Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

Using custom segmentations with recon-all
by james pardon 02 Jan '16

02 Jan '16

Dear All, I was wondering whether there is a simple way to pass T1 segmentations I have from another software to Freesurfer, in order to do the remaining recon-all steps? Thank you in advance, James

2 3

Longitudinal data analysis
by John Anderson 02 Jan '16

02 Jan '16

2 1

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.

2 2

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

2 3

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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Re: [Freesurfer] 答复: about functional ROIs
by Thomas Yeo 31 Dec '15

31 Dec '15

Hi Jintao, The difference comes from the fact that the MNI template I used is 256 x 256 x 256, which was obtained by passing the FSL MNI152 template through the FreeSurfer recon-all pipeline. Therefore even though the header information are different, they are still in the same space. You can convince yourself by using freesurfer's freeview to load both the MNI template I provide and the MNI template from FSL: >> freeview FSL_MNI152_FreeSurferConformed_1mm.nii.gz $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz You should observe they are in perfect alignment (although the values have been altered by recon-all intensity normalization process). If the different headers bother you, what you can do is to use freesurfer's function mri_vol2vol to re-interpolate the volume. For example: >> mri_vol2vol --mov FSL_MNI152_FreeSurferConformed_1mm.nii.gz --targ $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz --regheader --o new_volume.nii.gz --no-save-reg Regards, Thomas On Thu, Dec 31, 2015 at 2:59 PM, <shengjt2014(a)163.com> wrote: > Hello Professor Thomas， > > > > Thank you for your reply so quickly. > > > > I download the zip files on the webside you gave me, and the images look > like normal, but when I checked the header information, I found some > differences with common MNI images. > > > > Could you see the following pictures and notice the regions with blue > lines circled. > > > > > > > > Excuse me to bother you again. > > Best wishes, > > Jintao > > > > > > > *发件人: *Thomas Yeo <ythomas(a)csail.mit.edu> > *发送时间: *2015年12月31日 11:46 > *收件人: *shengjt2014(a)163.com > *抄送: *freesurfer <freesurfer(a)nmr.mgh.harvard.edu> > *主题: *Re: about functional ROIs > > > > Hi Jintao, > > > > This might be a header error in the original files. The error is not > apparent in the FreeSurfer or FSL environment, but might be problematic > with mricron (completely my fault). > > > > Can you try the files from this zip file instead: > https://dl.dropboxusercontent.com/u/5734119/Outgoing/Yeo2011MNIParcellation… > (courtesy of Chris Rorden). > > > > Please let me know if this resolves your issues. > > > > Regards, > > Thomas > > > > On Thu, Dec 31, 2015 at 10:23 AM, <shengjt2014(a)163.com> wrote: > > > > Dear Professor Yeo, > > > > My name is Sheng Jintao, and I am a master in China. > > Recently, I download the ‘Resting State Cortical Parcellation in > nonlinear MNI152 space’ in > https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011, > But when I opened images and found they are very stange. Just like this > sectional drawing. And I don’t know why, therefore, I would love to > consult you. > > Thank you, and I look forward to hearing from you. > > > > Best wishes, > > Jintao > > > > > > >

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Re: [Freesurfer] about functional ROIs
by Thomas Yeo 30 Dec '15

30 Dec '15

Hi Jintao, This might be a header error in the original files. The error is not apparent in the FreeSurfer or FSL environment, but might be problematic with mricron (completely my fault). Can you try the files from this zip file instead: https://dl.dropboxusercontent.com/u/5734119/Outgoing/Yeo2011MNIParcellation… (courtesy of Chris Rorden). Please let me know if this resolves your issues. Regards, Thomas On Thu, Dec 31, 2015 at 10:23 AM, <shengjt2014(a)163.com> wrote: > > > Dear Professor Yeo, > > > > My name is Sheng Jintao, and I am a master in China. > > Recently, I download the ‘Resting State Cortical Parcellation in nonlinear > MNI152 space’ in > https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011, > But when I opened images and found they are very stange. Just like this > sectional drawing. And I don’t know why, therefore, I would love to consult > you. > > Thank you, and I look forward to hearing from you. > > > > Best wishes, > > Jintao > > > >

1 0

Longitudinal data analysis
by John Anderson 30 Dec '15

30 Dec '15

1 0

minimum number of vertices for cluster-correction
by Tara Miskovich 29 Dec '15

29 Dec '15

Hi all, Can someone help me find how to get the minimum number of vertices required to pass the cluster-corrected threshold with monte carlo simulations? -- Thank you, Tara

1 0

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