Hi Angela
gyrification is the ratio of areas and hence dimensionless, so I would think it wouldn't be much affected by TIV.
cheers Bruce
On Sun, 21 Feb 2016, angela.favaro@unipd.it wrote:
In the case of a gyrification analysis, does correction for total brain volume make sense?
Angela
Inviato dal mio dispositivo Huawei
-------- Messaggio originale -------- Oggetto: Re: [Freesurfer] eTIV question Da: Bruce Fischl A: Freesurfer support list CC:
yes, it's a somewhat different and more conservative test. I guess you could check the talairach transforms of some of your subjects with eTIVs that don't make sense (or change the most over time) to try to see why this is happening. Or take Mike's suggestion and test a different (but probably still interesting) hypothesis On Sun, 21 Feb 2016, Angela Favaro wrote: > Hi, thank you > I think this would test something different: 'how much a brain area is > atrophic controlling for the average brain atrophy' and not 'how much > a brain area is atrophic controlling for the individual differences in > head size'. Doesn't it? > > Angela > > > "Harms, Michael" ha scritto: > >> Hi, >> Why not use a measurement of brain size rather than “eTIV”? >> >> 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 63110Email: mharms@wustl.edu >> >> >> >> >> On 2/21/16, 6:06 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of >> Angela Favaro" >> angela.favaro@unipd.it> wrote: >> >> there is a mistake in the graph, hippocampal volume is TIV2 >> I apologize for that! >> >> Angela Favaro ha scritto: >> >>> Hi Bruce, >>> please find attached the graph of the correlation between the two time >>> point. I did not find outliers or failures. However the discrepancy >>> between TIVs is particularly high in few cases. Obviously these data >>> are those before running longitudinal streaming >>> This is a sample of adolescents with low body weight (anorexia nervosa). >>> In my previous study (on young adults with low weight) I found no >>> correlation between TIV and body weight and high correlations between >>> fs estimated TIV and manually segmented TIV (r=0.94 in the whole >>> sample and r=0.93 in the underweight sample (n=38)). >>> Do you think that the young age can be a factor? or patients who are >>> more acutely underweight? >>> Thank you for any suggestion >>> >>> Angela >>> >>> >>> Bruce Fischl ha scritto: >>> >>>> Hi Angel >>>> >>>> the time1/time2 correlation of eTIV is pretty worrisome. Are you sure >>>> that there aren't outliers/failures in that set? >>>> >>>> Bruce >>>> >>>> >>>> On Sun, 14 Feb 2016, angela.favaro@unipd.it wrote: >>>> >>>>> Dear Freesurfer experts, >>>>> I have a question about eTIV (FS 5.3) which I use as a covariate where >>>>> appropriate. Is it in some way influenced by the presence of brain >>>>> atrophy? >>>>> I have a new sample of subjects in a longitudinal study: at time 1 they >>>>> have some atrophy (due to low body weight) that improves in time 2 (4 >>>>> months). I observed that eTIV-time1 is slightly correlated with weight >>>>> (r=0.3) whereas no correlation is present at time 2. The correlation >>>>> between eTIV-time1 and eTIV-time2 is somewhat lower than expected >>>>> (r=0.53) >>>>> and is lower than correlation between SegBrain_Vol_1 and SegBrain_Vol_2 >>>>> (0.65). >>>>> >>>>> Do you suggest in these cases to perform manual segmentation to obtain >>>>> TIV? or is there any other method (in freesurfer) to obtain an >>>>> estimate of >>>>> TIV not influenced by brain atrophy? What about using BrainMask_to_TIV? >>>>> >>>>> Thank you for any suggestion >>>>> >>>>> Angela >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>>> >>>> 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. >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> ________________________________ >> The materials in this message are private and may contain Protected >> Healthcare Information or other information of a sensitive nature. >> If you are not the intended recipient, be advised that any >> unauthorized use, disclosure, copying or the taking of any action in >> reliance on the contents of this information is strictly prohibited. >> If you have received this email in error, please immediately notify >> the sender via telephone or return mail. >> >> _______________________________________________ >> 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 > > > _______________________________________________ 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.
Hi Bruce, this is true, but I noticed that many papers used TIV as a covariate. In addition, in my samples (both pathological and healthy) there is a moderate positive correlation between gyrification and TIV (and brain volume). For the hemispheric overall gyrification index the correlation is 0.3-0.35 with TIV and 0.35-0.4 with total brain volume. I think that in pathological samples with possible brain atrophy, this is a way to control for a possible bias effect. Am I wrong?
Thank you Angela
Hi Angela
gyrification is the ratio of areas and hence dimensionless, so I would think it wouldn't be much affected by TIV.
cheers Bruce
On Sun, 21 Feb 2016, angela.favaro@unipd.it wrote:
In the case of a gyrification analysis, does correction for total brain volume make sense?
Angela
Inviato dal mio dispositivo Huawei
-------- Messaggio originale -------- Oggetto: Re: [Freesurfer] eTIV question Da: Bruce Fischl A: Freesurfer support list CC:
yes, it's a somewhat different and more conservative test. I guess you could check the talairach transforms of some of your subjects with eTIVs that don't make sense (or change the most over time) to try to see why this is happening. Or take Mike's suggestion and test a different (but probably still interesting) hypothesis On Sun, 21 Feb 2016, Angela Favaro wrote: > Hi, thank you > I think this would test something different: 'how much a brain area is > atrophic controlling for the average brain atrophy' and not 'how much > a brain area is atrophic controlling for the individual differences in > head size'. Doesn't it? > > Angela > > > "Harms, Michael" ha scritto: > >> Hi, >> Why not use a measurement of brain size rather than “eTIV”? >> >> 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 63110Email: mharms@wustl.edu >> >> >> >> >> On 2/21/16, 6:06 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of >> Angela Favaro" >> angela.favaro@unipd.it> wrote: >> >> there is a mistake in the graph, hippocampal volume is TIV2 >> I apologize for that! >> >> Angela Favaro ha scritto: >> >>> Hi Bruce, >>> please find attached the graph of the correlation between the two time >>> point. I did not find outliers or failures. However the discrepancy >>> between TIVs is particularly high in few cases. Obviously these data >>> are those before running longitudinal streaming >>> This is a sample of adolescents with low body weight (anorexia nervosa). >>> In my previous study (on young adults with low weight) I found no >>> correlation between TIV and body weight and high correlations between >>> fs estimated TIV and manually segmented TIV (r=0.94 in the whole >>> sample and r=0.93 in the underweight sample (n=38)). >>> Do you think that the young age can be a factor? or patients who are >>> more acutely underweight? >>> Thank you for any suggestion >>> >>> Angela >>> >>> >>> Bruce Fischl ha scritto: >>> >>>> Hi Angel >>>> >>>> the time1/time2 correlation of eTIV is pretty worrisome. Are you sure >>>> that there aren't outliers/failures in that set? >>>> >>>> Bruce >>>> >>>> >>>> On Sun, 14 Feb 2016, angela.favaro@unipd.it wrote: >>>> >>>>> Dear Freesurfer experts, >>>>> I have a question about eTIV (FS 5.3) which I use as a covariate where >>>>> appropriate. Is it in some way influenced by the presence of brain >>>>> atrophy? >>>>> I have a new sample of subjects in a longitudinal study: at time 1 they >>>>> have some atrophy (due to low body weight) that improves in time 2 (4 >>>>> months). I observed that eTIV-time1 is slightly correlated with weight >>>>> (r=0.3) whereas no correlation is present at time 2. The correlation >>>>> between eTIV-time1 and eTIV-time2 is somewhat lower than expected >>>>> (r=0.53) >>>>> and is lower than correlation between SegBrain_Vol_1 and SegBrain_Vol_2 >>>>> (0.65). >>>>> >>>>> Do you suggest in these cases to perform manual segmentation to obtain >>>>> TIV? or is there any other method (in freesurfer) to obtain an >>>>> estimate of >>>>> TIV not influenced by brain atrophy? What about using BrainMask_to_TIV? >>>>> >>>>> Thank you for any suggestion >>>>> >>>>> Angela >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>>> >>>> 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. >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> ________________________________ >> The materials in this message are private and may contain Protected >> Healthcare Information or other information of a sensitive nature. >> If you are not the intended recipient, be advised that any >> unauthorized use, disclosure, copying or the taking of any action in >> reliance on the contents of this information is strictly prohibited. >> If you have received this email in error, please immediately notify >> the sender via telephone or return mail. >> >> _______________________________________________ >> 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 > > > _______________________________________________ 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.
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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.
Hi Angela
yes, although if the eTIV is (incorrectly) correlated with atrophy you may be removing some of your effect (and slightly reducing your power)
cheers Bruce On Mon, 22 Feb 2016, angela.favaro@unipd.it wrote:
Hi Bruce, this is true, but I noticed that many papers used TIV as a covariate. In addition, in my samples (both pathological and healthy) there is a moderate positive correlation between gyrification and TIV (and brain volume). For the hemispheric overall gyrification index the correlation is 0.3-0.35 with TIV and 0.35-0.4 with total brain volume. I think that in pathological samples with possible brain atrophy, this is a way to control for a possible bias effect. Am I wrong?
Thank you Angela
Hi Angela
gyrification is the ratio of areas and hence dimensionless, so I would think it wouldn't be much affected by TIV.
cheers Bruce
On Sun, 21 Feb 2016, angela.favaro@unipd.it wrote:
In the case of a gyrification analysis, does correction for total brain volume make sense?
Angela
Inviato dal mio dispositivo Huawei
-------- Messaggio originale -------- Oggetto: Re: [Freesurfer] eTIV question Da: Bruce Fischl A: Freesurfer support list CC:
yes, it's a somewhat different and more conservative test. I guess you could check the talairach transforms of some of your subjects with eTIVs that don't make sense (or change the most over time) to try to see why this is happening. Or take Mike's suggestion and test a different (but probably still interesting) hypothesis On Sun, 21 Feb 2016, Angela Favaro wrote: > Hi, thank you > I think this would test something different: 'how much a brain area is > atrophic controlling for the average brain atrophy' and not 'how much > a brain area is atrophic controlling for the individual differences in > head size'. Doesn't it? > > Angela > > > "Harms, Michael" ha scritto: > >> Hi, >> Why not use a measurement of brain size rather than “eTIV”? >> >> 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 63110Email: mharms@wustl.edu >> >> >> >> >> On 2/21/16, 6:06 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of >> Angela Favaro" >> angela.favaro@unipd.it> wrote: >> >> there is a mistake in the graph, hippocampal volume is TIV2 >> I apologize for that! >> >> Angela Favaro ha scritto: >> >>> Hi Bruce, >>> please find attached the graph of the correlation between the two time >>> point. I did not find outliers or failures. However the discrepancy >>> between TIVs is particularly high in few cases. Obviously these data >>> are those before running longitudinal streaming >>> This is a sample of adolescents with low body weight (anorexia nervosa). >>> In my previous study (on young adults with low weight) I found no >>> correlation between TIV and body weight and high correlations between >>> fs estimated TIV and manually segmented TIV (r=0.94 in the whole >>> sample and r=0.93 in the underweight sample (n=38)). >>> Do you think that the young age can be a factor? or patients who are >>> more acutely underweight? >>> Thank you for any suggestion >>> >>> Angela >>> >>> >>> Bruce Fischl ha scritto: >>> >>>> Hi Angel >>>> >>>> the time1/time2 correlation of eTIV is pretty worrisome. Are you sure >>>> that there aren't outliers/failures in that set? >>>> >>>> Bruce >>>> >>>> >>>> On Sun, 14 Feb 2016, angela.favaro@unipd.it wrote: >>>> >>>>> Dear Freesurfer experts, >>>>> I have a question about eTIV (FS 5.3) which I use as a covariate where >>>>> appropriate. Is it in some way influenced by the presence of brain >>>>> atrophy? >>>>> I have a new sample of subjects in a longitudinal study: at time 1 they >>>>> have some atrophy (due to low body weight) that improves in time 2 (4 >>>>> months). I observed that eTIV-time1 is slightly correlated with weight >>>>> (r=0.3) whereas no correlation is present at time 2. The correlation >>>>> between eTIV-time1 and eTIV-time2 is somewhat lower than expected >>>>> (r=0.53) >>>>> and is lower than correlation between SegBrain_Vol_1 and SegBrain_Vol_2 >>>>> (0.65). >>>>> >>>>> Do you suggest in these cases to perform manual segmentation to obtain >>>>> TIV? or is there any other method (in freesurfer) to obtain an >>>>> estimate of >>>>> TIV not influenced by brain atrophy? What about using BrainMask_to_TIV? >>>>> >>>>> Thank you for any suggestion >>>>> >>>>> Angela >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>>> >>>> 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. >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> ________________________________ >> The materials in this message are private and may contain Protected >> Healthcare Information or other information of a sensitive nature. >> If you are not the intended recipient, be advised that any >> unauthorized use, disclosure, copying or the taking of any action in >> reliance on the contents of this information is strictly prohibited. >> If you have received this email in error, please immediately notify >> the sender via telephone or return mail. >> >> _______________________________________________ >> 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 > > > _______________________________________________ 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.
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Even assuming one had a true measure of TIV, if you get meaningfully different results when using TIV vs. brain size as a covariate, isn’t that a rather important thing to point out?
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 63110Email: mharms@wustl.edu
On 2/22/16, 4:44 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:
Hi Angela
yes, although if the eTIV is (incorrectly) correlated with atrophy you may be removing some of your effect (and slightly reducing your power)
cheers Bruce On Mon, 22 Feb 2016, angela.favaro@unipd.it wrote:
Hi Bruce, this is true, but I noticed that many papers used TIV as a covariate. In addition, in my samples (both pathological and healthy) there is a moderate positive correlation between gyrification and TIV (and brain volume). For the hemispheric overall gyrification index the correlation is 0.3-0.35 with TIV and 0.35-0.4 with total brain volume. I think that in pathological samples with possible brain atrophy, this is a way to control for a possible bias effect. Am I wrong?
Thank you Angela
Hi Angela
gyrification is the ratio of areas and hence dimensionless, so I would think it wouldn't be much affected by TIV.
cheers Bruce
On Sun, 21 Feb 2016, angela.favaro@unipd.it wrote:
In the case of a gyrification analysis, does correction for total brain volume make sense?
Angela
Inviato dal mio dispositivo Huawei
-------- Messaggio originale -------- Oggetto: Re: [Freesurfer] eTIV question Da: Bruce Fischl A: Freesurfer support list CC:
yes, it's a somewhat different and more conservative test. I guess you could check the talairach transforms of some of your subjects with eTIVs that don't make sense (or change the most over time) to try to see why this is happening. Or take Mike's suggestion and test a different (but probably still interesting) hypothesis On Sun, 21 Feb 2016, Angela Favaro wrote: > Hi, thank you > I think this would test something different: 'how much a brain area is > atrophic controlling for the average brain atrophy' and not 'how much > a brain area is atrophic controlling for the individual differences in > head size'. Doesn't it? > > Angela > > > "Harms, Michael" ha scritto: > >> Hi, >> Why not use a measurement of brain size rather than “eTIV”? >> >> 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 63110Email: mharms@wustl.edu >> >> >> >> >> On 2/21/16, 6:06 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of >> Angela Favaro" >> angela.favaro@unipd.it> wrote: >> >> there is a mistake in the graph, hippocampal volume is TIV2 >> I apologize for that! >> >> Angela Favaro ha scritto: >> >>> Hi Bruce, >>> please find attached the graph of the correlation between the two time >>> point. I did not find outliers or failures. However the discrepancy >>> between TIVs is particularly high in few cases. Obviously these data >>> are those before running longitudinal streaming >>> This is a sample of adolescents with low body weight (anorexia nervosa). >>> In my previous study (on young adults with low weight) I found no >>> correlation between TIV and body weight and high correlations between >>> fs estimated TIV and manually segmented TIV (r=0.94 in the whole >>> sample and r=0.93 in the underweight sample (n=38)). >>> Do you think that the young age can be a factor? or patients who are >>> more acutely underweight? >>> Thank you for any suggestion >>> >>> Angela >>> >>> >>> Bruce Fischl ha scritto: >>> >>>> Hi Angel >>>> >>>> the time1/time2 correlation of eTIV is pretty worrisome. Are you sure >>>> that there aren't outliers/failures in that set? >>>> >>>> Bruce >>>> >>>> >>>> On Sun, 14 Feb 2016, angela.favaro@unipd.it wrote: >>>> >>>>> Dear Freesurfer experts, >>>>> I have a question about eTIV (FS 5.3) which I use as a covariate where >>>>> appropriate. Is it in some way influenced by the presence of brain >>>>> atrophy? >>>>> I have a new sample of subjects in a longitudinal study: at time 1 they >>>>> have some atrophy (due to low body weight) that improves in time 2 (4 >>>>> months). I observed that eTIV-time1 is slightly correlated with weight >>>>> (r=0.3) whereas no correlation is present at time 2. The correlation >>>>> between eTIV-time1 and eTIV-time2 is somewhat lower than expected >>>>> (r=0.53) >>>>> and is lower than correlation between SegBrain_Vol_1 and SegBrain_Vol_2 >>>>> (0.65). >>>>> >>>>> Do you suggest in these cases to perform manual segmentation to obtain >>>>> TIV? or is there any other method (in freesurfer) to obtain an >>>>> estimate of >>>>> TIV not influenced by brain atrophy? What about using BrainMask_to_TIV? >>>>> >>>>> Thank you for any suggestion >>>>> >>>>> Angela >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>>> >>>> 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. >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> ________________________________ >> The materials in this message are private and may contain Protected >> Healthcare Information or other information of a sensitive nature. >> If you are not the intended recipient, be advised that any >> unauthorized use, disclosure, copying or the taking of any action in >> reliance on the contents of this information is strictly prohibited. >> If you have received this email in error, please immediately notify >> the sender via telephone or return mail. >> >> _______________________________________________ >> 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 > > > _______________________________________________ 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.
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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.
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________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
That is, going back to your earlier post, I personally don’t find it all that interesting whether a given brain area is atrophic relative to head size, especially in the situation where many regions are atrophic (i.e., global atrophy). I’m more interested in knowing whether the atrophy in a given region is greater (or less than) what would be predicted based on the global atrophy.
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 63110Email: mharms@wustl.edu
On 2/22/16, 10:19 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Harms, Michael" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of mharms@wustl.edu> wrote:
Even assuming one had a true measure of TIV, if you get meaningfully different results when using TIV vs. brain size as a covariate, isn’t that a rather important thing to point out?
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 63110Email: mharms@wustl.edu
On 2/22/16, 4:44 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:
Hi Angela
yes, although if the eTIV is (incorrectly) correlated with atrophy you may be removing some of your effect (and slightly reducing your power)
cheers Bruce On Mon, 22 Feb 2016, angela.favaro@unipd.it wrote:
Hi Bruce, this is true, but I noticed that many papers used TIV as a covariate. In addition, in my samples (both pathological and healthy) there is a moderate positive correlation between gyrification and TIV (and brain volume). For the hemispheric overall gyrification index the correlation is 0.3-0.35 with TIV and 0.35-0.4 with total brain volume. I think that in pathological samples with possible brain atrophy, this is a way to control for a possible bias effect. Am I wrong?
Thank you Angela
Hi Angela
gyrification is the ratio of areas and hence dimensionless, so I would think it wouldn't be much affected by TIV.
cheers Bruce
On Sun, 21 Feb 2016, angela.favaro@unipd.it wrote:
In the case of a gyrification analysis, does correction for total brain volume make sense?
Angela
Inviato dal mio dispositivo Huawei
-------- Messaggio originale -------- Oggetto: Re: [Freesurfer] eTIV question Da: Bruce Fischl A: Freesurfer support list CC:
yes, it's a somewhat different and more conservative test. I guess you could check the talairach transforms of some of your subjects with eTIVs that don't make sense (or change the most over time) to try to see why this is happening. Or take Mike's suggestion and test a different (but probably still interesting) hypothesis On Sun, 21 Feb 2016, Angela Favaro wrote: > Hi, thank you > I think this would test something different: 'how much a brain area is > atrophic controlling for the average brain atrophy' and not 'how much > a brain area is atrophic controlling for the individual differences in > head size'. Doesn't it? > > Angela > > > "Harms, Michael" ha scritto: > >> Hi, >> Why not use a measurement of brain size rather than “eTIV”? >> >> 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 63110Email: mharms@wustl.edu >> >> >> >> >> On 2/21/16, 6:06 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of >> Angela Favaro" >> angela.favaro@unipd.it> wrote: >> >> there is a mistake in the graph, hippocampal volume is TIV2 >> I apologize for that! >> >> Angela Favaro ha scritto: >> >>> Hi Bruce, >>> please find attached the graph of the correlation between the two time >>> point. I did not find outliers or failures. However the discrepancy >>> between TIVs is particularly high in few cases. Obviously these data >>> are those before running longitudinal streaming >>> This is a sample of adolescents with low body weight (anorexia nervosa). >>> In my previous study (on young adults with low weight) I found no >>> correlation between TIV and body weight and high correlations between >>> fs estimated TIV and manually segmented TIV (r=0.94 in the whole >>> sample and r=0.93 in the underweight sample (n=38)). >>> Do you think that the young age can be a factor? or patients who are >>> more acutely underweight? >>> Thank you for any suggestion >>> >>> Angela >>> >>> >>> Bruce Fischl ha scritto: >>> >>>> Hi Angel >>>> >>>> the time1/time2 correlation of eTIV is pretty worrisome. Are you sure >>>> that there aren't outliers/failures in that set? >>>> >>>> Bruce >>>> >>>> >>>> On Sun, 14 Feb 2016, angela.favaro@unipd.it wrote: >>>> >>>>> Dear Freesurfer experts, >>>>> I have a question about eTIV (FS 5.3) which I use as a covariate where >>>>> appropriate. Is it in some way influenced by the presence of brain >>>>> atrophy? >>>>> I have a new sample of subjects in a longitudinal study: at time 1 they >>>>> have some atrophy (due to low body weight) that improves in time 2 (4 >>>>> months). I observed that eTIV-time1 is slightly correlated with weight >>>>> (r=0.3) whereas no correlation is present at time 2. The correlation >>>>> between eTIV-time1 and eTIV-time2 is somewhat lower than expected >>>>> (r=0.53) >>>>> and is lower than correlation between SegBrain_Vol_1 and SegBrain_Vol_2 >>>>> (0.65). >>>>> >>>>> Do you suggest in these cases to perform manual segmentation to obtain >>>>> TIV? or is there any other method (in freesurfer) to obtain an >>>>> estimate of >>>>> TIV not influenced by brain atrophy? What about using BrainMask_to_TIV? >>>>> >>>>> Thank you for any suggestion >>>>> >>>>> Angela >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>>> >>>> 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. >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> ________________________________ >> The materials in this message are private and may contain Protected >> Healthcare Information or other information of a sensitive nature. >> If you are not the intended recipient, be advised that any >> unauthorized use, disclosure, copying or the taking of any action in >> reliance on the contents of this information is strictly prohibited. >> If you have received this email in error, please immediately notify >> the sender via telephone or return mail. >> >> _______________________________________________ >> 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 > > > _______________________________________________ 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.
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________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
yes, I agree. I will explore both thank you! Angela
That is, going back to your earlier post, I personally don’t find it all that interesting whether a given brain area is atrophic relative to head size, especially in the situation where many regions are atrophic (i.e., global atrophy). I’m more interested in knowing whether the atrophy in a given region is greater (or less than) what would be predicted based on the global atrophy.
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 63110Email: mharms@wustl.edu
On 2/22/16, 10:19 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Harms, Michael" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of mharms@wustl.edu> wrote:
Even assuming one had a true measure of TIV, if you get meaningfully different results when using TIV vs. brain size as a covariate, isn’t that a rather important thing to point out?
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 63110Email: mharms@wustl.edu
On 2/22/16, 4:44 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:
Hi Angela
yes, although if the eTIV is (incorrectly) correlated with atrophy you may be removing some of your effect (and slightly reducing your power)
cheers Bruce On Mon, 22 Feb 2016, angela.favaro@unipd.it wrote:
Hi Bruce, this is true, but I noticed that many papers used TIV as a covariate. In addition, in my samples (both pathological and healthy) there is a moderate positive correlation between gyrification and TIV (and brain volume). For the hemispheric overall gyrification index the correlation is 0.3-0.35 with TIV and 0.35-0.4 with total brain volume. I think that in pathological samples with possible brain atrophy, this is a way to control for a possible bias effect. Am I wrong?
Thank you Angela
Hi Angela
gyrification is the ratio of areas and hence dimensionless, so I would think it wouldn't be much affected by TIV.
cheers Bruce
On Sun, 21 Feb 2016, angela.favaro@unipd.it wrote:
In the case of a gyrification analysis, does correction for total brain volume make sense?
Angela
Inviato dal mio dispositivo Huawei
-------- Messaggio originale -------- Oggetto: Re: [Freesurfer] eTIV question Da: Bruce Fischl A: Freesurfer support list CC:
yes, it's a somewhat different and more conservative test. I guess you could check the talairach transforms of some of your subjects with eTIVs that don't make sense (or change the most over time) to try to see why this is happening. Or take Mike's suggestion and test a different (but probably still interesting) hypothesis On Sun, 21 Feb 2016, Angela Favaro wrote: > Hi, thank you > I think this would test something different: 'how much a brain area is > atrophic controlling for the average brain atrophy' and not 'how much > a brain area is atrophic controlling for the individual differences in > head size'. Doesn't it? > > Angela > > > "Harms, Michael" ha scritto: > >> Hi, >> Why not use a measurement of brain size rather than “eTIV”? >> >> 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 63110Email: mharms@wustl.edu >> >> >> >> >> On 2/21/16, 6:06 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of >> Angela Favaro" >> angela.favaro@unipd.it> wrote: >> >> there is a mistake in the graph, hippocampal volume is TIV2 >> I apologize for that! >> >> Angela Favaro ha scritto: >> >>> Hi Bruce, >>> please find attached the graph of the correlation between the two time >>> point. I did not find outliers or failures. However the discrepancy >>> between TIVs is particularly high in few cases. Obviously these data >>> are those before running longitudinal streaming >>> This is a sample of adolescents with low body weight (anorexia nervosa). >>> In my previous study (on young adults with low weight) I found no >>> correlation between TIV and body weight and high correlations between >>> fs estimated TIV and manually segmented TIV (r=0.94 in the whole >>> sample and r=0.93 in the underweight sample (n=38)). >>> Do you think that the young age can be a factor? or patients who are >>> more acutely underweight? >>> Thank you for any suggestion >>> >>> Angela >>> >>> >>> Bruce Fischl ha scritto: >>> >>>> Hi Angel >>>> >>>> the time1/time2 correlation of eTIV is pretty worrisome. Are you sure >>>> that there aren't outliers/failures in that set? >>>> >>>> Bruce >>>> >>>> >>>> On Sun, 14 Feb 2016, angela.favaro@unipd.it wrote: >>>> >>>>> Dear Freesurfer experts, >>>>> I have a question about eTIV (FS 5.3) which I use as a covariate where >>>>> appropriate. Is it in some way influenced by the presence of brain >>>>> atrophy? >>>>> I have a new sample of subjects in a longitudinal study: at time 1 they >>>>> have some atrophy (due to low body weight) that improves in time 2 (4 >>>>> months). I observed that eTIV-time1 is slightly correlated with weight >>>>> (r=0.3) whereas no correlation is present at time 2. The correlation >>>>> between eTIV-time1 and eTIV-time2 is somewhat lower than expected >>>>> (r=0.53) >>>>> and is lower than correlation between SegBrain_Vol_1 and SegBrain_Vol_2 >>>>> (0.65). >>>>> >>>>> Do you suggest in these cases to perform manual segmentation to obtain >>>>> TIV? or is there any other method (in freesurfer) to obtain an >>>>> estimate of >>>>> TIV not influenced by brain atrophy? What about using BrainMask_to_TIV? >>>>> >>>>> Thank you for any suggestion >>>>> >>>>> Angela >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>>> >>>> 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. >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> ________________________________ >> The materials in this message are private and may contain Protected >> Healthcare Information or other information of a sensitive nature. >> If you are not the intended recipient, be advised that any >> unauthorized use, disclosure, copying or the taking of any action in >> reliance on the contents of this information is strictly prohibited. >> If you have received this email in error, please immediately notify >> the sender via telephone or return mail. >> >> _______________________________________________ >> 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 > > > _______________________________________________ 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.
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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.
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The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
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The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
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angela.favaro＠unipd.it -
Bruce Fischl -
Harms, Michael