[Freesurfer] b0dc flag for Freesurfer7

External Email - Use Caution Dear Experts, I am wondering if there is additional documentation about the -b0dc flag for mkanalysis-sess. This flag is applying field distortion correction. Is it possible to use my topup information in order to correct it or it s a different

[Freesurfer] Export stats: HCP Multi Modal parcellation

External Email - Use Caution Dear Freesurfer experts, it is possible to export the stats of subjects reconstructed with freesurfer v.6 using the HCP Multi Modal parcellation? (Glasser et al., 2016). Thank you in advance. Best regards, -- *Miguel Ángel Rivas Fernández*

Re: [Freesurfer] Export stats: HCP Multi Modal parcellation

External Email - Use Caution What stats are you looking for? Matt. From: on behalf of Miguel Ángel Rivas Fernández Reply-To: Freesurfer support list Date: Wednesday, March 31, 2021 at 4:36 AM To: Freesurfer support list Subject: [Freesurfer] Export stats: HCP Multi Modal

[Freesurfer] quantification of volume of perivascular spaces

External Email - Use Caution Dear experts, We would like to quantify volume of brain perivascular spaces. Ideally longitudinally - i.e. to study the dynamics of perivascular spaces in multiple measurement of the same subject. Is it possible to use samseg for this? Do you

Re: [Freesurfer] Export stats: HCP Multi Modal parcellation

External Email - Use Caution It might be necessary to resample the atlas to the native mesh surfaces and convert it to the .annot file format from GIFTI. The former can be done using these instructions to get to fsaverage and then presumably FreeSurfer has a tool to get it to

Re: [Freesurfer] Export stats: HCP Multi Modal parcellation

External Email - Use Caution Hello Glasser, In addition to freesurfer's asegstats2table, I would be interested in volume, cortical thickness and area of the HCP atlas (please, see attached .csv file). Other software (e.g CAT12

Re: [Freesurfer] Left-Right labeled brain MRI

How about an aseg volume? The left and right are labeled with different numbers  From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Arman Avesta Sent: Wednesday, March 31, 2021 5:24 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer]

Re: [Freesurfer] fMRIPrep BOLD Output

External Email - Use Caution Hi FS Forum, I am following up on this post because after using mri_vol2surf to downsample my scans to fsaverage4, I ended up with empty files when viewed in Freeview. This is the command that I ran generally: mri_vol2surf --src bold_preproc.nii.gz

[Freesurfer] Research Assistant/Lab manager position at Brown

External Email - Use Caution A full-time Research Assistant position is available in the Oh Laboratory for Cognitive and Translational Neuroscience in the Department of Psychiatry and Human Behavior at Brown University. This position entails both administrative and research

[Freesurfer] Left-Right labeled brain MRI

External Email - Use Caution Hi, Thank you again for responding to my previous questions!  I'm writing a python class to show MR images, and I need to have one brain MRI volume (e.g. nifti or mgz) in which left and right are labeled in some way.  FSL website used to provide a

[Freesurfer] mri_glmfit error

External Email - Use Caution Hello FS experts, I attempted to execute mri_glmfit on my structural data through the following command - mri_glmfit --y final.lh.mTBI.volume.10.mgh --fsgd FSGD/mild.tbi.fsgd dods -C contrats/HC-mTBI.mtx --surf fsaverage --cortex --glmdir

[Freesurfer] Regarding recon all

External Email - Use Caution Dear Team, Actually I am trying to test my own data in recon all , but i have taken only one subject for recon. It shows me this error. ERROR! FOV=408.000 > 256 Include the flag -cw256 with recon-all! Inspect orig.mgz to ensure the head is fully