Freesurfer March 2014

freesurfer@nmr.mgh.harvard.edu

147 participants
247 discussions

One sample t-test in Qdec
by Buse Merve Ürgen 18 Mar '14

18 Mar '14

Hello, I would like to learn whether we can conduct one-sample t-test using Qdec. I'm working on a single-case study, and I want to compare a single subject's data with a group of controls (to see how this specific subject is different from the group) in terms of volume, thickness and meancurvature. As far as I know, we can do the analysis in Terminal, but I would like to see & have the brain figure output (cluster by cluster) in Qdec for one sample t-test as well. Is it possible? Thanks in advance, Buse.

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Restrict QDEC analysis to a region
by amirhossein manzouri 18 Mar '14

18 Mar '14

Dear Experts, I have read the previous posts in the list regarding restricted ROI analysis. So I generated my label from tksurfer and used that for group difference analysis by adding --label to mri_glmfit, but the result (sig.mgh) seems just a masked version of the analysis including whole brain ( no difference in significance! ). I expected to see a different pattern of significance by limiting the region. Would you please advise if I am doing this in a right way? Best regards, Amirhossein Manzouri

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Re: [Freesurfer] fMRI contrasts in Freesurfer
by Douglas N Greve 18 Mar '14

18 Mar '14

Hi Francesco, please remember to post to the list. Thanks! The baseline is a regressor with all ones, so it is measured throughout the scan, not just during the rests. This makes the other regression coefficients relative to baseline. doug On 03/17/2014 01:05 PM, Francesco Puccettone wrote: > thank you Doug, I am just still not sure about comparing to the > baseline vs comparing between conditions; since the baseline it's not > one of the predictors, how is it exactly used to define the contrasts > and influence the regression coefficients? > > And is it the case that the "baseline" is taken as the average of all > non-stimulus (rest) periods in the scan, i.e. the "zero" periods in > the block-design boxcar diagram? > > Thank you again, > --Francesco > > > On 17 March 2014 15:33, Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > On 03/15/2014 06:35 PM, Francesco Puccettone wrote: > > Dear Freesurfer community: > > > > I have some (perhaps silly, but I think fundamental) questions about > > contrasts in functional analyses: > > > > > > 1. When wanting to see what regions are activated by exposure to a > > certain stimulus (blocked-design), what is the exact stats that is > > happening voxel-wise: > > > > (i) correlation between the time series of the HRF-convoluted > BOLD and > > that of the behavioural stimulus that was used, or > > (ii) t-test between the BOLD signal during the stimulus and the BOLD > > signal during a resting baseline > > > > If ii) is the answer, then is "baseline" taken as an average of all > > non-stimulus (rest) periods in the scan, i.e. the "zero" periods in > > the block-design boxcar diagram? > Neither. A GLM is set up with regressors for you conditions and > nuisance > variables. The GLM is fit to the time course to compute a regression > coefficient for each regressor. This is a multivariate operation and > does not reduce to a simple correlation. For a task regressor, the > regression coefficient indicates the amplitude of the HRF. This > amplitude is tested with a t-test > > > > > > > > 2. When wanting, on the other hand, to see what regions are > active in > > condition A but not in condition B (so a comparison this time), > is it > > the case that i) is no longer a choice and a t-test always has to be > > used between condition A and condition B? If so, is the > > stimulus-vs-baseline situation from the previous question just a > > special case of this, where condition B = (passive) baseline? > This would be a conjunction analysis that does not reduce to a simple > contrast. > > > > > > > > 3. Is it the case that a contrast probing the difference between two > > groups is using independent samples t-tests, whereas one probing the > > within-subject difference between two time-points is using > > paired-samples t-tests? > Between groups is independent two-sample. Within subject uses a > GLM and > does not reduce to a simple paired formula (but that is basically the > right way to think about it) > doug > > > > > > Thank you for your help:-) > > > > --Francesco > > > > > > _______________________________________________ > > 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 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://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. > > -- 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/

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Re: [Freesurfer] hypothalamus?
by Koolschijn, Cédric 18 Mar '14

18 Mar '14

Hi Ella, There are a number of options: You can draw manual segmentations on individual subjects, though the time and cost required for this labor-intensive process of manual tracing has become prohibitive. Paul's suggestion would be a better one, maybe one of our protocols described in e.g. http://www.ncbi.nlm.nih.gov/pubmed/21733239 could be of use to you? In case of drawing on the fsaverage, I would add the suggestion to draw at least two times to see if you're segmentation is reliable (compare your two (or more) ROIs and check for overlap and non-overlapping parts, for non-overlap decide whether those voxels should be in- or excluded). Subsequently, you map your segmentation to individual subjects and check for correct registration. Another approach would be to use the ROI from the Wake Forest University PickAtlas. You can map this to FS-space, and follow similar procedures to map to native space. Though I must note that this ROI is not perfect. All depends on your research question of course, how detailed do you want your ROI to be. Best of luck, Cédric ---------------------------------------------------------------- P.C.M.P. Koolschijn (Cédric), PhD Dutch Autism & ADHD Research Center Brain and Cognition The Netherlands E P.C.M.P.Koolschijn(a)uva.nl<mailto:P.C.M.P.Koolschijn@uva.nl> W http://www.dutcharc.nl<http://www.dutcharc.nl/>/ On 3/18/14 1:04 PM, "Paul Beach" <pabeach1(a)gmail.com<mailto:pabeach1@gmail.com>> wrote: Ella, My understanding is the same. I've made my own ROI by hand drawing on the average subject and using various commands to map onto individual subjects. If you're doing resting analysis then you can check your general whole brain correlation results against the literature to see if your ROI performs well. It's not perfect, but it can give decent results. Cheers, Paul Sent from my iPhone On Mar 18, 2014, at 7:13 AM, Ella <ellahinton(a)hotmail.com<mailto:ellahinton@hotmail.com>> wrote: Hi all, I'm looking to create a mask for the hypothalamus on individual subjects. I've had a good look at the literature, and at the moment, am I right in thinking the automatic segmentation in Freesurfer doesn't currently include the hypothalamus? thanks in advance Ella _______________________________________________ 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.

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hypothalamus?
by Ella 18 Mar '14

18 Mar '14

Hi all, I'm looking to create a mask for the hypothalamus on individual subjects. I've had a good look at the literature, and at the moment, am I right in thinking the automatic segmentation in Freesurfer doesn't currently include the hypothalamus? thanks in advance Ella

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Problem about Surface-based Registration
by yufeng huang 18 Mar '14

18 Mar '14

I followed the process of creating a registration template from scratch(GW)( https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates) to do the surface-based registration. My question are as followed: 1 I want to know if I need to use the mri_cvs_registrater to replace mri_register. 2 I check the result and find it produce the lh.sphere.reg.newtemplate1 and rh.sphere.reg.newtemplate1 in each subjects's surf folder. I want to know how to check the result by using the new file. 3 Should I need to re-run recon-all after the mri_register for every subjects? Thanks very much for your help!

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tkmedit edit voxel tcl script
by Joerg Pfannmoeller 18 Mar '14

18 Mar '14

Hello, if I have selected a voxel in a volume with tkmedit with a tcl script, how can I set the voxel value to 0. Sincerely yours pfannmoe

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Fw: Re: view time course in freeview
by charujing123 17 Mar '14

17 Mar '14

Hi doug and other FS experts, Thanks very much doug. rh.ttest.thickness.10.mgh is created from the mris_preproc to merge all the subjects' thickness into one file. Then group t-test can be done. I try tksurfer -t rh.ttest.thickness.10.mgh, but the command window echoes its usage. Just as you told me freeview has a new version to see time course for this file. I wonder where I can download it. Thanks doug, All the best. Rujing Zha 2014-03-13 charujing123 发件人：Douglas Greve <greve(a)nmr.mgh.harvard.edu> 发送时间：2014-03-12 22:57 主题：Re: [Freesurfer] view time course in freeview 收件人："freesurfer"<freesurfer(a)nmr.mgh.harvard.edu> 抄送： But what is in rh.ttest.thickness.10.mgh? Is it a stack of all your subjects (the file you passed with --y to mri_glmfit)? If so, then add "-t rh.ttest.thickness.10.mgh" to your tksurfer command line. Ruopeng just added something to freeview to do it, but you'd have to get a new version doug On 3/11/14 9:46 PM, charujing123 wrote: Hi doug, sig.mgh is my result for two group t-test on pial thickness of whole brain. So I want to see the time course of thickness of rh.ttest.thickness.10.mgh vertex by vertex. Thanks. All the best. Rujing Zha 2014-03-12 charujing123 发件人：Douglas N Greve <greve(a)nmr.mgh.harvard.edu> 发送时间：2014-03-12 00:16 主题：Re: [Freesurfer] view time course in freeview 收件人："freesurfer"<freesurfer(a)nmr.mgh.harvard.edu> 抄送： the time course of what? On 03/11/2014 07:18 AM, charujing123 wrote: > Hi FS experts, > For the sig.mgh, can I see the time course vertex by vertex in freeview? > Thanks. > All the best. > Rujing Zha > > > _______________________________________________ > 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 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

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mris_preproc, mri_surf2surf and lme_mass_vw
by Eric Cunningham 17 Mar '14

17 Mar '14

Hello Freesurfer experts, The lme_mass_vw script runs for a long time and outputs info into the matlab terminal. Most look like this: Location #####: Algorithm did not converge. Initial and final likelihoods: ###, ### Running this script, for almost every line, the initial and final likelihoods are "Inf". Is this indicative of a problem? ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Getting these results made me wonder if the Y-input was built properly. Using mris_preproc and mri_surf2surf to smooth, we tested 10mm smoothing and no smoothing in addition to the 30mm smoothing we had been doing originally. The results: smoothed to 30 ~ almost every likelihood = Inf, Inf smoothed to 10 ~ some (1 in 5? 10?) likelihood = Inf not smoothed ~ no instances of likelihood = Inf, Inf Thanks, -Eric

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Consistent Dura issues
by Jonathan Holt 17 Mar '14

17 Mar '14

Hi all, I’m working with a particularly stubborn data set whose defining characteristic is dura along the posterior of the brain. It’s become so consistent that I’m hoping to find a way to perhaps tweak recon-all so as to take care of the issue in a more automated manner and save many many man hours of manual work. Is this possible? jon

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Freesurfer March 2014