Re: [Freesurfer] new 'dev' release for Linux rh9, centos4 and centos4_x86_64

Hi Nick,

I downloaded freesurfer-Linux-rh9-dev20050905-full.tar.gz and installed it on the following system: Fedora Core 4; AMD Sempron 2600+ on an ECS KT600-A board; Nvidia GeForce 2; 1 GB DDR 400 RAM.

'recon-all -subjid XXX -autorecon-all' would not run at first because it could not find some of the mni tools. The ones that it was having difficulty with were the perl scripts (not the binary MNI files). I noticed the first line in each of the scripts points to what looks like the MGH specific perl installation (i.e., /usr/pubsw/bin/perl), which does not exist on my system. I tested two different solutions 1) change the first line of each file and 2) mkdir -p /usr/pubsw/bin and then add a symbolic link to my perl binary. Both methods appear to work, and 'recon-all -subjid XXX -autorecon-all' has been running successfully for about 12 hours. I assume it is working!

I also noticed that recon-all expected the mgz files for each separate anatomical to both be located in $FREESURFER_HOME/subjects/XXX/mri/orig. This is opposed to what I recall for the old COR method of placing separate anats in 001 002 etc (for obvious overwriting reasons). I believe this is documented in the recon-all help file, but could be confusing for some users at first.

Csurf, tkmedit, and tksurfer gui's loaded without a problem on my FC4 machine. Csurf loads surfaces fine, but I cannot get it to load mgz files. It seems to expect COR files. Out of habit, I did all of my volume edits using 'Edit Segmentation' in csurf, but may have to switch tkmedit/tksurfer. No problem there.

In sum, the current dev version for Redhat 9 appears to be running fine on a basic Fedora Core 4 machine.

Thanks, Brian