[Freesurfer] Display results with tksurfer

External Email - Use Caution Thanks for the reply Doug, We used the tksurfer command lines because they were run in matlab after performing some analysis to obtain the figures of the results. With the scripts, these figures are automatically saved for later review. We would like t

Re: [Freesurfer] Tracula error: run list is longer than subject list

External Email - Use Caution Hi Anastasia Thanks for your reply. It was subjlist (sorry that was a typo in my email) I have attached the 1) log file 2) cognfiuration file 3) bvec and bval files I have used. I hope that's what you need- I am very new to FreeSurfer please let me k

Re: [Freesurfer] segmentHA on Human Connectome Project

This is most likely a problema with wmparc.mgz which is still at 1mm. Can you please try these commands from the mri directory of a subject and rerunning? The first one renames wmparc to wmparc.1mm and the second upscales it to the resolution of the other high resolution volumes using aseg.mgz as

Re: [Freesurfer] Error during skullstripping: numerical result out of range

Hi Julia Can you check the output of the skull stripping and see if it failed? Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Hye Min Shin Sent: Tuesday, October 20, 2020 1:13 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Error during skullstripping: numer

[Freesurfer] Error running mris_ca_label

External Email - Use Caution Experts, My group runs an older version of Freesurfer so that when we run recon-all, it creates the 2005 FS atlas. I've installed the current version of FS on a new machine and I'm trying to go back and create DKT atlases for each of our previous pa

[Freesurfer] Freesurfer edits

External Email - Use Caution Hi freesurfer editing experts. Below are snapshots of the brainmask, aseg and wm.mgz for a 2 year old run through FS 7.1.1 I'm hoping for feedback on the best way to make the relevant edits to the three blue-circled regions. 1. In the superio

Re: [Freesurfer] Error running mris_ca_label

You are missing a switch before the ../label/lh.cortex.label parameter (-l I think? Read the help). That makes all the positional parameters apparently in the wrong place From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Rollo, Patrick Sent: Tuesday, October 20, 2020 11:06 AM To: frees

[Freesurfer] white and pial surfaces appearing outside gray matter boundary

External Email - Use Caution Dear FreeSurfer experts, I wrote in this question around a week ago, but haven't heard back. I'm attempting again without attaching an image, since I didn't see this getting posted the first time. I'm seeing this type of error reoccur for around half

Re: [Freesurfer] replace the vertex_label_index in .annot file

Your best bet is using the FS matlab library to script annotation edits (see read_annotation.m and write_annotation.m). Otherwise, if you’re using freesurfer 6, you can use tksurfer to manually edit labels/annotations through the GUI (https://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit)

Re: [Freesurfer] please help me

Hi Saman Recon-all will give you a comprehensive assessment of most macroscopically visible structures in the brain. You don’t have to convert to nifty first – just point recon-all at a single slice in the proper dicom series (for your 3D T1-weighted scan), and it will spend a few hours doing s

Re: [Freesurfer] surface/volume editing

External Email - Use Caution Hi again, Doug, I am just checking to make sure that the thread didn't get lost in the pile of requests, and whether or not you have had a chance to look at the surfaces I sent. Thanks Jake Jensen On Tue, Oct 6, 2020 at 10:08 AM Jake Jensen wrote:

[Freesurfer] LGI output question

External Email - Use Caution Dear Freesurfer experts, I have performed LGI for one of my subject pools and I was wondering if I can compute the mean area for the different LGI values instead of the area in the output tables? How should I edit the code below to accomplish this? Tha

[Freesurfer] please help me

External Email - Use Caution hi I want to process MRI images to extract Morphology features. I convert my dcm file to nii format by mri-convert command and then  I used FSL software and BET(Best extraction Tool). Next I do not know what to do to extract morphological features? My