Hi, there,

Last week, we met a problem when we ran the recon-all long-base pipeline. 
%% After running this command with FS v4.5 :
recon-all -base 005_S_0221BASE -tp 005_S_0221_45_20070321.105506_1 -tp 005_S_0221v2_45_20061006.104318_1 -all -force

%% I get the following error:

mri_concatenate_lta -invert1 005_S_0221_45_20070321.105506_1_to_005_S_0221BASE.lta identity.nofile 005_S_0221BASE_to_005_S_0221_45_20070321.105506_1.lta

invert the first LTA before applying it
MatrixInverse: NULL input matrix!

Read individual LTAs
%%%%%%%%%%


Recently, my colleague  found an interesting thing from several tests he did,

For example, we have two subjects:

001_S_0001_20000101_11111_1 and 001_S_0001_20000202_22222_2, both of them have been processed by FreeSurfer cross-sectional pipeline.

We use the following command,

recon-all -base 001_S_0001_20000101_11111_1_to_001_S_0001_20000202_22222_2 -all 

The process will crash at the mri_concatenate_lta step

I change the command to:
recon-all -base 001_S_0001_20000101_to_001_S_0001_20000202 -tp 001_S_0001_20000101_11111_1 -tp 001_S_0001_20000202_22222_2 -all

The process will crash at the mri_concatenate_lta step, again.

However, if f we copied and renamed these two subjects as 001_S_0001_20000101 and 001_S_0001_20000202,
and run the following recon-all command,
recon-all -base 001_S_0001_20000101_to_20000202 -tp 001_S_0001_20000101 -tp 001_S_0001_20000202 -all

It works well, no crash,

So, it looks like recon-all or mri_concatenate_lta has a commandline length limit, is it true?

Thanks!
Guang




From: freesurfer_zg@hotmail.com
To: mreuter@nmr.mgh.harvard.edu
CC: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] longitudinal base error
Date: Fri, 29 Oct 2010 08:44:43 -0500

Hello, Martin,
 
I checked the norm.mgz of these two time points, nothing is wrong.
Maybe I can try the new version of mri_robust_register and ...template,
 
I checked the mailing list. Actually, someone met the same kind of problem in 2009 and 2008.
But it looks like this problem was unsolved.
 
Thanks!
Guang


 
From: mreuter@nmr.mgh.harvard.edu
Date: Thu, 28 Oct 2010 21:29:55 -0400
To: freesurfer_zg@hotmail.com
CC: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] longitudinal base error

Haven't seen this before. Can you send the lta file (should be in basid/MRI/transforms)
Probably the lta is not correct.
Also you can try to delete the base dir and rerun, maybe it was just a hiccup.

Does the norm.mgz look good in the base? If not registration did not work.
In that case download updated mri_robust_register and ...template (links on the wiki on the 5.0 release notes) and run again.

Best Martin

On 28.10.2010, at 20:24, Guang Zeng <freesurfer_zg@hotmail.com> wrote:

Hi, there, 

%% After running this command with FS v4.5 :
recon-all -base 005_S_0221BASE -tp 005_S_0221_45_20070321.105506_1 -tp 005_S_0221v2_45_20061006.104318_1 -all -force

%% I get the following error:

mri_concatenate_lta -invert1 005_S_0221_45_20070321.105506_1_to_005_S_0221BASE.lta identity.nofile 005_S_0221BASE_to_005_S_0221_45_20070321.105506_1.lta

invert the first LTA before applying it
MatrixInverse: NULL input matrix!

Read individual LTAs
%%%%%%%%%%

Any one can help me?

Thanks a lot!
uang
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