Freesurfer January 2019

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by Tefera, Getaneh B 22 Jan '19

22 Jan '19

External Email - Use Caution This is a test

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LME MATLAB tools
by Tefera, Getaneh B 22 Jan '19

22 Jan '19

External Email - Use Caution Dear Freesurfer Experts, I have a question about how to interpret cortical thickness difference between groups using LME MATLAB tools. I have three groups(g0, g1, and g2) and five time points(t= 0,0.5, 1,2,3). I am trying to use LME model with random effects y-int and time from the base line. Based on the LME tutorial and the questions and answers from Freesurfer support list: Y=B1+B2*t+B3*g1+B4*g1*t+B5*g2+B6*g2*t+ .... To see the difference between group g0 and group g1, I constructed the following contrast matrix using the tutorial provided in LME MATLAB tools C = [zeros(1,3) [1 0 0] zeros(1,4)]; CM.C=[zeros(1,3) [1 0 0] zeros(1,4)]; Based on the tutorial I run the following functions. rhstats = lme_mass_fit_Rgw(X,[1 2],rhY,ni,rhTh0,rhRgs,rhsphere); F_rhstats = lme_mass_F(rhstats,CM); fs_write_fstats(F_rhstats,rhmri,'/backup/cross/rh_AB_cross_sig.mgh','sig'); nv=length(rhstats); Beta2 = zeros(1,nv); for i=1:nv if ~isempty(rhstats(i).Bhat) Beta2(i) = rhstats(i).Bhat(2); end; end; rhmri1 = rhmri; rhmri1.volsz(4) = 1; fs_write_Y(Beta2,rhmri1,'rhBeta2.mgh'); [detvtx,sided_pval,pth] = lme_mass_FDR2(F_rhstats.pval,F_rhstats.sgn,rhcortex,0.05,0); fs_write_Y(sided_pval,rhmri1,'spval.mgh'); When I view sig.mgh using tksurfer I see regions with red and blue color. 1) Does the result shows the oveall change for all the five time points? 2) How do I know the difference between the two groups for each 5 time points? 3) Does red means thickness of group A is lgreater than thickness of group B? 4) what does rhBeta2.mgh and spval.mgh tell us? How can I extract the information from the file? With regards Getaneh Hi Kersten, I am sorry I did not make the question more specific. I have three groups. I want see the power analysis by checking the sample size calculation for the cortical thickness analysis . [sz1,sz2] = lme_plannedSampleSize(Zi,ZiCol,Dhat,phisqhat,effsz,... dr,pw,alpha,gr_pr) my question is how can I get Dhat ( Estimated random effects covariance matrix) and phisqhat (Estimated intra-subject variability) to calculate the sample size of the pairs . Based on your suggestion to get Dhat and phisqhat I have to run " lme_fit_FS(X,[1,2],y ,ni)" When I run lme_fit_FS(X,[1,2],y ,ni), where Y is obtained from the following [Y,mri] = fs_read_Y('lh.thickness_sm10.mgh'), I get error. Which function with what argument is good to use to find Dhat and phisqhat? Are these values the same for left and right cortical thickness data? I am sorry for the inconvenience . with regards Getaneh ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.ha "rvard.edu> on behalf of Diers, Kersten /DZNE <Kersten.Diers(a)dzne.de> Sent: Thursday, January 11, 2018 3:50 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] LME Hi, I am not entirely sure that I understand the goal of this particular analysis, so I don't have any suggestions at the moment. Maybe you could give some more detail, if this is still an issue. Best regards, Kersten -----Original Message----- From: "Tefera, Getaneh B" <Getaneh.B.Tefera(a)uth.tmc.edu> Reply-to: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] LME Date: Wed, 10 Jan 2018 17:58:58 +0100 Dear Kersten, Thank you so much. When I run the procedure with left and right cortical thickness data I get different phisqhat values Phisqhat:0.2530 for the left and Phisqhat:0.0903 for the right The Dhat matrix is also different. Is that Ok? If so , shall I consider two sample sizes for the left and right? With regards Getaneh -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces @nmr.mgh.harvard.edu] On Behalf Of Diers, Kersten /DZNE Sent: Wednesday, January 10, 2018 7:10 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] LME Hi Getaneh, the estimates for D and phisq for a given analysis are contained within the data structure that is returned by the lme_fit_FS procedure. I.e. for the tutorial data, the command was: total_hipp_vol_stats = lme_fit_FS(X,[1 2],Y(:,1)+Y(:,2),ni); Dhat and phisqhat are fields of the 'total_hipp_vol_stats' structure, and can be accessed by typing 'total_hipp_vol_stats.Dhat' and 'total_hipp_vol_stats.phisqhat', respectively. Best regards, Kersten -----Original Message----- From: "Tefera, Getaneh B" <Getaneh.B.Tefera(a)uth.tmc.edu> Reply-to: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] LME Date: Tue, 9 Jan 2018 23:02:08 +0100 Hi Kersten. Thank you very much . I am not planning a new design for sample size calculation. Can you please help me how to find those values? Thank you Getaneh ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mg h.harvard.edu> on behalf of Diers, Kersten /DZNE <Kersten.Diers(a)dzne.d e > > Sent: Tuesday, January 9, 2018 5:56 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] LME Hi Getaneh, please find my responses below. -----Original Message----- From: "Tefera, Getaneh B" <Getaneh.B.Tefera(a)uth.tmc.edu> Reply-to: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] LME Date: Mon, 8 Jan 2018 22:54:49 +0100 Dear Freesurfer experts, I have three groups g0, g1, and g2. I am trying to use LME model with random effects y-int and time from the base line. Based on the LME tutorial and the questions and answers from Freesurfer support list: Y=B1+B2*t+B3*g1+B4*g1*t+B5*g2+B6*g2*t+ ... The slope of g0 : 0 1 0 0 0 0 The slope of g1: 0 1 0 1 0 0 The slope of g2: 0 1 0 0 0 1 The slope difference between g0 and g1: 0 0 0 1 0 0 The slope difference between g0 and g2: 0 0 0 0 0 1 The slope difference between g1 and g2: 0 0 0 -1 0 1 1) Is this contrast matrix correct to observe pairwise slope difference? In the tutorial the contrast matrix C = [zeros(3,3) [1 0 0 0 0; -1 0 1 0 0; 0 0 -1 0 1] zeros(3,6)] This is a correct matrix, but only for the particular design given in the tutorial, i.e. 4 groups and several covariates. Also, it is not strictly speaking a pairwise test, but will indicate if there is *any* difference between the slopes of the groups (i.e. it will give only one F- and p-value). If you specifically want to test differences between particular pairs, use contrast matrices with just a single row. 2) Is it necessary to combine contrast matrix of the pair difference the same as the tutorial? If so, my contrast matrix can be C=[0 0 0 1 0 0; 0 0 0 -1 0 1] It makes sense to look at the overall effect prior to looking at pairwise differences. If you don't have any additional covariates, that matrix is OK for looking the overall effect. Otherwise, add as many columns of zeros as you have covariates, similar to the tutorial. 3) How can we interpret the result for this contrast matrix? This is an F-test to detect if there is any difference between the slopes of the groups. 4) How can I obtain B1, B2, ... ? Consider the following command from the tutorial: total_hipp_vol_stats = lme_fit_FS(X,[1 2],Y(:,1)+Y(:,2),ni); Then B1 and B2 will be the first two entries of total_hipp_vol_stats.Bhat [sz1,sz2] = lme_plannedSampleSize(Zi,ZiCol,Dhat,phisqhat,effsz,... dr,pw,alpha,gr _pr) 5) For sample size calculation how can I get Dhat ( Estimated random effects covariance matrix) and phisqhat (Estimated intra-subject variability)? If you are planning a new design, these estimates should be based on prior knowledge and can be derived e.g. from a pilot study or from the literature. Best regards, Kersten With regards Getaneh _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harva rd.edu_mailman_listinfo_freesurfer&d=DwIGaQ&c=6vgNTiRn9_pqCD9hKx9JgXN1V apJQ8JVoF8oWH1AgfQ&r=f2w_aQllkjZisjakf5SS_8h7m7gQVFtFYcFC7K0Nk8k&m=w3Go ND77ORaREflQR6B1sxt8pIPGPzd8Oh_hzfJ_rhk&s=7GFfEuDrrPYWE- NE_mVYzsQUEvfZizwe853OSP2n_Zo&e= 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 https://urldefense.proofpoint.com/v2/ur l?u=http-3A__www.partners.org_co mplianceline&d=DwIGaQ&c=6vgNTiRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ&r=f 2w_aQllkjZisjakf5SS_8h7m7gQVFtFYcFC7K0Nk8k&m=w3GoND77ORaREflQR6B1sxt8pI PGPzd8Oh_hzfJ_rhk&s=_JumR_-uS8QiP3xZfqqQ73pib0Pi-_MI1tUhsm2z5bA&e= . 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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. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harva rd.edu_mailman_listinfo_freesurfer&d=DwIGaQ&c=6vgNTiRn9_pqCD9hKx9JgXN1V apJQ8JVoF8oWH1AgfQ&r=f2w_aQllkjZisjakf5SS_8h7m7gQVFtFYcFC7K0Nk8k&m=hFe7 jo1OaOiJPYJN1sciBovML-jRiS7s_7h32CzMnCY&s=1X6nJq9b-3c- 2R4AgFUDMpC2l7itlL1ORo6Ipf9ljLs&e= _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e… 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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compli… . 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. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e…

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LME MATLAB tools
by Tefera, Getaneh B 22 Jan '19

22 Jan '19

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mapping a volumetric statistical map to the cerebellum surface
by john Anderson 22 Jan '19

22 Jan '19

External Email - Use Caution Dear FS experts, I have a statistical map from the output of a surface based analysis in subcortical regions. This statistical map shows significant difference between the groups in the cerebellum cortex. I reconstructed the cerebellar surfaces using the command "mri_tessalte). Now, I would like to map the volumetric statistical map to the constructed cerebellum surfaces. How can I do that? I tried the command "mri_vol2surf" in many different wants but it didn't work! Thanks for any guidance! John

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fsaverage, brainstem and cerebellum
by john Anderson 22 Jan '19

22 Jan '19

External Email - Use Caution Dear FS experts, For visualization purposes, is there any way to show the cerebellum and brain stem regions (similar to the attached figure), this figure was published used CONN toolbox but I am not sure how they were able to map functional data in brain surface and show the cerebellum and brain stem with fsaverage. I appreciate any suggestion Jon

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Problems with GM segmentation
by Rosalia Dacosta Aguayo 22 Jan '19

22 Jan '19

External Email - Use Caution Dear Free Surfer team, I few days ago I sent you personally the dicom files as well as the mask of the lesion you asked me for as I am having problems with GM segmentation. I would greatly appreciate if you could help me with this issue and tell me how I could manage the problem so I can solve it as I have many participants with the same issue. Yours sincerely, Rosalia

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problems with bbregister's output image
by Sam W. 22 Jan '19

22 Jan '19

External Email - Use Caution Hello, I have registered example_func.nii.gz to the anatomical image using bbregister and then I looked at the registered file with tkregister2. $ bbregister --bold --lta reg.lta --mov example_func.nii.gz --s sub001 --o f-in-anat.nii.gz $ tkregister2 --s sub001 --mov f-in-anat.nii.gz --reg reg.lta --surf However if I click "coronal" tkregister2 shows the coronal surface as expected, whereas it shows the horizontal volume. If I click "horizontal" it shows the horizontal surface, whereas it shows the coronal volume. When I click "sagittal" the sagittal surface and volume are loaded, but the orientations are different. When I use the example_func as the mov image in tkregister2 I don't get this issue. I don't understand why the registered image "f-in-anat.nii.gz" is not aligned with the anatomical image with the tkregister2 command, because "f-in-anat.nii.gz" is exactly the output image of the bbregister transformation from functional to anatomical space, isn't it? Could someone please help me understand this? Thanks Sam

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Error using mri_convert and recon-all
by Isil Bilgin 22 Jan '19

22 Jan '19

External Email - Use Caution Dear All, I want to convert my .nii structural file to .mgz file. I tried using mri_convert however I got a permission denied message. Since I am not the administrator in the system, hence I cannot change the permissions at the moment, so I guess I will have to wait for IT to help me soon. Instead, I wanted to try recon-all -i STRUCT_FOLDER1/xxx.dcm -i STRUCT_FOLDER2/xxx.dcm -autorecon1 -subjid 10 [/bash] command. However, I am getting an "if: Expression Syntax" error. So I am not sure why might be the cause for that, though. So I might really appreciate your helps please. I am using 4.4.0-139-generic #165-Ubuntu SMP Wed Oct 24 10:58:50 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux and bash. I found a similar discussion from the archive ( https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-September/02569…) but there was no agreed solution I guess. So I wonder if there is any other way of converting the structural nii file to .mgz until these problems are solved? Thank you very much for the help in advance Kind regards Isil

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Clinical Scan Thickness
by Sahnoune,Iman 22 Jan '19

22 Jan '19

External Email - Use Caution Hello, I’m writing to ask whether clinical scans with thickness of 5mm are currently able to be analyzed using Freesurfer? This question has been asked in the archives, but it has been about 5 years so just writing to see whether that has changed or if a work around has been developed. Alternatively, the option exists to computationally make the slices thinner. Would running the software either as 5mm or thinner slices yield accurate and useful information cortically and subcortically? Thank you in advance for your help. The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

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Calculating global thickness
by Arsenije Subotic 22 Jan '19

22 Jan '19

External Email - Use Caution Dear experts, When calculating global thickness, is it fine to simply use an average of lh.thickness and rh.thickness, or is it necessary to weight it according to the area of each hemisphere, so that the calculation is (lh.thickness x lh.area + rh.thickness x rh.area)/(lh.area +rh.area)? Thanks! Arsenije --- Arsenije Subotic | MSc Student Department of Clinical Neurosciences Hotchkiss Brain Institute, University of Calgary | T2N 4N1, Canada Tel: (403) 918-6970 arsenije.subotic1(a)ucalgary.ca

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Freesurfer January 2019