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Dear Bruce， I have fdr correction for sig.mgh obtained by mri_glmfit, but the corrected graphs are all 0. Why is this, the instructions and the running results are as follows:
mri_fdr --fdr .05 --i lh2.gender_age.glmdir/group2/sig.mgh lh2.gender_age.glmdir/mask.mgh 2.mgh $Id: mri_fdr.c,v 1.2 2016/01/07 22:23:57 greve Exp $ cwd /usr/local/freesurfer/subjects cmdline mri_fdr --fdr .05 --i lh2.gender_age.glmdir/group2/sig.mgh lh2.gender_age.glmdir/mask.mgh 2.mgh sysname Linux hostname xiaorn machine x86_64 user xiaorn fdr 0.050000 ninputs 1 MRIfdr2vwth: np = 149953, nv = 163842 MRIfdr2vwth: vwth = 0.000003, log10(vwhth) = 5.583609
voxel-wise-threshold 5.5836093010
Writing to 2.mgh mri_fdr done
yours yujunjie
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Dear expert
I am trying to calculate LGI for a subject. Now with some of your suggestions it runs, but after one hour and half it gives me this errors
remeasuring lGI value for vertex iV = 29501. It may take a few minutes. WARNING -- Problem for vertex iV = 29501, lGI value is aberrantly high (lGI=42.4705)... ...lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface.
ERROR: compute_lgi did not create output file '/Applications/freesurfer/subjects/bianchi/surf/tmp-mris_compute_lgi-lh.pial/lh.pial_lgi.asc’!
It is a problem of my original file or someone had the same problems? Any suggestions Thanks
Lorenzo
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Dear expert I am trying to calculate LGI for a subject. Now with some of your suggestions it runs, but after one hour and half it gives me this errors remeasuring lGI value for vertex iV = 29501. It may take a few minutes.WARNING -- Problem for vertex iV = 29501, lGI value is aberrantly high (lGI=42.4705)......lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface. ERROR: compute_lgi did not create output file '/Applications/freesurfer/subjects/bianchi/surf/tmp-mris_compute_lgi-lh.pial/lh.pial_lgi.asc’! I think that is a problem of my file, someone knows a way to fix it? Thanks Lorenzo
Sorry, the lGI code is not being maintained anymore
On 12/11/18 4:00 AM, Lorenzo Ferri wrote:
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Dear expert
I am trying to calculate LGI for a subject. Now with some of your suggestions it runs, but after one hour and half it gives me this errors
remeasuring lGI value for vertex iV = 29501. It may take a few minutes. WARNING -- Problem for vertex iV = 29501, lGI value is aberrantly high (lGI=42.4705)... ...lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface.
ERROR: compute_lgi did not create output file '/Applications/freesurfer/subjects/bianchi/surf/tmp-mris_compute_lgi-lh.pial/lh.pial_lgi.asc’!
I think that is a problem of my file, someone knows a way to fix it?
Thanks
Lorenzo
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do you mean that nothing survived threshold? That happens sometimes.
On 12/10/18 8:03 AM, 1013364183 wrote:
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Dear Bruce， I have fdr correction for sig.mgh obtained by mri_glmfit, but the corrected graphs are all 0. Why is this, the instructions and the running results are as follows:
mri_fdr --fdr .05 --i lh2.gender_age.glmdir/group2/sig.mgh lh2.gender_age.glmdir/mask.mgh 2.mgh $Id: mri_fdr.c,v 1.2 2016/01/07 22:23:57 greve Exp $ cwd /usr/local/freesurfer/subjects cmdline mri_fdr --fdr .05 --i lh2.gender_age.glmdir/group2/sig.mgh lh2.gender_age.glmdir/mask.mgh 2.mgh sysname Linux hostname xiaorn machine x86_64 user xiaorn fdr 0.050000 ninputs 1 MRIfdr2vwth: np = 149953, nv = 163842 MRIfdr2vwth: vwth = 0.000003, log10(vwhth) = 5.583609
voxel-wise-threshold 5.5836093010
Writing to 2.mgh mri_fdr done
yours yujunjie
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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1013364183 -
Greve, Douglas N.,Ph.D. -
Lorenzo Ferri