[Freesurfer] mask volume calculation

Hello FS experts, I'm trying to get the volume of a binary mask on orig.mgz. I know that FS uses a more sophisitcated approach than simply counting the number of voxels within the mask and I'd like to apply the same approach. Is there any way to get the volume for a defined mask with the same

Re: [Freesurfer] significant of long_mris_slopes

Hi Lanbo, the first command computes the slope of within-subject linear fits (the rate, so the unit is mm/time). You use —generic time which means that the time is 1 2 3 … It is better to put the real time, e.g. in years for a longitudinal study. the second command is a

Re: [Freesurfer] mris_jacobian error while running recon-all -make all

Hi Anne, Unfortunately, the “-make all” flag contains a bug in the stable6.0 release. However, this has been fixed in the dev version. This can be quickly fixed if you download this script - ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/centos6_x86_64/recon-all.makefile -

Re: [Freesurfer] (no subject)

Hi vidhu use recon-all to process the dataset, then mri_extract_labels or mri_binarize can be used to extract just the hippocampus cheers Bruce On Wed, 1 Nov 2017, Vidhu Agrawal wrote: Respected Sir, How can i scoop out or separate  only hippocampus from a 3D MRI of whole brain? With

[Freesurfer] cut-off clusters size

Hi, I wonder if there is a consensus to thershold the size of clusters obtained by FS-FAST after FDR correction?To cut-off clusters size>10-15 mm2 should be good? or do you advise more than? ThanksStefano ___ Freesurfer mailing list

Re: [Freesurfer] TRACULA

Hi Zheng - I'll need the trac-all.log file, the gradient table, and the b-value table. Please do not send other data at the moment. Thanks, Anastasia. From: 郑凤莲 <13181786...@163.com> Sent: Tuesday, October 31, 2017 9:48:52 PM To: Yendiki, Anastasia Subject:

[Freesurfer] Qdec question

Dear Freesurfer experts, I would like to use "Qdec" tool to study the between groups changes of volume/cortical thickness of one region (Perirhinal) belonging to the Brodmann areas. As I understand Qdec load only the aparc and aseg stat lists and not the BA stat list. I am wondering if we

Re: [Freesurfer] (no subject)

Hi Vidhu, After your standard recon-all, do: mri_binarize --i yoursubjectname/mri/aseg.mgz --match 17 --o left_hip.nii mri_binarize --i yoursubjectname/mri/aseg.mgz--match 53 --o right_hip.nii Hope that helps. Best Wishes, Elijah On Wed, Nov 1, 2017 at 5:57 AM, Vidhu Agrawal

Re: [Freesurfer] Freesurfer 6.0 - Hippocampal subfields segmentation (Mode B) - Registration error

Hi Patricia, Do you think you could send us an example? I’ve never seen the registration fail with good prealignment on an of my datasets, so this would be very, very helpful to improve the software. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging