I was able to get around this error by changing -invert1 to -invert2 in recon-all:

%%%% line 716
  # now create the inverse transforms
  cd $subjdir/mri/transforms > /dev/null
  $PWD |& tee -a $LF
  foreach s ($BaseSubjsList)
    set cmd = (mri_concatenate_lta -invert2) #MJE: invert1 to invert2
    set cmd = ($cmd ${s}_to_${subjid}.lta)
    set cmd = ($cmd identity.nofile)
    set cmd = ($cmd ${subjid}_to_${s}.lta)
    echo "\n $cmd \n" |& tee -a $LF |& tee -a $CF
    if($RunIt) then
      $fs_time $cmd |& tee -a $LF
      if($status) goto error_exit;
    endif
  end
  touch $touchdir/base.touch
endif
%%%% line 733

Is this a reasonable fix? Or am I doing something I shouldn't?

I've also attached my full log.

thanks!
Matt

On Fri, Oct 30, 2009 at 10:09 PM, Martin Reuter <mreuter@nmr.mgh.harvard.edu> wrote:
Hi Matt 
Looks like there is something wrong with the lta mapping tp1 to the base. Can you send the full log?

Thanks Martin


On Oct 30, 2009, at 23:32, Matt Erhart <mattjerhart@gmail.com> wrote:

Hello everyone,

%% After running this command with v4.5 and v4.4:
recon-all -base FREESURFERRECON_TEST_005_S_
0221BASE45 -tp FREESURFERRECON_TEST_005_S_0221_45_20070321.105506_1 -tp FREESURFERRECON_TEST_005_S_0221v2_45_20061006.104318_1 -all -force

%% I get this error:
%%%%%%%%%%
mri_concatenate_lta -invert1 FREESURFERRECON_TEST_005_S_0221_45_20070321.105506_1_to_FREESURFERRECON_TEST_005_S_0221BASE45.lta identity.nofile FREESURFERRECON_TEST_005_S_0221BASE45_to_FREESURFERRECON_TEST_005_S_0221_45_20070321.105506_1.lta

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

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

Any ideas on how to solve this?

A side note for other troubleshooters: getting to this stage takes around 5 minutes with 2 subjects and around 90 minutes with 3.

thanks!
Matt
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