Can't run mrAnatLoadSpmVol in deployed mode

[soichih]

We are running vistasoft in deployed (compiled) mode, and we are having an issue with mrAnatLoadSpmVol function.

Error using spm>spm_version (line 1269)
Can't obtain SPM Revision information.

Error in spm (line 875)


Error in mrAnatLoadSpmVol (line 32)

We are using spm8 and I think this is really a spm issue, but I am not sure if spm8 is still maintained or not.. So the easiest fix for us is to patch mrAnatLoadSpmVol with following.

diff --git a/mrAnatomy/VolumeUtilities/mrAnatLoadSpmVol.m b/mrAnatomy/VolumeUtilities/mrAnatLoadSpmVol.m
index 0fed6d6..eba7e1a 100644
--- a/mrAnatomy/VolumeUtilities/mrAnatLoadSpmVol.m
+++ b/mrAnatomy/VolumeUtilities/mrAnatLoadSpmVol.m
@@ -29,7 +29,7 @@ elseif(isstruct(fname)&&isfield(fname,'nifti_type'))
         elseif(strcmp(type,'double')), type = 'float64'; end
         type = spm_type(type);
     end
-    if(strcmp(spm('Ver'),'SPM2'))
+    if(strcmp('SPM8','SPM2'))
         V.dim = [V.dim type];
     else
         V.dt = [type 0];

Unless vistasoft is still supporting spm2, I was wondering if it can simply drop spm2 unless people are still using it?

[francopestilli]

@jyeatman @JWinawer @wandell would it be OK to remove the check for SPM2?

[JWinawer]

Yes, should be ok. I use SPM 12 with vistasoft. But I think this line won't work: + if(strcmp('SPM8','SPM2')) Since it will always be false. Meantime, I will check whether any of the validation functions call mrAnatLoadSpmVol.

…

On Thu, Feb 15, 2018 at 8:23 AM, Franco Pestilli ***@***.***> wrote: @jyeatman <https://github.com/jyeatman> @JWinawer <https://github.com/jwinawer> @wandell <https://github.com/wandell> would it be OK to remove the check for SPM2? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#278 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ACBX3uqz80mt5IXe8HRV6LYCL4vwDYFVks5tVC_igaJpZM4SG1Qn> .

-- Jonathan Winawer Assistant Professor of Psychology and Neural Science New York University 6 Washington Place New York, NY, 10003 (212) 998-7922 (phone) (212) 995-4018 (fax) jonathan.winawer@nyu.edu http://psych.nyu.edu/winawer/

[JWinawer]

As far as I can tell, this function is not called in any of the validation code and is only called in these two places in the repository: - mrAnatComputeSpmSpatialNorm.m 54 Vtemplate = mrAnatLoadSpmVol(templateFileName); - dtiLoadNormalizedMap.m 49 V = mrAnatLoadSpmVol(fullfile(p,fname)); If the desired functionality for any SPM version beyond 2 is V.dt = [type 0]; then I suggest eliminating the check, i.e. replacing this block, if(strcmp(spm('Ver'),'SPM2')) V.dim = [V.dim type]; else V.dt = [type 0]; end with V.dt = [type 0]; since SPM 2 is way out of date and need not be supported.

…

-Jon On Thu, Feb 15, 2018 at 8:39 AM, Jonathan A Winawer < jonathan.winawer@nyu.edu> wrote:

Yes, should be ok. I use SPM 12 with vistasoft. But I think this line won't work: + if(strcmp('SPM8','SPM2')) Since it will always be false. Meantime, I will check whether any of the validation functions call mrAnatLoadSpmVol. On Thu, Feb 15, 2018 at 8:23 AM, Franco Pestilli ***@***.*** > wrote: > @jyeatman <https://github.com/jyeatman> @JWinawer > <https://github.com/jwinawer> @wandell <https://github.com/wandell> > would it be OK to remove the check for SPM2? > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > <#278 (comment)>, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/ACBX3uqz80mt5IXe8HRV6LYCL4vwDYFVks5tVC_igaJpZM4SG1Qn> > . > -- Jonathan Winawer Assistant Professor of Psychology and Neural Science New York University 6 Washington Place New York, NY, 10003 (212) 998-7922 (phone) (212) 995-4018 (fax) ***@***.*** http://psych.nyu.edu/winawer/

-- Jonathan Winawer Assistant Professor of Psychology and Neural Science New York University 6 Washington Place New York, NY, 10003 (212) 998-7922 (phone) (212) 995-4018 (fax) jonathan.winawer@nyu.edu http://psych.nyu.edu/winawer/

[jyeatman]

AFQ uses this function and is currently only compatible with spm8. Shouldn’t be hard to update but I’m not sure when I’ll have the time to make that change. Is keeping som8 compatibility a problem? On Thu, Feb 15, 2018 at 6:18 AM Jonathan Winawer <notifications@github.com> wrote:

As far as I can tell, this function is not called in any of the validation code and is only called in these two places in the repository: - mrAnatComputeSpmSpatialNorm.m 54 Vtemplate = mrAnatLoadSpmVol(templateFileName); - dtiLoadNormalizedMap.m 49 V = mrAnatLoadSpmVol(fullfile(p,fname)); If the desired functionality for any SPM version beyond 2 is V.dt = [type 0]; then I suggest eliminating the check, i.e. replacing this block, if(strcmp(spm('Ver'),'SPM2')) V.dim = [V.dim type]; else V.dt = [type 0]; end with V.dt = [type 0]; since SPM 2 is way out of date and need not be supported. -Jon On Thu, Feb 15, 2018 at 8:39 AM, Jonathan A Winawer < ***@***.***> wrote: > Yes, should be ok. I use SPM 12 with vistasoft. > > But I think this line won't work: > > + if(strcmp('SPM8','SPM2')) > > > Since it will always be false. > > Meantime, I will check whether any of the validation functions call mrAnatLoadSpmVol. > > > On Thu, Feb 15, 2018 at 8:23 AM, Franco Pestilli < ***@***.*** > > wrote: > >> @jyeatman <https://github.com/jyeatman> @JWinawer >> <https://github.com/jwinawer> @wandell <https://github.com/wandell> >> would it be OK to remove the check for SPM2? >> >> — >> You are receiving this because you were mentioned. >> Reply to this email directly, view it on GitHub >> < #278 (comment)>, >> or mute the thread >> < https://github.com/notifications/unsubscribe-auth/ACBX3uqz80mt5IXe8HRV6LYCL4vwDYFVks5tVC_igaJpZM4SG1Qn > >> . >> > > > > -- > Jonathan Winawer > Assistant Professor of Psychology and Neural Science > > New York University > 6 Washington Place <https://maps.google.com/?q=6+Washington+Place+%0D+%3E+New+York,+NY,+10003&entry=gmail&source=g> <https://maps.google.com/?q=6+Washington+Place+%0D+%3E+New+York,+NY,+10003&entry=gmail&source=g>> New York, NY, 10003 <https://maps.google.com/?q=6+Washington+Place+%0D+%3E+New+York,+NY,+10003&entry=gmail&source=g> > (212) 998-7922 (phone) > (212) 995-4018 (fax) > ***@***.*** > http://psych.nyu.edu/winawer/ > -- Jonathan Winawer Assistant Professor of Psychology and Neural Science New York University 6 Washington Place <https://maps.google.com/?q=6+Washington+Place+%0D+New+York,+NY,+10003&entry=gmail&source=g> New York, NY, 10003 <https://maps.google.com/?q=6+Washington+Place+%0D+New+York,+NY,+10003&entry=gmail&source=g> (212) 998-7922 (phone) (212) 995-4018 (fax) ***@***.*** http://psych.nyu.edu/winawer/ — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#278 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABsYyi5hwMSh39AJnB_gRdnvAPe3ZRLeks5tVDx0gaJpZM4SG1Qn> .

-- Sent from a mobile device. Please excuse typos

[JWinawer]

I think SPM 8 is fine. It's just SPM 2 that I thought we should stop supporting. If you have unit testing for AFQ, then maybe you can just check that this change will not cause a problem. The change I suggested was to replace the if/then/else with the simplest line that would work: - if(strcmp(spm('Ver'),'SPM2')) - V.dim = [V.dim type]; - else - V.dt = [type 0]; - end + V.dt = [type 0]; On Thu, Feb 15, 2018 at 10:59 AM, Jason D. Yeatman <notifications@github.com

…

wrote: AFQ uses this function and is currently only compatible with spm8. Shouldn’t be hard to update but I’m not sure when I’ll have the time to make that change. Is keeping som8 compatibility a problem? On Thu, Feb 15, 2018 at 6:18 AM Jonathan Winawer ***@***.*** > wrote: > As far as I can tell, this function is not called in any of the validation > code and is only called in these two places in the repository: > > > - mrAnatComputeSpmSpatialNorm.m 54 Vtemplate = > mrAnatLoadSpmVol(templateFileName); > - dtiLoadNormalizedMap.m 49 V = mrAnatLoadSpmVol(fullfile(p,fname)); > > If the desired functionality for any SPM version beyond 2 is > > > V.dt = [type 0]; > > > then I suggest eliminating the check, i.e. replacing this block, > > > if(strcmp(spm('Ver'),'SPM2')) > > V.dim = [V.dim type]; > > else > > V.dt = [type 0]; > > end > > with > > V.dt = [type 0]; > > since SPM 2 is way out of date and need not be supported. > > > -Jon > > > > > On Thu, Feb 15, 2018 at 8:39 AM, Jonathan A Winawer < > ***@***.***> wrote: > > > Yes, should be ok. I use SPM 12 with vistasoft. > > > > But I think this line won't work: > > > > + if(strcmp('SPM8','SPM2')) > > > > > > Since it will always be false. > > > > Meantime, I will check whether any of the validation functions call > mrAnatLoadSpmVol. > > > > > > On Thu, Feb 15, 2018 at 8:23 AM, Franco Pestilli < > ***@***.*** > > > wrote: > > > >> @jyeatman <https://github.com/jyeatman> @JWinawer > >> <https://github.com/jwinawer> @wandell <https://github.com/wandell> > >> would it be OK to remove the check for SPM2? > >> > >> — > >> You are receiving this because you were mentioned. > >> Reply to this email directly, view it on GitHub > >> < > #278 (comment) >, > >> or mute the thread > >> < > https://github.com/notifications/unsubscribe-auth/ ACBX3uqz80mt5IXe8HRV6LYCL4vwDYFVks5tVC_igaJpZM4SG1Qn > > > >> . > >> > > > > > > > > -- > > Jonathan Winawer > > Assistant Professor of Psychology and Neural Science > > > > New York University > > 6 Washington Place <https://maps.google.com/?q=6+Washington+Place&entry=gmail&source=g> > <https://maps.google.com/?q=6+Washington+Place+%0D+%3E+New+ York,+NY,+10003&entry=gmail&source=g> > > <https://maps.google.com/?q=6+Washington+Place+%0D+%3E+New+ York,+NY,+10003&entry=gmail&source=g>> > New York, NY, 10003 > <https://maps.google.com/?q=6+Washington+Place+%0D+%3E+New+ York,+NY,+10003&entry=gmail&source=g> > > (212) 998-7922 (phone) > > (212) 995-4018 (fax) > > ***@***.*** > > http://psych.nyu.edu/winawer/ > > > > > > -- > Jonathan Winawer > Assistant Professor of Psychology and Neural Science > > New York University > 6 Washington Place <https://maps.google.com/?q=6+Washington+Place&entry=gmail&source=g> > <https://maps.google.com/?q=6+Washington+Place+%0D+New+York, +NY,+10003&entry=gmail&source=g> > New York, NY, 10003 > <https://maps.google.com/?q=6+Washington+Place+%0D+New+York, +NY,+10003&entry=gmail&source=g> > (212) 998-7922 (phone) > (212) 995-4018 (fax) > ***@***.*** > http://psych.nyu.edu/winawer/ > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > <#278 (comment) >, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/ABsYyi5hwMSh39AJnB_ gRdnvAPe3ZRLeks5tVDx0gaJpZM4SG1Qn> > . > -- Sent from a mobile device. Please excuse typos — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#278 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ACBX3ubKcv2TCz7ojARJ72KO9ZFumgAwks5tVFRVgaJpZM4SG1Qn> .

-- Jonathan Winawer Assistant Professor of Psychology and Neural Science New York University 6 Washington Place New York, NY, 10003 (212) 998-7922 (phone) (212) 995-4018 (fax) jonathan.winawer@nyu.edu http://psych.nyu.edu/winawer/

[francopestilli]

Correct. The issue is with SPM2.

[JWinawer]

@francopestilli , @soichih , @jyeatman :
Is this resolved? It's just a short bit of code. We just need someone to test it and commit it, if it hasn't already been done.

[soichih]

I can test it if this is already updated upstream. We are still using our locally patched version of vistasoft.

[soichih]

Can you merge my PR? We are unable to use the official version of vistasoft and our branch is diverging and affecting our workflow.