Good morning Bruce,
1). My LNX3 the only one which is working is a Fedora Linux, Kernel Linux
2.6.32.23-170.fc12.x86_64, GENOME 2.28.2
LNX2 where I get the weird surface display is a Linux CENTOS x86_64, GENOME
2.16.0
The Analyst computer where I got the multiple frames error is a Linux, Kernel
Linux 2.6.35.13-91.fc14.x86_64, GENOME 2.32.0
2). Also, when I am doing my data analysis after running the recon -all and
qcache -all for my subjects, what is the best steps order to be followed. While
reading the FreeSurfer Troubleshooting Reconstruction Work suggests the user
to
run all these steps at once before beginning to inspect the data since this
allows the user to see the final complete output before deciding on any
interventions.But this steps are in a different order that the one in the
tutorial and also in a different order that the one described in the attached
document.
FreeSurfer Troubleshooting Reconstruction Work Flow:1. Source the correct
version of FS
2. Set your SUBJECTS_DIR variable to your subjects directory
3. Import your data and create a subject data directory
4. Run the all the steps of recon-all
5. Check the talairach transform
6. Check the skull strip:
- After adding control points run the steps -autorecon-cp (this will run
-normalization, using control points, and everything else through the end of
-autorecon2) and -autorecon3 (this will update all your stat tables with the
new
changes).
- After adjusting the skullstrip, run the steps -autorecon2 and
-autorecon3.
7. Check the white and pial surfaces
- After editing the wm.mgz volume run the steps -autorecon2-wm (this will
run -fill, using new wm.mgz volume, and everything else through the end of
-autorecon2) and -autorecon3.
- After editing the brainmask.mgz volume to adjust the pial surface, run
the
steps -autorecon-pial (this will run -finalsurfs, using new brainmask.mgz
volume, and everything else through the end of -autorecon3.)
8. Check the segmentations
- After editing the wm.mgz volume run the following steps: -normalization
-maskbfs -segmentation -autorecon2-wm -autorecon3.
3). Sorry for the silly question: It is possible in order to save time to do
all
the corrections ones at the time and then run all the autorecon in one step?
Thank you for your help!
Antonella _______________________________________________
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