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:> <mailto:greve@nmr.mgh.harvard.edu
>
> 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:Freesurfer@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:greve@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>
> <tel:617-724-2358 <tel:617-724-2358>>
> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422
> <tel:617-726-7422>>> <mailto:Freesurfer@nmr.mgh.harvard.edu
>
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> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
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> 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>
>
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>
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> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
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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>
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>
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--
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
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www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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