Hello, The message being output to the screen regarding "?PATTERN?" is just a warning message and is not directly related to the error you are experiencing.
The problem is that when using a virtual machine, the MNI software will crash when subjects directory is on a shared folder between the host and virtual machine. The only known solution I am aware of is to import the subject data so that it resides completely in the virtual machine space. Best, -Zeke On 10/13/2015 09:46 AM, Julio Alberto González Torre wrote: > Hi everybody. I have the same problem. > > When I run the "recon-all -all", the first steps warns me about a > "deprecated" command when running the "nu_correct" step: > > nu_correct -clobber ./tmp.mri_nu_correct.mni.13923/nu0.mnc > ./tmp.mri_nu_correct.mni.13923/nu1.mnc -tmpdir > ./tmp.mri_nu_correct.mni.13923/0/ > [fsuser@xubuntu-VirtualBox:/home/fsuser/Desktop/sub01/mri/] > [2015-10-10 18:19:24] running: > /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log > -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask > -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber > -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.13923/0/ > ./tmp.mri_nu_correct.mni.13923/nu0.mnc > ./tmp.mri_nu_correct.mni.13923/nu1.imp > > Use of ?PATTERN? without explicit operator is deprecated at > /usr/local/freesurfer/mni/bin/sharpen_volume line 153. > > Processing:.................................................................Done > Use of ?PATTERN? without explicit operator is deprecated at > /usr/local/freesurfer/mni/bin/sharpen_volume line 153. > . > . > . > > [...] (the same error repeated several times) > > > > But the recon-all non stops and it seems that the reconstruction ends > correctly. Should I be worried about this error? > > I know that this may not be a problem concerning to Freesurfer software > but MNI software... but I'm using the virtualbox version with no > modifications or updates, and this error is present. Should not it be an > environment ready to carry out the reconstruction without compatibility > problems? > > Thanks. > > > 2013-06-05 8:04 GMT+02:00 Peter Wendorff <peter.wendo...@c-lab.de > <mailto:peter.wendo...@c-lab.de>>: > > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > The error is fixed upstream by this commit: > > https://github.com/BIC-MNI/N3/commit/0fdb7b069afec6983d5aa0be1f9156266cef393b > > I'm not sure if it's already part of any release, but probably that > helps. > > regards > Peter > > Am 03.06.2013 15:02, schrieb Christian Thode Larsen: > > Hi, > > > > While you're on the subject, there's a version 1.12 available from > > http://packages.bic.mni.mcgill.ca/tgz/ (dated January 2011, > > Freesurfer wraps and uses 1.10). I'm running tests with this > > version, and it also produces the errors mentioned. > > > > Best Regards, Christian > > > > On 06/03/2013 02:56 PM, Bruce Fischl wrote: > >> Hi Peter > >> > >> I would try this: > >> > >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > >> > >> Bruce On Mon, 3 Jun 2013, Peter Wendorff wrote: > >> > >> Hi Brucel yes, sure - sorry. I followed your advice (your > >> response to my first mail here), and found > >> http://www.bic.mni.mcgill.ca/Research/Homepage which - if I'm > >> not mistaken - is the MNI institute you pointed me to. As there's > >> no John Sled listed on their website I wrote to Jennifer Chew, > >> who is mentioned as general admnistrative questions or > >> assistance, but I did not get an answer yet. > >> > >> I'll wait for a response further, but if there's any more direct > >> contact, I would be happy to get an additional pointer ;) > >> > >> regards Peter > >> > >> > >> Am 03.06.2013 14:29, schrieb Bruce Fischl: > >>>>> Hi Peter, > >>>>> > >>>>> did you mean MNI when you said MRI? I think that they are > >>>>> still maintaining it - I would be surprised otherwise Bruce > >>>>> On Mon, 3 Jun 2013, Peter Wendorff wrote: > >>>>> > >>>>> Hi again. > >>>>> > >>>>> So: is the MRI stuff dead code? I wrote an email to > >>>>> Jennifer Chew asking for the right contact for bugs/issues > >>>>> regarding that code. That mail has been sent on May 22nd > >>>>> and I didn't get any response, yet. > >>>>> > >>>>> Is that code ever updated by the freesurfer team? Or only > >>>>> if there's anybody from MRI joining in by some kind of a > >>>>> pull request (in git terms)? If the latter: Are pull > >>>>> requests accepted even by other people than MRI stuff (e.g. > >>>>> by me, if I'm working out my patch, which I haven't done > >>>>> yet)? How to apply that patch then? > >>>>> > >>>>> regards Peter > >>>>> > >>>>> Am 15.05.2013 16:18, schrieb Peter Wendorff: > >>>>>>>> Hi Bruce. > >>>>>>>> > >>>>>>>> Thanks - kind of... > >>>>>>>> > >>>>>>>> Can you point me to anybody working on that stuff > >>>>>>>> there currently? The cprresponding code is from 1996, > >>>>>>>> and according to the MNI website, it's author John > >>>>>>>> Sled isn't there any more. > >>>>>>>> > >>>>>>>> Who's the maintainer of these code parts in the > >>>>>>>> freesurfer project? (Or isn't there anybody > >>>>>>>> responsible?) > >>>>>>>> > >>>>>>>> Is there some kind of master repository/project for > >>>>>>>> their code in Freesurfer (if the freesurfer project I > >>>>>>>> hoped to address here isn't responsible for it)? > >>>>>>>> > >>>>>>>> If I were a pearl guru and know exactly what could > >>>>>>>> and could not happen by this patch, I would probably > >>>>>>>> ask for repository access, but I'm not, so any > >>>>>>>> contact being responsible would be great. > >>>>>>>> > >>>>>>>> regards Peter > >>>>>>>> > >>>>>>>> Am 15.05.2013 15:04, schrieb Bruce Fischl: > >>>>>>>>> thanks Peter, > >>>>>>>> > >>>>>>>>> that's actually MNI code, so you might want to > >>>>>>>>> report it to them. > >>>>>>>> > >>>>>>>>> Bruce On Wed, 15 May 2013, Peter Wendorff wrote: > >>>>>>>> > >>>>>>>>> Hi. > >>>>>>>> > >>>>>>>>> I'm working with freesurfer as a software developer > >>>>>>>>> in a cloud project. My task is to enable control of > >>>>>>>>> freesurfer via network (e.g. REST interfaces). > >>>>>>>> > >>>>>>>>> That works fine so far, but I stumbled over the > >>>>>>>>> following pearl deprecated warning: > >>>>>>>> > >>>>>>>>> "Use of ?PATTERN? without explicit operator is > >>>>>>>>> deprecated at > >>>>>>>>> /usr/local/freesurfer//mni/bin/sharpen_volume line > >>>>>>>>> 153." > >>>>>>>> > >>>>>>>>> Which has been printed to the log files > >>>>>>>>> repeatingly. I'm not a pearl expert, but I think, > >>>>>>>>> it's due to a more up to date pearl version used > >>>>>>>>> here, that deprecated the usage of ? delimiters for > >>>>>>>>> patterns without explicit operator. Using / as a > >>>>>>>>> delimiter works fine. > >>>>>>>> > >>>>>>>>> I changed that locally to (new line 153): > >>>>>>>> > >>>>>>>>> ($output_volume =~ /^([\S]+).mnc/) && ($base_name = > >>>>>>>>> $1) || die "sharpen_volume failed: output volume > >>>>>>>>> does not appear to be" ." a minc volume.\n"; > >>>>>>>> > >>>>>>>>> (the original code here was): ($output_volume =~ > >>>>>>>>> ?^([\S]+).mnc?) && ($base_name = $1) || die > >>>>>>>>> "sharpen_volume failed: output volume does not > >>>>>>>>> appear to be" ." a minc volume.\n"; > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>>> I'm not sure this is the best solution. It's even > >>>>>>>>> not strictly necessary to change this - it's only a > >>>>>>>>> warning that's thrown; but I think, it's useful. > >>>>>>>> > >>>>>>>>> How can I submit this as a patch? Is it enough to > >>>>>>>>> report here? What to do? > >>>>>>>> > >>>>>>>>> regards Peter Wendorff > >>>>>>>> > >>>>>>>>> P.S.: For referene the header parameters of my > >>>>>>>>> sharpen_volume for revision comparison: > >>>>>>>> > >>>>>>>>> > >> > > #---------------------------------------------------------------------------- > >>>>>>>>> > >>>>>>>> > >>>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>>> > >>>>>>>>> > >> > >> > #$RCSfile: sharpen_volume.in <http://sharpen_volume.in>,v $ > #$Revision: 1.1 $ #$Author: > >>>>>>>>> bert $ #$Date: 2003/04/16 14:29:34 $ #$State: Exp > >>>>>>>>> $ > >>>>>>>>> > >> > > #--------------------------------------------------------------------------- > >>>>>>>>> > >>>>>>>> > >>>>>>>>> > >>>>>>>>> > >> > >> > # ------------------------------ MNI Header > >>>>>>>>> ---------------------------------- #@NAME : > >>>>>>>>> sharpen_volume #@INPUT : #@OUTPUT : > >>>>>>>>> #@RETURNS : #@DESCRIPTION: modifies intensities > >>>>>>>>> so as to produce a sharper histogram #@METHOD : > >>>>>>>>> #@GLOBALS : #@CALLS : #@CREATED : > >>>>>>>>> February 28, 1996 #@MODIFIED : > >>>>>>>>> > >> > > #----------------------------------------------------------------------------- > >>>>>>>>> > >>>>>>>> > >>>>>>>>> > >>>>>>>> > >>>>>>>>>> > >>>>>>>>> > >> > >> > _______________________________________________ Freesurfer > >>>>>>>>>> mailing list 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. > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> _______________________________________________ > >>>>>>>> Freesurfer mailing list > >>>>>>>> Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > >>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>>>>>>> > >>>>> > >>>>>> > >>>>>>>> > _______________________________________________ Freesurfer > >>>>>> mailing list Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>>>>> > >>>>>> > >>>>>> > >>>>> > >> > >>> > >>> > >>> > >> > >>>>>> > _______________________________________________ > >> Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > _______________________________________________ Freesurfer mailing > > list 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. > > > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.11 (GNU/Linux) > Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ > > iEYEARECAAYFAlGu1McACgkQi8ffXNvWmYSGJwCgpEhr7dDKiOTqtk3ckpOfp6Yx > DzYAn1NJaenXkkNuN/bkGkhrrNfZfNzV > =zdgQ > -----END PGP SIGNATURE----- > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
