[Freesurfer] Volume are different in asegstats vs matlab

Hi, I have a question about volume info from freesurfer vs matlab. I am looking at, say, the left hippocampus volume from asegstats, which was 3778.2 mm^3. When I try to get the same volume by loading aseg.nii on matlab, however, I get a different number, 3945. For matlab, I used the followi

Re: [Freesurfer] Hippocampal Subfields Module, output error

Thanks, Aura. What exact version of FreeSurfer are you using? I’m assuming it’s a development version, but from when? The results are indeed weird… -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.

[Freesurfer] Positions available in Dr. Zeynep Saygin's lab at OSU

TECHNICAL ASSISTANT, The Ohio State University, Dept. of Psychology – Dr. Zeynep Saygin’s Lab, to assist with neuroscience research on the functional and structural architecture of the human brain in adults and children. The Z-lab studies the functional differentiation of the human brain across

Re: [Freesurfer] Volume are different in asegstats vs matlab

Hi Kristine the aseg.stats volume uses partial volume correction to get subvoxel accuracy. cheers Bruce On Fri, 23 Mar 2018, Lee Subin Kristine wrote: Hi,   I have a question about volume info from freesurfer vs matlab. I am looking at, say, the left hippocampus volume from asegstats, w

[Freesurfer] using T2 for hippo subfields

Hi. We are acquiring sequences on a pediatric cohort that include a T1-mprage (0.8mm isotropic) and a T2-space (1mm isotropic), and I'd like to run the hippocampal subfields module on the subjects using FS 6.0. Is it recommended/useful to run the multispectral segmentation mode with the additio

Re: [Freesurfer] using T2 for hippo subfields

Hi Jim, In the end it’s an empirical question, but my gut feeling is that the T1 with hi-res flag will be best. Cheers, /E -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: on b

Re: [Freesurfer] Different DWI protocols

Hi, Have you been able to read my follow-up question? Thanks, M. Cano De: Cano Catala, Marta Enviado: lunes, 19 de marzo de 2018 13:33 Para: Freesurfer support list Asunto: Re: [Freesurfer] Different DWI protocols Thank you for your reply. I see that it is not a

Re: [Freesurfer] Different DWI protocols

It's possible that the differences between time points are different for each of the acquisition protocols. In that case, by adding a different acquisition protocol, you may be increasing the variability of your effect across subjects, in which case you'd need a bigger effect size to be able to

Re: [Freesurfer] Functional Overlap Map

Thank you very much! > On Mar 22, 2018, at 2:31 PM, Douglas Greve wrote: > > you can view it with > tksurferfv fsaverage lh inflated -aparc -overlay conjunction.nii.gz -fminmax > 2 5 > tksurferfv is a front-end for freeview. You can change the thresholds in > freeview > > On 3/22/18 12:27 PM,

Re: [Freesurfer] Hippocampal Subfields Module, output error

Thanks, Eugenio. We used the stable 6 version for reconall: reconall -all back in 06 13 2017, this is the build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-v6-20170215-dc3d7a6 reconall -long back in 02 27 2018, this is the build-stamp.txt: freesurfer-Linux-centos7_x86_64-stable-v6-20161229-