Freesurfer

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30132 discussions

Re: [Freesurfer] Error with mri_glmfit-sim \
by Douglas N Greve 02 Dec '11

02 Dec '11

Is this volume data? If so, then use --grf with mri_glmfit-sim instead of --cache. doug Antonella Kis wrote: > Dear Doug, > > Can you please advise me how I can do a multiple comparison for my DTI > group analysis? > > I tried and I ran: > > mri_glmfit --y group-fa-tal.nii > --fsgd DTI_group_analysis.fsgd dods --cwpvalthresh .99 \ --C > contrast.mtx --glmdir group_analysis-0.99.glmdir > > but I got: > > ERROR: Option --cwpvalthresh unknown > so I really don't know how I can do the multiple comparison in this > case: the DTI data. > > Also, I tried to run the: > > > mri_glmfit-sim \ > --glmdir group_analysis.glmdir \ > --cache 2 neg \ > --cwpvalthresh .99 \ > --overwrite > > but I got another ERROE: > > ERROR: cannot find > /usr/local/freesurfer//average/mult-comp-cor///cortex/fwhm04/neg/th20/mc-z.csd > > Thank you very much! > Antonella > -- 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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how to make lh.curv lh.sulc visible
by Maria Felber 02 Dec '11

02 Dec '11

Dear all, in the process of understanding freesurfer I like to see/inspect the created transforms visually. However, so far I am not able to see all the data that is stored in the transforms folder. So is it possible to see files like /transforms/lh.curv or /transfroms/lh.sulc? And if yes, what is the programm and command order? So far, I only figured out how to see data like /transforms/lh.pial lh.orig lh.inflated and so on. Thanks a lot, Maria -- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522

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Computing Volume of Segmentation Label Above or Below a User-Defined Plane
by Joshua Lee 01 Dec '11

01 Dec '11

Hi All, I would like to determine the volumes of a segmented region below or above an arbitrary line in one of the planes. For example, what would be the remaining volume of a label when z >= nth slice, where I would have previously determined the appropriate value of n. Thanks, Josh

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Re: [Freesurfer] Four Groups (Two Factors/Two Levels), One Covariate with very strange results
by Douglas N Greve 01 Dec '11

01 Dec '11

For thickness studies, if you have just one group, then the only thing to test is the slope, and it should not matter (but you might need DeMean to make it well conditioned). doug Knut J Bjuland wrote: > Hi > > Should i also add demean flag if I had just one group an one continus > variable like iq. I get in this case significant findings on the other > side of the brain in Fs 5.1 than in Fs 4.30 > > Thank you for you time > Knut j > > > Date: Thu, 1 Dec 2011 12:09:52 -0500 > > From: greve(a)nmr.mgh.harvard.edu > > To: knutjbj(a)hotmail.com > > Subject: Re: [Freesurfer] Four Groups (Two Factors/Two Levels), One > Covariate with very strange results > > > > I think the problem is just a scaling issue with the ages being 20x > more > > than the offset (which is 1). The next version will handle this > > internally, but you can go ahead and use the DeMean flag in the > FSGD. If > > your goal is to test for a difference in covariate slope across the > > groups, then adding the DeMean flag will not affect the results. > > However, if the continuous variables (covariates) are nuisance > > variables, then you should first test your contrast of interest on the > > slopes (using the DODS model). If there is no difference, then you > > should re-run the analysis with DOSS. > > doug > > > > Knut J Bjuland wrote: > > > Hi Nick > > > > > > Thank for the replay. > > > > > > > > > I have one group with premature that I compares to a group with term > > > born controls. However when I control for gender and age I get this > > > error message. > > > > > > ERROR: matrix is ill-conditioned or badly scaled, condno = 11065.5 > > > -------------------------------- > > > Possible problem with experimental design: > > > Check for duplicate entries and/or lack of range of > > > continuous variables within a class. > > > If you seek help with this problem, make sure to send: > > > 1. Your command line: > > > mri_glmfit --y lh.60.mgh --fsgd group_diff_gender_age_old.fsgd --C > > > Controls_VLBW.intercept.mtx --cortex --glmdir new --surf fsaverage lh > > > 2. The FSGD file (if using one) > > > 3. And the design matrix above > > > > > > > > > But when I added those subject that are commented I am able to run > > > mrl_glm fit without problems. I have checked for the usual errors and > > > there are none duplicated entries. The variables are 4 fixed > > > variables and one continuous variable named age in years. When I add > > > the subjects that are commented out I am able to produce an design > > > matrix. Having said that I am able to produce an matrix that works by > > > adding demean flag, but I am uncertain if it will is good idea. Could > > > you please take a look at my fsgd file and error message. > > > > > > I know that there is difference between Freesurfer versions in > > > results. But should the difference be huge or small. I am able to > > > reproduce results in previous Freesurfer when using group difference > > > in thickness, but not when I am adding continues variables for > > > instance in correlation analysis. I am enclosing two jpg files of the > > > results. > > > > > > > > > Best regards > > > Knut J > > > > > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > > ------------------------------------------------------------------------ > > > > > > > -- > > 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 > > > > > > > > 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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Tracula: Small Tracts
by Tyler Blazey 01 Dec '11

01 Dec '11

Hi List, I recently ran a group of around 70 subjects through trac-all. I have started to check the results, and have noticed that Tracula will often produce a tract with a really small volume and a posterior distribution that consists of just 0s and 1000s. When this occurs, the end point images usually contain only one voxel greater than 0. I am not sure what, if anything, is going wrong. The original recons are all of good quality, and the registrations to MNI space look good (the end point images look fine in MNI space as well). I also noticed this same issue in the right SLFP (bbregister version) of the Tracula tutorial subject. Is this a fixable error, or is it actually expected behavior? Thanks for any help. - Tyler

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talairach.xfm empty
by Christine Smith 30 Nov '11

30 Nov '11

Hello, I have a subject whose talairach.xfm file is present, but has no size (0 kb). I reran recon-all -talairach -s <subject name>. It does not fix the problem. The only error in that output was: error loading transform from /<path to subject data>/mri/transforms/talairach.xfm After rerunning the -talairach part of recon-all the talairach.xfm file does not have a new creation date. The date of the 0 kb file is from when the data was first analyzed with freesurfer (i.e., a year ago). How can I generate the transform file? Thanks, Christine

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entorhinal cortex excluded from wm.mgz and pial surface
by Christine Smith 30 Nov '11

30 Nov '11

Hello, I have a subject whose entorhinal cortex on one side of the brain is being excluded from the white matter surface and the pial surface. The cortex is included in the brain mask. I have tried a number of approaches to fix the problem but none have worked. First, I set some control points in the white matter band of the entorhinal cortex to encourage the white matter to extend out there. That didnt work. Next, edited the wm.mgz mask and drew in the white matter in that area. That didn't work either. The yellow white matter surface line still does not extend out where it should. The pial surface line skirts the white matter line as it cuts through the entorhinal cortex. Is there any other option for this subject? I wish I could pull the red pial line out to the right place... Thanks, Christine

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Re: [Freesurfer] Yeo_JNeurophysiol11_FreeSurfer networks
by Yolanda Vives 30 Nov '11

30 Nov '11

Hi Thomas, Thank you for your answer, I will try to project your parcellation in fsaverage space to BASGU space first. Regards, Yolanda 2011/11/26 Thomas Yeo <yeoyeo02(a)gmail.com> > Hi Yolanda, > > Just to understand what you are doing, you have run BASGU through > recon-all and you are trying to project the surface parcellation into > the anatomical volume of BASGU? > > The annotation we are providing is actually in fsaverage space, so you > need to first project the parcellation from fsaverage space to BASGU > native surface space before running mris_annot_to_segmentation to > project the parcellation into his/her anatomical volume. > > To project the parcellation from freesurfer surface space to the > subject's native surface space, I think you can use mri_surf2surf, > although I am not sure if there's a more specific freesurfer function > that is specialized for transferring annotation files. > > --Thomas > > On Thu, Nov 24, 2011 at 4:11 PM, Yolanda Vives <yvives(a)pic.es> wrote: > > Dear Freesurfer experts, > > > > I would like to use the Yeo_JNeurophysiol11_FreeSurfer parcellations > with my > > dataset and I am not sure what I have to do. I have used the > > mris_annot_to_segmentation command but I have the following error: > > > > mris_annot_to_segmentation BASGU lh inflated > > ./fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot > > ../Yeo_JNeurophysiol11_MNI152/Yeo2011_17Networks_ColorLUT.txt test > > reading /freesurfer/BASGU/surf/lh.inflated... > > reading colortable from annotation file... > > colortable with 18 entries read (originally MyColorLUT) > > mri_read(): couldn't determine type of file /freesurfer/BASGU/mri/T1 > > (null): could not read T1 for template volume > > > > I have a T1.mgz file inside mri/. Where could be the problem? Is this > > command appropriate? > > > > Thank you in advance, > > Yolanda > > > > _______________________________________________ > > 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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mac os questions and hypo/hyper intensity question
by Lindsay Ercole 30 Nov '11

30 Nov '11

Has anyone else had problems installing FS 5.1 on a Mac running OS 10.7.2? (i.e. Lion) Also - are the hypo and hyper-intensities only calculated for given regions, or are they segmented no matter where they occur in the tissue? Thanks, Lindsay

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Four Groups (Two Factors/Two Levels), One Covariate with very strange results
by Knut J Bjuland 30 Nov '11

30 Nov '11

I have ran an analysis similar to the analysis listed http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V. I get a results that was quite different from group analysis controlled for age compared to group difference controlled for both gender and sex. I have similar picture analyzed with a previous version of Freesurfer 4.30 that has different part of the brain highlighted. I get quite similar results for the group analysis when comparing Freesurfer 4.30 and Freesurfer 5.1. Knut J

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