On Mon, Jul 22, 2013 at 9:25 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

Hi Michelle

is the MNI stuff installed? If seems like ti can't find
"MNI/Startup.pm". Mine is under: $MNI_PERL5LIB/MNI/Startup.pm

cheers
Bruce

On Sun, 21 Jul
2013, Michelle W. Voss wrote:

> 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.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
> > <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/
> >
> > _______________________________________________
> > 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
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> >
> >
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> > Phone Number: 617-724-2358 <tel:617-724-2358>
> > Fax: 617-726-7422 <tel:617-726-7422>
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > <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
> greve@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/
>
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>
>
>
>