Re: [Freesurfer] how to dilate a mgh binary mask file in fsaverage space. The file is in .mgh format.

Hi Ani the dev version of freeview has some label morphology operations in the interface, including dilation. Try downloading the dev version and see if it solves your problem cheers Bruce p.s. I think mri_label2label can also do a dilation On Wed, 5 Sep 2018, Anik Dar wrote:

[Freesurfer] Resting-State and Brain Connectivity 2018: Early registration fee applies until September 14, 2018

External Email - Use Caution -- Forwarded message - *From:* Amir Shmuel, Dr. *Subject:* Resting-State and Brain Connectivity 2018: Early registration fee applies until September 14, 2018 *Resting-State and Brain Connectivity 2018: *Early registration fee applies

Re: [Freesurfer] Mean FA values for major tracts all greater than 1

You should probably be suspicious. From: Katherine Damme mailto:katherine.da...@gmail.com>> Date: Wednesday, September 5, 2018 at 1:48 PM To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>>, Anastasia Yendiki mailto:ayend...@nmr.mgh.harvard.edu>> Subject: Mean FA values for

[Freesurfer] Mean FA values for major tracts all greater than 1

External Email - Use Caution Hello Freesurfer Support group, I have run tracula on hundreds of subjects for a study and their primary tracts are all showing that MFA is greater than 1. Typically, I expected that MFA should be in the .3 to 1 range. Should I be suspicious that

Re: [Freesurfer] mris_compute_parc_overlap average minimum distance measurement

Hi Jared I think you description is accurate, but I believe we compute the distances both ways then average them, making it symmetric. As to surfae area corrections, I guess that kind of depends on what you care about. cheers Bruce On Wed, 5 Sep 2018, Zimmerman, Jared wrote:

[Freesurfer] mris_compute_parc_overlap average minimum distance measurement

External Email - Use Caution Hi Freesurfers, I’m using mris_compute_parc_overlap to compare the similarity between two parcellations and I’m curious about how the average minimum distance measurement is calculated. The help text for the function says “… a table of mean minimum

Re: [Freesurfer] long_mris_slopes: error: cannot create a table with longitudinal pc1

Hi Anwar, I see, you want to convert the mgh file back to some text table. Not sure how that worked, but I think mri_convert could do it (but maybe only for a single subject with several structures, not sure about multiple subjects - this is a stacked file). Another way is to open the mgh in

[Freesurfer] Get corresponding vertex of another subject

External Email - Use Caution Hi, i want to create a lookup table for the vertex correspondence between the subjects A & B (pial files). e.g verticesA(100) corresponds to verticesB(122) Of course the number of vertices is different between the subjects, e.g one vertex of A can

Re: [Freesurfer] Is voxel size resampled during recon-all? And different voxel size in longitudinal studies

External Email - Use Caution Hi Martin, Thank you very much for your answer. Best regards Dani 2018-09-04 16:38 GMT+02:00 Martin Reuter : > Hi Dani, > > the regular FreeSurfer stream samples everything to 1mm isotropic. This is > of course problematic, if you have one group

[Freesurfer] error in selxavg3-sess - mismatch TE

External Email - Use Caution Hi list, I have run the FS-FAST analysis in line with the standard procedures that I use routinely. With new data, selxavg3-sess produces an errror: there is a mis-matched between the TE in the analysis (=3) and the TE in the data (=0). I have

[Freesurfer] amygdala segmentation using additional scan error

External Email - Use Caution Hello, freesurfer experts I'm trying to run segmentation of hippocampal subfields and nuclei of amygdala with additional scan. I already ran segmentation of hippocampal subfields and nuclei of amygdala with only T1 image, using segmentHA_T1.sh command