[Freesurfer] Gray matter volume image per group

External Email - Use Caution Dear Freesurfer Community, I want to have an image of the average gray matter Volume in each of my 3 groups, and I did not find a good way to do it. I easily obtained an image from the GM thickness and area by using make_average_subject in each of m

Re: [Freesurfer] Gray matter volume image per group

What do you mean by "gray matter Volume"? Do you just want a map where the value at a voxel is the fraction of GM in that voxel? What space (eg, cvs, fsaverage, mni305) are you planning to make the average in? On 7/27/2020 4:33 AM, Oana Georgiana Rus wrote: > External Email - Use Cautio

Re: [Freesurfer] Coregistration to MNI

This command will allow you to have a registration file and sample into MNI152 2mm space mri_vol2vol --gcam pet.nii.gz register.dof6.lta $SUBJECTS_DIR/$subject/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/register.lta 0 1 pet.cvs.2mm.sm00.ni

Re: [Freesurfer] The input for Petsurfer

Sorry, no, not with PETsurfer On 7/26/2020 1:05 PM, Hengameh Marzbani wrote: External Email - Use Caution Thank you for the quick response. Could I use the T1 weighted MRI of an atlas as an alternative for T1-weighted MRI of each subject? If this solution is not applicable, is there a

Re: [Freesurfer] Working with cortical surface area - parcellation size?

I'm not sure what you are trying to do. If you want to look at differences in surface area, wouldn't making all the ROIs the same size defeat the purpose? On 7/24/2020 9:33 AM, Yash Patel wrote: External Email - Use Caution Hi Freesurfer colleagues, I want to analyze regional profil

Re: [Freesurfer] overlapping/ superimposing regions of one analysis over another

are you asking how to create positive and negative regions or are you asking how to operate the visualization? On 7/25/2020 9:40 AM, Sunil Khokhar wrote: External Email - Use Caution Dear Experts, I have done a between group (2 groups) difference in whole brain voxel based cortical

[Freesurfer] Question about QDEC Design Tab Measurement Parameter

External Email - Use Caution Hi, Hope you are having a wonderful morning! In QDEC in the Design tab under the measurement parameter, there are a variety of options (thickness, area, area.pial, volume, sulc, curv, white.K, white.H, w-g.pct.mgh, intensity.deep, intensity.superficial,

[Freesurfer] local gyrification index unit

External Email - Use Caution Hi FreeSurfer experts, I have recently been wondering about the correct unit for curvature and local gyrification index. For curvature I find inconsistent information like: mm^-2 (https://onlinelibrary.wiley.com/doi/epdf/10.1002/ima.20138, page 47),

Re: [Freesurfer] Question about QDEC Design Tab Measurement Parameter

area is the area of the white surface. It  is  not as clear a concept as, eg, thickness. Basically, when the surface is registered to the atlas, it has to be stretched in some places and compressed in others. The stretching and compression will be different in different subjects and there may

Re: [Freesurfer] overlapping/ superimposing regions of one analysis over another

External Email - Use Caution To operate the visualization and obtain the common regions of my between-group difference results and the correlation results in one image. In other words, overlapping/ superimposing my correlation results on the between-group results (to obtain the com

[Freesurfer] Postdoctoral position in the Haber laboratory at McLean Hospital/Harvard Medical School

Dear all - Please see below for a unique opportunity to join the Haber lab in Boston. While the amazing work of the Haber lab speaks for itself, I will also add here the questionable perk that you might have me as a collaborator. If interested, please contact Dr. Haber directly (see below). Be

Re: [Freesurfer] FreeSurfer 7.1.0 tkmedit not opening - please help

tkmedit is deprecated. Try tkmeditfv On 7/24/2020 8:03 AM, Nils Böer wrote: External Email - Use Caution Hello everyone, I'm having a problem with tkmedit on the pre-installed Freesurfer 7.1.0 version for as Ubuntu guest on a Windows 10 host (via Oracle VM). I did work with the 6.0

[Freesurfer] FreeSurfer 7.1.1 is released

FreeSurfer 7.1.1 is now available here https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads This new version fixes bugs and adds some new features. Unless the new features are employed, it will give the same result as 7.1.0; consequently, results from subjects analyzed with 7.1.1 CAN be mix

[Freesurfer] fsgd file - glmfit error

External Email - Use Caution Dear Freesurfer experts, Hope this email finds you well. I am having some trouble with the fsgd file for glmfit and I'm confused why. This is the error I'm getting when running glmfit: iMac-Pro:BAP_complete ajobsaid$ mri_glmfit --y mrip.rh_volume_F7_B

Re: [Freesurfer] fsgd file - glmfit error

Please send the fsgd file On 7/27/2020 11:34 PM, Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience wrote: External Email - Use Caution Dear Freesurfer experts, Hope this email finds you well. I am having some trouble with the fsgd file for gl