Hi there, I've run autorecon2 on a subject who has significant unilateral atrophy in the anterior temporal region. In the last few slices anteriorly, the pial surface does not include what is clearly atrophied cortical tissue without underlying white matter. What is the method to correct for this? Looking at previous queries, all of them refer to spots where one can manipulate the segmentation by adding control points in the neighbouring white matter, which is not present in this instance. Any suggestion appreciated. Olivier
~~~~~~~~~~~~~~~~~~~~~ Olivier Piguet Ph.D. NHMRC Fellow (Clinical Career Development Award) Conjoint Senior Lecturer UNSW Prince of Wales Medical Research Institute Barker St Randwick NSW 2031 Australia
Voice: +61 2 9399 1113 Fax: +61 2 9399 1047 E-mail: o.piguet@powmri.edu.au
<pastedGraphic.tiff> http://www.ftdrg.org/
Hi there, I haven't received a reply to my question below.
Just to clarify, I ran autorecon1 and autorecon2 on this subject. When examining the surfaces in tkmedit, the left temporal pole is not included in the pial surface. Is there a way to force freesurfer to recognise this as valid brain tissue, bearing in mind that there is no visible white matter underneath (and therefore the option of adding control points is not possible).
Thanks for any suggestion to resolve this problem.
Olivier On 13/05/2009, at 12:57, Olivier Piguet wrote:
Hi there, I've run autorecon2 on a subject who has significant unilateral atrophy in the anterior temporal region. In the last few slices anteriorly, the pial surface does not include what is clearly atrophied cortical tissue without underlying white matter. What is the method to correct for this? Looking at previous queries, all of them refer to spots where one can manipulate the segmentation by adding control points in the neighbouring white matter, which is not present in this instance. Any suggestion appreciated. Olivier
Olivier Piguet Ph.D. NHMRC Fellow (Clinical Career Development Award) Conjoint Senior Lecturer UNSW Prince of Wales Medical Research Institute Barker St Randwick NSW 2031 Australia Voice: +61 2 9399 1113 Fax: +61 2 9399 1047 E-mail: o.piguet@powmri.edu.au <pastedGraphic.tiff> http://www.ftdrg.org/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Oliver,
how far away is the nearest white matter?
Bruce On Fri, 15 May 2009, Olivier Piguet wrote:
Hi there, I haven't received a reply to my question below.
Just to clarify, I ran autorecon1 and autorecon2 on this subject. When examining the surfaces in tkmedit, the left temporal pole is not included in the pial surface. Is there a way to force freesurfer to recognise this as valid brain tissue, bearing in mind that there is no visible white matter underneath (and therefore the option of adding control points is not possible).
Thanks for any suggestion to resolve this problem.
Olivier On 13/05/2009, at 12:57, Olivier Piguet wrote:
Hi there, I've run autorecon2 on a subject who has significant unilateral atrophy in the anterior temporal region. In the last few slices anteriorly, the pial surface does not include what is clearly atrophied cortical tissue without underlying white matter. What is the method to correct for this? Looking at previous queries, all of them refer to spots where one can manipulate the segmentation by adding control points in the neighbouring white matter, which is not present in this instance. Any suggestion appreciated. Olivier
Olivier Piguet Ph.D. NHMRC Fellow (Clinical Career Development Award) Conjoint Senior Lecturer UNSW Prince of Wales Medical Research Institute Barker St Randwick NSW 2031 Australia Voice: +61 2 9399 1113 Fax: +61 2 9399 1047 E-mail: o.piguet@powmri.edu.au <pastedGraphic.tiff> http://www.ftdrg.org/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce, In the coronal plane, slice 152 is the last slice where white matter is clearly visible. Then, slices 153-158, only grey matter is recognised but not all of it, and slices 159-164, grey matter is not recognised at all. I added control points on slice 151-153 in the hope that it would help but no luck. Olivier
On 15/05/2009, at 8:39, Bruce Fischl wrote:
Hi Oliver,
how far away is the nearest white matter?
Bruce On Fri, 15 May 2009, Olivier Piguet wrote:
Hi there, I haven't received a reply to my question below.
Just to clarify, I ran autorecon1 and autorecon2 on this subject. When examining the surfaces in tkmedit, the left temporal pole is not included in the pial surface. Is there a way to force freesurfer to recognise this as valid brain tissue, bearing in mind that there is no visible white matter underneath (and therefore the option of adding control points is not possible).
Thanks for any suggestion to resolve this problem.
Olivier On 13/05/2009, at 12:57, Olivier Piguet wrote:
Hi there, I've run autorecon2 on a subject who has significant unilateral atrophy in the anterior temporal region. In the last few slices anteriorly, the pial surface does not include what is clearly atrophied cortical tissue without underlying white matter. What is the method to correct for this? Looking at previous queries, all of them refer to spots where one can manipulate the segmentation by adding control points in the neighbouring white matter, which is not present in this instance. Any suggestion appreciated. Olivier
Olivier Piguet Ph.D. NHMRC Fellow (Clinical Career Development Award) Conjoint Senior Lecturer UNSW Prince of Wales Medical Research Institute Barker St Randwick NSW 2031 Australia Voice: +61 2 9399 1113 Fax: +61 2 9399 1047 E-mail: o.piguet@powmri.edu.au <pastedGraphic.tiff> http://www.ftdrg.org/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
so there's 10mm or so of gray matter with no underlying wm? I didn't think that was ever the case. What pathology is this in? And you're sure it's cortex, not amygdala? Jean: any thoughts?
On Fri, 15 May 2009, Olivier Piguet wrote:
Hi Bruce, In the coronal plane, slice 152 is the last slice where white matter is clearly visible. Then, slices 153-158, only grey matter is recognised but not all of it, and slices 159-164, grey matter is not recognised at all. I added control points on slice 151-153 in the hope that it would help but no luck. Olivier
On 15/05/2009, at 8:39, Bruce Fischl wrote:
Hi Oliver,
how far away is the nearest white matter?
Bruce On Fri, 15 May 2009, Olivier Piguet wrote:
Hi there, I haven't received a reply to my question below.
Just to clarify, I ran autorecon1 and autorecon2 on this subject. When examining the surfaces in tkmedit, the left temporal pole is not included in the pial surface. Is there a way to force freesurfer to recognise this as valid brain tissue, bearing in mind that there is no visible white matter underneath (and therefore the option of adding control points is not possible).
Thanks for any suggestion to resolve this problem.
Olivier On 13/05/2009, at 12:57, Olivier Piguet wrote:
Hi there, I've run autorecon2 on a subject who has significant unilateral atrophy in the anterior temporal region. In the last few slices anteriorly, the pial surface does not include what is clearly atrophied cortical tissue without underlying white matter. What is the method to correct for this? Looking at previous queries, all of them refer to spots where one can manipulate the segmentation by adding control points in the neighbouring white matter, which is not present in this instance. Any suggestion appreciated. Olivier
Olivier Piguet Ph.D. NHMRC Fellow (Clinical Career Development Award) Conjoint Senior Lecturer UNSW Prince of Wales Medical Research Institute Barker St Randwick NSW 2031 Australia Voice: +61 2 9399 1113 Fax: +61 2 9399 1047 E-mail: o.piguet@powmri.edu.au <pastedGraphic.tiff> http://www.ftdrg.org/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
That is correct. This is case of semantic dementia where left anterior temporal region is markedly atrophic. Olivier
On 15/05/2009, at 9:15, Bruce Fischl wrote:
so there's 10mm or so of gray matter with no underlying wm? I didn't think that was ever the case. What pathology is this in? And you're sure it's cortex, not amygdala? Jean: any thoughts?
On Fri, 15 May 2009, Olivier Piguet wrote:
Hi Bruce, In the coronal plane, slice 152 is the last slice where white matter is clearly visible. Then, slices 153-158, only grey matter is recognised but not all of it, and slices 159-164, grey matter is not recognised at all. I added control points on slice 151-153 in the hope that it would help but no luck. Olivier
On 15/05/2009, at 8:39, Bruce Fischl wrote:
Hi Oliver, how far away is the nearest white matter? Bruce On Fri, 15 May 2009, Olivier Piguet wrote:
Hi there, I haven't received a reply to my question below. Just to clarify, I ran autorecon1 and autorecon2 on this subject. When examining the surfaces in tkmedit, the left temporal pole is not included in the pial surface. Is there a way to force freesurfer to recognise this as valid brain tissue, bearing in mind that there is no visible white matter underneath (and therefore the option of adding control points is not possible). Thanks for any suggestion to resolve this problem. Olivier On 13/05/2009, at 12:57, Olivier Piguet wrote:
Hi there, I've run autorecon2 on a subject who has significant unilateral atrophy in the anterior temporal region. In the last few slices anteriorly, the pial surface does not include what is clearly atrophied cortical tissue without underlying white matter. What is the method to correct for this? Looking at previous queries, all of them refer to spots where one can manipulate the segmentation by adding control points in the neighbouring white matter, which is not present in this instance. Any suggestion appreciated. Olivier
Olivier Piguet Ph.D. NHMRC Fellow (Clinical Career Development Award) Conjoint Senior Lecturer UNSW Prince of Wales Medical Research Institute Barker St Randwick NSW 2031 Australia Voice: +61 2 9399 1113 Fax: +61 2 9399 1047 E-mail: o.piguet@powmri.edu.au <pastedGraphic.tiff> http://www.ftdrg.org/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
As an aside, in a Alzheimer/ elderly cohort of ~250, we had 12 subjects that we had to exclude for what sounds like a very similar reason -- we just couldn't get the pial surface in the anterior temporal lobe to properly encapsulate the gray matter.
-Mike H.
On Fri, 2009-05-15 at 12:24 +1000, Olivier Piguet wrote:
That is correct. This is case of semantic dementia where left anterior temporal region is markedly atrophic. Olivier
On 15/05/2009, at 9:15, Bruce Fischl wrote:
so there's 10mm or so of gray matter with no underlying wm? I didn't think that was ever the case. What pathology is this in? And you're sure it's cortex, not amygdala? Jean: any thoughts?
On Fri, 15 May 2009, Olivier Piguet wrote:
Hi Bruce, In the coronal plane, slice 152 is the last slice where white matter is clearly visible. Then, slices 153-158, only grey matter is recognised but not all of it, and slices 159-164, grey matter is not recognised at all. I added control points on slice 151-153 in the hope that it would help but no luck. Olivier
On 15/05/2009, at 8:39, Bruce Fischl wrote:
Hi Oliver, how far away is the nearest white matter? Bruce On Fri, 15 May 2009, Olivier Piguet wrote:
Hi there, I haven't received a reply to my question below. Just to clarify, I ran autorecon1 and autorecon2 on this subject. When examining the surfaces in tkmedit, the left temporal pole is not included in the pial surface. Is there a way to force freesurfer to recognise this as valid brain tissue, bearing in mind that there is no visible white matter underneath (and therefore the option of adding control points is not possible). Thanks for any suggestion to resolve this problem. Olivier On 13/05/2009, at 12:57, Olivier Piguet wrote:
Hi there, I've run autorecon2 on a subject who has significant unilateral atrophy in the anterior temporal region. In the last few slices anteriorly, the pial surface does not include what is clearly atrophied cortical tissue without underlying white matter. What is the method to correct for this? Looking at previous queries, all of them refer to spots where one can manipulate the segmentation by adding control points in the neighbouring white matter, which is not present in this instance. Any suggestion appreciated. Olivier
Olivier Piguet Ph.D. NHMRC Fellow (Clinical Career Development Award) Conjoint Senior Lecturer UNSW Prince of Wales Medical Research Institute Barker St Randwick NSW 2031 Australia Voice: +61 2 9399 1113 Fax: +61 2 9399 1047 E-mail: o.piguet@powmri.edu.au <pastedGraphic.tiff> http://www.ftdrg.org/ _______________________________________________ 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
thanks Mike. Was it the same situation, where there is no nearby white matter? I guess I don't really understand the anatomy. Is there really a place where you have 10mm of gray matter with no underlying white matter? Or is it unmeylinated white matter that we just can't see?
On Fri, 15 May 2009, Michael Harms wrote:
As an aside, in a Alzheimer/ elderly cohort of ~250, we had 12 subjects that we had to exclude for what sounds like a very similar reason -- we just couldn't get the pial surface in the anterior temporal lobe to properly encapsulate the gray matter.
-Mike H.
On Fri, 2009-05-15 at 12:24 +1000, Olivier Piguet wrote:
That is correct. This is case of semantic dementia where left anterior temporal region is markedly atrophic. Olivier
On 15/05/2009, at 9:15, Bruce Fischl wrote:
so there's 10mm or so of gray matter with no underlying wm? I didn't think that was ever the case. What pathology is this in? And you're sure it's cortex, not amygdala? Jean: any thoughts?
On Fri, 15 May 2009, Olivier Piguet wrote:
Hi Bruce, In the coronal plane, slice 152 is the last slice where white matter is clearly visible. Then, slices 153-158, only grey matter is recognised but not all of it, and slices 159-164, grey matter is not recognised at all. I added control points on slice 151-153 in the hope that it would help but no luck. Olivier
On 15/05/2009, at 8:39, Bruce Fischl wrote:
Hi Oliver, how far away is the nearest white matter? Bruce On Fri, 15 May 2009, Olivier Piguet wrote:
Hi there, I haven't received a reply to my question below. Just to clarify, I ran autorecon1 and autorecon2 on this subject. When examining the surfaces in tkmedit, the left temporal pole is not included in the pial surface. Is there a way to force freesurfer to recognise this as valid brain tissue, bearing in mind that there is no visible white matter underneath (and therefore the option of adding control points is not possible). Thanks for any suggestion to resolve this problem. Olivier On 13/05/2009, at 12:57, Olivier Piguet wrote: > Hi there, > I've run autorecon2 on a subject who has significant unilateral > atrophy in the anterior temporal region. In the last few slices > anteriorly, the pial surface does not include what is clearly > atrophied cortical tissue without underlying white matter. What > is the method to correct for this? Looking at previous queries, > all of them refer to spots where one can manipulate the > segmentation by adding control points in the neighbouring white > matter, which is not present in this instance. > Any suggestion appreciated. > Olivier > ~~~~~~~~~~~~~~~~~~~~~ > Olivier Piguet Ph.D. > NHMRC Fellow (Clinical Career Development Award) > Conjoint Senior Lecturer UNSW > Prince of Wales Medical Research Institute > Barker St > Randwick NSW 2031 > Australia > Voice: +61 2 9399 1113 > Fax: +61 2 9399 1047 > E-mail: o.piguet@powmri.edu.au > <pastedGraphic.tiff> > http://www.ftdrg.org/ > _______________________________________________ > 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
Thanks for the info. In severe cases of semantic dementia, you will see overall atrophy where the anterior temporal pole becomes almost non existent (combination of neuronal loss and white matter loss), probably also contributing to reduced white/grey differentiation.
Is there a way to manually trace the pial surface on these slices or not? Because I have a large group of patients with semantic dementia that I would like to process, I am likely to encounter this problem again in the future.
Thanks again for any suggestions and comments Olivier
On 16/05/2009, at 0:20, Bruce Fischl wrote:
thanks Mike. Was it the same situation, where there is no nearby white matter? I guess I don't really understand the anatomy. Is there really a place where you have 10mm of gray matter with no underlying white matter? Or is it unmeylinated white matter that we just can't see?
On Fri, 15 May 2009, Michael Harms wrote:
As an aside, in a Alzheimer/ elderly cohort of ~250, we had 12 subjects that we had to exclude for what sounds like a very similar reason -- we just couldn't get the pial surface in the anterior temporal lobe to properly encapsulate the gray matter.
-Mike H.
On Fri, 2009-05-15 at 12:24 +1000, Olivier Piguet wrote:
That is correct. This is case of semantic dementia where left anterior temporal region is markedly atrophic. Olivier
On 15/05/2009, at 9:15, Bruce Fischl wrote:
so there's 10mm or so of gray matter with no underlying wm? I didn't think that was ever the case. What pathology is this in? And you're sure it's cortex, not amygdala? Jean: any thoughts?
On Fri, 15 May 2009, Olivier Piguet wrote:
Hi Bruce, In the coronal plane, slice 152 is the last slice where white matter is clearly visible. Then, slices 153-158, only grey matter is recognised but not all of it, and slices 159-164, grey matter is not recognised at all. I added control points on slice 151-153 in the hope that it would help but no luck. Olivier
On 15/05/2009, at 8:39, Bruce Fischl wrote:
Hi Oliver, how far away is the nearest white matter? Bruce On Fri, 15 May 2009, Olivier Piguet wrote: > Hi there, > I haven't received a reply to my question below. > Just to clarify, I ran autorecon1 and autorecon2 on this > subject. > When examining the surfaces in tkmedit, the left temporal pole > is > not included in the pial surface. Is there a way to force > freesurfer to recognise this as valid brain tissue, bearing in > mind that there is no visible white matter underneath (and > therefore the option of adding control points is not possible). > Thanks for any suggestion to resolve this problem. > Olivier > On 13/05/2009, at 12:57, Olivier Piguet wrote: >> Hi there, >> I've run autorecon2 on a subject who has significant unilateral >> atrophy in the anterior temporal region. In the last few slices >> anteriorly, the pial surface does not include what is clearly >> atrophied cortical tissue without underlying white matter. What >> is the method to correct for this? Looking at previous queries, >> all of them refer to spots where one can manipulate the >> segmentation by adding control points in the neighbouring white >> matter, which is not present in this instance. >> Any suggestion appreciated. >> Olivier >> ~~~~~~~~~~~~~~~~~~~~~ >> Olivier Piguet Ph.D. >> NHMRC Fellow (Clinical Career Development Award) >> Conjoint Senior Lecturer UNSW >> Prince of Wales Medical Research Institute >> Barker St >> Randwick NSW 2031 >> Australia >> Voice: +61 2 9399 1113 >> Fax: +61 2 9399 1047 >> E-mail: o.piguet@powmri.edu.au >> <pastedGraphic.tiff> >> http://www.ftdrg.org/ >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Oliver,
you might check with Mike Chee (ccd) who has some tools for editing of the mesh. Alternatively you could draw in some white matter (even if you can't see it) to get the pial surface a closer initialization.
cheers, Bruce On Sat, 16 May 2009, Olivier Piguet wrote:
Thanks for the info. In severe cases of semantic dementia, you will see overall atrophy where the anterior temporal pole becomes almost non existent (combination of neuronal loss and white matter loss), probably also contributing to reduced white/grey differentiation.
Is there a way to manually trace the pial surface on these slices or not? Because I have a large group of patients with semantic dementia that I would like to process, I am likely to encounter this problem again in the future.
Thanks again for any suggestions and comments Olivier
On 16/05/2009, at 0:20, Bruce Fischl wrote:
thanks Mike. Was it the same situation, where there is no nearby white matter? I guess I don't really understand the anatomy. Is there really a place where you have 10mm of gray matter with no underlying white matter? Or is it unmeylinated white matter that we just can't see?
On Fri, 15 May 2009, Michael Harms wrote:
As an aside, in a Alzheimer/ elderly cohort of ~250, we had 12 subjects that we had to exclude for what sounds like a very similar reason -- we just couldn't get the pial surface in the anterior temporal lobe to properly encapsulate the gray matter.
-Mike H.
On Fri, 2009-05-15 at 12:24 +1000, Olivier Piguet wrote:
That is correct. This is case of semantic dementia where left anterior temporal region is markedly atrophic. Olivier
On 15/05/2009, at 9:15, Bruce Fischl wrote:
so there's 10mm or so of gray matter with no underlying wm? I didn't think that was ever the case. What pathology is this in? And you're sure it's cortex, not amygdala? Jean: any thoughts?
On Fri, 15 May 2009, Olivier Piguet wrote:
Hi Bruce, In the coronal plane, slice 152 is the last slice where white matter is clearly visible. Then, slices 153-158, only grey matter is recognised but not all of it, and slices 159-164, grey matter is not recognised at all. I added control points on slice 151-153 in the hope that it would help but no luck. Olivier
On 15/05/2009, at 8:39, Bruce Fischl wrote:
> Hi Oliver, > how far away is the nearest white matter? > Bruce > On Fri, 15 May 2009, Olivier Piguet wrote: >> Hi there, >> I haven't received a reply to my question below. >> Just to clarify, I ran autorecon1 and autorecon2 on this subject. >> When examining the surfaces in tkmedit, the left temporal pole is >> not included in the pial surface. Is there a way to force >> freesurfer to recognise this as valid brain tissue, bearing in >> mind that there is no visible white matter underneath (and >> therefore the option of adding control points is not possible). >> Thanks for any suggestion to resolve this problem. >> Olivier >> On 13/05/2009, at 12:57, Olivier Piguet wrote: >>> Hi there, >>> I've run autorecon2 on a subject who has significant unilateral >>> atrophy in the anterior temporal region. In the last few slices >>> anteriorly, the pial surface does not include what is clearly >>> atrophied cortical tissue without underlying white matter. What >>> is the method to correct for this? Looking at previous queries, >>> all of them refer to spots where one can manipulate the >>> segmentation by adding control points in the neighbouring white >>> matter, which is not present in this instance. >>> Any suggestion appreciated. >>> Olivier >>> ~~~~~~~~~~~~~~~~~~~~~ >>> Olivier Piguet Ph.D. >>> NHMRC Fellow (Clinical Career Development Award) >>> Conjoint Senior Lecturer UNSW >>> Prince of Wales Medical Research Institute >>> Barker St >>> Randwick NSW 2031 >>> Australia >>> Voice: +61 2 9399 1113 >>> Fax: +61 2 9399 1047 >>> E-mail: o.piguet@powmri.edu.au >>> <pastedGraphic.tiff> >>> http://www.ftdrg.org/ >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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