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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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