Hi, I seem to be having the same error, recon all is crashing out with the mri_nu_correct.mni command, e.g., if I run in the mri directory of a subject, I get what is pasted below. Any ideas for the fix?
bash-3.2$ mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz /Users/mwvoss/Analysis/ChordLearning/Freesurfer/sub100/mri /Applications/freesurfer/bin/mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz nIters 1 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Darwin dhcp80ff9e7c.dynamic.uiowa.edu 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64 Sun Jul 21 09:25:15 CDT 2013 Can't locate MNI/Startup.pm in @INC (@INC contains: /Applications/freesurfer/mni/lib/../System/Library/Perl/5.8.6 /Library/Perl/5.12/darwin-thread-multi-2level /Library/Perl/5.12 /Network/Library/Perl/5.12/darwin-thread-multi-2level /Network/Library/Perl/5.12 /Library/Perl/Updates/5.12.3 /System/Library/Perl/5.12/darwin-thread-multi-2level /System/Library/Perl/5.12 /System/Library/Perl/Extras/5.12/darwin-thread-multi-2level /System/Library/Perl/Extras/5.12 .) at /Applications/freesurfer/mni/bin/nu_correct line 37. BEGIN failed--compilation aborted at /Applications/freesurfer/mni/bin/nu_correct line 37. tmpdir is ./tmp.mri_nu_correct.mni.30026 /Users/mwvoss/Analysis/ChordLearning/Freesurfer/sub100/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.30026/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.30026/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.30026/nu0.mnc... -------------------------------------------------------- Iteration 1 Sun Jul 21 09:25:18 CDT 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.30026/nu0.mnc ./tmp.mri_nu_correct.mni.30026/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.30026/0/ -iterations 1000 -distance 50 Can't locate MNI/Startup.pm in @INC (@INC contains: /Applications/freesurfer/mni/lib/../System/Library/Perl/5.8.6 /Library/Perl/5.12/darwin-thread-multi-2level /Library/Perl/5.12 /Network/Library/Perl/5.12/darwin-thread-multi-2level /Network/Library/Perl/5.12 /Library/Perl/Updates/5.12.3 /System/Library/Perl/5.12/darwin-thread-multi-2level /System/Library/Perl/5.12 /System/Library/Perl/Extras/5.12/darwin-thread-multi-2level /System/Library/Perl/Extras/5.12 .) at /Applications/freesurfer/mni/bin/nu_correct line 37. BEGIN failed--compilation aborted at /Applications/freesurfer/mni/bin/nu_correct line 37. ERROR: nu_correct On Tue, Jun 4, 2013 at 12:51 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > It looks like it is not finding the MNI tools. Maybe Zeke can chime in. > doug > On 06/04/2013 01:48 PM, Nitenson, Adam wrote: > > > > Hi Doug, > > > > The command runs a bit further now but then exits with errors. > > Unfortunately this time there is no specific stated error. The > > last few lines of the log are: > > > > INFO: extension is mgz > > #-------------------------------------------- > > #@# Talairach Tue Jun 4 13:22:08 EDT 2013 > > /gpfs/data/twhite/anitenso/FreesurferPractice/unpack4/mri > > > > mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 > > --no-rescale --i orig.mgz --o orig_nu.mgz > > > > Linux node271 2.6.32-279.2.1.el6.x86_64 #1 SMP Fri Jul 20 01:55:29 > > UTC 2012 x86_64 x86_64 x86_64 GNU/Linux > > > > recon-all -s unpack4 exited with ERRORS at Tue Jun 4 13:22:10 EDT > > 2013 > > > > > > > > The only other section of the log that seems like it could be > > related to an error is: > > > > Can't locate MNI/Startup.pm in @INC (@INC contains: > > /gpfs/runtime/opt/perl/5.16.0/lib > > /gpfs/runtime/opt/perl/5.16.0/lib/site_perl /usr/local/lib64/perl5 > > /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl > > /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) > > at /gpfs/runtime/opt/freesurfer/5.2.0/mni/bin/nu_correct line 37. > > BEGIN failed--compilation aborted at > > /gpfs/runtime/opt/freesurfer/5.2.0/mni/bin/nu_correct line 37. > > > > So, I'm not sure what it's not liking here. > > > > Thanks again, > > Adam > > > > > > On Tue, Jun 4, 2013 at 11:44 AM, Douglas N Greve > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> > wrote: > > > > That dcmunpack command will put the data into a file called > > unpack3/MPRAGE/002/struct.nii > > It needs to be put into upack3/mri/orig/002.mgz > > doug > > > > > > > > > > On 06/04/2013 11:22 AM, Nitenson, Adam wrote: > > > > Hi Doug, > > > > When I try the command as you suggested: > > recon-all -all -s unpack3 > > I get the following error: > > > > ERROR: no run data found in > > /gpfs/data/twhite/anitenso/FreesurferPractice/unpack3/mri. > > Make sure to > > have a volume called 001.mgz in > > > /gpfs/data/twhite/anitenso/FreesurferPractice/unpack3/mri/orig > > > > Do you know why I might be lacking that volume? This was > > not usually an issue after running the two unpacksdcmdir > > commands (for MPRAGE and bold runs). > > > > Thanks, > > Adam > > > > > > On Mon, Jun 3, 2013 at 3:44 PM, Douglas N Greve > > <gr...@nmr.mgh.harvard.edu > > <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu > > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: > > > > Hi Adam, if the subject folder exists and you pass > > recon-all a -i > > flag, > > then it will exit with error saying that the data > > exist (otherwise it > > would overwrite what is there). However, just because > > the subject > > folder > > exists does not mean that there is any data sitting in > > subject/mri/orig. > > Then it will tell you that it cannot find any data. > > > > Note that when you run recon-all, you need to tell it > > to do something > > (eg, add the "-all" flag to do everything) > > > > doug > > > > > > On 06/03/2013 03:21 PM, Nitenson, Adam wrote: > > > Hello users, > > > > > > I am trying to get Freesurfer (5.2) working properly > > off-site and am > > > encountering errors I did not have while working at > > the Martinos > > > center. We use the same Siemens 3T Tim Trio scanner > > at Brown, so I > > > would hope the data is similar to work with. > > > > > > I have been using dcmunpack since unpacksdcmdir is not > > identifying the > > > DICOM files properly. I have successfully unpacked the > > structural and > > > bold scans using the command (entered from the raw > > scan data folder: > > > > > > dcmunpack -src DICOM -targ > > (path)/FreesurferPractice/unpack3 -run 2 > > > MPRAGE nii struct (I also tried using mgz > > instead of nii, > > and also > > > changed struct to other things as it appears to be a > > naming > > argument) > > > > > > dcmunpack -src DICOM -targ > > (path)/FreesurferPractice/unpack3 -fsfast > > > -run 3 bold nii f.nii -run 4 bold nii f.nii -run 5 > > bold nii > > f.nii -run > > > 6 bold nii f.nii -run 7 bold nii f.nii -run 8 bold > > nii f.nii -run 9 > > > bold nii f.nii > > > > > > (path) just being an abbreviate piece of the > > relevant pathway > > > > > > These generate the MPRAGE and bold folders in the > > subject folder as > > > expected. I have difficulties with the next commands > > (environment has > > > been set). > > > > > > I try: > > > recon-all -i <path to structural data> -s <subject > > name> -force > > > recon-all -i > > (path)/FreesurferPractice/unpack/MPRAGE/002 -s unpack3 > > > (I got an error about using -force so I omitted that > > from my > > command) > > > > > > and get the following Error > > > ERROR: You are trying to re-run an existing subject > > with (possibly) > > > new input data (-i). If this is truly new input > > data, you > > should delete > > > the subject folder and re-run, or specify a > > different subject name. > > > If you are just continuing an analysis of an > > existing subject, then > > > omit all -i flags. > > > > > > Yet when I omit -i and just use "recon-all -s > > unpack3", I get > > "ERROR: > > > nothing to do" > > > > > > I tried a different tactic and used > > > > > > "recon-all -s unpack3 -autorecon1" as well as > "recon-all > > > -autorecon-all -s unpack3" > > > > > > which both created the various folders (bem, label, > > mri, surf, etc) > > > but failed with > > > "ERROR: no run data found in > > (path)/FreesurferPractice/unpack3/mri. > > > Make sure to have a volume called 001.mgz in > > > (path)/FreesurferPractice/unpack3/mri/orig. If you > > have a second run > > > of data call it 002.mgz, etc." > > > > > > I have tried these commands in both bash and tcsh > > shells with > > the same > > > effect. So the problem, it seems, is that my "mri" > > file is > > blank, and > > > this was not a problem I had running these commands > > at Martinos. Any > > > idea what the issue might be? > > > > > > Best, > > > > > > Adam Nitenson > > > Neuroscience Graduate Program > > > Laboratory of Affective Neuroscience > > > Brown University > > > > > > > > > > > > _______________________________________________ > > > 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://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...@nmr.mgh.harvard.edu > > <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu > > <mailto:gr...@nmr.mgh.harvard.edu>> > > Phone Number: 617-724-2358 <tel:617-724-2358> > > <tel:617-724-2358 <tel:617-724-2358>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > > <tel:617-726-7422>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > > > Outgoing: > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > _______________________________________________ > > 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://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > 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. > > > > > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > Phone Number: 617-724-2358 <tel:617-724-2358> > > Fax: 617-726-7422 <tel:617-726-7422> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
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