Hello Freesurfer Developers,
I am having an issue with values of 0 in certain areas of the visual cortex in my beta.mgh files.
I am looking at the effect of age on grey/white matter signal intensity contrast (grey devided by white times 100) with gender as a regressor. I ran mri_glmfit with the DODS Matrix 0 0 0.5 0.5 CLASS 1 and 2 were males and females respectively and age in months was the variable.
When I look at the beta.mgh files in Freeview there are identical parts of surface which contains 0 even tho there are contrast values in those areas in the contrast surface maps. If I understood correctly the 2 first beta files should be the average contrast for males and females at offset? and the 3rd and 4th should be the slope? So at least the first two files should not contain 0 other than in the medial wall.
Any idea what I might be doing wrong?
Thank you in advance! Cheers, Linn
Hi Linn can you show us a picture of the medial inflated surface with the overlay? The occipital horn of the ventricle is quite difficult to label and sometimes erroneously extends into the anterior calcarine. If this is tthe location of your 0s you should correct the aseg and rerun with -make all to get the ?h.cortex.label and the surfaces right
cheers Bruce
On Thu, 27 Oct 2016, l.c.b.norbom@psykologi.uio.no wrote:
Hello Freesurfer Developers,
I am having an issue with values of 0 in certain areas of the visual cortex in my beta.mgh files.
I am looking at the effect of age on grey/white matter signal intensity contrast (grey devided by white times 100) with gender as a regressor. I ran mri_glmfit with the DODS Matrix 0 0 0.5 0.5 CLASS 1 and 2 were males and females respectively and age in months was the variable.
When I look at the beta.mgh files in Freeview there are identical parts of surface which contains 0 even tho there are contrast values in those areas in the contrast surface maps. If I understood correctly the 2 first beta files should be the average contrast for males and females at offset? and the 3rd and 4th should be the slope? So at least the first two files should not contain 0 other than in the medial wall.
Any idea what I might be doing wrong?
Thank you in advance! Cheers, Linn _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Yes, if even one subject has a 0 at a vertex, then that vertex will be excluded from analysis
On 10/27/2016 10:34 AM, Bruce Fischl wrote:
Hi Linn can you show us a picture of the medial inflated surface with the overlay? The occipital horn of the ventricle is quite difficult to label and sometimes erroneously extends into the anterior calcarine. If this is tthe location of your 0s you should correct the aseg and rerun with -make all to get the ?h.cortex.label and the surfaces right
cheers Bruce
On Thu, 27 Oct 2016, l.c.b.norbom@psykologi.uio.no wrote:
Hello Freesurfer Developers,
I am having an issue with values of 0 in certain areas of the visual cortex in my beta.mgh files.
I am looking at the effect of age on grey/white matter signal intensity contrast (grey devided by white times 100) with gender as a regressor. I ran mri_glmfit with the DODS Matrix 0 0 0.5 0.5 CLASS 1 and 2 were males and females respectively and age in months was the variable.
When I look at the beta.mgh files in Freeview there are identical parts of surface which contains 0 even tho there are contrast values in those areas in the contrast surface maps. If I understood correctly the 2 first beta files should be the average contrast for males and females at offset? and the 3rd and 4th should be the slope? So at least the first two files should not contain 0 other than in the medial wall.
Any idea what I might be doing wrong?
Thank you in advance! Cheers, Linn _______________________________________________ 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
On 2016-10-27 17:26, Douglas N Greve wrote:
Yes, if even one subject has a 0 at a vertex, then that vertex will be excluded from analysis
On 10/27/2016 10:34 AM, Bruce Fischl wrote:
Hi Linn can you show us a picture of the medial inflated surface with the overlay? The occipital horn of the ventricle is quite difficult to label and sometimes erroneously extends into the anterior calcarine. If this is tthe location of your 0s you should correct the aseg and rerun with -make all to get the ?h.cortex.label and the surfaces right
cheers Bruce
On Thu, 27 Oct 2016, l.c.b.norbom@psykologi.uio.no wrote:
Hello Freesurfer Developers,
I am having an issue with values of 0 in certain areas of the visual cortex in my beta.mgh files.
I am looking at the effect of age on grey/white matter signal intensity contrast (grey devided by white times 100) with gender as a regressor. I ran mri_glmfit with the DODS Matrix 0 0 0.5 0.5 CLASS 1 and 2 were males and females respectively and age in months was the variable.
When I look at the beta.mgh files in Freeview there are identical parts of surface which contains 0 even tho there are contrast values in those areas in the contrast surface maps. If I understood correctly the 2 first beta files should be the average contrast for males and females at offset? and the 3rd and 4th should be the slope? So at least the first two files should not contain 0 other than in the medial wall.
Any idea what I might be doing wrong?
Thank you in advance! Cheers, Linn _______________________________________________ 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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
Thank you so much for the reply. Yes I do se now, that single subjects which have certain vertexes with a value of 0 thus excludes that vertex for analyses for all subjects. Is there a flag to exclude just the vertex of the individuals with 0 and keep the vertex for the rest of the subjects?
If not I Guess a possibility is the "--no-prune" flag.
Cheers,
If you use the --no-prune flag, then it will consider all subjects at a vertex regardless of whether it is 0 or not. But is this really what you want to do?
Thank you so much for the reply. Yes I do se now, that single
subjects which have certain vertexes with a value of 0 thus excludes that vertex for analyses for all subjects. Is there a flag to exclude just the >>vertex of the individuals with 0 and keep the vertex for the rest of the subjects?
If not I Guess a possibility is the "--no-prune" flag.
On 10/31/16 8:50 AM, l.c.b.norbom@psykologi.uio.no wrote:
On 2016-10-27 17:26, Douglas N Greve wrote:
Yes, if even one subject has a 0 at a vertex, then that vertex will be excluded from analysis
On 10/27/2016 10:34 AM, Bruce Fischl wrote:
Hi Linn can you show us a picture of the medial inflated surface with the overlay? The occipital horn of the ventricle is quite difficult to label and sometimes erroneously extends into the anterior calcarine. If this is tthe location of your 0s you should correct the aseg and rerun with -make all to get the ?h.cortex.label and the surfaces right
cheers Bruce
On Thu, 27 Oct 2016, l.c.b.norbom@psykologi.uio.no wrote:
Hello Freesurfer Developers,
I am having an issue with values of 0 in certain areas of the visual cortex in my beta.mgh files.
I am looking at the effect of age on grey/white matter signal intensity contrast (grey devided by white times 100) with gender as a regressor. I ran mri_glmfit with the DODS Matrix 0 0 0.5 0.5 CLASS 1 and 2 were males and females respectively and age in months was the variable.
When I look at the beta.mgh files in Freeview there are identical parts of surface which contains 0 even tho there are contrast values in those areas in the contrast surface maps. If I understood correctly the 2 first beta files should be the average contrast for males and females at offset? and the 3rd and 4th should be the slope? So at least the first two files should not contain 0 other than in the medial wall.
Any idea what I might be doing wrong?
Thank you in advance! Cheers, Linn _______________________________________________ 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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
Thank you so much for the reply. Yes I do se now, that single subjects which have certain vertexes with a value of 0 thus excludes that vertex for analyses for all subjects. Is there a flag to exclude just the vertex of the individuals with 0 and keep the vertex for the rest of the subjects?
If not I Guess a possibility is the "--no-prune" flag.
Cheers,
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas Greve -
Douglas N Greve
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l.c.b.norbom＠psykologi.uio.no