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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