[Freesurfer] Using Total Cortical White Matter Volume as a "whole brain" covariate

Dear FreeSurfer Developers, I am using FreeSurfer 5.3 to analyze whether a risk factor explains variation in brain structures related to surface area, mean thickness, and subcortical volumes. Documentation suggests using estimated Total Intracranial Volume (eTIV) as a covariate to adjust for

[Freesurfer] Interpretting Brain Segmentation Volume to eTIV ratio

Dear FreeSurfer community, I wanted to interpret the BrainSegVol.to.eTIV ratio that is outputted from FreeSurfer version 5.2.0. In my sample of normally developing adolescents of ages 8 to 21, this ratio is between 0.65 and 0.85 for 98% of subjects. However, the value is less than 0.65 for 2%

[Freesurfer] aparc.stats files from FreeSurfer 6.0

Dear FreeSurfer Users, I have run recon-all on data using both FreeSurfer versions 5.3.0 and 6.0. FS v6.0 generated files named lh.aparc.pial.stats and lh.aparc.stats, whereas FS v5.3.0 created only lh.aparc.stats. I wanted to verify two things: (a) Is it right that surface areas in lh.aparc.

[Freesurfer] Question on surface-based analysis

Dear FreeSurfer users, I am new to surface based analysis in FreeSurfer (version 6.0). My data consists of T1-weighted scan from normally developing youth of 8 to 21 years of age. I have two questions on assumptions of this analysis for pediatric data: (a) Is "fsaverage" an appropriate common

[Freesurfer] Running statistical analysis on surface data in R

Dear FreeSurfer users, I am using R to apply a statistical method on surface data registered to fsaverage (for example, left hemisphere area smoothed at bandwidth=10mm). This method requires data be in a matrix Y with NS rows and V columns, where NS = #subjects and V=#vertices. The output prod

[Freesurfer] Descriptions of regions in Yeo 2011 Network atlases

Dear Freesurfer users, I am examining the Yeo 2011 17 Network atlases in Freesurfer 6.0. The regions are labeled 1 through 17. Is there a reference table mapping these numbers with the names of cognitive networks described by Yeo, et al. (2011) (

Re: [Freesurfer] Descriptions of regions in Yeo 2011 Network atlases

Thank you Thomas! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail

[Freesurfer] TRACULA bedpostx step with gpu

Dear FreeSurfer users, I am using Freesurfer 6.0 and Tracula 6.0 for processing MRI and DTI scans. The second step of the trac-all pipeline performs the ball-and-stick fit with the bedpost function from FSL. Documentation for FSL suggests that the use of GPUs can considerably speed this process

Re: [Freesurfer] TRACULA bedpostx step with gpu

Thank you Anastasia! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-ma

[Freesurfer] Tracula --- Volume and path length are equal

Dear FreeSurfer users, I am using FreeSurfer 6.0 and Tracula 6.0. For many subjects that I'm processing, the volume and path length are equal to each other. For ~60% of subjects, the "pathstats.overall.txt" file shows something like: Count 1500 Volume 34 Len_Min 34 Len_Max 34 Len_Avg 34 Len_

[Freesurfer] Creating cached versions of Xhemi registrations

Dear FreeSurfer Users, I'm using FreeSurfer version 6.0. I've processing subjects with recon-all and performed surface-based interhemispheric registration (via Xhemi at https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi). I want to run a GLM on the subjects Area and Thickness from the differences

Re: [Freesurfer] mris_preproc srcsurfreg Freesurfer 6.0

Dear Doug, Are there reasons why registering to my_subject_average (template defined from, say, average in a cross-sectional sample) can be better than registering to fsaverage? Thank you. Best, Chintan ___ Freesurfer mailing list Freesurfer@nmr.mgh.har

Re: [Freesurfer] Creating cached versions of Xhemi registrations

Dear Doug, I think that is essentially what I figured. Based on remarks in other posts, my steps for evaluating laterality index entail applying: (1). Apply mri_preproc for each subject $SUB and $meas (area or thickness) individually using -xhemi flag but without any paired differences via: >

Re: [Freesurfer] mris_preproc srcsurfreg Freesurfer 6.0

Thank you for the insight; that is very interesting. I'm performing tests of continuous independent variables over a single sample of normally developing children (ages uniformly distributed from

[Freesurfer] dt_recon and Tracula

Dear FreeSurfer users, I've been using FreeSurfer and Tracula versions 6.0. I've run Tracula on DWI scans, and now I am seeking to run dt_recon on them as well. As a new user, it seems both programs follow similar initial pre-processing steps (eddy current & motion correction), which the docume

Re: [Freesurfer] dt_recon and Tracula

Dear FreeSurfer users, Sorry for adding the questions, I found most of my answers at https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/DiffusionV6.0#dMRIDataAnalysisProcessingStream I used FreeView and found that registrations of the lowb.nii, orig.mgz, lh.white, and rh.white aligned very ni

Re: [Freesurfer] dt_recon and Tracula

Dear Doug, I figured out the mistake I was making, which was that I ran: > freeview -v orig.mgz wmparc2diff.mgz:colormap=lut > lowb.nii.gz:reg=register.dat -f lh.white:edgecolor=green > rh.white:edgecolor=green -viewport coronal & Here the lowb, orig, and white surfaces were consistent. Since

[Freesurfer] Reference on measures computed by dt_recon

Dear FreeSurfer users, I'm using FS 6.0 and have computed summary statistics for different measures including adc, ivc, volume ratio, and radial diffusivity. Is there a reference on how the FreeSurfer software computes these measures (i.e. mathematical formulas)? Thank you. Best, Chintan

Re: [Freesurfer] Creating cached versions of Xhemi registrations

Dear Doug, I'm performing a linear regression over one sample with a design matrix including columns for one continuous-valued predictor whose effect on neural measures I'm interested in testing, several covariates to adjust for (continuous- or binary-valued such as age, sex, total intracranial

[Freesurfer] QC on CVS registration

Dear FreeSurfer users, I'm using FS 6.0. I registered MRI scans to the CVS-Avg35 template (mri_cvs_register) and viewed output. While the nonlinear warp of the scan to the template looked completely fine, the warping of the automatic segmentation (aseg) did not look as "clean". Attached is a

[Freesurfer] Simultaneously morphing to CVS + Downsampling.

Dear FreeSurfer community, I have applied mri_cvs_register to subjects' T1 scans using FreeSurfer 6.0 and mri_vol2vol to warp fractional anisotropy spatial maps warped to CVS space. A previous post talks about functionality of "morph + downsampling" in a single step coming in the future: htt