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:
> -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > 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 >> > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.11 (GNU/Linux) > Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ > > iEYEARECAAYFAlGsSiAACgkQi8ffXNvWmYTWpwCdGhXYy2rs3I9KO16TfitRxOAu > WUoAni/inOLTmQzOukHxNCqzNT+U/8vB > =9jEf > -----END PGP SIGNATURE----- > _______________________________________________ > 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
