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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>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>
>>>>>>
>>>>>>>
>>>>>>>>
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>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________ Freesurfer
>>>>>> mailing list Freesurfer@nmr.mgh.harvard.edu
>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>
>>>
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>>>>
>>>>
>>>>
>>>