Claudia,
I'll try to answer some of your questions, in each section below:
On Mon, 2006-09-25 at 18:29 +0100, claudia wheeler-kingshott wrote:
Hi,
I have just started to look at freesurfer and decided to run each step to try to understand what recon-all does.
Some resources to learn the processing stream in a step-by-step manner include this wiki page:
http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
and, in your freesurfer distribution, there is a sample subject, named bert. Look at the files:
$FREESURFER_HOME/subjects/bert/scripts/recon-all-status.log
and
$FREESURFER_HOME/subjects/bert/scripts/recon-all.log
Also, adding the flag -dontrun at the end of recon-all will show you what will run, but it will not execute. This is handy to see what it will do (ie. expose flags to commands).
Lastly, the --help command given to recon-all, and virtually all freesurfer commands, will give help info.
Well, after a bit of teething to put the data in the right orientation, we managed to start, but we have a few questions :-)
First of all, our SPGR data is 1.2x1.2x1.2mm^3 and it is acquired coronally. I used mri_convert to get the data resampled to 1x1x1mm^3.
- When I run the mri_nu_correct command to generate the nu file I get
a lot of "Not yet installed" errors. Do I have to generate this file at all? It seems redundant.
Do you mean messages that say:
Not implemented yet in cache_volume_range_has_changed()
These can be ignored. They originate in the mni toolkit distributed with freesurfer.
- When I get to the generation of the T1 file and then the brainmask,
this last file is not compatible with the original data or the nu data because of a different voxel size. This causes me the first problem with the mri_em_register command, which fails if I use the --mask option with my brainmask image and the nu data, giving me a segmentation fault. If I use the T1 data, then the command runs fine! Is there a reason why we can't use the T1 file instead of the nu or orig file?
Using the command:
recon-all -s <subjname> -autorecon1
is recommended for generating the T1 and brainmask files using the proper voxel sizes. Can you tell us which command is failing for you? Specify the whole command line.
- We also have a problem with the commands that use the
$FREESURFER_HOME/average/RB40_talairach_2005-12-30.gca file because it is not in the directory. Can we use the RB_all_2006-02-15.gca file instead? What is the difference between these two files?
RB_all_2006-02-15.gca is a newer version of RB40_talairach_2005-12-30.gca. I've updated the wiki and help info to correct this.
- Has anybody got a feeling on how freesurfer works on brains with MS
lesions?
Others will have to answer this.
- Is there any way to find descriptions and info on commands that do
not have an official page?
The --help flag to most commands provides description. Some commands are lacking though, so let me know if you think a command needs more -- help info.
Sorry for the basic questions and I hope to hear from you soon.
Claudia
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