Re: [Freesurfer] 4.5 and 4.4 longitudinal base creation error from mri_concatenate_lta

Hi Matt,

no that is not a fix. The command is supposed to invert the map from the current time point to the base (so that we have the map from base to this tp). Therefore the second transform in mri_concatenate is the identity. Your code is inverting the identity. Again, the error happens somewhere earlier. I will check your log. Maybe we will also need the data. I'll let you know.

Best, Martin

On Mon, 2009-11-09 at 01:26 -0600, Matt Erhart wrote:

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
    > 
    > _______________________________________________
    > Freesurfer mailing list
    > Freesurfer@nmr.mgh.harvard.edu
    > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer