Hi Bruce & surfers,

That's what I thought initially, but then I did edit the wm.mgz to remove topological defects, and re-ran the reconstruction from the 'fill' step, and this problem remains. I can't find a nearby defect in the wm.mgz volume to edit, but maybe there is something that isn't obvious to me.

I put up coronal, axial, and sagittal views of the problem area & neighborhood up at:

http://nmr.mgh.harvard.edu/~kdevaney/monkrecon/coronal_wm_defect.tif http://nmr.mgh.harvard.edu/~kdevaney/monkrecon/horizontal_wm_defect.tif http://nmr.mgh.harvard.edu/~kdevaney/monkrecon/sagittal_wm_defect.tif

Maybe there is a defect around this area which I'm not seeing? Otherwise, is there something else that I can do? Also, let me know if you'd like to check out the data, and I can put it somewhere accessible.

Thanks! Katie

Bruce Fischl wrote:

Hi Katie,

looks like an incorrectly fixed topological defect. You need to edit the wm.mgz to remove the defect and rerun autorecon2-wm

cheers, Bruce On Wed, 22 Apr 2009, Kathryn Devaney wrote:

...

Hello freesurfers,

I am running a reconstruction of a macaque in stabe4, and I am having a problem with the smooth white matter surface not following the wm boundary in the wm.mgz volume (please see attached for examples in the wm and T1 volumes).

The non-wm area included in the surface was never part of the wm volume, but I edited the other defects in wm.mgz and re-ran fill, tessellate, smooth1, inflate1, qsphere, fix, finalsurfs, smooth2, amd inflate2. Unsurprisingly, this problem persisted.

Is there anything that I can do to fix this?

Thanks! Katie

Hi Bruce,

Thanks! The lh.orig.nofix surface follows the white matter perfectly, but the lh.orig surface does not. So I suspect that the topology fixing step is creating this problem.

However, when I load lh.defect_labels this area is not marked as a defect, nor are there any major defects labeled nearby (see http://nmr.mgh.harvard.edu/~kdevaney/monkrecon/lh_wm_defect.tif for image). Does this mean that the topology fixing is not editing this area?

If it is the topology fixing, are there parameters of mris_fix_topology, mris_euler_number or mris_remove_intersection that I can alter in order to fix this problem, without wreaking havoc in other areas? Or any other suggestions would be much appreciated!

Best, Katie

Bruce Fischl wrote:

Hi Katie,

try looking at the lh.orig.nofix and lh.inflated.nofix surfaces to see if you can see the defect.

cheers, Bruce On Thu, 23 Apr 2009, Kathryn Devaney wrote:

...

Hi Bruce & surfers,

That's what I thought initially, but then I did edit the wm.mgz to remove topological defects, and re-ran the reconstruction from the 'fill' step, and this problem remains. I can't find a nearby defect in the wm.mgz volume to edit, but maybe there is something that isn't obvious to me.

I put up coronal, axial, and sagittal views of the problem area & neighborhood up at:

http://nmr.mgh.harvard.edu/~kdevaney/monkrecon/coronal_wm_defect.tif http://nmr.mgh.harvard.edu/~kdevaney/monkrecon/horizontal_wm_defect.tif http://nmr.mgh.harvard.edu/~kdevaney/monkrecon/sagittal_wm_defect.tif

Maybe there is a defect around this area which I'm not seeing? Otherwise, is there something else that I can do? Also, let me know if you'd like to check out the data, and I can put it somewhere accessible.

Thanks! Katie

Bruce Fischl wrote:

...

Hi Katie,

looks like an incorrectly fixed topological defect. You need to edit the wm.mgz to remove the defect and rerun autorecon2-wm

cheers, Bruce On Wed, 22 Apr 2009, Kathryn Devaney wrote:

...

Hello freesurfers,

I am running a reconstruction of a macaque in stabe4, and I am having a problem with the smooth white matter surface not following the wm boundary in the wm.mgz volume (please see attached for examples in the wm and T1 volumes).

The non-wm area included in the surface was never part of the wm volume, but I edited the other defects in wm.mgz and re-ran fill, tessellate, smooth1, inflate1, qsphere, fix, finalsurfs, smooth2, amd inflate2. Unsurprisingly, this problem persisted.

Is there anything that I can do to fix this?

Thanks! Katie

Sorry,

I meant to answer another email...

Roberto

Hello,

It is working fine for me

regards

Roberto

On Vie, 24 de Abril de 2009, 10:38 am, Kathryn Devaney dijo:

...

Hi Bruce,

Thanks! The lh.orig.nofix surface follows the white matter perfectly, but the lh.orig surface does not. So I suspect that the topology fixing step is creating this problem.

However, when I load lh.defect_labels this area is not marked as a defect, nor are there any major defects labeled nearby (see http://nmr.mgh.harvard.edu/~kdevaney/monkrecon/lh_wm_defect.tif for image). Does this mean that the topology fixing is not editing this area?

If it is the topology fixing, are there parameters of mris_fix_topology, mris_euler_number or mris_remove_intersection that I can alter in order to fix this problem, without wreaking havoc in other areas? Or any other suggestions would be much appreciated!

Best, Katie

Bruce Fischl wrote:

...

Hi Katie,

try looking at the lh.orig.nofix and lh.inflated.nofix surfaces to see if you can see the defect.

cheers, Bruce On Thu, 23 Apr 2009, Kathryn Devaney wrote:

...

Hi Bruce & surfers,

That's what I thought initially, but then I did edit the wm.mgz to remove topological defects, and re-ran the reconstruction from the 'fill' step, and this problem remains. I can't find a nearby defect in the wm.mgz volume to edit, but maybe there is something that isn't obvious to me.

I put up coronal, axial, and sagittal views of the problem area & neighborhood up at:

http://nmr.mgh.harvard.edu/~kdevaney/monkrecon/coronal_wm_defect.tif http://nmr.mgh.harvard.edu/~kdevaney/monkrecon/horizontal_wm_defect.tif http://nmr.mgh.harvard.edu/~kdevaney/monkrecon/sagittal_wm_defect.tif

Maybe there is a defect around this area which I'm not seeing? Otherwise, is there something else that I can do? Also, let me know if you'd like to check out the data, and I can put it somewhere accessible.

Thanks! Katie

Bruce Fischl wrote:

...

Hi Katie,

looks like an incorrectly fixed topological defect. You need to edit the wm.mgz to remove the defect and rerun autorecon2-wm

cheers, Bruce On Wed, 22 Apr 2009, Kathryn Devaney wrote:

...

Hello freesurfers,

I am running a reconstruction of a macaque in stabe4, and I am having a problem with the smooth white matter surface not following the wm boundary in the wm.mgz volume (please see attached for examples in the wm and T1 volumes).

The non-wm area included in the surface was never part of the wm volume, but I edited the other defects in wm.mgz and re-ran fill, tessellate, smooth1, inflate1, qsphere, fix, finalsurfs, smooth2, amd inflate2. Unsurprisingly, this problem persisted.

Is there anything that I can do to fix this?

Thanks! Katie

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-- Roberto Roiz Santiáñez Laboratorio de Neuroimagen en Psiquiatría Hospital Universitario Marqués de Valdecilla Santander, España Tel: +34 942202520 Ext: 73958 rroiz@humv.es _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer