[Freesurfer] Extract vertex-wise cortical thickness, surface area and lgi values in ascii files?

Hi all, I want to extract to extract thickness, area and lgi values vertex wise in ascii files for group of subjects. Could anyone suggest me on how to do it. Thank you for your help. -Sabin___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard

Re: [Freesurfer] Extract vertex-wise cortical thickness, surface area and lgi values in ascii files?

Hi Sabin mris_convert can convert binary "curvature" format files to ascii ones if the output file has the extension asc. Something like: mris_convert -c lh.thickness lh.orig lh.thickness.asc this will give you a 5 column ascii file in the format cheers Bruce On Thu, 17 Apr 2014, sabin

Re: [Freesurfer] Extract vertex-wise cortical thickness, surface area and lgi values in ascii files?

yes, you can use mri_surf2surf first to map them to fsaverage, then convert them to ascii On Thu, 17 Apr 2014, sabin khadka wrote: > Hi Bruce, > Thanks for the reply. I was wondering if I have to somehow resample or map > to fsaverage so as to have same # of vertices across all subjects. I tried

Re: [Freesurfer] Extract vertex-wise cortical thickness, surface area and lgi values in ascii files?

Hi Bruce, Thanks for the reply. I was wondering if I have to somehow resample or map to fsaverage so as to have same # of vertices across all subjects. I tried using mris_convert as you suggested above but I can see that different subjects have different #of vertices. Thanks for help. -Sabin

Re: [Freesurfer] recon-all error

Thanks Bruce! I will try it again then! Katica From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, April 16, 2014 10:10 PM To: Freesurfer support list Subje

[Freesurfer] Question about how to get Talairach step to work on brains with bright scalp areas

Hello, I have a question about how to get freesurfer to work correctly with images that have problematic contrast. We have a bunch of images that were taken with a new 32-channel head coil. For some of these images, the contrast value for the scalp cutaneous fat is dramatically higher than the

Re: [Freesurfer] Group Average Thickness

Anyone have any input? On Apr 16, 2014, at 11:27 AM, Jonathan Holt wrote: > Doug, > > Thanks for the quick reply. > > At this point all I want to do is calculate average thickness, per group, > then visualize the average whole brain thickness for each group. I’m thinking > I’m probably going

[Freesurfer] Cortical Thickness Correction Factor

We are working on a study that includes data from multiple scanners and initial indication suggest that there may be small differences in cortical thickness measures that are scanner related (human and other phantom data were acquired at both sites). Is it possible to include a correction facto

Re: [Freesurfer] Extract vertex-wise cortical thickness, surface area and lgi values in ascii files?

Hi all, I ran mri_surf2surf and then mris_convert to get vertexwise thickness and surface area values in ascii files. I found that some vertices had negative values of surface area for few subjects. Should not surface area values be positive only? -Sabin On Thursday, April 17, 2014 10:30 AM, s

Re: [Freesurfer] Group Average Thickness

I'm a little lost here. Why would you run mris_preproc with the average subject as input? That is not one of the options I listed below. It sounds like you would run mris_preproc with fsaverage as the target and your list of subjects for a group as input. Then take the mean of the output stack

Re: [Freesurfer] Cortical Thickness Correction Factor

I would probably just include scanner as a nuisance variable. Can you do that? On 04/17/2014 12:07 PM, David Tate wrote: > We are working on a study that includes data from multiple scanners > and initial indication suggest that there may be small differences in > cortical thickness measures t

Re: [Freesurfer] Group Average Thickness

Doug thank you for your patience. for you what seems natural can be a bit confusing for me. I'll do what you suggests, but I have to ask where does make_average_subject come into play. you recommended it as an option, but now it doesn't seem to be a part of the process Jon > On Apr 17, 2014

Re: [Freesurfer] Group Average Thickness

If you want to display the group mean on the average anatomy of your group, then you use make_average_subject. This is different that just creating an average map of cortical thickness (as is done with mris_preproc). make_average_subject actually creates surfaces, the whole freesurfer subject

[Freesurfer] dt_recon using weighted least squares for diffusion tensor estimation

Dear freesurfer experts, As far as I understand, dt_recon uses linear least squares method as default to estimate the diffusion tensor. Is it possible to use weighted linear least squares in dt_recon? Thank you. Estephan Moana-Filho, DDS, MS, PhD Clinical Fellow, Oral & Maxillofacial Pain Pr

Re: [Freesurfer] dt_recon using weighted least squares for diffusion tensor estimation

In principle if you knew the weights you could weight each direction (but not across weights). But it will not compute such weights for you doug On 4/17/14 7:35 PM, Estephan Moana wrote: Dear freesurfer experts, As far as I understand, dt_recon uses linear least squares method as default

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Hi FS experts, I have a ROI mask in tlrc coordinates in *.tlrc file format, which represents functional activation. Also I have a significant area in sig.mgh which represents cortical thickness difference between two groups, and I created a mask based on surface for it. Now I want to compare the

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