Hi Matt,
looked at the log. Everything before seems fine. Not sure what's going
on. Can you send the following files:
>From the two cross sectional runs (tp1 and tp2):
The two norms:
/space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221_45_20070321.105506_1/mri/norm.mgz
/space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221v2_45_20061006.104318_1/mri/norm.mgz
the two orig.mgz:
/space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221_45_20070321.105506_1/mri/orig.mgz
/space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221v2_45_20061006.104318_1/mri/orig.mgz
(if you like, you can call the files norm1.mgz and norm2.mgz, same with
orig, or pack them with their respective subject dir in the path)
in the Base directory:
the two created ltas:
/space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221BASE45/mri/transforms/FREESURFERRECON_TEST_005_S_0221_45_20070321.105506_1_to_FREESURFERRECON_TEST_005_S_0221BASE45.lta
/space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221BASE45/mri/transforms/FREESURFERRECON_TEST_005_S_0221v2_45_20061006.104318_1_to_FREESURFERRECON_TEST_005_S_0221BASE45.lta
the created base nrom_template:
/space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221BASE45/mri/norm_template.mgz
the created base 001.mgz:
/space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221BASE45/mri/orig/001.mgz
Then I can rerun the steps here.
It is strange that it complains about the NULL input matrix, as the two
transforms are successfully used in the step before (when the 001.mgz is
created). We'll see if I can recreate the error..
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
> <mreu...@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 <mattjerh...@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
>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
