Freesurfer

freesurfer@nmr.mgh.harvard.edu

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Missing files after recon-all
by Zhi Li 14 Feb '19

14 Feb '19

External Email - Use Caution Hello FreeSurfer experts, I am trying recon-all in a SGE cluster. However, the size of of the results was smaller than that executed in a local CentOs system. I did not found error in the recon-all log file which ended with "recon-all -s sub001 finished without error". But when I used QAtools, it reported: Checking if all files exist...FAILED (read ../a003/scripts/recon_checker.log) ERROR: Subject a003 missing output file ../mri/transforms/talairach.m3z.inv.x.mgz ERROR: Subject a003 missing output file ../mri/transforms/talairach.m3z.inv.y.mgz ERROR: Subject a003 missing output file ../mri/transforms/talairach.m3z.inv.z.mgz ERROR: Subject a003 missing output file ../mri/nu_noneck.mgz ERROR: Subject a003 missing output file ../label/lh.BA1.label ERROR: Subject a003 missing output file ../label/lh.BA2.label ERROR: Subject a003 missing output file ../label/lh.BA3a.label ERROR: Subject a003 missing output file ../label/lh.BA3b.label ERROR: Subject a003 missing output file ../label/lh.BA4a.label ERROR: Subject a003 missing output file ../label/lh.BA4p.label ERROR: Subject a003 missing output file ../label/lh.BA6.label ERROR: Subject a003 missing output file ../label/lh.BA44.label ERROR: Subject a003 missing output file ../label/lh.BA45.label ERROR: Subject a003 missing output file ../label/lh.V1.label ERROR: Subject a003 missing output file ../label/lh.V2.label ERROR: Subject a003 missing output file ../label/lh.MT.label ERROR: Subject a003 missing output file ../label/lh.BA.annot ERROR: Subject a003 missing output file ../stats/lh.BA.stats ERROR: Subject a003 missing output file ../label/rh.BA1.label ERROR: Subject a003 missing output file ../label/rh.BA2.label ERROR: Subject a003 missing output file ../label/rh.BA3a.label ERROR: Subject a003 missing output file ../label/rh.BA3b.label ERROR: Subject a003 missing output file ../label/rh.BA4a.label ERROR: Subject a003 missing output file ../label/rh.BA4p.label ERROR: Subject a003 missing output file ../label/rh.BA6.label ERROR: Subject a003 missing output file ../label/rh.BA44.label ERROR: Subject a003 missing output file ../label/rh.BA45.label ERROR: Subject a003 missing output file ../label/rh.V1.label ERROR: Subject a003 missing output file ../label/rh.V2.label ERROR: Subject a003 missing output file ../label/rh.MT.label ERROR: Subject a003 missing output file ../label/rh.BA.annot ERROR: Subject a003 missing output file ../label/BA.ctab ERROR: Subject a003 missing output file ../stats/rh.BA.stats ERROR: Subject a003 missing output file ../stats/lh.entorhinal_exvivo.stats ERROR: Subject a003 missing output file ../stats/rh.entorhinal_exvivo.stats In addition, the QA results were black. But if I apply QATools on these results in a local CentOs system, the results seemed normal. Should this QA problem be caused by X11? I did not install FSL in the SGE cluster, would this be the problem of missing files after recon-all? Any suggestions would be appreciated. Thanks and best wishes, Lizhi

2 6

Re: [Freesurfer] dt_recon issue
by Greve, Douglas N.,Ph.D. 14 Feb '19

14 Feb '19

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(a)gmail.com <mailto:ddcc2442@gmail.com>_ > 443-254-6298 > > > On Thu, Feb 14, 2019 at 4:03 PM Greve, Douglas N.,Ph.D. > <DGREVE(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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. > > >

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dt_recon issue
by Daniel Davidson Callow 14 Feb '19

14 Feb '19

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 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 $LF tee -a echo exit 1 ; exit 1 Again the DICOM files are named image000001.dcm through image000065.dcm. These were 64 gradient images acquired on a SIEMENS scanner with 1 bo image. I assume there is an issue with how I am naming the input volumes for dt_recon. Any advice on how I should structure this command would be greatly appreciated! Thanks, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park dcallow(a)umd.edu <dcallow(a)gmail.com> 443-254-6298 *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298 On Wed, Feb 13, 2019 at 3:04 PM fsbuild <fsbuild(a)contbay.com> wrote: > Hello Daniel. > > It looks like you need a slash in front of Volumes for the path after —I > /Volumes > > - R. > > On Feb 13, 2019, at 14:44, Daniel Davidson Callow <dcallow(a)umd.edu> wrote: > > External Email - Use Caution > > Hello, > > I am trying to run dt_recon on my dti data using the following script. > > dt_recon --debug --i > Volumes/DANIEL/tutorial_data/diffusion_recons/${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(a)umd.edu <dcallow(a)gmail.com> > 443-254-6298 > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

4 9

Thalamic nuclei segmentation
by Antti Cajanus 14 Feb '19

14 Feb '19

External Email - Use Caution Hi! Few weeks ago I found the thalamic nuclei segmentation tool in Freesurfer development version and I had it working fine. However, I can’t find the web page anymore with the instructions how to use the tool. Is the tool still in use and if so, where can I find the instructions? Also, does free surfer have a similar segmentation tool for cerebellar subsegments? Thank you in advance! -Antti

2 1

Re: [Freesurfer] problem using recon-all
by Shachar Gal 14 Feb '19

14 Feb '19

External Email - Use Caution Hey, So I disabled SIP, and tried to run the subject from the beginning, and sadly I encountered an error while running the PreFreesurfer Pipeline, which worked fine until disabling SIP. This is the error message: ** ERROR (nifti_image_read): short header read '/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11.nii' ** ERROR: nifti_image_open(/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11): bad header info ERROR: failed to open file /Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11 ERROR: Could not open file ** ERROR (nifti_image_read): short header read '/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11.nii' ** ERROR: nifti_image_open(/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11): bad header info ERROR: failed to open file /Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11 ERROR: Could not open file /usr/local/fsl/bin/fslreorient2std: line 99: [: too many arguments /usr/local/fsl/bin/fslreorient2std: line 108: [: =: unary operator expected ** ERROR (nifti_image_read): short header read '/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11.nii' ** ERROR: nifti_image_open(/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11): bad header info ERROR: failed to open file /Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11 ERROR: Could not open file (standard_in) 1: parse error ** ERROR (nifti_image_read): short header read '/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11.nii' ** ERROR: nifti_image_open(/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11): bad header info ERROR: failed to open file /Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11 ERROR: Could not open file /usr/local/fsl/bin/fslswapdim: line 107: [: =: unary operator expected ** ERROR (nifti_image_read): short header read '/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11.nii' ** ERROR: nifti_image_open(/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11): bad header info ERROR: failed to open file /Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11 ERROR: Could not open file /usr/local/fsl/bin/fslswapdim: line 115: [: -gt: unary operator expected ** ERROR (nifti_image_read): short header read '/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11.nii' ** ERROR: nifti_image_open(/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11): bad header info ERROR: failed to open file /Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11 ERROR: Could not open file /usr/local/fsl/bin/fslswapdim: line 117: [: -gt: unary operator expected Cannot use RLAPSI notation for nifti files without either sform or qform set Thu Feb 14 11:04:26 IST 2019 - PreFreeSurferPipeline.sh: Not Averaging T1w Images Thu Feb 14 11:04:26 IST 2019 - PreFreeSurferPipeline.sh: ONLY ONE AVERAGE FOUND: COPYING Traceback (most recent call last): File "/usr/local/fsl/bin/imcp", line 11, in <module> load_entry_point('fslpy==1.7.0', 'console_scripts', 'imcp')() File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/pkg_resources/__init__.py", line 479, in load_entry_point return get_distribution(dist).load_entry_point(group, name) File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2703, in load_entry_point return ep.load() File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2321, in load return self.resolve() File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2327, in resolve module = __import__(self.module_name, fromlist=['__name__'], level=0) File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/fsl/scripts/imcp.py", line 26, in <module> import fsl.utils.imcp as imcp File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/fsl/utils/imcp.py", line 24, in <module> import fsl.data.image as fslimage File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/fsl/data/image.py", line 44, in <module> import scipy.ndimage as ndimage File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/scipy/ndimage/__init__.py", line 161, in <module> from .filters import * File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/scipy/ndimage/filters.py", line 37, in <module> from scipy.misc import doccer File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/scipy/misc/__init__.py", line 67, in <module> from scipy.interpolate._pade import pade as _pade File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/scipy/interpolate/__init__.py", line 175, in <module> from .interpolate import * File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/scipy/interpolate/interpolate.py", line 21, in <module> import scipy.special as spec File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/scipy/special/__init__.py", line 640, in <module> from ._ufuncs import * ImportError: dlopen(/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/scipy/special/_ufuncs.cpython-36m-darwin.so, 2): Symbol not found: __gfortran_stop_numeric_f08 Referenced from: /usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/scipy/special/_ufuncs.cpython-36m-darwin.so Expected in: /Applications/MATLAB_R2017b.app/sys/os/maci64/libgfortran.3.dylib in /usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/scipy/special/_ufuncs.cpython-36m-darwin.so Any thoughts? Thanks, Shachar

2 2

fsgd and contrasts
by John Absher 14 Feb '19

14 Feb '19

External Email - Use Caution Hi, I realize this is fairly straightforward for most of you, but I am relatively new to freesurfer and want to make sure I'm proceeding correctly with group analysis. We have ~35 TBI subjects and a similar number of age- and sex-matched controls, and we're trying to see if we can identify differences between groups in cortical thickness, curvature and volume. We're using parasagittal T1 post-contrast 3D volumes obtained as part of routine clinical care, and hope our data show that it is feasible to do retrospective analysis like this, when axial 3D T1 MRI volumes are unavailable. So we have: Nclasses=4 (TBI+, TBI-, M, and F) Nvariables=1 (age) NregressorsDODS = 8 Each of the contrasts is repeated for lh (left hemisphere) and rh (right hemisphere), and the 3 values for MeasurementName. The "Title" in the fsgd file is changed to specify a separate output directory for each contrast. We figure there should be 24 lh directories, and 24 rh directories when we're all done, with 8 contrasts (below) for thickness, volume and curvature (8*3), for each hemisphere (i.e., 48 total). The contrast names and matrix specifications are: Male.TBI-vs-Controls.intercept.mtx 1 -1 0 0 0 0 0 0 Male.TBI-vs-Controls.slope.mtx 0 0 0 0 1 -1 0 0 Male-female.intercept.mtx 0.5 0.5 -0.5 -0.5 0 0 0 0 Male-female.slope.mtx 0 0 0 0 0.5 0.5 -0.5 -0.5 TBI-Controls.intercept.mtx 0.5 -0.5 0.5 -0.5 0 0 0 0 TBI-Controls.slope.mtx 0 0 0 0 0.5 -0.5 0.5 -0.5 Gender-x-TBI.intercept.mtx 0.5 -0.5 -0.5 0.5 0 0 0 0 Gender-x-TBI.slope.mtx 0 0 0 0 0.5 -0.5 -0.5 0.5 Should we do other contrasts? Female.TBI-vs-Controls.intercept.mtx Female.TBI-vs-Controls.slope.mtx Age-x-TBI.intercept.mtx Age-x-TBI.slope.mtx Finally, does a permutation analysis need to be done once, or once for each contrast? Here are the first few lines of the FSGD file: GroupDescriptorFile 1 Title lh.gender_age.glmdir MeasurementName thickness Class TBIMale plus blue Class ControlMale square red Class TBIFemale circle pink Class ControlFemale black triangle Variables Age Input TBI1_002 TBIMale 45.000 Input TBI1_003 TBIFemale 46.000 Does this approach look correct? Apologies for the long post. Thanks, John John R. Absher, MD, FAAN Department of Internal Medicine, Division of Neurology Prisma Health-Upstate 200 Patewood Drive, Suite 350B Greenville, SC 29615 864-454-4500 (office) 864-350-6655 (mobile) 864-454-4505 (fax) [cid:image003.png@01D4C465.CD87B130] Inspire health. Serve with compassion. Be the difference.

2 1

Pediatric Cortical Thickness Normalization by ICV
by Williamson, Brady 14 Feb '19

14 Feb '19

External Email - Use Caution Hi, I am running an analysis in a group of pediatric subjects (4-6 years old) and want to correct cortical thickness values by ICV before running the statistical model, since we have limited degrees of freedom. While I know this is not recommended for adults, I believe it is routinely done in pediatrics but I cannot find the implementation in freesurfer. Is there a straightforward way to normalize cortical thickness by ICV before running the glm? Thanks, Brady Williamson

2 4

talairach.m3z question
by Tim Schäfer 14 Feb '19

14 Feb '19

External Email - Use Caution Dear FreeSurfer experts, I have 2 questions on the talairach.m3z file generated by recon-all. 1) What exactly does it contain? I read its the displacement field for a non-linear transform from native space to some freesurfer space. But from which input file (or space) to which other one does it transform? 2) What's the file format? Is there a spec somewhere? Thanks, -- Tim

3 2

GLM - correction for multiple comparisons
by Barletta, Valeria 14 Feb '19

14 Feb '19

Dear Freesurfers, I am performing a GLM analysis on two groups (patients versus controls) and one variable (age). We are using the following option to correct for multiple comparisons: mri_glmfit-sim --glmdir ${glm_dir}/${hemi}_contrast-${contrast}_${surfname_t1} --cache 1.3 pos/abs Is it normal to have those 2 different results when using pos or abs option? (see screenshots) Thank you! Vale

2 2

Re: [Freesurfer] Task Design Question
by Rockhill, Alexander P. 14 Feb '19

14 Feb '19

Hello Freesurfer experts, I am working on designing a task using opt seq to determine the optimal ITI and I had a question about task timing. Does it matter if the stimulus period during a task starts at the start of a TR or that the stimulus presentation lasts uninterrupted an amount of time that is an integer multiple the TR? Thanks in advance for any help. Best, Alex Translational NeuroEngineering Laboratory Division of Neurotherapeutics, Department of Psychiatry Massachusetts General Hospital, Martinos Center 149 13th St Charlestown #2301, Boston, MA 02129

2 1

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