[Freesurfer] significant of long_mris_slopes

thickness.lh.aparc-rate --table thickness.lh.aparc-rate.stack.txt I got results sig.table.dat in folder of 'thickness.lh.aparc-rate'. I want to ask what's meaning of this results. Is it the significant results or just directly result? All best, Lanbo Wang sig.table.dat Descripti

[Freesurfer] Questions about BA template

Dear experts, I have questions about BA template: 1. What's different between BA and BA.thresh? 2. I want to check the size of each structure of BA and BA.thresh template. How can I got it? Thank you in advance. All best, Lanbo Wang ___ Frees

[Freesurfer] Question about Xhemi

Dear Freesurfer experts, When I try run mris_apply_reg according to Xhemi: "the error is lh.map.mgh does not exist or is not readable by you" lh.map.mgh is made by which step? Thank you in advance. best, Lanbo ___ Freesurfer mailing list Freesurfer@nmr

[Freesurfer] mris_apply_reg

Dear Freesurfer experts, I try run this code according to Xhemi： mris_apply_reg --src-label label/rh.V1_exvivo.thresh.label --trg rh-on-lh.V1_exvivo.thresh.label \ --streg xhemi/surf/lh.fsaverage_sym.sphere.reg surf/lh.fsaverage_sym.sphere.reg However, error shows: Option --src-label unknown. And

Re: [Freesurfer] mris_apply_reg

not > part of FS5.3 > > > > Best, > > M_ > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@ > nmr.mgh.harvard.edu] *On Behalf Of *lanbo Wang > *Sent:* Friday, November 3, 2017 11:49 AM > *To:* freesurfer@nmr.mgh.harvard.edu &g

Re: [Freesurfer] Question about Xhemi

the hemisphere from left-right to symptom-nosymptom according to body symptom side record and compare different between symptom hemisphere and nosymptom hemisphere. Can I use freesurfer to do it? Thanks for your patient and help. All best, Lanbo Wang On Sun, Nov 5, 2017 at 1:27 PM, Douglas Greve wr

[Freesurfer] hemisphere analysis

-nosymptom according to body symptom side record and compare different between symptom hemisphere and nosymptom hemisphere. Can I use freesurfer to do it? Thanks for your patient and help. All best, Lanbo Wang ___ Freesurfer mailing list Freesurfer

Re: [Freesurfer] hemisphere analysis

-cor.mtx. All best, Lanbo Wang On Tue, Nov 7, 2017 at 10:18 AM, Bruce Fischl wrote: > Hi Danny > > you need to give us more information if you want us to help you. Please > include the command you ran and the entire screen output. > > cheers > Bruce > > > On Tue

Re: [Freesurfer] hemisphere analysis

t, and then run that fscalc command > > > On 11/07/2017 11:33 AM, lanbo Wang wrote: > > Hi Douglas, > > > > Thanks for your reply. > > I created the fsgd file as you show me, and run code like this. Am I > > right? > > 1. > > mris_preproc --fsgd S

Re: [Freesurfer] hemisphere analysis

ou use? > > > On 11/07/2017 02:43 PM, lanbo Wang wrote: > > I try to use this code to compare left and right hemisphere by paired > > t-test and add age as covariate. > > > > Thanks, > > Lanbo > > > > On Tue, Nov 7, 2017 at 11:40 AM, Dou

Re: [Freesurfer] hemisphere analysis

at 11:17 AM, Douglas Greve wrote: > Do you only have one subject in your input file? You need to run > mris_preproc separately for each subject, create a different file for each, > then mri_concat the files together > > On 11/9/17 6:20 PM, lanbo Wang wrote: > > Dr. Douglas

Re: [Freesurfer] hemisphere analysis

You need to run >> mris_preproc separately for each subject, create a different file for each, >> then mri_concat the files together >> >> On 11/9/17 6:20 PM, lanbo Wang wrote: >> >> Dr. Douglas, >> >> I try #3 method, when I run mri_glmfit, get erro

Re: [Freesurfer] hemisphere analysis

Can I use data processed by other tool like FSL, or I can only use DTI image after Freesurfer processing? On Fri, Nov 10, 2017 at 3:07 PM, Douglas Greve wrote: > Yes > > On 11/10/17 2:45 PM, lanbo Wang wrote: > > Thank you very much, it's work. > I have another question,

[Freesurfer] dmrirc.tutorial problem

recommended to run this step on a cluster bedpostx_mgh -n 2 HD4/DTI/DBK08.4th/dmri Thanks for your patient and help. All best, Lanbo Wang dmrirc.tutorial Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] Question about compare left and right hemi of longitudinal data

Hi, all experts. I want to compare changes rate between left and right hemisphere of longitudinal data, How should I do that, how to combine xhemi with two stage or LME? Best, Lanbo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.

[Freesurfer] Question about LME modle

Dear all freesurfer experts, Hi, When use lme_lowessPlot, the plot shows black and green two lines. What the meaning of two line? Thank you, Lanbo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listi

Re: [Freesurfer] Question about compare left and right hemi of longitudinal data

ness map (I have never > done that, but probably works similarly, construct left -right > registration, compute difference, then run the LME on that). > > Best, Martin > > Am 17.12.2017 um 17:54 schrieb lanbo Wang: > > Hi, all experts. > I want to compare changes rate be

[Freesurfer] Question about combine longitudinal analysis and xhemi

​ xhemireg.lh.log ​Thanks for replying me. But I still have two questions. Firstly, when I try xhemi on pre-possessed longitudinal data, it showed error like this: Performing left-right swap of l

Re: [Freesurfer] Question about compare left and right hemi of longitudinal data

tlab LME code. https://surfer.nmr.mgh.harvard.edu/fswiki/ > LinearMixedEffectsModels > > > Best, Martin > > Am 27.12.2017 um 16:11 schrieb lanbo Wang: > > Thanks for replying me. But I still have two questions. > Firstly, when I try xhemi on pre-possessed longitudinal data, it showed > error li

[Freesurfer] Linear Mixed Effect Modle

Hi, all experts. When I try to use LME model. There is a code "mris_preproc --qdec-long qdec.table.dat --target fsaverage --hemi lh --meas thickness --out lh.thickness.mgh" in LME tutorials website under *"b)Mass-univariate". * When I ran it, error happened: """ [mtobia@localhost PD]$ mris_preproc

Re: [Freesurfer] Linear Mixed Effect Modle

gt; then we need to look for something else. > > Best regards, > > Kersten > > > > -Original Message- > From: lanbo Wang > Reply-to: Freesurfer support list > To: Freesurfer support list > Subject: [Freesurfer] Linear Mixed Effect Modle > Date: Sat, 20 Jan 20

Re: [Freesurfer] Question about compare left and right hemi of longitudinal data

The problem is that the surfreg command is failing. Thanks, Lanbo On Thu, Jan 18, 2018 at 5:14 PM, Douglas Greve wrote: > Is the problem that the surfreg command is failing or that you don't know > how to apply LME? > > On 1/17/18 9:55 AM, lanbo Wang wrote: > > Hi Mart

[Freesurfer] LME univariate data

Dear Experts, Hi, There is no example detail on website of LME tutorial. I have some question about it. Could you send me the table of ADNI univariate example data? Thanks, Lanbo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.n

Re: [Freesurfer] LME univariate data

b tools can be found here". The linked > tar.gz archive contains two folders, one for the univariate and one for > the mass-univariate example data. > > Best regards, > > Kersten > > On Di, 2018-03-13 at 13:38 +0100, lanbo Wang wrote: > > Dear Experts, > > &

Re: [Freesurfer] LME univariate data

Dear Kersten, Thanks a lot, it's really help. I have another question, after I got results that two group have significant, then how could I get direction? Thanks, Lanbo On Tue, Mar 13, 2018 at 5:40 PM, Diers, Kersten /DZNE wrote: > Hello, > > On Di, 2018-03-13 at 21:48 +01

Re: [Freesurfer] LME univariate data

Dear Kersten, I have a question about LME model. After I acquired p value, could I know which group is bigger? Thanks, Lanbo On Fri, Mar 16, 2018 at 12:13 AM, lanbo Wang wrote: > Dear Kersten, > > Thanks a lot, it's really help. I have another question, after I got > resul

Re: [Freesurfer] LME univariate data

icant difference among the several groups. To get an > idea which groups actually differ, and in which direction, one needs to > take a closer look, for example at those effects that are reflected in > the rows of the contrast matrix; for this, one option is to use the > signed p-values