[Freesurfer] Mixed Block Event-related Design Optseq Question

External Email - Use Caution Hello Experts, I am wondering if any of you are aware of any commands of optseq for a mixed design? We are specifically not sure how to specify block duration. It seems like optseq is designed for event related design according to the help page, but

Re: [Freesurfer] Ex vivo segmentations

Cool. Thanks again! Panagiotis Fotiadis Senior Imaging Research Technologist J. P. Kistler Stroke Research Center, Department of Neurology Massachusetts General Hospital, Boston, MA T: (617) 643-3869 From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruc

Re: [Freesurfer] Ex vivo segmentations

as I said, I don't think I would trust the ex vivo thicknesses. Definitely not in an absolute sense On Mon, 30 Jul 2018, Fotiadis, Panagiotis wrote: Hi Bruce, Thanks, that is actually really helpful.  Also, I realized I misspoke earlier when I was talking about the cortical thickness rang

Re: [Freesurfer] Ex vivo segmentations

Hi Bruce, Thanks, that is actually really helpful. Also, I realized I misspoke earlier when I was talking about the cortical thickness range. The 3.7-3.9 mm range that I mentioned was referring to global cortical thickness across (not within) the different brains I have processed. The range o

Re: [Freesurfer] Ex vivo segmentations

Hi Panos I think you can trust the white surface (more or less), it's the pial that is tougher. So you might sample say 1mm out from the white and not use the pial at all cheers Bruce On Mon, 30 Jul 2018, Fotiadis, Panagiotis wrote: Hi Bruce, Thanks for your prompt response! I see, in tha

Re: [Freesurfer] Ex vivo segmentations

Hi Bruce, Thanks for your prompt response! I see, in that case I will disregard cortical thickness for now. I was also interested in measuring the average signal intensities of the gray and white matter in those ex vivo brains. Do you think it would be prudent to use the resulting surfaces fro

Re: [Freesurfer] Ex vivo segmentations

Hi Panos I wouldn't trust the thickness from the ex vivo pipeline, and in any case those number are way to narrow a range. The normal cortex thickness ranges from about 1.5mm to 4 or 4.5mm. Getting reasonable thickness from ex vivo data is high on our to-do list cheers Bruce On Mon, 30 Jul

[Freesurfer] Ex vivo segmentations

Hi Bruce and Doug, I have processed a few ex vivo brains with the help of the ex vivo freesurfer pipeline (outlined in https://surfer.nmr.mgh.harvard.edu/fswiki/ExvivoRecon), and have extracted their cortical thickness. So far the range of the cortical thicknesses have been approximately betwe

Re: [Freesurfer] masking cortical thickness

Yes, that should work. You can create a mask by breaking the annotation into labels (mri_annotation2label), then converting the label into a binary mask (mri_label2label with --mask option), then mri_binarize --i lh.thickness --mask youmask.mgh --o lh.thickness.masked.mgh On 07/30/2018 01:47 A

Re: [Freesurfer] Atlases in FreeSurfer

Hi Siti it is more or less the same protocol, but I exepect there are some differences as for example neuromorphometrics used differentt (probably better) visualization and editing tools. We rebuild the atlas for every release to account for changes in registration, normalization, etc We

[Freesurfer] Surface editing: recon-all exited with errors

External Email - Use Caution Hello. I manually edited the brainmask.mgz file for three subjects. This was done to prevent the pial surface from extending into non-cortical areas, in particular the soft-tissue near the brain stem, and some cerebellar areas. Usually this type of

[Freesurfer] Atlases in FreeSurfer

External Email - Use Caution Hello, I’m working on a comparison of atlas and segmentation methods. One of the atlas sets I’m using is the subset of Neuromorphometrics data from the MICCAI 2012 Grand Challenge and Workshop on Multi-Atlas Labeling. From what I understand, the “ge

Re: [Freesurfer] hippocampal subfields segmentation error

External Email - Use Caution Dear Eugenio Thank you for your help. As I need to segment the nuclei of amygdala, I'll try to download the development version. Thanks!! Jinyoung 2018-07-30 17:39 GMT+09:00 Iglesias Gonzalez, Eugenio : > External Email - Use Caution > > D

Re: [Freesurfer] hippocampal subfields segmentation error

External Email - Use Caution Dear Jin, 6.0 does not segment the nuclei of the amygdala; you can ignore that line, assuming the code runs to completion (I am assuming it does?) If you want to segment the nuclei of the amygdala, you’ll have to download the development version: http

Re: [Freesurfer] hippocampal subfields segmentation error

External Email - Use Caution Dear Jinyoung, Can you please send us the log, or at least the last few lines before the error? Also, which exact version are you using? 6.0 or dev? Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing