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 : > >>>>>>> > #----------------------------------------------------------------------------- > >>>>>>> > >>>>>> > >>>>>>> > >>>>>> > >>>>>>>> > >>>>>>> > _______________________________________________ Freesurfer > >>>>>>>> mailing list 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 > >>>>>> 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
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