Freesurfer

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30089 discussions

MNI to RAS
by Jared Deck 23 Jul '12

23 Jul '12

Hi Doug, I am trying to convert MNI to RAS. I know the formula to convert from RAS to MNI is: MNI305RAS = TalXFM*Norig*inv(Torig)*[tkrR tkrA tkrS 1]' In theory, I should just be able to just invert this, but I am having difficulties because TalXFM is a non-square matrix and therefore not invertible. In addition, I tried using the moore-penrose pseudoinverse of the matrix but the values obtained do not match those in tkmedit. Do you have a formula for going from MNI to RAS or any advice about how would go about doing this? Thank you, Jared

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issues with the Talairach transformation
by Mojdeh Zamyadi 23 Jul '12

23 Jul '12

Hi all, I've just started to do cortical thickness analysis on some subjects and I'm noticing some miss-registrations, more specifically the Talairach image is smaller than the target image no matter what subject I look at! I just wanted to make sure if this is something normal and to what extend it's going to effect the individual cortical thickness calculations. I guess I'm not sure how the Talairach trasnformation is used in further steps of the cortical thickness calculation. I've attached example coronal, sagittal and horizontal slices of one of my subjects. I greatly appreciate your advice. Thanks, Mojdeh Zamyadi, MSc Clinical Research Project Assistant The Hospital for Sick Children 555 University Avenue Toronto ON M5G 1X8

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Questions about correction over 2 hemispheres and MCC
by Reem Jan 22 Jul '12

22 Jul '12

Hi Doug I hope it's okay that I double check I'm doing the correction over 2 hemispheres correctly and ask a question regarding correction for multiple comparisons. I will briefly describe what I have done: I have 2 groups of subjects - Drug addicts (n= 17) and controls (n=20). 1. I ran a surface thickness study: · For the 'mri_glmfit' command, I used DOSS and specified a contrast of +1 -1 0 (Controls > MA) · I ran a pre-cached simulation with the following command: mri_glmfit-sim --glmdir lh.group_age.glmdir --cache 4 pos · This simulation should only have corrected for the left hemisphere as I understand it. My cluster summary text file showed me that a cluster survived in the insula. I interpreted this as 'controls had higher grey matter thickness in this cluster located in the insula than drug addicts'. However, this was only corrected over the left hemisphere (when I ran the same simulation in the right hemisphere, nothing survived multiple comparison correction). · I now wanted to correct the lh results for 2 hemispheres. From the help menu of 'mri_glmfit-sim', I understood you can do this in 2 ways, are both of these correct and give the same result? a. mri_glmfit-sim --glmdir lh.group_age.glmdir --cache 4 pos --2 spaces --no-sim csdbase b. mri_glmfit-sim --glmdir lh.group_age.glmdir --cache 4 pos --cwpvalthresh 0.025 Ø No clusters survived the Bonferroni correction over both hemispheres. So I assume I can no longer report this result? 2. I ran a subcortical volume study: · I used SPSS to perform the statistical analysis on each of 14 subcortical structures (left and right). Is there a good way to correct for multiple comparisons, apart from Bonferroni, which would be very conservative? Many thanks for your advice. Kind regards Reem Reem Jan BPharm (Hons), RegPharmNZ PhD Student / Pharmacist School of Pharmacy, Faculty of Medical & Health Sciences, The University of Auckland, Private Bag 92019, Auckland, New Zealand. Ph: +64 9 373 7599 ext 81138. DDI: +64 9 923 1138 F: +64 9 367 7192 From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve Sent: Friday, 20 July 2012 11:52 a.m. To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] slice-by-slice predictors Sorry, not possible. On 7/19/12 6:56 PM, Caspar M. Schwiedrzik wrote: Hi! Is it possible to have slice-by-slice predictors in Freesurfer, and if so, how? Thanks, Caspar _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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mris_refine_surfaces
by Colin Reveley 20 Jul '12

20 Jul '12

Hi - I'm using freesurfer with an ex-vivo MTR of a monkey, at 0.25mm. unfortunately the data doesn't fit into 256^3, and anyway things are much faster, and decent results are to be had by downsampling to 0.5mm. I did notice this mris_refine_surfaces. That looked great. I can fit 0.32mm into 256^3, so I did that, and called it 0.64mm, and treated it the same way I treated the 0.5mm (nu_correct etc etc) to get my "hires.mgz" for mris_refine_surfaces then I noticed mris_refine_surfaces wants ?h_hires.label as well. a) how would I make ?h_hires.label b) does my hires.mgz even have to be 256^3? If not, I could use the actual 250um data to refine the surface, and that would be nice. c) I don't suppose there would be any chance of not only using a hi res volume to refine the surfaces, but also upsampling the surfaces too? There is a reason I might want them upsampled. It would be nice for the ?h.white mesh to sort of approximately have a node for each voxel face. It's to do with more accurately mapping certain data in CARET later on. I'd settle for just how to make ?h_hires.label and use mris_refine_surfaces though :) cheers, Colin

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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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