[Freesurfer] Lobe parcellation without cingulate from --lobesStrict

External Email - Use Caution Dear FreeSurfer experts, I want to get with mris_anatomical_stats the stats from the four lobes, Frontal, Parietal, Temporal and Occipital as suggest here ( https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation), but without the cingulate. I

[Freesurfer] Resting-State and Brain Connectivity 2018: abstract submission remains open until August 11

External Email - Use Caution -- *From:* Amir Shmuel, Dr. *Sent:* 03 August 2018 15:55 *Subject:* Resting-State and Brain Connectivity 2018: abstract submission remains open until August 11 *Resting-State and Brain Connectivity 2018: abstract submission

[Freesurfer] ICV bias in CV measures

External Email - Use Caution Dear FS experts, This paper was published in 2013: https://www.sciencedirect.com/science/article/pii/S1053811913007064?via%3Dihub#s0040 I was just wondering if the current version of FreeSurfer can still introduce bias in cortical volume measures if I

Re: [Freesurfer] SNA covariate in cortical thickness between groups analysis

I don't think it is correct conceptually.  By including SNR as a covariate, you are saying that you expect the thickness to increase with higher SNR and decrease with lower SNR. This does not make sense to me. It sounds like you are trying to do a mixed effects analysis where you weight by the

Re: [Freesurfer] Origin of freesusrfer output

To add on, the origin is changed in that the "first voxel" is not the same in the 256^3 volume as it is in the original dicom. Having said that, all our files (eg, mgz and nifti) have a  matrix that converts a col, row, slice into the scanner RAS, so you can always find your way back to the dic

[Freesurfer] SNA covariate in cortical thickness between groups analysis

External Email - Use Caution Daer FS experts, I would like to inquire about including SNR as a covariate for the between groups cpmparison in cortical thickness. Is this procedure correct mathematically? Do I need to demean the SNA values before including it covariates? Finally,

Re: [Freesurfer] Origin of freesusrfer output

Hi Ritesh Doug can correct any inaccuracies, but 1. Yes, unless you tell recon-all not to. 2. I'm not sure what you mean by the origin, but we do keep track of the ras coordinates of the center of the volume after resampling (the so-called "cras"). 3. We do keep track of the original dicom

Re: [Freesurfer] Anterior / Posterior Partition in Hippocampus parcellation atlas

External Email - Use Caution Dear Vasudev, It is expected that you get different volume estimates with different atlases (FreeSurfer vs CobraLab), as the manual delineation protocols that were used to create them are very different (e.g., see Yushkevich et al., NeuroImage, 2015).