[Freesurfer] make_average_subject for subcortical volumes in children

Dear FS experts, I am new to freesurfer and have a few basic questions. I have a sample of 8-17 year olds in which I will be looking at both cortical thickness and subcortical volumes. I understand that the surface-based registrations seem to be fine for this age range (as per Ghosh et al, 201

Re: [Freesurfer] where to start recon-all after edits

Hi, If the surfaces are 'done' and we update/edit the the aseg.mgz with recon-all -surfsegedit and then run recon-all -autorecon2-cp -autorecon3 to update the .stats, this also creates new wm and pial surfaces that may be different to those used for -surfsegedit. Is that right? As another alt

[Freesurfer] help with using optseq2

Hello, I'm trying to create trial sequences for a slow event related fMRI experiment. I have 10 classes of stimuli, and each stimulus lasts 5 sec and repeats twice in a run. Environment: Linux 3.13.0-35-generic #62-Ubuntu SMP UTC 2014 x86_64 x86_64 x86_64 GNU/Linux I ran: ./optseq2 --ntp

[Freesurfer] QA measures

Dear Freesurfer Team, We would like to have a Q/A measure (or two) that would give us indication of how well your software worked on each of our data sets. Obviously some image sets will be noisier than others for a variety of reasons. Could you point us towards what options we may have for e

[Freesurfer] mri_vol2vol

Hi Freesurfer experts, We are analyzing data for a simultaneous PET-MRI study, and are having trouble registering individual subject BPnd maps to fsaverage space. I attached a photo of a post-registration subject (the left side is cut off). I had previously registered each individual BPnd volum

[Freesurfer] tracula reinit failure filled my hard drive

Hi, I'm using freesurfer-Darwin-lion-stable-pub-v5.3.0 and the latest version of tracula (downloaded Sept 2014). I was running 'trac-all -prior -c mydmrircfile.txt' with reinit=1 on a few tracts that initially reconstructed to look like single voxels. The log file indicated there was difficulty co

Re: [Freesurfer] (no subject)

Hi Amirhossein we will reformat them all to 1mm iso during recon-all. Hopefully those differences are small enough not to cause a bias. cheers Bruce On Thu, 16 Jul 2015, amirhossein manzouri wrote: Hi FS, MR images of two of my subjects in a group have been acquired with different T1 pro

[Freesurfer] (no subject)

Hi FS, MR images of two of my subjects in a group have been acquired with different T1 protocol from the rest. All the subjects has been acquired with sagittal 1mm iso : Width: 230.00 mm (256) Height: 230.00 mm (256) Resolution: 1.113 pixels per mm Pixel size: 0.90x0.90 mm and these two with cor

Re: [Freesurfer] help

As the error message indicates, this is a permissions issue. To solve the license problem, your best bet is to create the license files in your home directory (or anywhere you have adequate permissions) and copy it to /Applications/freesurfer. This is described in a little more detail in the "Licen

[Freesurfer] help

I am very new to Freesurfer and are having problems getting it up and running. I have followed, successfully the set up and configuration instructions up the license. At this point, after entering the license information received in the email I try and to exit and save and I get a message that r

[Freesurfer] Regarding: Qdec GLM design error

Dear freesurfer experts, I am new to Qdec analysis and I trying to do( using the information provided in the qdec wiki page) group surface analysis in SCA patients 1and 2 and compare their surface thickness using qdec command. The data table is loading successfully but when I go the design and cl

Re: [Freesurfer] Tksurfer and Tkregister2 in Ubuntu 14.04

Hi Zeke, I am wondering if you had a chance to look at this. Thanks, Reza Hello Reza, > > > I wasn't able to replicate on Ubuntu 12 but it's entirely possible this but > exists only in Ubuntu 14. It's tough because we don't have test machines with > every Linux distro that people post to the li