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.

1. 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.

2. 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.

3. 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.

4. Has anybody got a feeling on how freesurfer works on brains with MS

lesions?

Others will have to answer this.

5. 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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