Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

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

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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

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

09 Jan '14

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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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Question about Monte Carlo and significant clusters
by Maller, Jerome 09 Jan '14

09 Jan '14

Hi everyone, I have a question related to Monte Carlo tests of multiple comparisons. When I conduct some of my analyses, there is no difference between before and after Monte Carlo (i.e. same size and coloured regions appear on the inflated brain after I click on the analysis in the Description box), whereas for other analyses I get large matt coloured clusters with significance values stated for those clusters in the terminal. Also, I have completed one analysis whereby the before and after Monte Carlo coloured clusters are the same but only one of the clusters is stated as significant in the terminal. Does anyone know whether the clusters that appear after Monte Carlo simulation, but are not stated as clusters in the terminal, are significant? Thankyou! Jerome Maller -- Dr Jerome J Maller BSc,GradDipPsych,MSc,PhD Neuroscientist NHMRC Industry Career Development Fellow (CDF) CETBIR (Centre for Excellence in Traumatic Brain Injury) Postdoctoral Research Fellow Monash Alfred Psychiatry Research Centre (MAPrc) Central Clinical School, Monash University and Alfred Hospital 4th Floor, 607 St Kilda Rd, Melbourne VIC Adjunct Associate Professor Centre for Research on Ageing, Health and Wellbeing, Research School of Population Health, ANU College of Medicine, Biology and Environment at the Australian National University. Phone: +61 3 9076 2404 Fax: +61 3 9076 6588 Mobile: +61 419 221 454

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Fwd: Anatomical segmentation - question
by Rotem Saar 09 Jan '14

09 Jan '14

Dear freesurfer experts, I'm performing anatomical segmentation for Philips dicoms (3T scanner). I got these two images from the same slice while performing step number 4 in the script below – from some reason, the two images don't fit. Should I use "scale brain" ? I know this is not recommended thus want to consult with u first – Can u please comment on why this is happening? Is there any value that corresponds to "how good is the segmentation" ? if yes, where can I find it ? My script is written below. Thanks, Rotem Anatomical segmentation: first step- 23 hours: *recon-all -autorecon-all -i ~/Desktop/ FOLDER-NAME /I00001.dcm -s FOLDER-NAME* second step:(gyrus=green, sulcus=red) *tksurfer -curv FOLDER-NAME lh/rh inflated* third step: (talairch registretion) *tkmedit FOLDER-NAME brainmask.mgz* File-> transforms-> load transform AUX-> Browse-> talairch.xfm forth step: (simetry - allows changing 12df transformation. if we made any changes we should click "save reg" and run this command again) *tkregister2 --mgz --s FOLDER-NAME --fstal --surf orig* IF WE CHANGE ANYTHING, CLICK "SAVE REG" AND RUN FROM STARTING POING: recon-all -all -subjectid FOLDER-NAME fifth step: (scalp removal: if removed too much, rise up from the value 25: *recon-all -skullstrip -wsthresh 25 -clean-bm -no-wsgcaatlas -s FOLDER-NAME * to check the result press: *tkmedit FOLDER-NAME brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white *) for hand correction: *tkmedit FOLDER-NAME brainmask.mgz -aux T1.mgz* tools-> configure volume brush -> MARK: mode=clone, source=Aux tools-> configure brush info (for choosing brush size) click on edit voxels: click in MIDDLE for adding voxels, RIGHT for removing voxels : slice by slice. when finish, click: File-> save main volume sisxt step: (cp for correcting segmentation) *tkmedit FOLDER-NAME brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white* seventh step: (done) *recon-all -autorecon2-cp -autorecon3 -s FOLDER-NAME* Rotem Saar-Ashkenazy Department of Brain and Cognitive Science Ben Gurion University of the Negev Beer-Sheva 84105 Israel

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Re: [Freesurfer] Freesurfer templates for cross-ethnicity comparisons
by Bruce Fischl 09 Jan '14

09 Jan '14

Hi Mike nice to be right once in a while :). You shouldn't have to register to an atlas brain to build the folding pattern template though - you can pick one of your own dataset to start with. cheers Bruce On Thu, 9 Jan 2014, Michael Chee wrote: > Hi Bruce and Linda, > > Yes, this is my work email. Pacific internet shut down email operations in > Singapore in Dec 2012… > > We built an ‘Asian Only’ template with around 30 Chinese participants but > the use of this template did not generate a result that differed from that > obtained using the stock MGH template. We were quite disbelieving of Bruce’s > prediction that this would be so but he proved to be correct. The caveat > (and its not a small one) is that to BUILD the template, one has to register > to an atlas brain which is presumably Caucasian weighted. > > The paper comparing predominantly Caucasian and Chinese brains using FS was > published in 2011 in J Cog Neurosci and can be found on my lab website. We > did not mention building the custom atlas in that work because of the lack > of a difference in using this vs. the standard template. > > Zheng Hui (copied) did all the hard work on this. > > > Michael Chee MBBS, FRCP(Edin) > Professor > Cognitive Neuroscience Laboratory > Neuroscience and Behavioral Disorders Program > Duke-NUS Graduate Medical School > 8 College Rd, #06-18 > Singapore 169857. > > email: michael.chee(a)duke-nus.edu.sg > office: (65) 65164916 > CNL Home page: http://www.cogneuro-lab.org > > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Date: Thursday, 9 January, 2014 5:24 am > To: Linda Zhang <lzhang87(a)gmail.com> > Cc: Freesurfer <freesurfer(a)nmr.mgh.harvard.edu>, Michael Chee > <michael.chee(a)duke-nus.edu.sg> > Subject: Re: Freesurfer templates for cross-ethnicity comparisons > > Hi Linda > > I had an old address for Mike in the first email. I think this one is > correct. Building a folding atlas is pretty quick, depending on how many > subjects you have. You'll need to pick one subject, run mris_make_template > to build a single-subject template (for each hemi), register everyone to > it, rerun mris_make_template to build a multi-subject atlas, rerun > mris_register with the new atlas as the target and iterate this procedure > until it converges (atlas building and reregistering). Usually it does > after only one additional round. > > cheers > Bruce > > > > > On Wed, 8 Jan 2014, Linda Zhang wrote: > > Thanks Bruce! How long would it take to build an atlas? > > What are your thoughts Mike? > > > On 7 January 2014 14:38, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > wrote: > Hi Linda > > I actually don't know the ethnicity of the subjects in our > atlas. I wouldn't > expect it to be an issue for folding patterns, but it is > possible. You could > build your own atlas and redo the analyses if you want to see if > that > changes things. I'll cc Mike Chee who I think has looked at this > question as > well. > > cheers > Bruce > > > > > > On Tue, 7 Jan 2014, Linda Zhang wrote: > > Hi Bruce, > > I've been using Freesurfer to compare subcortical volumes > and cortical > thickness between Caucasian and Chinese controls. There > are some > significant findings, but the question of whether or not > these may be > biased due to the template has been raised (the assumption > being that > the majority of subjects used in the template are > Caucasian). Is it > possible to reduce the weight of the atlas during > normalisation (or > some other method to address the issue)? I would greatly > appreciate > your thoughts on this. > > Cheers, > Linda > > > > > > 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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Fwd: questions about cortical thickness using qdec.
by yaya ya 09 Jan '14

09 Jan '14

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>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 > > 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. > >

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Re: [Freesurfer] absolute value of effect size
by Douglas N Greve 08 Jan '14

08 Jan '14

Several potential problems. It makes the statistics non-gaussian and the abs(ces) becomes noise dependent (and so there will be a noise dependent bias). This makes interpretation more difficult (eg, is a difference between groups a difference in ces or a difference in noise?). The non-gaussianity could be addressed with a permutation test. doug On 01/08/2014 07:11 PM, shahin(a)nmr.mgh.harvard.edu wrote: > Exactly! I need ces and cesvar files for a second order analysis. More > specifically, I need to subtract this absolute map from another map. > Would you be more specific about what I should check when I am doing this > second order analysis? > > > >> You can do it to the sig file (the p-value already assumes a two-sided >> test). Why do you want to do it with the ces and cesvar files? If you >> are planning to use the abs(ces) for a higher level analysis then you >> need to be very careful as you can get some unintended effects >> doug >> >> >> >> >> On 01/07/2014 03:46 PM, SHAHIN NASR wrote: >>> Hi, >>> I have two related questions. I have two conditions (e.g. C1 and >>> C2) and I want to generate a map that shows all voxels that can >>> differentiate C1 from C2 _irrespective_ of whether C1>C2 or C1<C2. I >>> think it can be done easily by: >>> >>> mris_calc -o sig.nii abs_sig.nii abs >>> >>> If I am right, then: >>> 1) Can I apply the same command to ces.nii file to have the absolute >>> value of the effect size (i.e. abs(C1-C2 effect size)) or should I >>> consider other factors? >>> 2) Do I need to apply the same routine to cesvar? >>> >>> Thanks >>> -- >>> Shahin Nasr >>> >>> PhD in Cognitive Neuroscience >>> Martinos Imaging Center, MGH >>> Harvard Medical School >> -- >> 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/ >> >> >> > -- 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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