Re: [Freesurfer] Editing masks

2013-06-12 Thread Joshua deSouza
Hello Bruce, Yes, I am using the surfaces for this. I am trying to find cortical thickness differences between populations. I do not think that the mask covers the entire hippocampal area, just leaving out the corpus callosum. How would I include these areas into the mask? Thank you, Joshua On

Re: [Freesurfer] Editing masks

2013-06-12 Thread Bruce Fischl
Hi Joshua The thickness isn't well defined in the hippocampus, so you don't want to use it there. Use volumes of the subfields instead Cheers Bruce On Jun 12, 2013, at 10:35 PM, Joshua deSouza desouzajoshu...@gmail.com wrote: Hello Bruce, Yes, I am using the surfaces for this. I am trying

[Freesurfer] Editing masks

2013-06-11 Thread Joshua deSouza
Hello all, I am having a problem with generating values of the vertices at the hippocampal area. I believe it is a masking issue as reviewing the mask after the glmfit analysis I see that the mask does not cover the entire medial region excluding the corpus callosum. Can I do anything to change

Re: [Freesurfer] Editing masks

2013-06-11 Thread Bruce Fischl
Hi Joshua are you using the surfaces for this? If so, you shouldn't as they are undefined in those regions (since they have internal laminar structure that is different than what we expect). What are you trying to achieve? cheers Bruce On Tue, 11 Jun 2013, Joshua deSouza wrote: Hello all,

[Freesurfer] editing masks

2008-08-05 Thread Daniel H Choi
Hi, I have a binary mask that I apply to my .mgz files. It allows me to block everything outside of the STG as 0 and everything inside the way it is. I was wondering though how I might go about editing the mask? I see that there are random voxels that have been left out and I would like to fill

Re: [Freesurfer] editing masks

2008-08-05 Thread Bruce Fischl
Sorry, I don't understand. Where did you get the mask? Or are you trying to create it from scratch? On Tue, 5 Aug 2008, Daniel H Choi wrote: Hi, I have a binary mask that I apply to my .mgz files. It allows me to block everything outside of the STG as 0 and everything inside the way it is. I