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 greve@nmr.mgh.harvard.eduwrote:
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 <greve@nmr.mgh.harvard.edu <mailto:greve@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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <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/
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