[Freesurfer] ventricular volumes - freesurfer 6 vs 7

External Email - Use Caution Hi All, I have some datasets processed with freesurfer 6 and other datasets processed with version 7. Is it ok to combine the ventricular volume results from version 6 and version 7 ? Please advise, Thank you Ani ___

[Freesurfer] ERROR! FOV=265.909 > 256

External Email - Use Caution Hello All, I am running recon-all highres on 10 7T MP2RAGE datasets that has been skull striped and in two subjects, I get the following error - I tried the suggested workaround ie I included the flag -cw256 but that didnt help and I got the error ag

[Freesurfer] plotting mean T1/T2 values in the different cortical layers

External Email - Use Caution Hi All, I have created cortical surfaces corresponding to 25%, 50%, 75% of the cortex. Now I want to plot the T1/T2 values corresponding to these different layers.I believe I have to use mri_vol2surf. What options in the mri_vol2surf do I need to use

[Freesurfer] volume and mean intensity values from single nii file with multiple ROIs

External Email - Use Caution Dear All, I have segmented the midbrain of each subjects into different subregions (peduncle, substantia nigra, red nucleus etc) using an atlas. I am trying to extract the volume of each region (the regions are labeled 101, 102, 103 etc) and also tryin

[Freesurfer] freesurfer development version for mac incomplete

External Email - Use Caution Hi When I try to download the development version of freesurfer for mac, the file size is only 138 MB and doesnt unzip once downloaded. Is there another link where the complete development version for mac can be found ? Thanks Ani __

[Freesurfer] T2 seq. for hippocampus ??

External Email - Use Caution Hi All, I have 1x1x3 cubic mm T2 and 1x1x1 cubic mm FLAIR, in addition to 1x1x1 cubic mm MPRAGE. Can you please let me know whether I should use only T1 or should I use one of the additional seq. for hippocampal subfield segmentation ? cheers Nik ___

Re: [Freesurfer] question about hippocampal vols

r Ani, > > What was the exact command you used? > > Cheers, > > /Eugenio > > > > -- > > Juan Eugenio Iglesias > > ERC Senior Research Fellow > > Translational Imaging Group > > University College London > > http://www.jeiglesias.com

[Freesurfer] question about hippocampal vols

External Email - Use Caution Hi All, I have run quantifyHAsubregions.sh hippoSf - and have the volumes for the hippocampal subfields. From which of the following segmentation files are these volumes computed from ? lh.hippoAmygLabels-T1.v21.CA.FSvoxelSpace.mgz lh.hippoAmygLab

[Freesurfer] which dev version for amygdala segmentation

Hi All, How do I download reqd. files / FS developmental version to run hippocampal/amygdala pipeline as described in the wiki https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala I tried downloading the el capitan version of the development version of freesurfer fro