Freesurfer January 2016

freesurfer@nmr.mgh.harvard.edu

130 participants
204 discussions

Fwd: LME FDR2 corrected results
by Hanbyul Cho 01 Jan '16

01 Jan '16

Dear FreeSurfer Team, My name is Han. I am wondering how I can save the FDR2 corrected results. I processed in MATLAB for Linear mixed effects models analysis, as follow: [lhTh01,lhRe01] = lme_mass_fit_EMinit(X,[1],Y,ni,lhcortex,3,4) [lhRgs01,lhRgMeans01] = lme_mass_RgGrow(lhsphere, lhRe01, lhTh01,lhcortex,2,95); lhstats01 = lme_mass_fit_Rgw(X,[1],Y,ni, lhTh01, lhRgs01, lhsphere,[],'euc','exp',4) F_lhstats01=lme_mass_F(lhstats01,CM,4); dvtx = lme_mass_FDR2(F_lhstats01.pval, F_lhstats01.sgn, lhcortex, 0.05, 0); length(dvtx) ans = 8000 In this case, I search the corrected results that were 8000 vertices. I think the dvtx value was for saving the significant each vertex numbering label, is it right? However, I don't know the next step for save the 8000 corrected vertices. fs_write_fstats(F_lhstats01,mri,'%%$.mgh','sig'); I can save the whole results 'F_lhstats01' as the mgh format. However these were uncorrected results, is it right? Could you let me know the method for saving the FDR2 corrected results as a mgh format? Best Regards, Han.

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Question on longitudinal stats directory
by Govindarajan, Koushik Athreya 01 Jan '16

01 Jan '16

Hi there, I have run my subjects from multiple time points through a cross-sectional stream and a longitudinal stream. When I look at the 'stats' directory for the same subject from the cross-sectional pipeline and the longitudinal pipeline, I see that the numbers are different. For example, the cortical thickness values in the lh.aparc file for the same subject are different. Is one estimation more accurate than the other? Where is the difference coming from? Thanks Koushik Govindarajan

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Files needed for qdec
by Tara Miskovich 01 Jan '16

01 Jan '16

Hello Freesurfer experts, I need to upload some data to a public domain and I am trying to best limit the amount of files needed. I am wondering what subjects files are absolutely necessary to run an analysis in qdec. This is for an lgi analysis. I tried only using the surf directory, but qdec would fail. Could someone let me know what other directories/files from freesurfer are needed just to recreate one surface analysis in qdec. -- Thank you, Tara

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minimum number of vertices for cluster-correction
by Tara Miskovich 01 Jan '16

01 Jan '16

Hello Freesurfer experts, I need help me finding how to get the minimum number of vertices required to pass the cluster-corrected threshold with monte carlo simulations? Is there a way to figure this out? -- Thank you, Tara

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Freesurfer January 2016