Re: [Freesurfer] dev version

Dear Zheng, Question 1: In the dev version, all labels are rendered by default. In previous versions: it’s probably best to open the file twice, and render the hippo with the range 200-249 and the amygdala with the range 7000-7020. Question 2: open lh.hippoAmygLabels-T1.v2x.mgz instead of lh.h

Re: [Freesurfer] segmentHA_T2.sh

We are looking into all this. We’ll have updates soon. Cheers, /Eugenio -- 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 behalf of Eva Hilland Reply-To: Freesurfer support

Re: [Freesurfer] annotation to volume with custom color scheme (Yeo parcellations)

Hi Dorit, The reason why the colors look off is that mri_aparc2aseg will automatically add 1000 for left cerebral cortex and add 2000 for right cerebral cortex. Therefore, for example, a left hemisphere voxel in network 5 will have a value of 1005 in your test.mgz. Here is my suggestion: 1. Find

Re: [Freesurfer] Differences between version 5.2.0 and 6.0.0

Hi Patrik we report both the number of voxels and the volume of each structure in the stats files. Even for 1mm data we use partial volume estimation in the newer versions so that these numbers will not be the same. In general we find that the partial volume estimation helps accuracy, and that

Re: [Freesurfer] Combining scans with different protocols

Dear FreeSurfer Team, Unsure whether this is the correct email for queries, apologies it not. I am wondering if it is possible to combine data set from two different protocols with different slice numbers. For example, (see attached screenshots): 1st - SAG ADNI GO ACC SPGR – 196 slice

[Freesurfer] Fwd: Differences between version 5.2.0 and 6.0.0

Hello! Thank You for the answer. So, If I understand this in good way - version 6.0 works with original data voxel size and the data are not conformed to voxel size 1x1x1 mm. Can I ask if also version 5.3 conform data that have different voxel size from 1x1x1 mm. Thank You very much! patrik krump

Re: [Freesurfer] Combining scans with different protocols

Hi Maria you could but they have different contrast/distortion properties, so it isn't clear to me that it is a win. I guess the easiest thing to do would be to "conform" them both with mri_convert, then try registering/averaging them. cheers Bruce On Thu, 1 Feb 2018, Gudbrandsen, Maria wr

Re: [Freesurfer] Fwd: Differences between version 5.2.0 and 6.0.0

Hi Patrik They both can conform if you ask them to or not if you tell them not to. 6.0 does a much better job using the native highres data though cheers Bruce On Thu, 1 Feb 2018, Patrik Krumpolec wrote: Hello!Thank You for the answer. So, If I understand this in good way - version 6.0 wor

Re: [Freesurfer] options for a poor T1

Hello Jason, The freesurfer folks may have some suggestions for adjusting certain parameters, but you can also try some denoising approaches before going into the freesurfer pipeline. There are a number of flavors. The link below is a good place to start I think. https://www.sciencedirect.com/

[Freesurfer] White matter hypointensities

Dear Experts, I was wondering if anyone might know why the WM hypointensities total number in aseg does not match the sum of left and right white matter hypointensities. Thanks, Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Departmen

[Freesurfer] Control Points Not Working

Dear experts, I’m currently performing quality control for my data, and most of my issues so far have been that in many cases adding control points has not been able to extend the white surface. I’ve also noticed that most of the regions where I have needed to add CPs are in the parietal region

Re: [Freesurfer] [freesurfer] Extracting values of cortical thickness in each vertex.

Hi Bruce I found a directory having a file with ".curv", open terminal and run following command. [root@localhost surf]# mris_convert rh.curv rh.curv.asc nquads=4587523, nvertices=476 ERROR: MRISread: file 'rh.curv' has many more faces than vertices! Probably trying to use a scalar data file as a