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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