-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 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 >> >> >> > -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iEYEARECAAYFAlGskhMACgkQi8ffXNvWmYQoYgCbBvHqOJcAvNkJiINqoz5s9WdC U2AAoMPh5UN4WhHIYCf6c14gSQMH/8Ma =fFxr -----END PGP SIGNATURE----- _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
