Hi Bruce,

Thanks, this makes sense. I somehow assumed 1 defect wouldn't be bad but failed to notice how large the defect is.

I was using the "-washu_mprage" option as it is for the HCP data and the gm looked quite dark to me. I will try to run FS without that option.

Best,

Martin

On 11/07/13 11:17, Bruce Fischl wrote:

Hi Martin

see my response to a similar question just a minute or two ago. This is the same issue (a defect that is too big)

cheers Bruce On Thu, 7 Nov 2013, Martin Luessi wrote:

...

Hi,

I'm running recon-all on a subject from the human connectome project, and for some reason "mris_fix_topology" seems to be hanging, or at least it has been using 100% of a CPU for more than 24h with no new output. Is this normal or is there a way to fix this problem?

Best,

Martin

PS: I'm using FS 5.3

... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 28 iterations marking ambiguous vertices... 127679 ambiguous faces found in tessellation segmenting defects... 1 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 1 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/fusion/mluessi/hcp_data/subjects/100307/surf/lh.qsphere.nofix...

reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -10.9679 (-5.4839) -vertex loglikelihood: -10.8878 (-5.4439) -normal dot loglikelihood: -3.6700 (-3.6700) -quad curv loglikelihood: -8.7258 (-4.3629) Total Loglikelihood : -34.2514

CORRECTING DEFECT 0 (vertices=65102, convex hull=346) _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

yes, it is quite old and applies to a set of mprage parameters that result in *very* dark gray matter (the gray is actually closer to CSF than white matter in that sequence).

Thanks for pointing this out Mike Bruce

On Thu, 7 Nov 2013, Harms, Michael wrote:

We are not using the -washu_mprage option in the HCP pipelines. My understanding is that flag dates way back to when WashU was running a "non-standard" MPRAGE.

cheers, -MH

-- Michael Harms, Ph.D.

---

Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mharms@wustl.edu

On 11/7/13 10:28 AM, "Martin Luessi" mluessi@nmr.mgh.harvard.edu wrote:

...

Hi Bruce,

Thanks, this makes sense. I somehow assumed 1 defect wouldn't be bad but failed to notice how large the defect is.

I was using the "-washu_mprage" option as it is for the HCP data and the gm looked quite dark to me. I will try to run FS without that option.

Best,

Martin

On 11/07/13 11:17, Bruce Fischl wrote:

...

Hi Martin

see my response to a similar question just a minute or two ago. This is the same issue (a defect that is too big)

cheers Bruce On Thu, 7 Nov 2013, Martin Luessi wrote:

...

Hi,

I'm running recon-all on a subject from the human connectome project, and for some reason "mris_fix_topology" seems to be hanging, or at least it has been using 100% of a CPU for more than 24h with no new output. Is this normal or is there a way to fix this problem?

Best,

Martin

PS: I'm using FS 5.3

... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 28 iterations marking ambiguous vertices... 127679 ambiguous faces found in tessellation segmenting defects... 1 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 1 defects to be corrected 0 vertices coincident reading input surface

/autofs/cluster/fusion/mluessi/hcp_data/subjects/100307/surf/lh.qsphere. nofix...

reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -10.9679 (-5.4839) -vertex loglikelihood: -10.8878 (-5.4439) -normal dot loglikelihood: -3.6700 (-3.6700) -quad curv loglikelihood: -8.7258 (-4.3629) Total Loglikelihood : -34.2514

CORRECTING DEFECT 0 (vertices=65102, convex hull=346) _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Martin Luessi, Ph.D.

Research Fellow

Department of Radiology Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School 149 13th Street Charlestown, MA 02129

Fax: +1 617 726-7422 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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