[Freesurfer] QDEC failed due to missing files

Hello Freesurfers, In the past I have been able to run QDEC v 4.5 on images without any problem. Recently I ran recon-all on some new set of images. I was able to run the regression analyses using command line options. However, when I tried running qdec..it failed and I get the following messa

[Freesurfer] Measuring the distance relative to a path

Hi Surfers, I need to measure the ''minimum' distance between a cortical vertex and a manually defined path (e.g. V2-V3 border). Is there any command or straightforward way to do that? Thanks -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School __

[Freesurfer] Freesurfer errors on using .nii images

Good afternoon, We are trying to use Freesurfer to work out NifTi images are on using recon script run into this error message below. . It doesn't seem to move past motion correction in the run. Any input will be greatly appreciated! Adam [mcarlsonspronew:/] m_carlson% recon-all -i

Re: [Freesurfer] Optseq2: efficiency and vrf

Thanks for this. I should be more clear. The reasoning and figures tasks are completely separate and are not being compared to each other. Each task has two conditions. For example, in the reasoning task, I have two conditions: Spatial and Nonspatial. I want to compare Spatial and Nonspatial

[Freesurfer] Segmentation label map

Hi, I am having trouble creating a segmentation label map of the amygdala. So far I manually edited the amygdala to create 3 separate sub-regions of the amygdala of 5 subjects. I want to create a label map from these 5 subjects and apply it to the rest of my population. My end goal is to get th

Re: [Freesurfer] Auditory cortex ROIs Freesurfer versions 5.0-5.3

Hi Narly I think it was in 5.3, but you would have to look at the release notes (or maybe Nick remembers). We fixed some bugs and improved some things. cheers Bruce On Tue, 21 Apr 2015, Narly Golestani wrote: Dear Bruce,  Thanks for your answer. Did the surface-based registration procedu

Re: [Freesurfer] Auditory cortex ROIs Freesurfer versions 5.0-5.3

Dear Bruce, Thanks for your answer. Did the surface-based registration procedure change between each successive freesurfer version 5, 5.1, 5.2 and 5.3 or did the main (or bigger) changes occur between 2 specific versions? If so, which please? Many thanks and best, Narly. __

[Freesurfer] problem while running mkcontrast-sess

Dear all, I am trying to repeat FS-Fast tutorial on my data. The system that I use is a Neurodebian running through a virtual machine CentOS 4 x86_64 and freesurfer version is v5.3.0 The error that I get during mkcontrast is as below: mkcontrast-sess log file $Id: mkcontrast-sess,v 1.17 2011/03/1