Freesurfer

freesurfer@nmr.mgh.harvard.edu

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Re: [Freesurfer] average values per cluster
by maaike rive 27 May '16

27 May '16

Hi Douglas, Can I ask another question relating to an issue I ran into already a year ago? My lGI data were very smooth at the time (after smoothing for 10mm). I decided to use the unsmoothed data, since the fwmh is in the order of 10 then (according to the fwhm.dat file). My results are valid then, right? Just to check. For area and thickness I did smooth, resulting in comparable fwhm values. Thanks, Maaike Date: Mon, 9 Feb 2015 10:46:40 -0500 From: greve(a)nmr.mgh.harvard.edu To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] average values per cluster On 2/8/15 1:48 PM, maaike rive wrote: But how can i run the appropriate preprocessing and smoothing? The --X flag s not recognised using mris_preproc. mri_preproc only uses the fsgd file to get the list of subjects to assure that they are ordered in the same way as when mri_glmfit builds the X matrix. I used the same matrix as X in an FSGD file to do this now, it seems to work, but I do not no if it is correct. Furthermore, If I try to run mri_glmfit --sim for the lGI data, I get an error because fwmh66 is not available. I did not smooth the lGI data and with the DODS/DOSS FSGD models there was no problem, so does this mean my new models are not correct? Wow, it is 66 without smoothing? I'm not sure what to tell you. The lGI is often very smooth, but that seems excessive. You can look for outliers by loading the y files as a "time coures" in tksurfer (-t flag). If it says at 66 then I don't think you can do the voxel-wise analysis. Was it that way when you used the FSGD file? It could be that your design matrix does not remove the mean offset, so check that too. > From: r_maaike(a)hotmail.com > Date: Fri, 6 Feb 2015 21:41:53 +0100 > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] average values per cluster > > Ok, thanks! > Maaike > > > Op 6 feb. 2015 om 17:49 heeft "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> het volgende geschreven: > > > > > > There is not a way to build more flexible models in the FSGD structure. > > However, you can create your own design matrix and include anything you > > want in it and pass it to mri_glmfit with --X instead of --fsgd. > > > > doug > > > >> On 02/05/2015 06:13 AM, maaike rive wrote: > >> > >> Hi Doug, > >> > >> I hope I'm not driving you crazy, but I have some additional questions > >> regardig the DOSS/DODS models. Also because of the SPSS discrepancies. > >> > >> First, the model I discussed with you I used to assess diagn x age > >> interactions, regressing out the effects of state and gender. However, > >> in this model all interaction terms are incorporated. Is there a way > >> to build the model only incorporating main effects of diagn, state, > >> gender, age and diagn*age and diagn*state interactions? Since I do not > >> expect any higher order interactions or state* age interactions, for > >> instance (this is biologically not very plausible, although I did not > >> formally test it). > >> > >> Second, for areas where there is no diagn*age interaction I want to > >> use a model without any interaction term with age, so I was thinking > >> to use DOSS (I still want to regress out the effects of age, so it was > >> added as a regressor): > >> > >> diagn1*state1*gender1 > >> > >> diagn1*state1*gender2 > >> > >> diagn1*state2*gender1 > >> > >> diagn1*state2*gender2 > >> > >> diagn2*state1*gender1 > >> > >> diagn2*state1*gender2 > >> > >> diagn2*state2*gender1 > >> > >> diagn2*state2*gender2 > >> > >> age > >> > >> However, here there are still interaction terms with gender in the > >> model. I do want to regress out the effects of gender (since I expect > >> this to be a confounder), without incorporating the interaction term. > >> How should I do this? The only solution I can think of is building a > >> model with gender as additional regressor (containing 0 en 1) and > >> using DOSS. So: > >> > >> diagn1*state1 > >> > >> diagn1*state2 > >> > >> diagn2*state1 > >> > >> diagn2*state2 > >> > >> age > >> > >> gender > >> > >> Does this make sense? > >> > >> Third, if so, it implies that for areas where there is no diagn*state > >> interaction, and where I want to test diagn1 vs diagn2 (regressing out > >> the effects of state, since I expect this to be a confounder), I > >> should again build a new model: > >> > >> diagn1 > >> > >> diagn2 > >> > >> age > >> > >> gender > >> > >> state > >> > >> I realize this is a lot of work, hence I hope you could give me > >> any advice about this. > >> > >> Thanks, > >> > >> Maaike > >> > >> ------------------------------------------------------------------------ > >> From: r_maaike(a)hotmail.com > >> To: freesurfer(a)nmr.mgh.harvard.edu > >> Date: Tue, 3 Feb 2015 13:18:55 +0100 > >> Subject: Re: [Freesurfer] average values per cluster > >> > >> Hi Doug, > >> > >> Sorry, the statistician doesn't understand it yet; we're currently > >> building freesurfer and SPSS models step by step to find out what's > >> going on, but it's a litte time consuming... so, to be continued! > >> > >> Maaike > >> > >> ------------------------------------------------------------------------ > >> From: r_maaike(a)hotmail.com > >> To: freesurfer(a)nmr.mgh.harvard.edu > >> Date: Fri, 30 Jan 2015 20:55:27 +0100 > >> Subject: Re: [Freesurfer] average values per cluster > >> > >> On second thought, I think the reason for the discrepancy is that I > >> included state as a factor instead of covariate in the SPSS model. I > >> ran the model again after having adjusted this and included every > >> possible interaction; now I reach a p value of 0.009 (which is still > >> different but at least significant). But I'll check again Monday! > >> > >> ------------------------------------------------------------------------ > >> From: r_maaike(a)hotmail.com > >> To: freesurfer(a)nmr.mgh.harvard.edu > >> Date: Fri, 30 Jan 2015 20:15:07 +0100 > >> Subject: Re: [Freesurfer] average values per cluster > >> > >> I thought so, but I will check with the statistician next Monday, I'll > >> get back to you as soon as I'm sure. > >> > >> ------------------------------------------------------------------------ > >> Date: Fri, 30 Jan 2015 14:12:32 -0500 > >> From: greve(a)nmr.mgh.harvard.edu > >> To: freesurfer(a)nmr.mgh.harvard.edu > >> Subject: Re: [Freesurfer] average values per cluster > >> > >> > >> Actually, that looks correct. Is this what you fed to SPSS? > >> > >> On 1/30/15 2:07 PM, maaike rive wrote: > >> > >> Ok, I'm so sorry, I'm afraid I mixed things up. I indeed used > >> DODS, and assumed these were may regressors: > >> > >> diagn1*state1*gender1 > >> > >> diagn1*state1*gender2 > >> > >> diagn1*state2*gender1 > >> > >> diagn1*state2*gender2 > >> > >> diagn2*state1*gender1 > >> > >> diagn2*state1*gender2 > >> > >> diagn2*state2*gender1 > >> > >> diagn2*state2*gender2 > >> > >> diagn1*state1*gender1*age > >> > >> diagn1*state1*gender2*age > >> > >> diagn1*state2*gender1*age > >> > >> diagn1*state2*gender2*age > >> > >> diagn2*state1*gender1*age > >> > >> diagn2*state1*gender2*age > >> > >> diagn2*state2*gender1*age > >> > >> diagn2*state2*gender2*age > >> > >> > >> However what I actually meant to do was testing for the effects of > >> diagnosis and interactions (e.g. diagnosis*age) by using the > >> appropriate contrasts, so I thought that if I used the contrast > >> for the diagnosis*age interaction, I was testing whether or not > >> this interaction was significant regressing out the effects of > >> state and gender. Another example, I thought that if I used the > >> contrast for diagnosis1 versus diagnosis2, I was testing wether or > >> not there was a significant effect of diagnosis regressing out the > >> effects of state, gender and age. > >> > >> > >> But that is not the case than? How should I build the model to > >> answer these questions? > >> > >> > >> Maaike > >> > >> > >> > >> > >> Date: Fri, 30 Jan 2015 13:33:40 -0500 > >> From: greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > >> To: freesurfer(a)nmr.mgh.harvard.edu > >> <mailto:freesurfer@nmr.mgh.harvard.edu> > >> Subject: Re: [Freesurfer] average values per cluster > >> > >> > >> It depends on the actual covariates and whether you used DOSS or > >> DODS. The default is DODS, which is a full interaction model. > >> Assuming that state is a categorical variable with 2 levels, you'd > >> have 4 regressors (gender by state) + 4 more regressors (gender by > >> state by age). If the SPSS model did not have 8 regressors, then > >> it is not the same. > >> > >> doug > >> > >> On 1/30/15 1:26 PM, maaike rive wrote: > >> > >> How should I have described the model? > >> > >> ------------------------------------------------------------------------ > >> Date: Fri, 30 Jan 2015 13:09:40 -0500 > >> From: greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > >> To: freesurfer(a)nmr.mgh.harvard.edu > >> <mailto:freesurfer@nmr.mgh.harvard.edu> > >> Subject: Re: [Freesurfer] average values per cluster > >> > >>>>> I told him it the model is a GLM with age, gender and state > >> as covariates > >> > >> This is not a sufficient description. Several design matrices > >> could be derived from this description. > >> > >> On 1/30/15 11:58 AM, maaike rive wrote: > >> > >> The p value from SPSS is 0.156. I checked with a > >> statistician, just to be sure, but he says the SPSS model > >> is correct... (he doesn't know anything about freesurfer > >> and FSGD files, but I told him it the model is a GLM with > >> age, gender and state as covariates). > >> ------------------------------------------------------------------------ > >> Date: Fri, 30 Jan 2015 11:46:37 -0500 > >> From: greve(a)nmr.mgh.harvard.edu > >> <mailto:greve@nmr.mgh.harvard.edu> > >> To: freesurfer(a)nmr.mgh.harvard.edu > >> <mailto:freesurfer@nmr.mgh.harvard.edu> > >> Subject: Re: [Freesurfer] average values per cluster > >> > >> > >> You should report the clusterwise p-value. The p-value > >> that you have computed is not interpretable. If it did not > >> come out significant, then it would be worrisome, but it > >> is only a check and cannot be used for anything. What > >> p-value did you get from SPSS? I'd be curious to know what > >> the source of the descrpancy is since this has happened > >> several times now. > >> > >> doug > >> > >> On 1/30/15 3:25 AM, maaike rive wrote: > >> > >> Hi Douglas, > >> > >> I used the matlab code and the p value is signifiant, > >> although less so than the p-value I get from the > >> clusterwise statistics (0.0027 vs 0.00010). (Indeed I > >> used an abs threshold for the clusterwise statistics). > >> > >> Which p-value should I report? > >> > >> Thanks, > >> > >> Maaike > >> > >> ------------------------------------------------------------------------ > >> From: r_maaike(a)hotmail.com <mailto:r_maaike@hotmail.com> > >> To: freesurfer(a)nmr.mgh.harvard.edu > >> <mailto:freesurfer@nmr.mgh.harvard.edu> > >> Date: Thu, 29 Jan 2015 19:48:44 +0100 > >> Subject: Re: [Freesurfer] average values per cluster > >> > >> No not yet; I will do so! > >> > >>> Date: Thu, 29 Jan 2015 13:44:33 -0500 > >>> From: greve(a)nmr.mgh.harvard.edu > >> <mailto:greve@nmr.mgh.harvard.edu> > >>> To: freesurfer(a)nmr.mgh.harvard.edu > >> <mailto:freesurfer@nmr.mgh.harvard.edu> > >>> Subject: Re: [Freesurfer] average values per cluster > >>> > >>> > >>> The t is correct. When the contrast matrix only has > >> one row, then the F > >>> is just an unsigned t. I don't know anything about > >> SPSS so I can't tell > >>> from what you have sent whether it is the same model > >> or not. Try to get > >>> SPSS to output the design matrix. Did you try the > >> matlab code below? > >>> > >>>> On 01/29/2015 01:40 PM, maaike rive wrote: > >>>> Hi Douglas, > >>>> > >>>> I checked but as far as I see it I used the same > >> models. I attached > >>>> the SPSS model and output as wel as the FSGD file > >> and contrast file > >>>> (to test a diagnosis x age interaction). Now that > >> I come to think of > >>>> it, I think the reason for the discrepant findings > >> is that I used a > >>>> t-contrast instead of an F-contrast for the > >> interaction in Freesurfer. > >>>> Apologies I did not think about this earlier. But > >> maybe there is > >>>> something else I did completely wrong. > >>>> > >>>> What do you think? > >>>> > >>>> If it is indeed the t vs F contrast, than how > >> should I specify that > >>>> the contrast is an F-contrast? Is it ok to just > >> add another line to > >>>> the contrastfile (so > >>>> 0 0 0 0 0 0 0 0 1 1 1 1 -1 -1 -1 -1 > >>>> 0 0 0 0 0 0 0 0 -1 -1 -1 -1 1 1 1 1)? > >>>> > >>>> Thanks again, > >>>> > >>>> Maaike > >>>> > >>>>> Date: Mon, 26 Jan 2015 11:23:59 -0500 > >>>>> From: greve(a)nmr.mgh.harvard.edu > >> <mailto:greve@nmr.mgh.harvard.edu> > >>>>> To: freesurfer(a)nmr.mgh.harvard.edu > >> <mailto:freesurfer@nmr.mgh.harvard.edu> > >>>>> Subject: Re: [Freesurfer] average values per cluster > >>>>> > >>>>> > >>>>> We get these kind of reports occasionally. When > >> I ask people to confirm > >>>>> that they use exactly the same design matrix in > >> SPSS, I never hear > >>>> back, > >>>>> so I assume that it gets resolved. So please > >> check. The other thing you > >>>>> can do is to run in matlab, something like > >>>>> > >>>>> cd glmdir/contrast > >>>>> X = load('Xg.dat'); > >>>>> y = load('ocn.dat'); > >>>>> C = load('C.dat'); > >>>>> [beta rvar] = fast_glmfit(y,X); > >>>>> [F p] = fast_fratio(beta,X,rvar,C); > >>>>> p will be the p-value > >>>>> > >>>>> If you used an unsigned cluster-forming > >> threshold (ie, abs), then it is > >>>>> possible that some of the voxels are pos and > >> some are neg so that they > >>>>> average out > >>>>> > >>>>> doug > >>>>> > >>>>> > >>>>> > >>>>> > >>>>>> On 01/26/2015 09:03 AM, maaike rive wrote: > >>>>>> Dear Freesurfer experts, > >>>>>> > >>>>>> Sorry to bother you again, but I have two more > >> questions about > >>>>>> extracting (thickness/surface/GI) values from > >> a certain cluster. > >>>>>> > >>>>>> As I understood, the abs.y.ocn.dat file gives > >> the average values > >>>> for a > >>>>>> given significant cluster (e.g. a cluster > >> where there is a > >>>> significant > >>>>>> AxB interaction). > >>>>>> > >>>>>> I may be completely misunderstanding things, > >> but if I use these > >>>> values > >>>>>> in SPSS for further statistics and test the > >> same interaction (AxB), > >>>>>> than according to SPSS this interaction is > >> /not /significant > >>>>>> (corrected for the same covariates as in the > >> FSGD file). > >>>>>> > >>>>>> Could you tell me what is going wrong here? I > >> do not trust my > >>>> results now. > >>>>>> > >>>>>> Furthermore, is it possible (and if so, how?) > >> to extract the average > >>>>>> values of exactly the same cluster, but in an > >> independent group not > >>>>>> used in the analysis, for post-hoc comparisons > >> in SPSS? > >>>>>> > >>>>>> Thanks, > >>>>>> > >>>>>> Maaike > >>>>>> > >>>>>> > >>>>>> _______________________________________________ > >>>>>> Freesurfer mailing list > >>>>>> Freesurfer(a)nmr.mgh.harvard.edu > >> <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>>>> > >>>>> -- > >>>>> Douglas N. Greve, Ph.D. > >>>>> MGH-NMR Center > >>>>> greve(a)nmr.mgh.harvard.edu > >> <mailto:greve@nmr.mgh.harvard.edu> > >>>>> Phone Number: 617-724-2358 > >>>>> Fax: 617-726-7422 > >>>>> > >>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >>>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html > >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >>>>> Outgoing: > >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >>>>> > >>>>> _______________________________________________ > >>>>> Freesurfer mailing list > >>>>> Freesurfer(a)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(a)nmr.mgh.harvard.edu > >> <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >>> -- > >>> Douglas N. Greve, Ph.D. > >>> MGH-NMR Center > >>> greve(a)nmr.mgh.harvard.edu > >> <mailto:greve@nmr.mgh.harvard.edu> > >>> Phone Number: 617-724-2358 > >>> Fax: 617-726-7422 > >>> > >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html > >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >>> Outgoing: > >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer(a)nmr.mgh.harvard.edu > >> <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> _______________________________________________ > >> Freesurfer mailing list Freesurfer(a)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(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> > >> _______________________________________________ Freesurfer > >> mailing list Freesurfer(a)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(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> > >> _______________________________________________ Freesurfer > >> mailing list Freesurfer(a)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(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> > >> _______________________________________________ Freesurfer mailing > >> list Freesurfer(a)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(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> > >> _______________________________________________ Freesurfer mailing > >> list Freesurfer(a)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(a)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(a)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(a)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(a)nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve(a)nmr.mgh.harvard.edu > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)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.

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Cluster-wise correction error with mri_glmfit-sim
by Hao wen 27 May '16

27 May '16

Hello: Freesurfers, follow the tutorial ' * FsTutorial<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial> * GroupAnalysis<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis?action=f…>', my task is to find the thickness differences between groups(Controls(30) & AD(30)), and it works well for the first part which is to fit the linear model and get the uncorrected P_values, and I got the expected P-value map, but when I followed the clusterwise correction for multiple comparision, with this command below: mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --cache 4 neg \ --cwp 0.05\ --2spaces I got two questions: 1) with the flag --2spaces, i got the error that this command not found; 2) also, with or without the --2spaces, after the freeview open, i got another error, which said did not find any volume geometry information in the surface, I googled, and I know Doug has answered in this post: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg42911.html, but I think my freesurfer is the newest version:freesurfer-5.3.0-15052013-x86_64-centos! As below, these are my command and the output: §§Command: export SUBJECTS_DIR=/aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/ cd $SUBJECTS_DIR/glm/AD_CN_NO_COVARIATE mri_glmfit-sim \ --glmdir lh.AD_CN_NO_COVARIATE.glmdir \ --cache 1.3 neg \ --cwp 0.05\ --2spaces # load the cluster annotation in freeview freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.annot -viewport 3d §§Output: cmdline mri_glmfit --y lh.AD_CN_NO_COVARIATE.thickness.15.mgh --fsgd AD_CN_NO_COVARIATE.fsgd dods --C group.diff.mtx --surf fsaverage lh --cortex --glmdir lh.AD_CN_NO_COVARIATE.glmdir SURFACE: fsaverage lh log file is lh.AD_CN_NO_COVARIATE.glmdir/cache.mri_glmfit-sim.log cd /aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/glm/AD_CN_NO_COVARIATE /aramis/dartagnan2/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos/bin/mri_glmfit-sim --glmdir lh.AD_CN_NO_COVARIATE.glmdir --cache 1.3 neg --cwp 0.05 $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $ Thu May 26 16:20:39 CEST 2016 Linux HP1973 3.11.0-26-generic #45~precise1-Ubuntu SMP Tue Jul 15 04:02:35 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux wen setenv SUBJECTS_DIR /aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/ FREESURFER_HOME /aramis/dartagnan2/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos Original mri_glmfit command line: cmdline mri_glmfit --y lh.AD_CN_NO_COVARIATE.thickness.15.mgh --fsgd AD_CN_NO_COVARIATE.fsgd dods --C group.diff.mtx --surf fsaverage lh --cortex --glmdir lh.AD_CN_NO_COVARIATE.glmdir DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 22.776285 CSD /aramis/dartagnan2/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos/average/mult-comp-cor/fsaverage/lh/cortex/fwhm23/neg/th13/mc-z.csd mri_surfcluster --in lh.AD_CN_NO_COVARIATE.glmdir/group.diff/sig.mgh --csd /aramis/dartagnan2/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos/average/mult-comp-cor/fsaverage/lh/cortex/fwhm23/neg/th13/mc-z.csd --mask lh.AD_CN_NO_COVARIATE.glmdir/mask.mgh --cwsig lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh --vwsig lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.voxel.mgh --sum lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.summary --ocn lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.mgh --oannot lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.annot --annot aparc --csdpdf lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.pdf.dat --cwpvalthresh 0.05 --o lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.masked.mgh --no-fixmni --surf white Creating CDFs from CSD files csd->threshsign = -1 thsign = neg, id = -1 version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $ hemi = lh srcid = lh.AD_CN_NO_COVARIATE.glmdir/group.diff/sig.mgh srcsubjid = fsaverage srcsurf = white srcframe = 0 thsign = neg thmin = 1.3 thmax = -1 fdr = -1 minarea = 0 xfmfile = talairach.xfm nth = -1 outid = lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.masked.mgh MGH ocnid = lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.mgh MGH sumfile = lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.summary subjectsdir = /aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/ FixMNI = 0 Found 149955 vertices in mask Found 149955 vertices in mask Found 149955 points in clabel. ------------- XFM matrix (RAS2RAS) --------------- /aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//fsaverage/mri/transforms/talairach.xfm 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; ---------------------------------------------------- Reading source surface /aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//fsaverage/surf/lh.white Done reading source surface Reading annotation /aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//fsaverage/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Computing metric properties Loading source values number of voxels in search space = 149955 Done loading source values (nvtxs = 163842) overall max = 8.58718 at vertex 22205 overall min = -1.57802 at vertex 24019 surface nvertices 163842 surface area 65417.097656 surface area 65416.648438 Computing voxel-wise significance CSDpvalMaxSigMap(): found 0/163842 above 0 Adjusting threshold for 1-tailed test. If the input is not a -log10(p) volume, re-run with --no-adjust. Searching for Clusters ... thmin=1.300000 (0.998970), thmax=-1.000000 (-1), thsignid=-1, minarea=0.000000 Found 2 clusters Max cluster size 132.153870 Pruning by CW P-Value 0.05 Saving thresholded output to lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.masked.mgh Saving cluster numbers to lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.mgh Saving cluster pval lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh Constructing output annotation Writing annotation lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.annot mri_segstats --seg lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.mgh --exclude 0 --i /aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/glm/AD_CN_NO_COVARIATE/lh.AD_CN_NO_COVARIATE.thickness.15.mgh --avgwf lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.2688 $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.mgh --exclude 0 --i /aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/glm/AD_CN_NO_COVARIATE/lh.AD_CN_NO_COVARIATE.thickness.15.mgh --avgwf lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.2688 sysname Linux hostname HP1973 machine x86_64 user wen UseRobust 0 Loading lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.mgh Loading /aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/glm/AD_CN_NO_COVARIATE/lh.AD_CN_NO_COVARIATE.thickness.15.mgh Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 0 segmentations Computing spatial average of each frame Writing to lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.y.ocn.dat mri_segstats done mri_convert lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh --frame 0 mri_convert lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) keeping frame 0 writing to lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh... Thu May 26 16:20:39 CEST 2016 Thu May 26 16:20:45 CEST 2016 mri_glmfit-sim done ./cluster_wise_correction_for_multiple_comparisons.sh: line 23: --2spaces: command not found Did not find any volume geometry information in the surface p-Breading colortable from annotation file... colortable with 1 entries read (originally none) colortable with 1 entries read (originally none) CTABisEntryValid: index -1 was OOB Resource temporarily unavailable Resource temporarily unavailable B ginally none) CTABisEntryValid: index -1 was OOB Resource temporarily unavailable Resource temporarily unavailable B ginally none) CTABisEntryValid: index -1 was OOB Resource temporarily unavailable Resource temporarily unavailable B ginally none) CTABisEntryValid: index -1 was OOB Resource temporarily unavailable Resource temporarily unavailable B ginally none) Can you give me some answer? Thank you very much!

3 13

Segmentation of a 3D IR-deskulled volume
by Aquino Domenico 26 May '16

26 May '16

Dear Freesurfer team, I'm trying to segment a brain from a non standard sequence. It is a 3D IR sequence that I have previously pre-elaborated and deskulled. The software is running from a long time and at the moment is correcting defects (17/128) but I'm not sure it's working properly. I have previously sent you the NIFTI_GZ file but, if you prefer, I'll send it using FTP. Could you please help me in detecting some possible issues? Thanks a lot, Domenico ___________________________________________ Eng. Domenico Aquino Department of Neuroradiology IRCCS Foundation Neurological Institute "Carlo Besta" Via Celoria,11-20133 Milano Phone: +39 02 23942472 Fax +39 02 23942543 [1463859753944_LogoWhite.jpg]

1 0

Merging Brain Hemispheres
by Saeed Mahdizadeh Bakhshmand 26 May '16

26 May '16

Hello, As we know, Freesurfer generates separate surface models and associated labels for each brain hemisphere, is there any way to merge two hemisphere and come up with a single cortex surface? My best, Saeed _______________________________________________ Freesurfer mailing list Freesurfer(a)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.

1 0

LME MATLAB, X matrix error
by Hanbyul Cho 26 May '16

26 May '16

Dear FreeSurfer Team, I processed in MATLAB for Linear Mixed Effects Models Analysis with this X matrix: X matrix is 'Subjects N X 11', 11 columns are as follow, 1. Intercept (all '1') 2. time (from baseline time point) 3. time2 4. Patients group = 1, Control = 0 5. 4.X time 6. 4.X time2 7. Patients group = 0, Control = 1 8. 7. X time 9. 8. X time2 10. age 11. extra values for covariate 1. When I process this command, [lhTh01,lhRe01] = lme_mass_fit_EMinit(X,[1],Y,ni,lhcortex,3,4) The MATLAB windows print the warning alarm repeatedly. " Warning: Matrix is close to singular or badly scaled. Results may be inaccurate." Is this X matrix something wrong? 2. After complete 'lme_mass_fit_EMinit' process with the warning, I tried the next command, [lhRgs01,lhRgMeans01] = lme_mass_RgGrow(lhsphere, lhRe01, lhTh01,lhcortex,2,95); This command took a long time to process, and it caused the whole stop MATLAB works. Is it also because of the X matrix...? Could you let me know the solution for the X matrix problems ? Best Wishes, Han

2 4

Design Matrix Creation
by Timothy Hendrickson 26 May '16

26 May '16

Freesurfer Support, I'd like to create a design matrix for a group analysis outside of the DODS and DOSS models. I understand that in order to do this the -X flag must be used. However, I have been unable to find examples of how to do this. I am hoping to reveal a difference in thickness or gyrification amongst a clinical population. The data set contains two factors: diagnosis, and study site and one covariate: age. Diagnosis has two levels: controls, and patients. Study site has four levels, one level for each location the data has been collected from. What I would ideally like to do is: 1) Take into account offset differences amongst diagnosis and study site. 2) Allowing a difference in age slope amongst the diagnosis levels 3) Modeling the age slope as the same for the study site levels My FSGD file is designed as follows Class SITE 1-Control Class SITE 1-PATIENT Class SITE 2-Control Class SITE 2-PATIENT Class SITE 3-Control Class SITE 3-PATIENT Class SITE 4-Control Class SITE 4-PATIENT Variables age_at_scan study site levels = 1,2,3 and 4 diagnosis levels = PATIENT and Control age_at_scan = covariate age Any advice would be greatly appreciated. Respectfully, Tim -- Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay)

2 3

(no subject)
by Saeed Mahdizadeh Bakhshmand 26 May '16

26 May '16

1 0

mri_glmfit version
by Victor Montal Blancafort 26 May '16

26 May '16

Dear FS experts We have been playing around with different mri_glmfit versions. I processed all my data with FS v5.1, and then I run the mri_glmfit with both the 5.1 and 5.3 versions, using exactly the same X, same contrasts matrix and obviously the same images. Our concern is that the results differ significantly between both versions. Concretely, the results from the 5.3 mri_glmfit version are shifted 0.3 points with respect from the 5.1 one. More precisely, the results using the 5.1 version at 1.0 look the same as the 5.3 at 1.3 significance level. Is there any difference in parameter estimation or anything else between both versions? Should the results be the same given that we use the same data, parameters, etc? Thanks in advance for your replies, Best regards, V.

2 1

Connectivity design ill-conditioned
by Zimmerman, Jared Perry 26 May '16

26 May '16

Hi, I'm having a problem running first level connectivity analysis on my resting-state data. When I run selxavg3-sess I keep getting a notice that my design is ill-conditioned but I can't figure out why. I am trying to run analysis on two 124 volume rsfMRI runs in my fsd and the design matrix looks fine to me with dimensions 248x47 (although should ncols be an even number since I'm doing two runs?). Poking around the Xtmp.mat I noticed a few things that are confusing. Notably, flac.funcfspec points only to one of my runs in the fsd, and flac.X is a 124x24 matrix which appears to be the design matrix for just one of my runs (and if there are 24 columns in that, should there be 28 columns in the design matrix for combining both runs?). Any help figuring out why this design is ill-conditioned would be great. I've attached my Xtmp.mat, selxavg3.log and analysis design file to this email, but it's unclear to me if the mailing list will scrub them off. If so I can make them available some other way. Thanks, Jared

2 1

Fwd: Re: XQuartz 2.7.9 Update Inquiry
by Rockers, Elijah D. 26 May '16

26 May '16

Quick update on the GLX errors we experience with remote access of freesurfer, and qdec The below conversations may be of interest. -Eli -------- Forwarded Message -------- Subject: Re: XQuartz 2.7.9 Update Inquiry Date: Wed, 25 May 2016 20:59:55 -0400 From: Magda Tsintou <magda.tsintou(a)gmail.com><mailto:magda.tsintou@gmail.com> To: Ambrose LI <ambrose.li(a)gmail.com><mailto:ambrose.li@gmail.com> CC: MacQueen, Don <macqueen1(a)llnl.gov><mailto:macqueen1@llnl.gov>, Rich Cook <wealthychef(a)gmail.com><mailto:wealthychef@gmail.com>, x11-users(a)lists.apple.com<mailto:x11-users@lists.apple.com> <x11-users(a)lists.apple.com><mailto:x11-users@lists.apple.com>, Rockers, Elijah D. <edrockers(a)houstonmethodist.org><mailto:edrockers@houstonmethodist.org> Hi Ambrose, Thanks a lot for letting us know. That is very helpful. I would encourage everyone to send to the x.org<https://urldefense.proofpoint.com/v2/url?u=http-3A__x.org&d=DQMFaQ&c=QmPtDi…> mailing list so that we see if they could help us find the support we need to continue our work. I have already emailed them. Let's see how it goes. Thanks again! Best, Magda. On Wed, May 25, 2016 at 8:21 PM, Ambrose LI <ambrose.li(a)gmail.com<mailto:ambrose.li@gmail.com>> wrote: For anyone who need this to continue working: I mentioned this thread on Twitter and it got picked up by the X.org<https://urldefense.proofpoint.com/v2/url?u=http-3A__X.org&d=DQQFaQ&c=QmPtDi…> Foundation. They are requesting that anyone who need IGLX to work to send email to the x.org<https://urldefense.proofpoint.com/v2/url?u=http-3A__x.org&d=DQMFaQ&c=QmPtDi…> mailing lists to let them know what you need. They have no idea that people don't even know IGLX has been deprecated, let alone people are actually still depending on it for work. https://mobile.twitter.com/XOrgFoundation/status/733516667737628674<https://urldefense.proofpoint.com/v2/url?u=https-3A__mobile.twitter.com_XOr…> 2016-05-25 18:59 GMT-04:00 MacQueen, Don <macqueen1(a)llnl.gov<mailto:macqueen1@llnl.gov>>: For what it's worth, see, <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.x.org_wiki_Develop…>https://www.x.org/wiki/Development/Security/Advisory-2014-12-09/ -- Don MacQueen Lawrence Livermore National Laboratory 7000 East Ave., L-627 Livermore, CA 94550 925-423-1062<tel:925-423-1062> From: <<mailto:x11-users-bounces+macq=llnl.gov@lists.apple.com>x11-users-bounces+macq=llnl.gov(a)lists.apple.com<mailto:x11-users-bounces+macq=llnl.gov@lists.apple.com>> on behalf of Rich Cook <<mailto:wealthychef@gmail.com>wealthychef(a)gmail.com<mailto:wealthychef@gmail.com>> Date: Wednesday, May 18, 2016 at 4:43 PM To: Magda Tsintou <magda.tsintou(a)gmail.com<mailto:magda.tsintou@gmail.com>> Cc: "<mailto:x11-users@lists.apple.com>x11-users(a)lists.apple.com<mailto:x11-users@lists.apple.com>" <x11-users(a)lists.apple.com<mailto:x11-users@lists.apple.com>>, "Rockers, Elijah D." <<mailto:edrockers@houstonmethodist.org>edrockers(a)houstonmethodist.org<mailto:edrockers@houstonmethodist.org>> Subject: Re: XQuartz 2.7.9 Update Inquiry There will be a tsunami of interest in this if IGLX goes away. This is a legitimate user need. -- Rich On May 18, 2016, at 4:31 PM, Magda Tsintou <<mailto:magda.tsintou@gmail.com>magda.tsintou(a)gmail.com<mailto:magda.tsintou@gmail.com>> wrote: Yes indeed this will be a serious problem in my lab too. We all rely on that to work on our research projects and I think that most neuroimaging labs do the same and I am sure that there are tons of other applications I can not even think of right now. I really hope that a solution for this will come up so that there will be no problems. When I notified my lab they did not even know how to guide me on this. At least there should be some sort of awareness in the labs about that issue so that not everyone needs to figure it out alone. On Wed, May 18, 2016 at 6:39 PM, Rich Cook <<mailto:wealthychef@gmail.com>wealthychef(a)gmail.com<mailto:wealthychef@gmail.com>> wrote: There's nothing to transition to! I cannot believe that XOrg thinks that nobody needs to do this, it's mind boggling to me. It's going to be a big problem at our lab. > On May 18, 2016, at 8:46 AM, Rockers, Elijah D. <<mailto:edrockers@houstonmethodist.org>edrockers(a)houstonmethodist.org<mailto:edrockers@houstonmethodist.org>> wrote: > > Hello again experts, > > Being that XQ is no longer going to support IGLX, this could interfere > with some current application's functionality in our lab. Should I > notify the application developers that they should consider looking to > transition away from GLX? Or is this kind of ssh X forwarding to the mac > not even possible without GLX (are there alternatives to GLX they could > consider?) > > Apologies, even as a computer nerd, the complexity of graphics > software/hardware remains somewhat of a mystery to me, so I'm not 100% > sure I'm even asking the right questions here.. > > Thanks, > > On 05/18/2016 01:00 AM, <mailto:x11-users-request@lists.apple.com> x11-users-request(a)lists.apple.com<mailto:x11-users-request@lists.apple.com> wrote: >> Send X11-users mailing list submissions to >> <mailto:x11-users@lists.apple.com> x11-users(a)lists.apple.com<mailto:x11-users@lists.apple.com> >> >> To subscribe or unsubscribe via the World Wide Web, visit >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma…> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma… >> or, via email, send a message with subject or body 'help' to >> <mailto:x11-users-request@lists.apple.com> x11-users-request(a)lists.apple.com<mailto:x11-users-request@lists.apple.com> >> >> You can reach the person managing the list at >> <mailto:x11-users-owner@lists.apple.com> x11-users-owner(a)lists.apple.com<mailto:x11-users-owner@lists.apple.com> >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of X11-users digest..." >> >> >> Today's Topics: >> >> 1. Re: XQuartz 2.7.9 Update Inquiry (Jeremy Huddleston Sequoia) >> 2. Re: XQuartz 2.7.9 Update Inquiry (Richard Cook) >> 3. Re: XQuartz 2.7.9 Update Inquiry (Jeremy Huddleston Sequoia) >> 4. Re: XQuartz 2.7.9 Update Inquiry (Rich Cook) >> 5. Re: XQuartz 2.7.9 Update Inquiry (James Gunning) >> 6. Re: XQuartz 2.7.9 Update Inquiry (César) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Tue, 17 May 2016 21:59:06 -0700 >> From: Jeremy Huddleston Sequoia <<mailto:jeremyhu@apple.com>jeremyhu(a)apple.com<mailto:jeremyhu@apple.com>> >> To: César <<mailto:cesarmensajes@gmail.com>cesarmensajes(a)gmail.com<mailto:cesarmensajes@gmail.com>> >> Cc: "<mailto:x11-users@lists.apple.com>x11-users(a)lists.apple.com<mailto:x11-users@lists.apple.com>" <<mailto:x11-users@lists.apple.com>x11-users(a)lists.apple.com<mailto:x11-users@lists.apple.com>> >> Subject: Re: XQuartz 2.7.9 Update Inquiry >> Message-ID: <<mailto:31F32838-10D2-424F-A417-7213F78E67A2@apple.com>31F32838-10D2-424F-A417-7213F78E67A2(a)apple.com<mailto:31F32838-10D2-424F-A417-7213F78E67A2@apple.com>> >> Content-Type: text/plain; charset="utf-8" >> >> There was one change, but it didn't completely address the problem. >> >>> On May 17, 2016, at 21:53, César <<mailto:cesarmensajes@gmail.com>cesarmensajes(a)gmail.com<mailto:cesarmensajes@gmail.com>> wrote: >>> >>> Jeremy, was the OpenGL context clipping bug addressed in 2.7.9, or is it still pending? (I sent you a minimal working example showing the bug some time ago) >>> >>> Thanks, >>> >>> César >>> >>> >>> >>> El miércoles, 18 de mayo de 2016, Jeremy Huddleston Sequoia <<mailto:jeremyhu@apple.com>jeremyhu(a)apple.com<mailto:jeremyhu@apple.com>> escribió: >>> FWIW, there are security vulnerabilities addressed in the versions of libpng in 2.7.9, so you might want to update at least for the security reasons. >>> >>> The only issues that I'm aware of as regressions are the issues with IGLX (which isn't really going to be supported much longer) and a regression in the support for tcp connections (which is off by default and discouraged). >>> >>> --Jeremy >>> >>>> On May 17, 2016, at 14:39, Christopher Fick <<mailto:spacecarrider@gmail.com>spacecarrider(a)gmail.com<mailto:spacecarrider@gmail.com>> wrote: >>>> >>>> Magda, thank you so much for your thoughts! I did notice that v2.7.9 was just released earlier this month, and bugs were one thing I wondered about. I'm pretty out of the loop on this stuff. >>>> >>>> And, no I don't think I have anything to gain from an upgrade. Nothing prompted me to look into an upgrade aside from curiosity and an attempt to stay up to date. I just use XQ to run Inkscape, and so far I haven't had any issues in the little I've used it. It also appears that Inkscape is still standing at the same version (0.91) as when I initially installed it with XQ So, I will take your advice. If it ain't broken... >>>> >>>> Many Thanks! >>>> Christopher >>>> >>>> >>>> >>>> On Tue, May 17, 2016 at 4:25 PM, Magda Tsintou <<mailto:magda.tsintou@gmail.com>magda.tsintou(a)gmail.com<mailto:magda.tsintou@gmail.com>> wrote: >>>> Note: Sorry forgot to reply to all so that everyone can keep track of the conversation... >>>> >>>> Hi Christopher, >>>> >>>> With your OSX you would certainly not need to update. We recently were discussing some bugs in XQ 2.7.9 that have not been resolved while the version 2.7.8 works perfectly fine and I am running El Capitan 10.11.5. XQ 2.7.9 did not allow me to work with certain commands that needed forwarding over ssh and given the limited people who have been working on that fix this may cause problems for some time. I would strongly recommend from my personal experience to stick with XQ 2.7.8 if you have nothing in particular to gain from upgrading. I hope this helps a bit. Good luck! >>>> >>>> Best regards, >>>> Magda. >>>> >>>> >>>> On Tue, May 17, 2016 at 5:17 PM, Christopher Fick <<mailto:spacecarrider@gmail.com>spacecarrider(a)gmail.com<mailto:spacecarrider@gmail.com>> wrote: >>>> Hi I'm running XQ 2.7.8, and I see that 2.7.9 is now available. If I check for updates through the XQ "app" it says I'm up to date with 2.7.8. >>>> >>>> So, if I manually download and install 2.7.9 from the website should I just install it over the previous version? >>>> >>>> And on a side note, should I be able to update through 2.7.8, or is it common knowledge that it doesn't work that way since this is more of a framework (for lack of better words) rather than a normal application. >>>> >>>> Macbook Pro Mid 2012 15" >>>> OSX 10.8.5 >>>> >>>> Thanks! >>>> Christopher >>>> >>>> _______________________________________________ >>>> Do not post admin requests to the list. They will be ignored. >>>> X11-users mailing list (<mailto:X11-users@lists.apple.com>X11-users(a)lists.apple.com<mailto:X11-users@lists.apple.com>) >>>> Help/Unsubscribe/Update your Subscription: <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma…> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma… >>>> >>>> This email sent to <mailto:magda.tsintou@gmail.com> magda.tsintou(a)gmail.com<mailto:magda.tsintou@gmail.com> >>>> >>>> >>>> _______________________________________________ >>>> Do not post admin requests to the list. They will be ignored. >>>> X11-users mailing list (<mailto:X11-users@lists.apple.com>X11-users(a)lists.apple.com<mailto:X11-users@lists.apple.com>) >>>> Help/Unsubscribe/Update your Subscription: <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma…> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma… >>>> >>>> This email sent to <mailto:jeremyhu@freedesktop.org> jeremyhu(a)freedesktop.org<mailto:jeremyhu@freedesktop.org> >> -------------- next part -------------- >> A non-text attachment was scrubbed... >> Name: smime.p7s >> Type: application/pkcs7-signature >> Size: 4465 bytes >> Desc: not available >> URL: <<https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.apple.com_archive…>https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.apple.com_archive… > >> >> ------------------------------ >> >> Message: 2 >> Date: Tue, 17 May 2016 22:18:27 -0700 >> From: Richard Cook <<mailto:wealthychef@gmail.com>wealthychef(a)gmail.com<mailto:wealthychef@gmail.com>> >> To: Jeremy Huddleston Sequoia <<mailto:jeremyhu@apple.com>jeremyhu(a)apple.com<mailto:jeremyhu@apple.com>> >> Cc: <mailto:x11-users@lists.apple.com> x11-users(a)lists.apple.com<mailto:x11-users@lists.apple.com> >> Subject: Re: XQuartz 2.7.9 Update Inquiry >> Message-ID: <<mailto:4479A8B5-7740-4BFB-B533-B95364D78F23@gmail.com>4479A8B5-7740-4BFB-B533-B95364D78F23(a)gmail.com<mailto:4479A8B5-7740-4BFB-B533-B95364D78F23@gmail.com>> >> Content-Type: text/plain; charset=us-ascii >> >> I don't know what IGLX is, but GLX did not seem to work for me at all when I tried it in 2.7.9. Specifically, I could not run glxgears on a remote linux box, which is the canonical GLX test I always use. But the good news it that switching back to 2.7.8 was painless and made my problems with 2.7.9 go away. >> >>> On May 17, 2016, at 9:40 PM, Jeremy Huddleston Sequoia <<mailto:jeremyhu@apple.com>jeremyhu(a)apple.com<mailto:jeremyhu@apple.com>> wrote: >>> >>> FWIW, there are security vulnerabilities addressed in the versions of libpng in 2.7.9, so you might want to update at least for the security reasons. >>> >>> The only issues that I'm aware of as regressions are the issues with IGLX (which isn't really going to be supported much longer) and a regression in the support for tcp connections (which is off by default and discouraged). >>> >>> --Jeremy >>> >>>> On May 17, 2016, at 14:39, Christopher Fick <<mailto:spacecarrider@gmail.com>spacecarrider(a)gmail.com<mailto:spacecarrider@gmail.com>> wrote: >>>> >>>> Magda, thank you so much for your thoughts! I did notice that v2.7.9 was just released earlier this month, and bugs were one thing I wondered about. I'm pretty out of the loop on this stuff. >>>> >>>> And, no I don't think I have anything to gain from an upgrade. Nothing prompted me to look into an upgrade aside from curiosity and an attempt to stay up to date. I just use XQ to run Inkscape, and so far I haven't had any issues in the little I've used it. It also appears that Inkscape is still standing at the same version (0.91) as when I initially installed it with XQ So, I will take your advice. If it ain't broken... >>>> >>>> Many Thanks! >>>> Christopher >>>> >>>> >>>> >>>> On Tue, May 17, 2016 at 4:25 PM, Magda Tsintou <<mailto:magda.tsintou@gmail.com>magda.tsintou(a)gmail.com<mailto:magda.tsintou@gmail.com>> wrote: >>>> Note: Sorry forgot to reply to all so that everyone can keep track of the conversation... >>>> >>>> Hi Christopher, >>>> >>>> With your OSX you would certainly not need to update. We recently were discussing some bugs in XQ 2.7.9 that have not been resolved while the version 2.7.8 works perfectly fine and I am running El Capitan 10.11.5. XQ 2.7.9 did not allow me to work with certain commands that needed forwarding over ssh and given the limited people who have been working on that fix this may cause problems for some time. I would strongly recommend from my personal experience to stick with XQ 2.7.8 if you have nothing in particular to gain from upgrading. I hope this helps a bit. Good luck! >>>> >>>> Best regards, >>>> Magda. >>>> >>>> >>>> On Tue, May 17, 2016 at 5:17 PM, Christopher Fick <<mailto:spacecarrider@gmail.com>spacecarrider(a)gmail.com<mailto:spacecarrider@gmail.com>> wrote: >>>> Hi I'm running XQ 2.7.8, and I see that 2.7.9 is now available. If I check for updates through the XQ "app" it says I'm up to date with 2.7.8. >>>> >>>> So, if I manually download and install 2.7.9 from the website should I just install it over the previous version? >>>> >>>> And on a side note, should I be able to update through 2.7.8, or is it common knowledge that it doesn't work that way since this is more of a framework (for lack of better words) rather than a normal application. >>>> >>>> Macbook Pro Mid 2012 15" >>>> OSX 10.8.5 >>>> >>>> Thanks! >>>> Christopher >>>> >>>> _______________________________________________ >>>> Do not post admin requests to the list. They will be ignored. >>>> X11-users mailing list (<mailto:X11-users@lists.apple.com>X11-users(a)lists.apple.com<mailto:X11-users@lists.apple.com>) >>>> Help/Unsubscribe/Update your Subscription: <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma…> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma… >>>> >>>> This email sent to <mailto:magda.tsintou@gmail.com> magda.tsintou(a)gmail.com<mailto:magda.tsintou@gmail.com> >>>> >>>> >>>> _______________________________________________ >>>> Do not post admin requests to the list. They will be ignored. >>>> X11-users mailing list (<mailto:X11-users@lists.apple.com>X11-users(a)lists.apple.com<mailto:X11-users@lists.apple.com>) >>>> Help/Unsubscribe/Update your Subscription: <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma…> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma… >>>> >>>> This email sent to <mailto:jeremyhu@freedesktop.org> jeremyhu(a)freedesktop.org<mailto:jeremyhu@freedesktop.org> >>> _______________________________________________ >>> Do not post admin requests to the list. They will be ignored. >>> X11-users mailing list (<mailto:X11-users@lists.apple.com>X11-users(a)lists.apple.com<mailto:X11-users@lists.apple.com>) >>> Help/Unsubscribe/Update your Subscription: <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma…> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma… >>> >>> This email sent to <mailto:wealthychef@gmail.com> wealthychef(a)gmail.com<mailto:wealthychef@gmail.com> >> >> >> >> ------------------------------ >> >> Message: 3 >> Date: Tue, 17 May 2016 22:38:13 -0700 >> From: Jeremy Huddleston Sequoia <<mailto:jeremyhu@apple.com>jeremyhu(a)apple.com<mailto:jeremyhu@apple.com>> >> To: Richard Cook <<mailto:wealthychef@gmail.com>wealthychef(a)gmail.com<mailto:wealthychef@gmail.com>> >> Cc: <mailto:x11-users@lists.apple.com> x11-users(a)lists.apple.com<mailto:x11-users@lists.apple.com> >> Subject: Re: XQuartz 2.7.9 Update Inquiry >> Message-ID: <<mailto:6C53050F-0731-4FBB-B83C-E02B54AA3F08@apple.com>6C53050F-0731-4FBB-B83C-E02B54AA3F08(a)apple.com<mailto:6C53050F-0731-4FBB-B83C-E02B54AA3F08@apple.com>> >> Content-Type: text/plain; charset="utf-8" >> >> >>> On May 17, 2016, at 22:18, Richard Cook <<mailto:wealthychef@gmail.com>wealthychef(a)gmail.com<mailto:wealthychef@gmail.com>> wrote: >>> >>> I don't know what IGLX is, but GLX did not seem to work for me at all when I tried it in 2.7.9. Specifically, I could not run glxgears on a remote linux box, which is the canonical GLX test I always use. >> That is IGLX. >> >>> But the good news it that switching back to 2.7.8 was painless and made my problems with 2.7.9 go away. >>> >>>> On May 17, 2016, at 9:40 PM, Jeremy Huddleston Sequoia <<mailto:jeremyhu@apple.com>jeremyhu(a)apple.com<mailto:jeremyhu@apple.com>> wrote: >>>> >>>> FWIW, there are security vulnerabilities addressed in the versions of libpng in 2.7.9, so you might want to update at least for the security reasons. >>>> >>>> The only issues that I'm aware of as regressions are the issues with IGLX (which isn't really going to be supported much longer) and a regression in the support for tcp connections (which is off by default and discouraged). >>>> >>>> --Jeremy >>>> >>>>> On May 17, 2016, at 14:39, Christopher Fick <<mailto:spacecarrider@gmail.com>spacecarrider(a)gmail.com<mailto:spacecarrider@gmail.com>> wrote: >>>>> >>>>> Magda, thank you so much for your thoughts! I did notice that v2.7.9 was just released earlier this month, and bugs were one thing I wondered about. I'm pretty out of the loop on this stuff. >>>>> >>>>> And, no I don't think I have anything to gain from an upgrade. Nothing prompted me to look into an upgrade aside from curiosity and an attempt to stay up to date. I just use XQ to run Inkscape, and so far I haven't had any issues in the little I've used it. It also appears that Inkscape is still standing at the same version (0.91) as when I initially installed it with XQ So, I will take your advice. If it ain't broken... >>>>> >>>>> Many Thanks! >>>>> Christopher >>>>> >>>>> >>>>> >>>>> On Tue, May 17, 2016 at 4:25 PM, Magda Tsintou <<mailto:magda.tsintou@gmail.com>magda.tsintou(a)gmail.com<mailto:magda.tsintou@gmail.com>> wrote: >>>>> Note: Sorry forgot to reply to all so that everyone can keep track of the conversation... >>>>> >>>>> Hi Christopher, >>>>> >>>>> With your OSX you would certainly not need to update. We recently were discussing some bugs in XQ 2.7.9 that have not been resolved while the version 2.7.8 works perfectly fine and I am running El Capitan 10.11.5. XQ 2.7.9 did not allow me to work with certain commands that needed forwarding over ssh and given the limited people who have been working on that fix this may cause problems for some time. I would strongly recommend from my personal experience to stick with XQ 2.7.8 if you have nothing in particular to gain from upgrading. I hope this helps a bit. Good luck! >>>>> >>>>> Best regards, >>>>> Magda. >>>>> >>>>> >>>>> On Tue, May 17, 2016 at 5:17 PM, Christopher Fick <<mailto:spacecarrider@gmail.com>spacecarrider(a)gmail.com<mailto:spacecarrider@gmail.com>> wrote: >>>>> Hi I'm running XQ 2.7.8, and I see that 2.7.9 is now available. If I check for updates through the XQ "app" it says I'm up to date with 2.7.8. >>>>> >>>>> So, if I manually download and install 2.7.9 from the website should I just install it over the previous version? >>>>> >>>>> And on a side note, should I be able to update through 2.7.8, or is it common knowledge that it doesn't work that way since this is more of a framework (for lack of better words) rather than a normal application. >>>>> >>>>> Macbook Pro Mid 2012 15" >>>>> OSX 10.8.5 >>>>> >>>>> Thanks! >>>>> Christopher >>>>> >>>>> _______________________________________________ >>>>> Do not post admin requests to the list. They will be ignored. >>>>> X11-users mailing list (<mailto:X11-users@lists.apple.com>X11-users(a)lists.apple.com<mailto:X11-users@lists.apple.com>) >>>>> Help/Unsubscribe/Update your Subscription: <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma…> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma… >>>>> >>>>> This email sent to <mailto:magda.tsintou@gmail.com> magda.tsintou(a)gmail.com<mailto:magda.tsintou@gmail.com> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Do not post admin requests to the list. They will be ignored. >>>>> X11-users mailing list (<mailto:X11-users@lists.apple.com>X11-users(a)lists.apple.com<mailto:X11-users@lists.apple.com>) >>>>> Help/Unsubscribe/Update your Subscription: <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma…> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma… >>>>> >>>>> This email sent to <mailto:jeremyhu@freedesktop.org> jeremyhu(a)freedesktop.org<mailto:jeremyhu@freedesktop.org> >>>> _______________________________________________ >>>> Do not post admin requests to the list. They will be ignored. >>>> X11-users mailing list (<mailto:X11-users@lists.apple.com>X11-users(a)lists.apple.com<mailto:X11-users@lists.apple.com>) >>>> Help/Unsubscribe/Update your Subscription: <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma…> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma… >>>> >>>> This email sent to <mailto:wealthychef@gmail.com> wealthychef(a)gmail.com<mailto:wealthychef@gmail.com> >> -------------- next part -------------- >> A non-text attachment was scrubbed... >> Name: smime.p7s >> Type: application/pkcs7-signature >> Size: 4465 bytes >> Desc: not available >> URL: <<https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.apple.com_archive…>https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.apple.com_archive… > >> >> ------------------------------ >> >> Message: 4 >> Date: Tue, 17 May 2016 22:42:44 -0700 >> From: Rich Cook <<mailto:wealthychef@gmail.com>wealthychef(a)gmail.com<mailto:wealthychef@gmail.com>> >> To: Jeremy Huddleston Sequoia <<mailto:jeremyhu@apple.com>jeremyhu(a)apple.com<mailto:jeremyhu@apple.com>> >> Cc: <mailto:x11-users@lists.apple.com> x11-users(a)lists.apple.com<mailto:x11-users@lists.apple.com> >> Subject: Re: XQuartz 2.7.9 Update Inquiry >> Message-ID: <<mailto:B3A6C40B-0280-4068-A564-2D29D14FF451@gmail.com>B3A6C40B-0280-4068-A564-2D29D14FF451(a)gmail.com<mailto:B3A6C40B-0280-4068-A564-2D29D14FF451@gmail.com>> >> Content-Type: text/plain; charset=utf-8 >> >> Hmm, what is going to replace IGLX? How are people going to display OpenGL graphics over remote X11 if not by GLX? Sorry if this is offtopic. >> >>> On May 17, 2016, at 10:38 PM, Jeremy Huddleston Sequoia <<mailto:jeremyhu@apple.com>jeremyhu(a)apple.com<mailto:jeremyhu@apple.com>> wrote: >>> >>> >>>> On May 17, 2016, at 22:18, Richard Cook <<mailto:wealthychef@gmail.com>wealthychef(a)gmail.com<mailto:wealthychef@gmail.com>> wrote: >>>> >>>> I don't know what IGLX is, but GLX did not seem to work for me at all when I tried it in 2.7.9. Specifically, I could not run glxgears on a remote linux box, which is the canonical GLX test I always use. >>> That is IGLX. >>> >>>> But the good news it that switching back to 2.7.8 was painless and made my problems with 2.7.9 go away. >>>> >>>>> On May 17, 2016, at 9:40 PM, Jeremy Huddleston Sequoia <<mailto:jeremyhu@apple.com>jeremyhu(a)apple.com<mailto:jeremyhu@apple.com>> wrote: >>>>> >>>>> FWIW, there are security vulnerabilities addressed in the versions of libpng in 2.7.9, so you might want to update at least for the security reasons. >>>>> >>>>> The only issues that I'm aware of as regressions are the issues with IGLX (which isn't really going to be supported much longer) and a regression in the support for tcp connections (which is off by default and discouraged). >>>>> >>>>> --Jeremy >>>>> >>>>>> On May 17, 2016, at 14:39, Christopher Fick <<mailto:spacecarrider@gmail.com>spacecarrider(a)gmail.com<mailto:spacecarrider@gmail.com>> wrote: >>>>>> >>>>>> Magda, thank you so much for your thoughts! I did notice that v2.7.9 was just released earlier this month, and bugs were one thing I wondered about. I'm pretty out of the loop on this stuff. >>>>>> >>>>>> And, no I don't think I have anything to gain from an upgrade. Nothing prompted me to look into an upgrade aside from curiosity and an attempt to stay up to date. I just use XQ to run Inkscape, and so far I haven't had any issues in the little I've used it. It also appears that Inkscape is still standing at the same version (0.91) as when I initially installed it with XQ So, I will take your advice. If it ain't broken... >>>>>> >>>>>> Many Thanks! >>>>>> Christopher >>>>>> >>>>>> >>>>>> >>>>>> On Tue, May 17, 2016 at 4:25 PM, Magda Tsintou <<mailto:magda.tsintou@gmail.com>magda.tsintou(a)gmail.com<mailto:magda.tsintou@gmail.com>> wrote: >>>>>> Note: Sorry forgot to reply to all so that everyone can keep track of the conversation... >>>>>> >>>>>> Hi Christopher, >>>>>> >>>>>> With your OSX you would certainly not need to update. We recently were discussing some bugs in XQ 2.7.9 that have not been resolved while the version 2.7.8 works perfectly fine and I am running El Capitan 10.11.5. XQ 2.7.9 did not allow me to work with certain commands that needed forwarding over ssh and given the limited people who have been working on that fix this may cause problems for some time. I would strongly recommend from my personal experience to stick with XQ 2.7.8 if you have nothing in particular to gain from upgrading. I hope this helps a bit. Good luck! >>>>>> >>>>>> Best regards, >>>>>> Magda. >>>>>> >>>>>> >>>>>> On Tue, May 17, 2016 at 5:17 PM, Christopher Fick <<mailto:spacecarrider@gmail.com>spacecarrider(a)gmail.com<mailto:spacecarrider@gmail.com>> wrote: >>>>>> Hi I'm running XQ 2.7.8, and I see that 2.7.9 is now available. If I check for updates through the XQ "app" it says I'm up to date with 2.7.8. >>>>>> >>>>>> So, if I manually download and install 2.7.9 from the website should I just install it over the previous version? >>>>>> >>>>>> And on a side note, should I be able to update through 2.7.8, or is it common knowledge that it doesn't work that way since this is more of a framework (for lack of better words) rather than a normal application. >>>>>> >>>>>> Macbook Pro Mid 2012 15" >>>>>> OSX 10.8.5 >>>>>> >>>>>> Thanks! >>>>>> Christopher >>>>>> >>>>>> _______________________________________________ >>>>>> Do not post admin requests to the list. They will be ignored. >>>>>> X11-users mailing list (<mailto:X11-users@lists.apple.com>X11-users(a)lists.apple.com<mailto:X11-users@lists.apple.com>) >>>>>> Help/Unsubscribe/Update your Subscription: <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma…> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma… >>>>>> >>>>>> This email sent to <mailto:magda.tsintou@gmail.com> magda.tsintou(a)gmail.com<mailto:magda.tsintou@gmail.com> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Do not post admin requests to the list. They will be ignored. >>>>>> X11-users mailing list (<mailto:X11-users@lists.apple.com>X11-users(a)lists.apple.com<mailto:X11-users@lists.apple.com>) >>>>>> Help/Unsubscribe/Update your Subscription: <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma…> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma… >>>>>> >>>>>> This email sent to <mailto:jeremyhu@freedesktop.org> jeremyhu(a)freedesktop.org<mailto:jeremyhu@freedesktop.org> >>>>> _______________________________________________ >>>>> Do not post admin requests to the list. They will be ignored. >>>>> X11-users mailing list (<mailto:X11-users@lists.apple.com>X11-users(a)lists.apple.com<mailto:X11-users@lists.apple.com>) >>>>> Help/Unsubscribe/Update your Subscription: <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma…> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma… >>>>> >>>>> This email sent to <mailto:wealthychef@gmail.com> wealthychef(a)gmail.com<mailto:wealthychef@gmail.com> >> ————— >> Cheers from Rich Cook >> =============================== >> Success is the ability to go from one failure to the next with no loss of enthusiasm. --Winston Churchill >> >> >> >> >> ------------------------------ >> >> Message: 5 >> Date: Wed, 18 May 2016 15:56:13 +1000 >> From: James Gunning <<mailto:James.Gunning@csiro.au>James.Gunning(a)csiro.au<mailto:James.Gunning@csiro.au>> >> To: Rich Cook <<mailto:wealthychef@gmail.com>wealthychef(a)gmail.com<mailto:wealthychef@gmail.com>>, Jeremy Huddleston Sequoia >> <<mailto:jeremyhu@apple.com>jeremyhu(a)apple.com<mailto:jeremyhu@apple.com>> >> Cc: <mailto:x11-users@lists.apple.com> x11-users(a)lists.apple.com<mailto:x11-users@lists.apple.com> >> Subject: Re: XQuartz 2.7.9 Update Inquiry >> Message-ID: <<mailto:573C03FD.8080509@csiro.au>573C03FD.8080509(a)csiro.au<mailto:573C03FD.8080509@csiro.au>> >> Content-Type: text/plain; charset="utf-8"; Format="flowed" >> >> Hi Rich, Jeremy, all, >> Yes, I think a lot of us care about this a deal. >> Any news welcome. >> James. >> >> >> Rich Cook wrote: >>> Hmm, what is going to replace IGLX? How are people going to display OpenGL graphics over remote X11 if not by GLX? Sorry if this is offtopic. >>> >>>> On May 17, 2016, at 10:38 PM, Jeremy Huddleston Sequoia <<mailto:jeremyhu@apple.com>jeremyhu(a)apple.com<mailto:jeremyhu@apple.com>> wrote: >>>> >>>> >>>>> On May 17, 2016, at 22:18, Richard Cook <<mailto:wealthychef@gmail.com>wealthychef(a)gmail.com<mailto:wealthychef@gmail.com>> wrote: >>>>> >>>>> I don't know what IGLX is, but GLX did not seem to work for me at all when I tried it in 2.7.9. Specifically, I could not run glxgears on a remote linux box, which is the canonical GLX test I always use. >>>> That is IGLX. >>>> >>>>> But the good news it that switching back to 2.7.8 was painless and made my problems with 2.7.9 go away. >>>>> >>>>>> On May 17, 2016, at 9:40 PM, Jeremy Huddleston Sequoia <<mailto:jeremyhu@apple.com>jeremyhu(a)apple.com<mailto:jeremyhu@apple.com>> wrote: >>>>>> >>>>>> FWIW, there are security vulnerabilities addressed in the versions of libpng in 2.7.9, so you might want to update at least for the security reasons. >>>>>> >>>>>> The only issues that I'm aware of as regressions are the issues with IGLX (which isn't really going to be supported much longer) and a regression in the support for tcp connections (which is off by default and discouraged). >>>>>> >>>>>> --Jeremy >>>>>> >>>>>>> On May 17, 2016, at 14:39, Christopher Fick <<mailto:spacecarrider@gmail.com>spacecarrider(a)gmail.com<mailto:spacecarrider@gmail.com>> wrote: >>>>>>> >>>>>>> Magda, thank you so much for your thoughts! I did notice that v2.7.9 was just released earlier this month, and bugs were one thing I wondered about. I'm pretty out of the loop on this stuff. >>>>>>> >>>>>>> And, no I don't think I have anything to gain from an upgrade. Nothing prompted me to look into an upgrade aside from curiosity and an attempt to stay up to date. I just use XQ to run Inkscape, and so far I haven't had any issues in the little I've used it. It also appears that Inkscape is still standing at the same version (0.91) as when I initially installed it with XQ So, I will take your advice. If it ain't broken... >>>>>>> >>>>>>> Many Thanks! >>>>>>> Christopher >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Tue, May 17, 2016 at 4:25 PM, Magda Tsintou <<mailto:magda.tsintou@gmail.com>magda.tsintou(a)gmail.com<mailto:magda.tsintou@gmail.com>> wrote: >>>>>>> Note: Sorry forgot to reply to all so that everyone can keep track of the conversation... >>>>>>> >>>>>>> Hi Christopher, >>>>>>> >>>>>>> With your OSX you would certainly not need to update. We recently were discussing some bugs in XQ 2.7.9 that have not been resolved while the version 2.7.8 works perfectly fine and I am running El Capitan 10.11.5. XQ 2.7.9 did not allow me to work with certain commands that needed forwarding over ssh and given the limited people who have been working on that fix this may cause problems for some time. I would strongly recommend from my personal experience to stick with XQ 2.7.8 if you have nothing in particular to gain from upgrading. I hope this helps a bit. Good luck! >>>>>>> >>>>>>> Best regards, >>>>>>> Magda. >>>>>>> >>>>>>> >>>>>>> On Tue, May 17, 2016 at 5:17 PM, Christopher Fick <<mailto:spacecarrider@gmail.com>spacecarrider(a)gmail.com<mailto:spacecarrider@gmail.com>> wrote: >>>>>>> Hi I'm running XQ 2.7.8, and I see that 2.7.9 is now available. If I check for updates through the XQ "app" it says I'm up to date with 2.7.8. >>>>>>> >>>>>>> So, if I manually download and install 2.7.9 from the website should I just install it over the previous version? >>>>>>> >>>>>>> And on a side note, should I be able to update through 2.7.8, or is it common knowledge that it doesn't work that way since this is more of a framework (for lack of better words) rather than a normal application. >>>>>>> >>>>>>> Macbook Pro Mid 2012 15" >>>>>>> OSX 10.8.5 >>>>>>> >>>>>>> Thanks! >>>>>>> Christopher >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Do not post admin requests to the list. They will be ignored. >>>>>>> X11-users mailing list (<mailto:X11-users@lists.apple.com>X11-users(a)lists.apple.com<mailto:X11-users@lists.apple.com>) >>>>>>> Help/Unsubscribe/Update your Subscription: <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma…> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma… >>>>>>> >>>>>>> This email sent to <mailto:magda.tsintou@gmail.com> magda.tsintou(a)gmail.com<mailto:magda.tsintou@gmail.com> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Do not post admin requests to the list. They will be ignored. >>>>>>> X11-users mailing list (<mailto:X11-users@lists.apple.com>X11-users(a)lists.apple.com<mailto:X11-users@lists.apple.com>) >>>>>>> Help/Unsubscribe/Update your Subscription: <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma…> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma… >>>>>>> >>>>>>> This email sent to <mailto:jeremyhu@freedesktop.org> jeremyhu(a)freedesktop.org<mailto:jeremyhu@freedesktop.org> >>>>>> _______________________________________________ >>>>>> Do not post admin requests to the list. They will be ignored. >>>>>> X11-users mailing list (<mailto:X11-users@lists.apple.com>X11-users(a)lists.apple.com<mailto:X11-users@lists.apple.com>) >>>>>> Help/Unsubscribe/Update your Subscription: <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma…> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma… >>>>>> >>>>>> This email sent to <mailto:wealthychef@gmail.com> wealthychef(a)gmail.com<mailto:wealthychef@gmail.com> >>> ————— >>> Cheers from Rich Cook >>> =============================== >>> Success is the ability to go from one failure to the next with no loss of enthusiasm. --Winston Churchill >>> >>> >>> _______________________________________________ >>> Do not post admin requests to the list. They will be ignored. >>> X11-users mailing list (<mailto:X11-users@lists.apple.com>X11-users(a)lists.apple.com<mailto:X11-users@lists.apple.com>) >>> Help/Unsubscribe/Update your Subscription: <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma…> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma… >>> >>> This email sent to <mailto:james.gunning@csiro.au> james.gunning(a)csiro.au<mailto:james.gunning@csiro.au> >> -------------- next part -------------- >> A non-text attachment was scrubbed... >> Name: James_Gunning.vcf >> Type: text/x-vcard >> Size: 223 bytes >> Desc: not available >> URL: <<https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.apple.com_archive…>https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.apple.com_archive… > >> >> ------------------------------ >> >> Message: 6 >> Date: Wed, 18 May 2016 07:59:37 +0200 >> From: César <<mailto:cesarmensajes@gmail.com>cesarmensajes(a)gmail.com<mailto:cesarmensajes@gmail.com>> >> To: Jeremy Huddleston Sequoia <<mailto:jeremyhu@apple.com>jeremyhu(a)apple.com<mailto:jeremyhu@apple.com>> >> Cc: "<mailto:x11-users@lists.apple.com>x11-users(a)lists.apple.com<mailto:x11-users@lists.apple.com>" <<mailto:x11-users@lists.apple.com>x11-users(a)lists.apple.com<mailto:x11-users@lists.apple.com>> >> Subject: Re: XQuartz 2.7.9 Update Inquiry >> Message-ID: >> <<mailto:CALGOyxrDB8O1WXGFG-H1AOrDq0XekRb1tE3B4UFqtFo4hxyx6A@mail.gmail.com>CALGOyxrDB8O1WXGFG-H1AOrDq0XekRb1tE3B4UFqtFo4hxyx6A(a)mail.gmail.com<mailto:CALGOyxrDB8O1WXGFG-H1AOrDq0XekRb1tE3B4UFqtFo4hxyx6A@mail.gmail.com>> >> Content-Type: text/plain; charset="utf-8" >> >> Ok, thanks a lot, I look forward to the final fix (it's not a critical bug, >> but it does make my apps look like if they were broken -they run fine, but >> their UI looks broken) >> >> Thanks, >> >> César >> >> >> >> El miércoles, 18 de mayo de 2016, Jeremy Huddleston Sequoia < >> <mailto:jeremyhu@apple.com> jeremyhu(a)apple.com<mailto:jeremyhu@apple.com>> escribió: >> >>> There was one change, but it didn't completely address the problem. >>> >>>> On May 17, 2016, at 21:53, César <<mailto:cesarmensajes@gmail.com>cesarmensajes(a)gmail.com<mailto:cesarmensajes@gmail.com> <javascript:;><javascript:;>> >>> wrote: >>>> Jeremy, was the OpenGL context clipping bug addressed in 2.7.9, or is it >>> still pending? (I sent you a minimal working example showing the bug some >>> time ago) >>>> Thanks, >>>> >>>> César >>>> >>>> >>>> >>>> El miércoles, 18 de mayo de 2016, Jeremy Huddleston Sequoia < >>> <mailto:jeremyhu@apple.com> jeremyhu(a)apple.com<mailto:jeremyhu@apple.com> <javascript:;><javascript:;>> escribió: >>>> FWIW, there are security vulnerabilities addressed in the versions of >>> libpng in 2.7.9, so you might want to update at least for the security >>> reasons. >>>> The only issues that I'm aware of as regressions are the issues with >>> IGLX (which isn't really going to be supported much longer) and a >>> regression in the support for tcp connections (which is off by default and >>> discouraged). >>>> --Jeremy >>>> >>>>> On May 17, 2016, at 14:39, Christopher Fick <<mailto:spacecarrider@gmail.com>spacecarrider(a)gmail.com<mailto:spacecarrider@gmail.com> >>> <javascript:;><javascript:;>> wrote: >>>>> Magda, thank you so much for your thoughts! I did notice that v2.7.9 >>> was just released earlier this month, and bugs were one thing I wondered >>> about. I'm pretty out of the loop on this stuff. >>>>> And, no I don't think I have anything to gain from an upgrade. >>> Nothing prompted me to look into an upgrade aside from curiosity and an >>> attempt to stay up to date. I just use XQ to run Inkscape, and so far I >>> haven't had any issues in the little I've used it. It also appears that >>> Inkscape is still standing at the same version (0.91) as when I initially >>> installed it with XQ So, I will take your advice. If it ain't broken... >>>>> Many Thanks! >>>>> Christopher >>>>> >>>>> >>>>> >>>>> On Tue, May 17, 2016 at 4:25 PM, Magda Tsintou < >>> <mailto:magda.tsintou@gmail.com> magda.tsintou(a)gmail.com<mailto:magda.tsintou@gmail.com> <javascript:;><javascript:;>> wrote: >>>>> Note: Sorry forgot to reply to all so that everyone can keep track of >>> the conversation... >>>>> Hi Christopher, >>>>> >>>>> With your OSX you would certainly not need to update. We recently were >>> discussing some bugs in XQ 2.7.9 that have not been resolved while the >>> version 2.7.8 works perfectly fine and I am running El Capitan 10.11.5. XQ >>> 2.7.9 did not allow me to work with certain commands that needed forwarding >>> over ssh and given the limited people who have been working on that fix >>> this may cause problems for some time. I would strongly recommend from my >>> personal experience to stick with XQ 2.7.8 if you have nothing in >>> particular to gain from upgrading. I hope this helps a bit. Good luck! >>>>> Best regards, >>>>> Magda. >>>>> >>>>> >>>>> On Tue, May 17, 2016 at 5:17 PM, Christopher Fick < >>> <mailto:spacecarrider@gmail.com> spacecarrider(a)gmail.com<mailto:spacecarrider@gmail.com> <javascript:;><javascript:;>> wrote: >>>>> Hi I'm running XQ 2.7.8, and I see that 2.7.9 is now available. If I >>> check for updates through the XQ "app" it says I'm up to date with 2.7.8. >>>>> So, if I manually download and install 2.7.9 from the website should I >>> just install it over the previous version? >>>>> And on a side note, should I be able to update through 2.7.8, or is >>> it common knowledge that it doesn't work that way since this is more of a >>> framework (for lack of better words) rather than a normal application. >>>>> Macbook Pro Mid 2012 15" >>>>> OSX 10.8.5 >>>>> >>>>> Thanks! >>>>> Christopher >>>>> >>>>> _______________________________________________ >>>>> Do not post admin requests to the list. They will be ignored. >>>>> X11-users mailing list (<mailto:X11-users@lists.apple.com>X11-users(a)lists.apple.com<mailto:X11-users@lists.apple.com> <javascript:;><javascript:;>) >>>>> Help/Unsubscribe/Update your Subscription: >>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma…> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma… >>>>> This email sent to <mailto:magda.tsintou@gmail.com> magda.tsintou(a)gmail.com<mailto:magda.tsintou@gmail.com> <javascript:;><javascript:;> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Do not post admin requests to the list. They will be ignored. >>>>> X11-users mailing list (<mailto:X11-users@lists.apple.com>X11-users(a)lists.apple.com<mailto:X11-users@lists.apple.com> <javascript:;><javascript:;>) >>>>> Help/Unsubscribe/Update your Subscription: >>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma…> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma… >>>>> This email sent to <mailto:jeremyhu@freedesktop.org> jeremyhu(a)freedesktop.org<mailto:jeremyhu@freedesktop.org> <javascript:;><javascript:;> >>> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: <<https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.apple.com_archive…>https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.apple.com_archive… > >> >> ------------------------------ >> >> _______________________________________________ >> X11-users mailing list >> <mailto:X11-users@lists.apple.com> X11-users(a)lists.apple.com<mailto:X11-users@lists.apple.com> >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma…> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma… >> >> End of X11-users Digest, Vol 13, Issue 35 >> ***************************************** > > Houston Methodist. Leading Medicine. > > Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 11 specialties. Named to FORTUNE® Magazine's "100 Best Companies to Work For®" list 10 years in a row. Designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org<http://houstonmethodist.org/>. Follow us at twitter.com/MethodistHosp<https://urldefense.proofpoint.com/v2/url?u=http-3A__twitter.com_MethodistHo…> and www.facebook.com/HoustonMethodist<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.facebook.com_Housto…>. > > ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you. > > _______________________________________________ > Do not post admin requests to the list. They will be ignored. > X11-users mailing list (<mailto:X11-users@lists.apple.com>X11-users(a)lists.apple.com<mailto:X11-users@lists.apple.com>) > Help/Unsubscribe/Update your Subscription: <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma…> https://lists.apple.com/mailman/options/x11-users/wealthychef%40gmail.com > > This email sent to <mailto:wealthychef@gmail.com> wealthychef(a)gmail.com<mailto:wealthychef@gmail.com> ————— Cheers from Rich Cook =============================== Success is the ability to go from one failure to the next with no loss of enthusiasm. --Winston Churchill _______________________________________________ Do not post admin requests to the list. They will be ignored. X11-users mailing list (<mailto:X11-users@lists.apple.com>X11-users(a)lists.apple.com<mailto:X11-users@lists.apple.com>) Help/Unsubscribe/Update your Subscription: <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.apple.com_mailma…> https://lists.apple.com/mailman/options/x11-users/magda.tsintou%40gmail.com This email sent to <mailto:magda.tsintou@gmail.com> magda.tsintou(a)gmail.com<mailto:magda.tsintou@gmail.com> ————— Cheers from Rich Cook =============================== Success is the ability to go from one failure to the next with no loss of enthusiasm. --Winston Churchill _______________________________________________ Do not post admin requests to the list. They will be ignored. 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Houston Methodist has also been named to FORTUNE® Magazine's "100 Best Companies to Work For®" list for 10 years in a row. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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