[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] 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

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 list

[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

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

[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

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 

[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

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

[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

[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