000050.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000051.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000052.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000053.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000054.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000055.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000056.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000057.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000058.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000059.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000060.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000061.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000062.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000063.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000064.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000065.dcm --s AES101.Ex --o /Volumes/DANIEL/tutorial_data/dtrecon
Darwin hlhp-105.umd.edu http://hlhp-105.umd.edu 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 10 20:06:00 PDT 2018; root:xnu-3789.73.24~1/RELEASE_X86_64 x86_64
dt_recon exited with ERRORS at Thu Feb 14 16:09:17 EST 2019
I am unsure why it is not reading these DICOM volumes in? They should be in the path I specify? Is it something to do with the way I am naming the files?
*Daniel Callow* /PhD Student, Neuroscience and Cognitive Science/ Exercise for Brain Health Lab University of Maryland, College Park _ddcc2442@gmail.com mailto:ddcc2442@gmail.com_ 443-254-6298
On Thu, Feb 14, 2019 at 4:03 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
You are trying to pass dt_recon the file 1-65.dcm but this does not exist in that folder On 2/14/19 3:41 PM, Daniel Callow wrote: > > External Email - Use Caution > > Oh sorry, for some reason the emails I am sending are not going > through to the listserv then. I have been sending them to > freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > and for some reason, they seem to have stopped going through? > > Anyways this is what I got when running the ls -l > > administrator% ls -l > /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/ > > total 172928 > > -rwxrwxrwx1 administratorstaff1276058 Feb 13 17:13 image000001.dcm > > -rwxrwxrwx1 administratorstaff1276462 Feb 13 17:13 image000002.dcm > > -rwxrwxrwx1 administratorstaff1276462 Feb 13 17:13 image000003.dcm > > -rwxrwxrwx1 administratorstaff1276470 Feb 13 17:13 image000004.dcm > > -rwxrwxrwx1 administratorstaff1276476 Feb 13 17:13 image000005.dcm > > -rwxrwxrwx1 administratorstaff1276480 Feb 13 17:13 image000006.dcm > > -rwxrwxrwx1 administratorstaff1276480 Feb 13 17:13 image000007.dcm > > -rwxrwxrwx1 administratorstaff1276476 Feb 13 17:13 image000008.dcm > > -rwxrwxrwx1 administratorstaff1276476 Feb 13 17:13 image000009.dcm > > -rwxrwxrwx1 administratorstaff1276476 Feb 13 17:13 image000010.dcm > > -rwxrwxrwx1 administratorstaff1276476 Feb 13 17:13 image000011.dcm > > -rwxrwxrwx1 administratorstaff1276484 Feb 13 17:13 image000012.dcm > > -rwxrwxrwx1 administratorstaff1276484 Feb 13 17:13 image000013.dcm > > -rwxrwxrwx1 administratorstaff1276486 Feb 13 17:13 image000014.dcm > > -rwxrwxrwx1 administratorstaff1276486 Feb 13 17:13 image000015.dcm > > -rwxrwxrwx1 administratorstaff1276478 Feb 13 17:13 image000016.dcm > > -rwxrwxrwx1 administratorstaff1276486 Feb 13 17:13 image000017.dcm > > -rwxrwxrwx1 administratorstaff1276474 Feb 13 17:13 image000018.dcm > > -rwxrwxrwx1 administratorstaff1276484 Feb 13 17:13 image000019.dcm > > -rwxrwxrwx1 administratorstaff1276474 Feb 13 17:13 image000020.dcm > > -rwxrwxrwx1 administratorstaff1276488 Feb 13 17:13 image000021.dcm > > -rwxrwxrwx1 administratorstaff1276484 Feb 13 17:13 image000022.dcm > > -rwxrwxrwx1 administratorstaff1276486 Feb 13 17:13 image000023.dcm > > -rwxrwxrwx1 administratorstaff1276480 Feb 13 17:13 image000024.dcm > > -rwxrwxrwx1 administratorstaff1276486 Feb 13 17:13 image000025.dcm > > -rwxrwxrwx1 administratorstaff1276476 Feb 13 17:13 image000026.dcm > > -rwxrwxrwx1 administratorstaff1276480 Feb 13 17:13 image000027.dcm > > -rwxrwxrwx1 administratorstaff1276484 Feb 13 17:13 image000028.dcm > > -rwxrwxrwx1 administratorstaff1276480 Feb 13 17:13 image000029.dcm > > -rwxrwxrwx1 administratorstaff1276484 Feb 13 17:13 image000030.dcm > > -rwxrwxrwx1 administratorstaff1276482 Feb 13 17:13 image000031.dcm > > -rwxrwxrwx1 administratorstaff1276486 Feb 13 17:13 image000032.dcm > > -rwxrwxrwx1 administratorstaff1276482 Feb 13 17:13 image000033.dcm > > -rwxrwxrwx1 administratorstaff1276480 Feb 13 17:13 image000034.dcm > > -rwxrwxrwx1 administratorstaff1276482 Feb 13 17:13 image000035.dcm > > -rwxrwxrwx1 administratorstaff1276476 Feb 13 17:13 image000036.dcm > > -rwxrwxrwx1 administratorstaff1276474 Feb 13 17:13 image000037.dcm > > -rwxrwxrwx1 administratorstaff1276484 Feb 13 17:13 image000038.dcm > > -rwxrwxrwx1 administratorstaff1276476 Feb 13 17:13 image000039.dcm > > -rwxrwxrwx1 administratorstaff1276490 Feb 13 17:13 image000040.dcm > > -rwxrwxrwx1 administratorstaff1276476 Feb 13 17:13 image000041.dcm > > -rwxrwxrwx1 administratorstaff1276490 Feb 13 17:13 image000042.dcm > > -rwxrwxrwx1 administratorstaff1276480 Feb 13 17:13 image000043.dcm > > -rwxrwxrwx1 administratorstaff1276488 Feb 13 17:13 image000044.dcm > > -rwxrwxrwx1 administratorstaff1276476 Feb 13 17:13 image000045.dcm > > -rwxrwxrwx1 administratorstaff1276488 Feb 13 17:13 image000046.dcm > > -rwxrwxrwx1 administratorstaff1276482 Feb 13 17:13 image000047.dcm > > -rwxrwxrwx1 administratorstaff1276486 Feb 13 17:13 image000048.dcm > > -rwxrwxrwx1 administratorstaff1276486 Feb 13 17:13 image000049.dcm > > -rwxrwxrwx1 administratorstaff1276490 Feb 13 17:13 image000050.dcm > > -rwxrwxrwx1 administratorstaff1276480 Feb 13 17:13 image000051.dcm > > -rwxrwxrwx1 administratorstaff1276474 Feb 13 17:13 image000052.dcm > > -rwxrwxrwx1 administratorstaff1276488 Feb 13 17:13 image000053.dcm > > -rwxrwxrwx1 administratorstaff1276486 Feb 13 17:13 image000054.dcm > > -rwxrwxrwx1 administratorstaff1276484 Feb 13 17:13 image000055.dcm > > -rwxrwxrwx1 administratorstaff1276488 Feb 13 17:13 image000056.dcm > > -rwxrwxrwx1 administratorstaff1276490 Feb 13 17:13 image000057.dcm > > -rwxrwxrwx1 administratorstaff1276484 Feb 13 17:13 image000058.dcm > > -rwxrwxrwx1 administratorstaff1276480 Feb 13 17:13 image000059.dcm > > -rwxrwxrwx1 administratorstaff1276472 Feb 13 17:13 image000060.dcm > > -rwxrwxrwx1 administratorstaff1276480 Feb 13 17:13 image000061.dcm > > -rwxrwxrwx1 administratorstaff1276484 Feb 13 17:13 image000062.dcm > > -rwxrwxrwx1 administratorstaff1276476 Feb 13 17:13 image000063.dcm > > -rwxrwxrwx1 administratorstaff1276490 Feb 13 17:13 image000064.dcm > > -rwxrwxrwx1 administratorstaff1276478 Feb 13 17:13 image000065.dcm > > -rwxrwxrwx1 administratorstaff5458789 Feb 13 17:13 orig.mgz > > Thank you! > *Daniel Callow* > /PhD Student, Neuroscience and Cognitive Science/ > Exercise for Brain Health Lab > University of Maryland, College Park > _ddcc2442@gmail.com <mailto:ddcc2442@gmail.com> <mailto:ddcc2442@gmail.com <mailto:ddcc2442@gmail.com>>_ > 443-254-6298 > > > On Thu, Feb 14, 2019 at 3:39 PM Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: > > I never saw an email with the result of the ls -l command > > On 2/14/19 3:36 PM, Daniel Callow wrote: > > > > External Email - Use Caution > > > > Hi Douglas, > > > > I was unsure if the emails I had been replying with were going > > through. They did not seem to come up on the mailing list so I > wasn’t > > sure if they had reached you. I recently responded to your question > > about the ls -l path output and the —debug output after fixing the > > path to the input Volumes. I wonder if you have any idea why this > > might still produce the same error? Is it an issue with the > setenv or > > the naming of the DICOM files?. Sorry for any questions. Any > help is > > greatly appreciated! > > > > On Wed, Feb 13, 2019 at 6:30 PM Greve, Douglas N.,Ph.D. > > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>> > wrote: > > > > Yes. Can you run it with --debug with the slash in front of > "Volumes"? > > > > On 2/13/19 6:25 PM, Daniel Callow wrote: > > > > > > External Email - Use Caution > > > > > > > > > Is this what you mean by no variables?? > > > > > > dt_recon --debug --i > > > > > > /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm --s > > > AES101.Ex --o /Volumes/DANIEL/tutorial_data/dtrecon > > > > > > *Daniel Callow* > > > /PhD Student, Neuroscience and Cognitive Science/ > > > Exercise for Brain Health Lab > > > University of Maryland, College Park > > > _ddcc2442@gmail.com <mailto:ddcc2442@gmail.com> <mailto:ddcc2442@gmail.com <mailto:ddcc2442@gmail.com>> > <mailto:ddcc2442@gmail.com <mailto:ddcc2442@gmail.com> <mailto:ddcc2442@gmail.com <mailto:ddcc2442@gmail.com>>> > > <mailto:ddcc2442@gmail.com <mailto:ddcc2442@gmail.com> <mailto:ddcc2442@gmail.com <mailto:ddcc2442@gmail.com>> > <mailto:ddcc2442@gmail.com <mailto:ddcc2442@gmail.com> <mailto:ddcc2442@gmail.com <mailto:ddcc2442@gmail.com>>>>_ > > > 443-254-6298 > > > > > > > > > On Wed, Feb 13, 2019 at 6:15 PM Greve, Douglas N.,Ph.D. > > > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> > > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>>> > > wrote: > > > > > > can you send the command line without the variables? > > > > > > > > > On 2/13/19 5:19 PM, Daniel Davidson Callow wrote: > > > > > > > > External Email - Use Caution > > > > > > > > Thanks for pointing that out! Unfortunately after making > > the change > > > > > > > > dt_recon --debug --i > > > > > > > > > > /Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/1-65.dcm > > > > > > > --s ${subj}.${cond} --o > /Volumes/DANIEL/tutorial_data/dtrecon > > > > > > > > > > > > I still get the error. > > > > > > > > > > > > ./dt_recon.sh > > > > > > > > mkdir: tutorial_data: File exists > > > > > > > > mkdir: diffusion_recons: File exists > > > > > > > > subj =AES101 , cond =Ex > > > > > > > > mkdir: > > /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex: > > > File > > > > exists > > > > > > > > set echo = 1 ; > > > > > > > > breaksw > > > > > > > > breaksw > > > > > > > > end > > > > > > > > end > > > > > > > > while ( $#argv != 0 ) > > > > > > > > while ( 6 != 0 ) > > > > > > > > > > > > set flag = $argv[1] ; shift ; > > > > > > > > set flag = --i > > > > > > > > shift > > > > > > > > > > > > switch ( $flag ) > > > > > > > > switch ( --i ) > > > > > > > > if ( $#argv < 1 ) goto arg1err ; > > > > > > > > if ( 5 < 1 ) goto arg1err > > > > > > > > set InputVol = "$argv[1]" ; shift ; > > > > > > > > set InputVol = > > > > > > Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm > > > > > > > > shift > > > > > > > > if ( ! -e "$InputVol" ) then > > > > > > > > if ( ! -e > > > > > > Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm > > > ) then > > > > > > > > echo "ERROR: cannot find $InputVol" > > > > > > > > echo ERROR: cannot find > > > > > > Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm > > > > > > > > ERROR: cannot find > > > > > > Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm > > > > > > > > goto error_exit ; > > > > > > > > goto error_exit > > > > > > > > uname -a | tee -a $LF > > > > > > > > uname -a > > > > > > > > tee -a > > > > > > > > Darwin hlhp-105.umd.edu <http://hlhp-105.umd.edu> <http://hlhp-105.umd.edu> > <http://hlhp-105.umd.edu> > > <http://hlhp-105.umd.edu> > > > <http://hlhp-105.umd.edu> 16.7.0 Darwin Kernel > > > > Version 16.7.0: Wed Oct 10 20:06:00 PDT 2018; > > > > root:xnu-3789.73.24~1/RELEASE_X86_64 x86_64 > > > > > > > > echo "" | & tee -a $LF > > > > > > > > tee -a > > > > > > > > echo > > > > > > > > > > > > echo "dt_recon exited with ERRORS at `date`" | & tee > -a $LF > > > > > > > > tee -a > > > > > > > > echo dt_recon exited with ERRORS at `date` > > > > > > > > date > > > > > > > > dt_recon exited with ERRORS at Wed Feb 13 17:12:30 > EST 2019 > > > > > > > > echo "" | & tee -a $LF > > > > > > > > tee -a > > > > > > > > echo > > > > > > > > > > > > exit 1 ; > > > > > > > > exit 1 > > > > > > > > > > > > Again the DICOM files are named image000001.dcm through > > > > image000065.dcm. These were 64 gradient images > acquired on a > > > SIEMENS > > > > scanner with 1 bo image. I assume there is an issue with > > how I am > > > > naming the input volumes for dt_recon. Any advice on > how I > > should > > > > structure this command would be greatly appreciated! > > > > > > > > > > > > Thanks, > > > > > > > > *Daniel Callow* > > > > /PhD Student, Neuroscience and Cognitive Science/ > > > > Exercise for Brain Health Lab > > > > University of Maryland, College Park > > > > dcallow@umd.edu <mailto:dcallow@umd.edu> <mailto:dcallow@umd.edu <mailto:dcallow@umd.edu>> > <mailto:dcallow@umd.edu <mailto:dcallow@umd.edu> <mailto:dcallow@umd.edu <mailto:dcallow@umd.edu>>> > > <mailto:dcallow@umd.edu <mailto:dcallow@umd.edu> <mailto:dcallow@umd.edu <mailto:dcallow@umd.edu>> > <mailto:dcallow@umd.edu <mailto:dcallow@umd.edu> <mailto:dcallow@umd.edu <mailto:dcallow@umd.edu>>>> > > > <mailto:dcallow@gmail.com <mailto:dcallow@gmail.com> <mailto:dcallow@gmail.com <mailto:dcallow@gmail.com>> > <mailto:dcallow@gmail.com <mailto:dcallow@gmail.com> <mailto:dcallow@gmail.com <mailto:dcallow@gmail.com>>> > > <mailto:dcallow@gmail.com <mailto:dcallow@gmail.com> <mailto:dcallow@gmail.com <mailto:dcallow@gmail.com>> > <mailto:dcallow@gmail.com <mailto:dcallow@gmail.com> <mailto:dcallow@gmail.com <mailto:dcallow@gmail.com>>>>> > > > > 443-254-6298 > > > > *Daniel Callow* > > > > /PhD Student, Neuroscience and Cognitive Science/ > > > > Exercise for Brain Health Lab > > > > University of Maryland, College Park > > > > _ddcc2442@gmail.com <mailto:ddcc2442@gmail.com> <mailto:ddcc2442@gmail.com <mailto:ddcc2442@gmail.com>> > <mailto:ddcc2442@gmail.com <mailto:ddcc2442@gmail.com> <mailto:ddcc2442@gmail.com <mailto:ddcc2442@gmail.com>>> > > <mailto:ddcc2442@gmail.com <mailto:ddcc2442@gmail.com> <mailto:ddcc2442@gmail.com <mailto:ddcc2442@gmail.com>> > <mailto:ddcc2442@gmail.com <mailto:ddcc2442@gmail.com> <mailto:ddcc2442@gmail.com <mailto:ddcc2442@gmail.com>>>> > > > <mailto:ddcc2442@gmail.com <mailto:ddcc2442@gmail.com> <mailto:ddcc2442@gmail.com <mailto:ddcc2442@gmail.com>> > <mailto:ddcc2442@gmail.com <mailto:ddcc2442@gmail.com> <mailto:ddcc2442@gmail.com <mailto:ddcc2442@gmail.com>>> > > <mailto:ddcc2442@gmail.com <mailto:ddcc2442@gmail.com> <mailto:ddcc2442@gmail.com <mailto:ddcc2442@gmail.com>> > <mailto:ddcc2442@gmail.com <mailto:ddcc2442@gmail.com> <mailto:ddcc2442@gmail.com <mailto:ddcc2442@gmail.com>>>>>_ > > > > 443-254-6298 > > > > > > > > > > > > On Wed, Feb 13, 2019 at 3:04 PM fsbuild > > <fsbuild@contbay.com <mailto:fsbuild@contbay.com> <mailto:fsbuild@contbay.com <mailto:fsbuild@contbay.com>> > <mailto:fsbuild@contbay.com <mailto:fsbuild@contbay.com> <mailto:fsbuild@contbay.com <mailto:fsbuild@contbay.com>>> > > > <mailto:fsbuild@contbay.com <mailto:fsbuild@contbay.com> > <mailto:fsbuild@contbay.com <mailto:fsbuild@contbay.com>> <mailto:fsbuild@contbay.com <mailto:fsbuild@contbay.com> > <mailto:fsbuild@contbay.com <mailto:fsbuild@contbay.com>>>> > > > > <mailto:fsbuild@contbay.com <mailto:fsbuild@contbay.com> > <mailto:fsbuild@contbay.com <mailto:fsbuild@contbay.com>> <mailto:fsbuild@contbay.com <mailto:fsbuild@contbay.com> > <mailto:fsbuild@contbay.com <mailto:fsbuild@contbay.com>>> > > <mailto:fsbuild@contbay.com <mailto:fsbuild@contbay.com> <mailto:fsbuild@contbay.com <mailto:fsbuild@contbay.com>> > <mailto:fsbuild@contbay.com <mailto:fsbuild@contbay.com> <mailto:fsbuild@contbay.com <mailto:fsbuild@contbay.com>>>>>> wrote: > > > > > > > > Hello Daniel. > > > > > > > > It looks like you need a slash in front of > Volumes for > > the path > > > > after —I > > > > /Volumes > > > > > > > > - R. > > > > > > > >> On Feb 13, 2019, at 14:44, Daniel Davidson Callow > > > >> <dcallow@umd.edu <mailto:dcallow@umd.edu> <mailto:dcallow@umd.edu <mailto:dcallow@umd.edu>> > <mailto:dcallow@umd.edu <mailto:dcallow@umd.edu> <mailto:dcallow@umd.edu <mailto:dcallow@umd.edu>>> > > <mailto:dcallow@umd.edu <mailto:dcallow@umd.edu> <mailto:dcallow@umd.edu <mailto:dcallow@umd.edu>> > <mailto:dcallow@umd.edu <mailto:dcallow@umd.edu> <mailto:dcallow@umd.edu <mailto:dcallow@umd.edu>>>> > > > <mailto:dcallow@umd.edu <mailto:dcallow@umd.edu> <mailto:dcallow@umd.edu <mailto:dcallow@umd.edu>> > <mailto:dcallow@umd.edu <mailto:dcallow@umd.edu> <mailto:dcallow@umd.edu <mailto:dcallow@umd.edu>>> > > <mailto:dcallow@umd.edu <mailto:dcallow@umd.edu> <mailto:dcallow@umd.edu <mailto:dcallow@umd.edu>> > <mailto:dcallow@umd.edu <mailto:dcallow@umd.edu> <mailto:dcallow@umd.edu <mailto:dcallow@umd.edu>>>>>> wrote: > > > >> > > > >> External Email - Use Caution > > > >> > > > >> > > > >> Hello, > > > >> > > > >> I am trying to run dt_recon on my dti data > using the > > following > > > >> script. > > > >> > > > >> dt_recon --debug --i > > > >> > > > > > > Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/1-65.dcm > > > >> --s ${subj}.${cond} --o > > /Volumes/DANIEL/tutorial_data/dtrecon > > > >> > > > >> > > > >> with the following error > > > >> > > > >> echo "ERROR: cannot find $InputVol" > > > >> echo ERROR: cannot find > > > >> > > Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm > > > >> ERROR: cannot find > > > >> > > Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm > > > >> goto error_exit ; > > > >> > > > >> the DICOM files are > > > named image000001.dcm through image000065.dcm > > > >> > > > >> These were 64 gradient images acquired on a SIEMENS > > scanner > > > with > > > >> 1 bo image. Any advice on how I should > structure this > > command > > > >> would be greatly appreciated! > > > >> > > > >> *Daniel Callow* > > > >> /PhD Student, Neuroscience and Cognitive Science/ > > > >> Exercise for Brain Health Lab > > > >> University of Maryland, College Park > > > >> dcallow@umd.edu <mailto:dcallow@umd.edu> <mailto:dcallow@umd.edu <mailto:dcallow@umd.edu>> > <mailto:dcallow@umd.edu <mailto:dcallow@umd.edu> <mailto:dcallow@umd.edu <mailto:dcallow@umd.edu>>> > > <mailto:dcallow@umd.edu <mailto:dcallow@umd.edu> <mailto:dcallow@umd.edu <mailto:dcallow@umd.edu>> > <mailto:dcallow@umd.edu <mailto:dcallow@umd.edu> <mailto:dcallow@umd.edu <mailto:dcallow@umd.edu>>>> > > > <mailto:dcallow@gmail.com <mailto:dcallow@gmail.com> <mailto:dcallow@gmail.com <mailto:dcallow@gmail.com>> > <mailto:dcallow@gmail.com <mailto:dcallow@gmail.com> <mailto:dcallow@gmail.com <mailto:dcallow@gmail.com>>> > > <mailto:dcallow@gmail.com <mailto:dcallow@gmail.com> <mailto:dcallow@gmail.com <mailto:dcallow@gmail.com>> > <mailto:dcallow@gmail.com <mailto:dcallow@gmail.com> <mailto:dcallow@gmail.com <mailto:dcallow@gmail.com>>>>> > > > >> 443-254-6298 > > > >> > > > >> _______________________________________________ > > > >> 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>>>> > > > >> <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 <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> > > > >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > _______________________________________________ > > > > 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://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > _______________________________________________ > > > 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://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > _______________________________________________ > > > 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://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > 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://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > *Daniel Callow* > > /PhD Student, Neuroscience and Cognitive Science/ > > Exercise for Brain Health Lab > > University of Maryland, College Park > > _ddcc2442@gmail.com <mailto:ddcc2442@gmail.com> <mailto:ddcc2442@gmail.com <mailto:ddcc2442@gmail.com>> > <mailto:ddcc2442@gmail.com <mailto:ddcc2442@gmail.com> <mailto:ddcc2442@gmail.com <mailto:ddcc2442@gmail.com>>>_ > > 443-254-6298 > > > > 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 > http://www.partners.org/complianceline . 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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Greve, Douglas N.,Ph.D.