Freesurfer July 2012

freesurfer@nmr.mgh.harvard.edu

128 participants
194 discussions

Re: [Freesurfer] stats
by Douglas N Greve 20 Jul '12

20 Jul '12

Hi Viola, those stats tables are unrelated to your map-based exploratory analysis. If you have clusters in your map, you should run the correction for multiple comparisons. This will give you significant clusters. It will also produce a table of mean thicknesses in each cluster for each subject which you can then import to SPSS. doug On 07/19/2012 04:35 PM, Oertel, Viola wrote: > Yes. I did the contrast pat. vs. cont and see some significant regions on the display. After that, I did this "generate" stats table. My idea was to put this scores into SPSS and run the inferential statistics there. But I am not sure which table I have to use. What I want to use are the thickness values of each participant of all significant regions which I can see on the template. > Currently, I am not sure what kind of regions the tables show? Are that all regions, only the significant ones of the specific contrast I compute? I have seen that both tables show different regions. But I currently don't how the selection works. > > May you help with that? > > Thanks and best regards, > > Viola > > ________________________________________ > Von: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu]" im Auftrag von"Douglas N Greve [greve(a)nmr.mgh.harvard.edu] > Gesendet: Donnerstag, 19. Juli 2012 17:30 > Bis: freesurfer(a)nmr.mgh.harvard.edu > Betreff: Re: [Freesurfer] stats > > Those stats tables just gives statistics (means, standard deviations) > for thickness in different regions. They do not have inferential > statistics. Have you run an analysis on patients vs controls? > doug > > On 07/19/2012 09:27 AM, Oertel, Viola wrote: >> Dear Doug, >> >> I have a question: when I create the stats tables, there are two tables: >> >> lh.aparc.a2005s.thickness.stats and >> >> lh.aparc.thickness.stats >> >> which one is the right one if I want to get the thickness values of >> the significant clusters from the main effect (pat. / controls)? >> >> Thanks and best regards, >> >> Viola >> >> >> >> _______________________________________________ >> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > _______________________________________________ > 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. > > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] freesurfer issue
by Douglas N Greve 20 Jul '12

20 Jul '12

It is supposed to be created by recon-all. If you already ran recon-all, then it probably failed. Look at the log file. doug On 07/20/2012 12:27 PM, David Eugene Klein wrote: > I suppose not. How do I create one? > > These are the options I get when I list (ls): > > brainmask.auto.mgz > brainmask.mgz > ctrl_pts.mgz > mri_nu_correct.mni.log > mri_nu_correct.mni.log.bak > norm.mgz > nu.mgz > orig > orig,mgz > rawavg.mgz > T1.mgz > talairach.label_intensitites.txt > talairach.log > talairach_with_skill.og > transforms > > > On Jul 20, 2012, at 11:21 AM, Douglas N Greve wrote: > >> ls $SUBJECTS_DIR/subject/mri/wm.mgz >> >> >> On 07/20/2012 11:55 AM, David Eugene Klein wrote: >>> It should…how can I check if it does? >>> On Jul 20, 2012, at 10:48 AM, Douglas N Greve wrote: >>> >>>> Does wm.mgz exist? >>>> doug >>>> >>>> On 07/20/2012 11:02 AM, David Eugene Klein wrote: >>>>> Hello, >>>>> >>>>> I'm using freesurfer edit in the tkmedit format and running into issues. >>>>> >>>>> I'm editing them in quest server. I type the following command: >>>>> >>>>> tkmedit<subjid> brainmask.mgz -aux wm.mgz -surfs >>>>> >>>>> where<subjid> is the subject. >>>>> >>>>> The subject loads but I get the following error message, and the red and yellow lines that are supposed to appear do not: >>>>> >>>>>> Error: Loading volume wm.mgz >>>>>> >>>>>> Couldn't read the anatomical volume. >>>>>> Tkmedit couldn't read the volume you specified. >>>>>> >>>>>> This could be because the image format wasn't recognized, >>>>>> or it couldn't find the proper header, >>>>>> or the file (s) were unreadable, >>>>>> or it was the wrong size. >>>>>> >>>>> I have run recon-all so I don't think that's the problem. If someone could help me figure this out it would be greatly appreciated. >>>>> >>>>> Thank you. >>>>> >>>>> David Klein >>>>> _______________________________________________ >>>>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> >>>> _______________________________________________ >>>> 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. >>>> >>> >> -- >> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> > > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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(no subject)
by Emilia Lentini 20 Jul '12

20 Jul '12

Hi. I´m working on a correlation analysis with a seed-region. With FDR correction I can see that the region correlate stronger with itself. But when I do the Monte Carlo simulation, I can´t see this color difference in the correlation. (see attached images). So my question is: why is it like this? Should not the seed region correlate stronger with it self when using monte-carlo simulation? Best regards, Emilia

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Re: [Freesurfer] FWHM smoothing for surface based
by Douglas N Greve 20 Jul '12

20 Jul '12

Yea, that is pretty smooth to start with. How did you choose to smooth by (an additional) 15mm? How are your results if you don't do anymore smoothing? doug On 07/20/2012 11:22 AM, jm wrote: > On 07/18/2012 11:14 AM, Douglas N Greve wrote: >> I think that the LGI is a very smooth measure, so even if you only >> smoothed by 15mm, there is a lot of smoothness in the unsmoothed data. >> This is what fwhm.dat is picking up. What happens if you do not smooth >> the data? What fwhm do you get? >> doug > > if I not smooth lgi data I get fwhm=13.2 into fwhm.dat > >> >> On 07/18/2012 08:02 AM, jm wrote: >>> Dear Freesurfer Team: >>> >>> I would like some information on FWHM.dat folder glmdir and its >>> relationship with mri_glmfit-sim. >>> It happens that when I use mri_glmfit-sim with --cache-in can't find >>> the data for fwhm 51 - which is logical because they exist only to >>> 1..30, but my data were smoothed previously for fwhm 15 (pial_lgi). >>> That interpretation would take this outcome? Something could go wrong >>> when he observed these differences between the smoothing of my data >>> and the reported in fwhm.dat >>> >>> thanks in advance >>> >>> >>> >>> _______________________________________________ >>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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freesurfer issue
by David Eugene Klein 20 Jul '12

20 Jul '12

Hello, I'm using freesurfer edit in the tkmedit format and running into issues. I'm editing them in quest server. I type the following command: tkmedit <subjid> brainmask.mgz -aux wm.mgz -surfs where <subjid> is the subject. The subject loads but I get the following error message, and the red and yellow lines that are supposed to appear do not: > >>>> > > Error: Loading volume wm.mgz > > Couldn't read the anatomical volume. > Tkmedit couldn't read the volume you specified. > > This could be because the image format wasn't recognized, > or it couldn't find the proper header, > or the file (s) were unreadable, > or it was the wrong size. > > >>>>>> I have run recon-all so I don't think that's the problem. If someone could help me figure this out it would be greatly appreciated. Thank you. David Klein

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covariation analysis
by Ivanka Savic Berglund 20 Jul '12

20 Jul '12

We are trying to evaluate the covariation pattern in cortical thickness from a selected cortical ROI along the entire brain cortex. However, the output received gives only positive values. Is this inherent in the program, or could it be a matter of the input command? Sincerely I Savic

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Longitudinal analysis question
by Kairys, Anson 20 Jul '12

20 Jul '12

Hello FS experts, I am running a group up subjects pre/post treatment. When trying to do group analysis, after converting data with the mri_slope command, when I made the long table into a cross table, I noticed in qdec it averaged my "time" variable and only supplies a mean and there is no longer separate timepoints for subjects, just one value per subject. Do I need to define time as something more descriptive than 0 (tp1) and 1 (tp2)? I am so close to analyzing these data, just need a little help with the group analysis Thanks Anson ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

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slice-by-slice predictors
by Caspar M. Schwiedrzik 19 Jul '12

19 Jul '12

Hi! Is it possible to have slice-by-slice predictors in Freesurfer, and if so, how? Thanks, Caspar

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stats
by Oertel, Viola 19 Jul '12

19 Jul '12

Dear Doug, I have a question: when I create the stats tables, there are two tables: lh.aparc.a2005s.thickness.stats and lh.aparc.thickness.stats which one is the right one if I want to get the thickness values of the significant clusters from the main effect (pat. / controls)? Thanks and best regards, Viola

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retroicor
by Caspar M. Schwiedrzik 19 Jul '12

19 Jul '12

Hi! Has someone used retroicor (retroactive correction of physiological noise; Glover at al. 2000) with Freesurfer? I would like to create nuisance regressors for EPI data based on cardiac and respiratory signals. The AFNI version of retroicor produces slice-based regressors, and I am not sure how to use them in Freesurfer. Suggestions for alternative implementations would also be appreciated. Thanks! Caspar

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Freesurfer July 2012