Re: [Freesurfer] Correcting pial surface with Flair sequence

External Email - Use Caution You can always give it a try and put slice thickness as a covariate of no interest. Matt. From: on behalf of Georgia Kapizioni Reply-To: Freesurfer support list Date: Friday, January 8, 2021 at 10:22 AM To: "freesurfer@nmr.mgh.harvard.edu" Subje

Re: [Freesurfer] write .annot files

Hi Octavian Yes, we do usually embed the LUTs into the .annot and .mgz files to make them self-contained. I think Doug has something to read them from at least the .mgz. Maybe mri_info? Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Octavian Lie Sent: Friday, January

Re: [Freesurfer] write .annot files

External Email - Use Caution Thank you, Bruce. Just to exhaust the annot issue. I assume that the labels (parcel names) are not embedded in .annot or aparc+aseg.mgz per se, but they are read from the LUT table by matching annot vertex indices to col 1 in the LUT. Is there any .m fi

Re: [Freesurfer] write .annot files

Alas there is not – there are large parts of the cortex that have not yet been mapped for microstructural boundaries From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Octavian Lie Sent: Friday, January 8, 2021 11:59 AM To: Freesurfer support list Subject: Re: [Freesurfer] write .annot

Re: [Freesurfer] write .annot files

Hi Octavian 1. Yes, there is a write_annotation.m that you can use. 2. We output an annot of the max probability labels at each point I think called BA_exvivo.thresh.annot Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Octavian Lie Sent: Friday, January 8, 2021

[Freesurfer] write .annot files

External Email - Use Caution Dear All, These are probably rookie questions. 1. I can read an .annot file with read_annotation.m, is there a way to write one? (for example read it to matlab, modify, and save, or create a combined (lh+rh) aparc.annot file etc. 2. On the same line,

Re: [Freesurfer] Correcting pial surface with Flair sequence

External Email - Use Caution Let me rephrase: I am running an analysis with two groups, a patient group (n=23) and a healthy control group (n=24). I have accomplished 3DT1 recons for all participants. Now I want to correct pial surface using 3D Flair images. However, I have dif

Re: [Freesurfer] recon-all issue in vmPFC with high-res T1/T2 data {Disarmed}

External Email - Use Caution Yes, the lh.orig is changing, but not lh.white. (I responded to this on the 23rd, but the reply didn't show up in the archive and I'm not sure it went through, so I'm trying again.) Thanks, Ben On Wed, Dec 23, 2020 at 12:37 PM Greve, Douglas N.,Ph.D.

[Freesurfer] Recon-all with Tumor lesion

External Email - Use Caution Dear all, I want to process brains with tumor lesions with the recon-all -all command. Recon-all (freesurfer version 6) gets always stucked when calling the function mris_fix_topology. It used to work with freesurfer version 4.5, but I still want to

[Freesurfer] question on GLM

Good morning Freesurfers! I am building a GLM with 4 classes (control_F, control_M, patient_F, patient_M) to check for differences in cortical thickness between patients and control accounting for the effect of gender and age on cortical thickness. How should my contrast be? Thanks a lot, Val

[Freesurfer] Contrast and cache for one group correlation analysis

External Email - Use Caution To Freesurfer team, Hi everyone, sorry for bothering. I am looking for correlation analysis in a cohort of subject between cortical thickness and an external score (and corrected for age). Because I am only working on one group (with 2 covariates),