-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1
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 : #-----------------------------------------------------------------------------
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:
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1
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 : #----------------------------------------------------------------------------- -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/
iEYEARECAAYFAlGTa5kACgkQi8ffXNvWmYSCUQCghMg1EffqfeJK4PSfo20uF8/J H0MAnjJc0WbHPf5gLDUw70K8fnQPjS+L =g+6e -----END PGP SIGNATURE----- _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1
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.
-----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
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
-----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
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:
-----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-----
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 : >>
#-----------------------------------------------------------------------------
>> > >> > >>> >>
_______________________________________________ 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1
The error is fixed upstream by this commit: https://github.com/BIC-MNI/N3/commit/0fdb7b069afec6983d5aa0be1f9156266cef393...
I'm not sure if it's already part of any release, but probably that helps.
regards Peter
Am 03.06.2013 15:02, schrieb Christian Thode Larsen:
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 : >>>
#-----------------------------------------------------------------------------
>>> >> >>> >> >>>> >>>
_______________________________________________ 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
_______________________________________________
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
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.
Hi everybody. I have the same problem.
When I run the "recon-all -all", the first steps warns me about a "deprecated" command when running the "nu_correct" step:
nu_correct -clobber ./tmp.mri_nu_correct.mni.13923/nu0.mnc ./tmp.mri_nu_correct.mni.13923/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.13923/0/ [fsuser@xubuntu-VirtualBox:/home/fsuser/Desktop/sub01/mri/] [2015-10-10 18:19:24] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.13923/0/ ./tmp.mri_nu_correct.mni.13923/nu0.mnc ./tmp.mri_nu_correct.mni.13923/nu1.imp
Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. . . .
[...] (the same error repeated several times)
But the recon-all non stops and it seems that the reconstruction ends correctly. Should I be worried about this error?
I know that this may not be a problem concerning to Freesurfer software but MNI software... but I'm using the virtualbox version with no modifications or updates, and this error is present. Should not it be an environment ready to carry out the reconstruction without compatibility problems?
Thanks.
2013-06-05 8:04 GMT+02:00 Peter Wendorff peter.wendorff@c-lab.de:
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1
The error is fixed upstream by this commit:
https://github.com/BIC-MNI/N3/commit/0fdb7b069afec6983d5aa0be1f9156266cef393...
I'm not sure if it's already part of any release, but probably that helps.
regards Peter
Am 03.06.2013 15:02, schrieb Christian Thode Larsen:
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 : >>>>
#-----------------------------------------------------------------------------
>>>> >>> >>>> >>> >>>>> >>>>
_______________________________________________ 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 > > >
>
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
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.
-----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/
iEYEARECAAYFAlGu1McACgkQi8ffXNvWmYSGJwCgpEhr7dDKiOTqtk3ckpOfp6Yx DzYAn1NJaenXkkNuN/bkGkhrrNfZfNzV =zdgQ -----END PGP SIGNATURE----- _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello,
The message being output to the screen regarding "?PATTERN?" is just a warning message and is not directly related to the error you are experiencing.
The problem is that when using a virtual machine, the MNI software will crash when subjects directory is on a shared folder between the host and virtual machine. The only known solution I am aware of is to import the subject data so that it resides completely in the virtual machine space.
Best,
-Zeke
On 10/13/2015 09:46 AM, Julio Alberto González Torre wrote:
Hi everybody. I have the same problem.
When I run the "recon-all -all", the first steps warns me about a "deprecated" command when running the "nu_correct" step:
nu_correct -clobber ./tmp.mri_nu_correct.mni.13923/nu0.mnc ./tmp.mri_nu_correct.mni.13923/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.13923/0/ [fsuser@xubuntu-VirtualBox:/home/fsuser/Desktop/sub01/mri/] [2015-10-10 18:19:24] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.13923/0/ ./tmp.mri_nu_correct.mni.13923/nu0.mnc ./tmp.mri_nu_correct.mni.13923/nu1.imp Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. . . . [...] (the same error repeated several times)But the recon-all non stops and it seems that the reconstruction ends correctly. Should I be worried about this error?
I know that this may not be a problem concerning to Freesurfer software but MNI software... but I'm using the virtualbox version with no modifications or updates, and this error is present. Should not it be an environment ready to carry out the reconstruction without compatibility problems?
Thanks.
2013-06-05 8:04 GMT+02:00 Peter Wendorff <peter.wendorff@c-lab.de mailto:peter.wendorff@c-lab.de>:
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 The error is fixed upstream by this commit: https://github.com/BIC-MNI/N3/commit/0fdb7b069afec6983d5aa0be1f9156266cef393b I'm not sure if it's already part of any release, but probably that helps. regards Peter Am 03.06.2013 15:02, schrieb Christian Thode Larsen: > 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 <http://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 <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>> >>>>> >>>>>> >>>>>>>> _______________________________________________ Freesurfer >>>>>> mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>>> >>>>> >> >>> >>> >>> >> >>>>>> _______________________________________________ >> Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ Freesurfer mailing > list Freesurfer@nmr.mgh.harvard.edu <mailto: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. > -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iEYEARECAAYFAlGu1McACgkQi8ffXNvWmYSGJwCgpEhr7dDKiOTqtk3ckpOfp6Yx DzYAn1NJaenXkkNuN/bkGkhrrNfZfNzV =zdgQ -----END PGP SIGNATURE----- _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Christian Thode Larsen -
Julio Alberto González Torre -
Peter Wendorff -
Z K