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.wendorff@c-lab.de:
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The error is fixed upstream by this commit:
https://github.com/BIC-MNI/N3/commit/0fdb7b069afec6983d5aa0be1f9156266cef393...
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,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 : >>>>
#-----------------------------------------------------------------------------
>>>> >>> >>>> >>> >>>>> >>>>
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