Freesurfer

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Re: [Freesurfer] Connectivity design ill-conditioned
by Zimmerman, Jared Perry 27 May '16

27 May '16

Thanks Doug, this worked. Misconfigured my nuisance regressor seeds. Matrix still has 47 columns, but it seems to be appropriately designed. Best, Jared Message: 2 Date: Thu, 26 May 2016 12:14:27 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Connectivity design ill-conditioned To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <574720E3.30603(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed It is strange that it has 47 columns, I would have expected 48, however, the current problem is caused by the wm.dat and vcsf.dat having the same content. Probably it was an error when you set up the command line for fcseed-config On 05/25/2016 06:40 PM, Zimmerman, Jared Perry wrote: > 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 > > > _______________________________________________ > 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

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mri_cc
by Arash Nazeri 27 May '16

27 May '16

Dear all, mri_cc does not seem to be working properly to parcellate corpus callosum. As per one of the previous posts, there is a bug in the current release of mri_cc. However, the link provided in the same thread for an updated version of mri_cc is no longer existent. Our cluster runs on 64bit Ubuntu 14.04 systems. I'd be grateful if someone can post a new link for the corrected mri_cc. Thanks in advance. Cheers, Arash

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(no subject)
by Saturne Fox 27 May '16

27 May '16

[image: Inline image 3][image: Inline image 1][image: Inline image 2][image: Inline image 4] Dear freesurfer community, These days I am manually editing some data and this subject is giving me such a hard time. In fact I would like the near-to-cortexartefacts at the top right hand corner to be excluded from the surface but even after changing the intensity of the wanted part to 255 and the one of the excluded parts to 1 (which is nevertheless not visible on these images) the surface is still not what I would like it to become. In adition to editing the wm.mgz file, I also modified the aseg.presurf file to exclude these parts and I re-runned the -normalization2 and -maskbfs flags to generate new brain.mgz and brain.finalsurfs.mgz files. Any idea why these modifications are not affecting the surface ? Best regards, Antoine

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roi mask?
by Marja Caverlé 27 May '16

27 May '16

Hi all, So I ran a recon-all -all on one of my subjects, and it completed without errors (according to the log). Now I would like to get cortical thickness numbers from this subject, but when I open the tutorial regarding this, it says it assumes that you already have a roi mask and a T1 in the same coordinate space as the roi mask. Did the recon -all -all by any chance create these files? And if not, how can I? So basically the question is; what do I have to do after recon -all -all in order to get cortical thickness numbers in roi's of my subjects? Thanks in advance. Marja

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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.

1 0

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)

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