[Freesurfer] Hippocampus ROI

External Email - Use Caution Dear FreeSurfer experts, I am trying to create a hippocampus ROI in FSL (MNI 152_2mm brain space) from the FreeSurfer 7.0 hippocampal/amygdala segmentation. How do I create this ROI? Best, Jessica ___ Free

[Freesurfer] Desikan Killiany Atlas Node Coordinates

External Email - Use Caution Dear FreeSurfer, I would like to conduct a network based statistical analysis. One of the inputs in the NBS toolbox is to provide a list of MNI coordinates for each of the brain regions in the parcellation. Is there an established list of MNI coordi

[Freesurfer] Extract Area from ROI

External Email - Use Caution Hi FreeSurfer Experts, I am tryinig to extract area from a volume-defined ROI. I used code from the FreeSurfer websiite (https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness) to extract thickness, but I was not able to extract area.

[Freesurfer] Convert FSL .nii ROI into FreeSurfer Label

External Email - Use Caution Hi FreeSurfer Experts, How can I convert a .nii ROI into a FreeSurfer label? I was able to convert the .nii into a .mgh file but could not figure out how to convert to a label file. Thank you, Jessica ___

Re: [Freesurfer] FreeSurfer v5.1 {Disarmed}

External Email - Use Caution Thanks, that did the trick! From: Tyler Ward Sent: Wednesday, August 12, 2020 8:46 PM To: freesurfer@nmr.mgh.harvard.edu Cc: Hua, Jessica Subject: Re: [Freesurfer] FreeSurfer v5.1 {Disarmed} Hi Jessica, Freesurfer

Re: [Freesurfer] FreeSurfer v5.1 {Disarmed}

have attached the error log in case helpful. Jessica Hua From: fsbuild Sent: Wednesday, August 12, 2020 3:14 PM To: freesurfer@nmr.mgh.harvard.edu Cc: Hua, Jessica Subject: Re: [Freesurfer] FreeSurfer v5.1 Hello Jessica, I believe the environment var

Re: [Freesurfer] FreeSurfer v5.1

o the Applications/freesurfer folder, but I am still getting the same error message. How do I get a .license file? I checked to unhide hidden files, and there is no .license file. Jessica From: Hua, Jessica Sent: Wednesday, August 12, 2020 12:36 PM To: frees

[Freesurfer] FreeSurfer v5.1

External Email - Use Caution Hi FreeSurfer, To be consistent with old analyses, I need to process my data using FreeSurfer v5.1 on my Mac. Do you know where I can find the link to install v5.1? Best, Jessica Hua ___ Freesurfer mailin

Re: [Freesurfer] Convert mgz to nii

External Email - Use Caution Hi FreeSurfer experts, Also in case the code is different, how would I convert my T1.mgz file to a .nii file to be used in DTI analyses? Thanks! Jessica --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psycho

[Freesurfer] Convert mgz to nii

External Email - Use Caution Hi FreeSurfer experts, I would like to convert my .mgz parcellation file to a .nii file to be used in DTI analyses. How would I convert my participant's aparc+aseg.mgz file to a .nii file? Best, Jessica --- Jessica Hua, M.A. Cognitive and Emotio

Re: [Freesurfer] Group Analysis Covariates

ouglas N. Greve) 2. Re: question on partial volume correction (Barletta, Valeria) 3. Re: question on partial volume correction (Douglas N. Greve) 4. Re: Group Analysis Covariates (Hua, Jessica) 5. Re: Group Analysis Covariates (Douglas N. Greve) 6. Re: mris_register intermediate resul

Re: [Freesurfer] Group Analysis Covariates

External Email - Use Caution I apologize for resending all of this info, but my email is acting up and every time I try to respond to the other email, my Outlook freezes. Here is info from our thread. I modified it to include the analysis in which I found significant clusters (i

Re: [Freesurfer] Robust Regression with Univariate LME

External Email - Use Caution Hi FreeSurfer Experts, Just bumping this item up. There are a couple of outliers in my data. I had winsorized the variable, but now I am trying to use robust regression to weight these outliers in my longitudinal analyses. In Matlab there is a rob

Re: [Freesurfer] Group Analysis Covariates

External Email - Use Caution Attached are the fsgd and Xg.dat files. --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri GroupComparison_AllMRI.AgeSexICV.fsgd Description: GroupComparison_AllMRI.AgeSexICV.fsgd

Re: [Freesurfer] Group Analysis Covariates

External Email - Use Caution I was not sure how to modify the last line in your code in order to calculate adjusted values accounting for age, sex, and ICV for each participant (this is a three group design). Your code: There is not an easy way to do it, but you can do it in ma

Re: [Freesurfer] Group Analysis Covariates

External Email - Use Caution Sure, attached are the files again and here is our previous correspondence: Original question: After running the permutation and finding significant clusters, I am trying to calculate the value for each participant for these significant clusters. Th

Re: [Freesurfer] Group Analysis Covariates

External Email - Use Caution Sure, attached is the FSGD file. In case helpful, I have also attached the Xg.dat file. --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri GroupComparison_AllMRI.AgeSexICV.fsgd De

Re: [Freesurfer] Group Analysis Covariates

External Email - Use Caution After running the permutation and finding significant clusters, I am trying to calculate the value for each participant for these significant clusters. The perm.th30.abs.y.ocn.dat contain the raw values, and I am trying to get the adjusted values acc

[Freesurfer] Group Analysis Covariates

External Email - Use Caution Hi FreeSurfer Experts, I am trying to extract or calculate the adjusted values for each participant in each cluster after accounting for covariates in my permutation analysis. This is a 3 group analysis with 3 covariates (age, sex, and ICV). After

[Freesurfer] Robust Regression with Univariate LME

External Email - Use Caution Hi FreeSurfer Experts, There are a couple of outliers in my data. I had winsorized the variable, but now I am trying to use robust regression to weight these outliers in my longitudinal analyses. In Matlab there is a robustfit function. Is there a

[Freesurfer] Trac-All NaN

External Email - Use Caution Hi FreeSurfer, I ran the trac-all -stat command on some of my participants, and I noticed that some of the values that were outputted contained NaN. Why are the values coming out as NaN? fmajor_PP.avg33_mni_bbr.AD_Avg.txt S11018a_LGI S11019a_LGI S1

Re: [Freesurfer] Trac-All Error

External Email - Use Caution Hi Dr. Yendiki, Thanks! That fixed the issue I was having. Jessica --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri ___ Freesurfer mai

Re: [Freesurfer] Trac-All Error

External Email - Use Caution Attached are bvecs and bvals. --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri 0,0,0 0,0,0 0,0,0 0,0,0 0,0,0 1,

Re: [Freesurfer] Trac-All Error

External Email - Use Caution Hi Dr. Yendiki, I wasn't sure if I could attach files to the FreeSurfer, so I have also emailed your work email. Attached is my full configuration file as well as my error log. Best, Jessica --- Jessica Hua, M.A. Cognitive and Emotional Control

[Freesurfer] Trac-all Error

External Email - Use Caution Hi FreeSurfer, I am running trac-all prepocessing using a configuration file. I tried preprocessing a couple of participants, and I keep getting this error: #- #@# Tensor fit Sat Apr 11 21:29:36 PDT 2020 dtifit

Re: [Freesurfer] Permutation with Non-Orthogonal Matrices

External Email - Use Caution I had a question regarding the output for permutation. perm.th40.abs.y.ocn.dat -- the average value of each subject in each cluster Is this average value the raw value of each subject, or does this also account for my covariates (age, sex, and ICV)?

Re: [Freesurfer] Permutation with Non-Orthogonal Matrices

External Email - Use Caution Thanks for your help! I downloaded the patch, and the analysis is now running. Hopefully, I will not run into any other issues with the permutation. Jessica --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psycho

[Freesurfer] Permutation with Non-Orthogonal Matrices

External Email - Use Caution Hi FreeSurfer Experts, As recommended I ran the following command: mri_glmfit-sim --glmdir rh.volume.AgeSex.10.glmdir --perm 1000 3.0 abs --perm-resid --cwp 0.05 --2spaces And I got the following error message: ERROR: Flag --perm-resid unrecognize

[Freesurfer] Permutation with Non-Orthogonal Matrices

External Email - Use Caution Hi FreeSurfer Experts, Reposting this message. I am trying to correct for multiple comparisons by running a permutation for a non-orthogonal design. Based on reading through the blog, I came up with the following script: mri_glmfit-sim --glmdir rh.

[Freesurfer] Permutation with Non-Ortohgonal Matrices

External Email - Use Caution Hi FreeSurfer Experts, I am trying to correct for multiple comparisons by running a permutation for a non-orthogonal design. Based on reading through the blog, I came up with the follow script: mri_glmfit-sim --glmdir rh.volume.AgeSex.10.glmdir --s

[Freesurfer] LME Contrast Question

External Email - Use Caution Hi FreeSurfer Experts, I had a question regarding contrasts for univariate LME models. I am interested in looking at the interaction of alcohol with change in volume across two time-points. Included in my model are covariates Gender, ICV, and Previ

[Freesurfer] Plotting Longitudinal Data and Calculating Effect Sizes

External Email - Use Caution Hi FreeSurfer Experts, I used the longitudinal pipeline and analyzed my data using the univariate linear mixed effects models. I had a couple of questions: 1) The model outputted the F and p values. How do I calculate the effect size? 2) How do I p

Re: [Freesurfer] Longitudinal Masking and FDR

External Email - Use Caution Hi Kersten, I used this code to calculate the threshold: P = [ F_lhstats1.pval(lhcortex) F_rhstats1.pval(rhcortex) ]; G = [ F_lhstats1.sgn(lhcortex) F_rhstats1.sgn(rhcortex) ]; [detvtx,sided_pval,pth] = lme_mass_FDR2(P,G,[],0.05,0); pcor = -log10(pth)

Re: [Freesurfer] Longitudinal Masking and FDR

External Email - Use Caution Dear Kersten, Thank you so much for your help! 1. As recommended, I masked my analyses using the label. 2. And that would be great if you could take a look at it when you have time. In the mean time, I will continue to try to figure out how to modif

[Freesurfer] Longitudinal Masking and FDR

External Email - Use Caution Hi FreeSurfer Experts, I had two questions regarding the longitudinal process. 1) I am using the linear mixed effects mass-univariate approach to analyze my longitudinal data. A priori I am interested in the orbitofrontal cortex and the parahippoca

[Freesurfer] Problem with lme_mass_fit_vw

External Email - Use Caution Dear Kersten, Thank you so much for your help! I made a duplicate copy of the matlab directory, and the scripts worked perfectly. I had one quick question regarding the CM.C. Based on the Linear Mixed Effects model page, I modified the CM.C to fi

[Freesurfer] Problem with lme_mass_fit_vw

External Email - Use Caution Dear FreeSurfer Experts, Just reposting this since I did not see it on the forum. I am trying to run longitudinal gyrification analyses following the FreeSurfer Linear Mixed Effects Models instructions, and I ran into a problem using lme_mass_fit_vw

[Freesurfer] Visualizing Overlapping Areas in Significant Clusters

External Email - Use Caution Dear FreeSurfer Experts, I finished running my analyses, and FreeSurfer calculated the significant clusters for my contrasts (cache.th13.abs.sig.cluster.mgh). I am trying to show where significant clusters overlap between two different models. Do y

Re: [Freesurfer] Qdecrc File

--- Jessica Hua, M.A. From: Hua, Jessica Sent: Sunday, February 17, 2019 5:39:38 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Qdecrc File Hi FreeSurfer Experts, I am trying to modify my .Qdecrc file in order to run lGI analyses. However, I cannot seem to

[Freesurfer] Qdecrc File

External Email - Use Caution Hi FreeSurfer Experts, I am trying to modify my .Qdecrc file in order to run lGI analyses. However, I cannot seem to find it. Do you know where I can find this file? Best, Jessica --- Jessica Hua, M.A. ___

Re: [Freesurfer] Group Analysis Covariates

External Email - Use Caution Hi FreeSurfer experts, Just bringing this question back up to the top: I analyzed my data following the guidelines on the FreeSurfer Tutorial/Group Analysis page . I am trying to plot the adjusted values (covariates: age, sex, and ICV) for the signi

[Freesurfer] Group Analysis Covariates

External Email - Use Caution Dear Freesurfer Experts: I analyzed my data following the guidelines on the FSL Tutorial/Group Analysis page . I am trying to plot the adjusted values (covariates: age, sex, and ICV) for the significant clusters for each of my participants. I set