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
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
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
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 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
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
freesurfer@nmr.mgh.harvard.edu
-
Martin Reuter -
Matt Erhart