Re: [Freesurfer] trac-all inquiry

2013-11-16 Thread Anastasia Yendiki
Hi David - This log only shows output from the -path step and not from the -prep step. The file that's missing should be created during the -prep step, so there's no way to figure out what went wrong without seeing the output from the pre-processing. Please cc the freesurfer list on your rep

Re: [Freesurfer] trac-all inquiry

2013-11-16 Thread David Soto
Thanks! for some weird unknown reason the log for the preprocessing file of this subject is unusually big (2.8 megabytes) please get it from this link https://dl.dropboxusercontent.com/u/8209026/Archive.zip cheers ds On Sat, Nov 16, 2013 at 3:13 PM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.e

Re: [Freesurfer] Linux recon-all error

2013-11-16 Thread krista kelly
Thanks Alan for your response! I've tried typing sudo yum update into the terminal window, however it does not work. It says yum:command not found. I've tried googling how to do this, but I can't find anything. This is what I type into the terminal window: sudo yum command Am I doing it wrong? T

Re: [Freesurfer] Linux recon-all error

2013-11-16 Thread Chris Watson
You need to type "sudo yum update", not "command". On 11/16/2013 01:29 PM, krista kelly wrote: Thanks Alan for your response! I've tried typing sudo yum update into the terminal window, however it does not work. It says yum:command not found. I've tried googling how to do this, but I can't find

[Freesurfer] aparc.DKTatlas40

2013-11-16 Thread krista kelly
I'm using freesurfer v. 5.3 and I see a new annotation, aparc.DKTatlas40.annot in the labels folder. Can anyone tell me what the difference between this and the apart.annot is? Does it just have 40 labels versus the 36 found in the older version? Thanks! ___

[Freesurfer] problem feeding design matrix to mri_glmfit

2013-11-16 Thread Laura M. Tully
Hello freesurfers, I'm trying to run mri_glmfit between groups analysis (patients vs. controls) with gender, age, medication (continuous), and duration of illness as covariates. Because the control group have values of zeros for medication and duration of illness (which results in an illconditione