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QAtools_v1.1 package
by Harms, Michael 10 Jan '14

10 Jan '14

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qdec error
by Cherise R. Chin Fatt 10 Jan '14

10 Jan '14

Hello All: I am hoping someone can help me with qdec. I am running -qcache and running into the following error: ERROR: number of vertices in /Recon/subj1/surf/lh.volume does not match surface (129774,129379) I tried running "recon-all -s subj1 -make all" but still getting the same error. I did manual edits after running the entire reconstruction so I am not sure if this is the problem. Can someone please help me? Thank you, Cherise.

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spatialsmooth-sess with option to set mask file name
by Caspar M. Schwiedrzik 10 Jan '14

10 Jan '14

Hi Doug, do you have a version of spatialsmooth-sess with the option to set mask file name? Thanks, Caspar

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Comparison of surface and euclidean distances
by Jörg Pfannmöller 10 Jan '14

10 Jan '14

Dear FreeSurfer experts, I computed distances on the cortex surface using mris_pmake on a data set acquired at a 3T scanner (using an MPRAGE sequence and protocol recommendations for FreeSurfer). The exact syntax of the distance computation was: mris_pmake --subject SUBJECT_ID --hemi lh --surface0 smoothwm --curv0 sulc --curv1 sulc --mpmOverlay euclidean --mpmProg pathFind --mpmArgs startVertex:66245,endVertex:59104 . Subsequently, the euclidean distance was computed using the Talairach coordinates displayed by tksurfer if the startVertex and the stopVertex are selected: distance_euc = sqrt[(startTal_x-stopTal_x)^2+(startTal_y-stopTal_y)^2+(startTal_z-stopTal_z)^2] . As you all know from your Tutorials, the in-surface distance must be larger or equal to the euclidean distance. Surprisingly, in the majority of cases investigated the opposite is computed. Typical distances calculated are in the range of 7 mm. Do you have an explanation for this outcome and a possible solution how it can be corrected? I am using FreeSurfer 5.1 and did not encounter any other problems in data evaluation. Any help us highly appreciated! Sincerely yours pfannmoe

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Re: [Freesurfer] questions about cortical thickness using qdec.
by Douglas N Greve 10 Jan '14

10 Jan '14

Please remember to post to the list. For the 0 0 1 -1 contrast, did any results survive multiple comparisons correction? If so, then at least the voxels in that region cannot be used with DOSS. I'm not sure why the patter was opposite between the two contrasts. I could mean that there is a nonlinear relationship with age. doug On 01/09/2014 03:54 AM, yaya ya wrote: > Dear Greve, > > Thank you very much for your response. I am now a little more clear, > although I still have some further questions. > > According to your suggestion, I just tried to test whether there is a > difference between group age. I included age as a continuous variable > in qdec. After running, I got the results arising from the contrast 0 > 0 1 -1 (which is called does the thickness-age correlation differ > between two groups?). That is, the results revealed the thinner in > some brain areas. But when I checked the results relating to the > comparision of groups (1 -1 0 0 ), the results were the same expect > the opposite pattern. That is, the results became thicker in the same > region. > > Does this imply that there is an age effect? It means I could not use > DOSS to do analysis, right? > > Best, > Lickey > > > On Thu, Jan 9, 2014 at 12:32 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > On 01/08/2014 04:28 PM, yaya ya wrote: > > Dear Freesurfer experts, > > > > I have a question about cortical thickness analysis using > freesurfer. > > Since I don't know how to post my question in freesurfer mailing > > list, that is why I am writing to you to get some help. > Hopefully, my > > email will not cause you any troubles. > Thanks for posting to the list. > > > > My question is : When I compared thickness from two groups (a > patient > > group and a healthy contrl group), that is say I got the thinner > in a > > subdivision of a particular brain region in patients than that in > > controls. But when I added age as a nusiance factors (not in the > > continuous covariate because I want to control for or regress > out the > > age effect) in qdec, the results changed. In the same region, the > > thickness became thicker in the patients than that in the > controls. I > > have no idea what happened. Which of them do I need to trust? > The age > > between two groups has been matched. > It depends on several things. It might be that there is an interaction > between group and age. Try testing for a difference between the age > slopes of the two groups. If there is no difference, then re-run using > DOSS (DOSS was removed from QDEC so you'll have to create an FSGD file > and use mri_glmfit). > > > > In addition, when I do FDR correction on the results, the min in the > > threshold jumped to more than 5 , making all the clusters > disappear. I > > think this correction is too high, unabling the genious effects to > > show up. How to deal with it? > Try using a cluster correction instead of FDR. > doug > > > > > By the way, our lab's IT staffs install the lastest released > > freesurfer. But when I use the qdec, I could not find the option of > > DODS and DOSS, as discussed in the mailing list. I am wondering > if it > > has been deleted in this new version. > > > > I really appreciate your help in advance. > > > > Best, > > Lickey > > > > > > _______________________________________________ > > 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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Download FS not working?
by Anderson M. Winkler 09 Jan '14

09 Jan '14

Hi guys, I've been trying in the last days to download FS but it doesn't seem to work: ================ winkler@volans:~ $ wget ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Linux… --2014-01-09 20:47:12-- ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Linux… => 'freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz' Resolving surfer.nmr.mgh.harvard.edu (surfer.nmr.mgh.harvard.edu) 132.183.202.158 Connecting to surfer.nmr.mgh.harvard.edu (surfer.nmr.mgh.harvard.edu)|132.183.202.158|:21... connected. Logging in as anonymous ... ================ It never goes beyond this point. It isn't working for any of the FS versions available, neither trying from different computers or different networks. Neither using different download methods. Looks like an issue with the FTP server, not sure... Thanks and sorry for bothering. All the best, Anderson

2 1

LME model
by Seán Froudist Walsh 09 Jan '14

09 Jan '14

Dear Jorge and FreeSurfers, Would you mind having a look at my set-up and advising on whether it is correct or needs changing? I have participants with one or two scans, who are divided into two groups. I'm interested in the longitudinal effects of aging, and the difference in the effect of age on the two groups. Not all people were scanned at exactly the same age, and the interscan interval in not exactly the same for each person. Rather, the age at scan looks like a bimodal distribution around the mean 1st and 2nd timepoint. I believe I read on the list that you should have more timepoints than random effects. I guess I should then only name one random effect (intercept). At the moment I have my model set up as follows: X = Intercept Group Age(at scan) Group*Age Gender [stats, st] = lme_mass_fit_vw(X,1,Y,ni,Mask,[],12); CM.C = [0 0 0 1 0] I guess I should then run * lme_mass_F(stats,CM);* and *lme_mass_FDR2.* Here I am trying to look find the areas that develop differently between the two groups over the timespan we are studying. If you would be able to advise me as to whether I have set up the model wrong it would be greatly appreciated. Age in this case refers to the the age at scan time, regardless of whether it is the first or second scan, so many participants will have two distinct values in the age column. Also, is it possible within this set-up to test the effect of age within a group, or would that require re-doing the design matrix? Finally, is it possible to include the by-subject random slopes for the effect of age? In R (lmer) it would be something like (1+age|subject). Best wishes y gracias, Seán

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ROI masks created in FreeSurfer used in FSL??
by Frank Hsieh 09 Jan '14

09 Jan '14

Dear FreeSurfer Users, I ran recon -all on my structural image and created ROI masks (using mri_label2vol) based on FreeSurfer's cortical parcellation. I'd like to use these masks for further analysis with FSL. However, it seems that the ROI masks generated with mri_label2vol have different header information than that of the original structural image. As a result, I was unable to carry out further analysis with FSL (e.g., converting these ROI masks into functional space with hires2example_func.mat). I was wondering if there is a way to solve this issue. Many thanks in advance. Frank

3 5

Question about qdec analysis
by carina＠van-vlodrop.de 09 Jan '14

09 Jan '14

2 1

Re: [Freesurfer] xhemi vertices
by Douglas N Greve 09 Jan '14

09 Jan '14

Hi Sofie, please remember to post to the list. The trickiness is that if you map the lh to the rh, then there will be interpoolation in the lh that is not in the rh which can cause a false difference. Our symmetric stream is set up to avoid this problem. doug On 01/09/2014 04:39 AM, Sofie Valk wrote: > Dear Doug, > > thanks, yes it does make some sense. Can I ask what the trickiness is you refer to, when mapping rh on lh? > Sofie > > ----- Original Message ----- > From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> > To: freesurfer(a)nmr.mgh.harvard.edu > Sent: Wednesday, January 8, 2014 9:11:04 PM > Subject: Re: [Freesurfer] xhemi vertices > > > To follow up, it is intended that you will map both hemispheres of a > given subject to one of the hemispheres of fsaverage_sym (it does not > matter which, but we usually use lh). You can then do the comparisons on > that hemisphere. Does that make sense? > doug > > > On 01/08/2014 02:09 PM, Bruce Fischl wrote: >> Hi Sofie, >> >> no, they don't correspond. You need to use mri_surf2surf to map one to >> the other (which is a bit tricky). >> >> cheers >> Bruce >> On Wed, 8 Jan 2014, Sofie Valk wrote: >> >>> Dear Free Surfers, >>> >>> I have a short question regarding the mapping of vertices of the fsaverage_sym, how do vertices in the left hemisphere correspond to vertices in the right hemisphere? >>> When I tested it, it did not seem that the first-indexed vertex on the left hemisphere corresponded to the first-indexed vertex on the right hemisphere defined by me as : (total vertexes/2 + 1) >>> if so, how to calculate the difference between lh and rh? >>> >>> Thank you very much!! >>> >>> Kind regards, >>> >>> >>> Sofie Valk >>> >>> ... >>> >>> PhD Candidate, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany >>> >>> >> _______________________________________________ >> 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/

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