Re: [Freesurfer] eTIV question
My experience with eTIV is that it's great with a perfect Talairach transform but otherwise is less accurate than other measures. Manually fixing the transforms and reprocessing as necessary will result in great eTIVs but requires quite a bit of manual work. What we do instead is just use the brainmask volume (but our data are MRIs of non-demented older adults so there's not typically extensive atrophy). We've found that brainmask has a Dice Similarity Coefficient of 0.95 and an ICC of 0.92 with manually traced intracranial masks (inferior termination on a straight line between the lowest portion of the clivus and occipital bone). eTIV had an ICC of 0.67 with our manual masks (but we didn't fix the transformations). Jared Jared Tanner, Ph.D. Research Assistant Professor Clinical and Health Psychology University of Florida > -- Forwarded message -- > From: "Harms, Michael" > To: "freesurfer@nmr.mgh.harvard.edu" > Cc: > Date: Sun, 21 Feb 2016 18:10:12 + > Subject: Re: [Freesurfer] eTIV question > > 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: mha...@wustl.edu > > ___ 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.
Re: [Freesurfer] eTIV question
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: mha...@wustl.edu On 2/21/16, 6:06 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Angela Favaro" 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.fav...@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-ma
Re: [Freesurfer] eTIV question
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: mha...@wustl.edu > > > > > On 2/21/16, 6:06 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of > Angela Favaro" angela.fav...@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.fav...@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
Re: [Freesurfer] eTIV question
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: mha...@wustl.edu On 2/21/16, 6:06 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Angela Favaro" 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.fav...@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
Re: [Freesurfer] eTIV question
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.fav...@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
Re: [Freesurfer] eTIV question
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.fav...@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.
Re: [Freesurfer] eTIV question and longitudinal issue
Hi all, I would be very grateful of any advice for the problem below with e-TIV. I have another problem with the longitudinal streaming (it is the first time I use it). I am running the .base and .long procedure in subjects with only one measure to include them in a mixed liner model analysis (as suggested in the wiki). I run the following commands: recon-all -base template100 -tp subj025 -all recon-all -long subj025 template100 -all However at the second command line an error occur (attached is the log): BEGIN failed--compilation aborted at /Applications/freesurfer/mni/bin/nu_correct line 37. ERROR: nu_correct Darwin iMac-di-Angela.local 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64 recon-all -s subj025.long.template100 exited with ERRORS Which is my mistake? I looked for a solution in the mailing list, but I did not find an answer. Thank you for any help! Angela > 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 > > > 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. > > recon-all.log Description: Binary data ___ 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.
