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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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