Hello, Martin,

I checked the norm.mgz of these two time points, nothing is wrong. Maybe I can try the new version of mri_robust_register and ...template,

I checked the mailing list. Actually, someone met the same kind of problem in 2009 and 2008. But it looks like this problem was unsolved.

Thanks! Guang

From: mreuter@nmr.mgh.harvard.edu Date: Thu, 28 Oct 2010 21:29:55 -0400 To: freesurfer_zg@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] longitudinal base error

Haven't seen this before. Can you send the lta file (should be in basid/MRI/transforms) Probably the lta is not correct. Also you can try to delete the base dir and rerun, maybe it was just a hiccup.

Does the norm.mgz look good in the base? If not registration did not work. In that case download updated mri_robust_register and ...template (links on the wiki on the 5.0 release notes) and run again.

Best Martin

On 28.10.2010, at 20:24, Guang Zeng freesurfer_zg@hotmail.com wrote:

Hi, there,

%% After running this command with FS v4.5 : recon-all -base 005_S_0221BASE -tp 005_S_0221_45_20070321.105506_1 -tp 005_S_0221v2_45_20061006.104318_1 -all -force

%% I get the following error:

mri_concatenate_lta -invert1 005_S_0221_45_20070321.105506_1_to_005_S_0221BASE.lta identity.nofile 005_S_0221BASE_to_005_S_0221_45_20070321.105506_1.lta

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

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

Any one can help me? Thanks a lot!uang

_______________________________________________ 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

Hi, there,

Last week, we met a problem when we ran the recon-all long-base pipeline. %% After running this command with FS v4.5 : recon-all -base 005_S_0221BASE -tp 005_S_0221_45_20070321.105506_1 -tp 005_S_0221v2_45_20061006.104318_1 -all -force

%% I get the following error:

mri_concatenate_lta -invert1 005_S_0221_45_20070321.105506_1_to_005_S_0221BASE.lta identity.nofile 005_S_0221BASE_to_005_S_0221_45_20070321.105506_1.lta

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

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

Recently, my colleague found an interesting thing from several tests he did,

For example, we have two subjects:

001_S_0001_20000101_11111_1 and 001_S_0001_20000202_22222_2, both of them have been processed by FreeSurfer cross-sectional pipeline.

We use the following command,

recon-all -base 001_S_0001_20000101_11111_1_to_001_S_0001_20000202_22222_2 -all

The process will crash at the mri_concatenate_lta step

I change the command to: recon-all -base 001_S_0001_20000101_to_001_S_0001_20000202 -tp 001_S_0001_20000101_11111_1 -tp 001_S_0001_20000202_22222_2 -all

The process will crash at the mri_concatenate_lta step, again.

However, if f we copied and renamed these two subjects as 001_S_0001_20000101 and 001_S_0001_20000202, and run the following recon-all command, recon-all -base 001_S_0001_20000101_to_20000202 -tp 001_S_0001_20000101 -tp 001_S_0001_20000202 -all

It works well, no crash,

So, it looks like recon-all or mri_concatenate_lta has a commandline length limit, is it true?

Thanks! Guang

From: freesurfer_zg@hotmail.com To: mreuter@nmr.mgh.harvard.edu CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] longitudinal base error Date: Fri, 29 Oct 2010 08:44:43 -0500

Hello, Martin,

I checked the norm.mgz of these two time points, nothing is wrong.

Maybe I can try the new version of mri_robust_register and ...template,

I checked the mailing list. Actually, someone met the same kind of problem in 2009 and 2008.

But it looks like this problem was unsolved.

Thanks!

Guang

From: mreuter@nmr.mgh.harvard.edu Date: Thu, 28 Oct 2010 21:29:55 -0400 To: freesurfer_zg@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] longitudinal base error

Haven't seen this before. Can you send the lta file (should be in basid/MRI/transforms) Probably the lta is not correct. Also you can try to delete the base dir and rerun, maybe it was just a hiccup.

Does the norm.mgz look good in the base? If not registration did not work. In that case download updated mri_robust_register and ...template (links on the wiki on the 5.0 release notes) and run again.

Best Martin

On 28.10.2010, at 20:24, Guang Zeng freesurfer_zg@hotmail.com wrote:

Hi, there,

%% After running this command with FS v4.5 : recon-all -base 005_S_0221BASE -tp 005_S_0221_45_20070321.105506_1 -tp 005_S_0221v2_45_20061006.104318_1 -all -force

%% I get the following error:

mri_concatenate_lta -invert1 005_S_0221_45_20070321.105506_1_to_005_S_0221BASE.lta identity.nofile 005_S_0221BASE_to_005_S_0221_45_20070321.105506_1.lta

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

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

Any one can help me? Thanks a lot!uang

_______________________________________________ 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

Hi Guang,

yes, fixed it. The mri_concatenate_lta had difficulties reading the lta if the filename field in the lta was too long.

Workaround: use short names especially for the base.

There will be a fixed version of mri_concatenate_lta in the 5.1 release coming up in a few weeks.

Best, Martin

On Mon, 2010-11-08 at 21:06 -0600, Guang Zeng wrote:

Hi, there,

Last week, we met a problem when we ran the recon-all long-base pipeline. %% After running this command with FS v4.5 : recon-all -base 005_S_0221BASE -tp 005_S_0221_45_20070321.105506_1 -tp 005_S_0221v2_45_20061006.104318_1 -all -force

%% I get the following error:

mri_concatenate_lta -invert1 005_S_0221_45_20070321.105506_1_to_005_S_0221BASE.lta identity.nofile 005_S_0221BASE_to_005_S_0221_45_20070321.105506_1.lta

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

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

Recently, my colleague found an interesting thing from several tests he did,

For example, we have two subjects:

001_S_0001_20000101_11111_1 and 001_S_0001_20000202_22222_2, both of them have been processed by FreeSurfer cross-sectional pipeline.

We use the following command,

recon-all -base 001_S_0001_20000101_11111_1_to_001_S_0001_20000202_22222_2 -all

The process will crash at the mri_concatenate_lta step

I change the command to: recon-all -base 001_S_0001_20000101_to_001_S_0001_20000202 -tp 001_S_0001_20000101_11111_1 -tp 001_S_0001_20000202_22222_2 -all

The process will crash at the mri_concatenate_lta step, again.

However, if f we copied and renamed these two subjects as 001_S_0001_20000101 and 001_S_0001_20000202, and run the following recon-all command, recon-all -base 001_S_0001_20000101_to_20000202 -tp 001_S_0001_20000101 -tp 001_S_0001_20000202 -all

It works well, no crash,

So, it looks like recon-all or mri_concatenate_lta has a commandline length limit, is it true?

Thanks! Guang

---

From: freesurfer_zg@hotmail.com To: mreuter@nmr.mgh.harvard.edu CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] longitudinal base error Date: Fri, 29 Oct 2010 08:44:43 -0500

Hello, Martin,

I checked the norm.mgz of these two time points, nothing is wrong. Maybe I can try the new version of mri_robust_register and ...template,

I checked the mailing list. Actually, someone met the same kind of problem in 2009 and 2008. But it looks like this problem was unsolved.

Thanks! Guang

---

From: mreuter@nmr.mgh.harvard.edu Date: Thu, 28 Oct 2010 21:29:55 -0400 To: freesurfer_zg@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] longitudinal base error

Haven't seen this before. Can you send the lta file (should be in basid/MRI/transforms) Probably the lta is not correct. Also you can try to delete the base dir and rerun, maybe it was just a hiccup.

Does the norm.mgz look good in the base? If not registration did not work. In that case download updated mri_robust_register and ...template (links on the wiki on the 5.0 release notes) and run again.

Best Martin

On 28.10.2010, at 20:24, Guang Zeng freesurfer_zg@hotmail.com wrote:

    Hi, there, 


    %% After running this command with FS v4.5 :
    recon-all -base 005_S_0221BASE -tp 005_S_0221_45_20070321.105506_1 -tp 005_S_0221v2_45_20061006.104318_1 -all -force

    %% I get the following error:

    mri_concatenate_lta -invert1 005_S_0221_45_20070321.105506_1_to_005_S_0221BASE.lta identity.nofile 005_S_0221BASE_to_005_S_0221_45_20070321.105506_1.lta

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

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

    Any one can help me?

    Thanks a lot!
    uang
    _______________________________________________
    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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer