Dear Doug and experts
I've analyzed structural changes of the subcortical GM by using both VBM (DARTEL in SPM8) and subcortical volumemetric measurement using FreeSurfer 5.1. While there is no significant volumetric difference between the groups in VBM (corrected p<0.05), FS results showed that some subcortical GM had significant volume reductions in patients relative to controls (MANCOVA controlling for the effect of ICV, age, gender, followed by Bonferroni correction). One of the referees raised the question regarding this discrepancy between the VBM and FS findings. How can I cope with it?
Thank you in advance for your help.
Kim
Hi Kim
what structure is it? Our definitions are different - for example I believe we include lateral thalamic nuclei in the thalamus and they do not. Have you visually inspected both sets of segmentations?
cheers Bruce
On Mon, 4 Nov 2013, jh kim wrote:
Dear Doug and experts I've analyzed structural changes of the subcortical GM by using both VBM (DARTEL in SPM8) and subcortical volumemetric measurement using FreeSurfer 5.1. While there is no significant volumetric difference between the groups in VBM (corrected p<0.05), FS results showed that some subcortical GM had significant volume reductions in patients relative to controls (MANCOVA controlling for the effect of ICV, age, gender, followed by Bonferroni correction). One of the referees raised the question regarding this discrepancy between the VBM and FS findings. How can I cope with it?
Thank you in advance for your help.
Kim
Hi Kim, the answer is both easy and difficult. The easy answer is that they are completely different methods and will often give inconsistent results. I'm not sure what answer the reviewer will accept, and you might need to post the same question to the VBM and DARTEL crews. In your VBM analysis, I assume that you used modulation (ie, you were looking at volume and not "GM density")? VBM performs a voxel by voxel comparison and you probably smoothed by 10mm or so. Either of those could have washed out the effect. Certainly a reasonable response is that the FS analysis is for the entire ROI and and the VBM is voxelwise. Hope that help.s
doug
On 11/03/2013 11:55 PM, jh kim wrote:
Dear Doug and experts
I've analyzed structural changes of the subcortical GM by using both VBM (DARTEL in SPM8) and subcortical volumemetric measurement using FreeSurfer 5.1. While there is no significant volumetric difference between the groups in VBM (corrected p<0.05), FS results showed that some subcortical GM had significant volume reductions in patients relative to controls (MANCOVA controlling for the effect of ICV, age, gender, followed by Bonferroni correction). One of the referees raised the question regarding this discrepancy between the VBM and FS findings. How can I cope with it?
Thank you in advance for your help.
Kim
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Drs. Bruce and Doug Thanks for the valuable comments.
Discrepancy between FS and VBM lies in putamen and hippocampus. Would you please briefly comment regarding segmentation method of above structures in FS? I'm just wondering whether segmentation of grey matter in FS is largely different from that of VBM? Sorry for bothering you again with my silly question.
Thanks. Kim
2013/11/5 Douglas N Greve greve@nmr.mgh.harvard.edu
Hi Kim, the answer is both easy and difficult. The easy answer is that they are completely different methods and will often give inconsistent results. I'm not sure what answer the reviewer will accept, and you might need to post the same question to the VBM and DARTEL crews. In your VBM analysis, I assume that you used modulation (ie, you were looking at volume and not "GM density")? VBM performs a voxel by voxel comparison and you probably smoothed by 10mm or so. Either of those could have washed out the effect. Certainly a reasonable response is that the FS analysis is for the entire ROI and and the VBM is voxelwise. Hope that help.s
doug
On 11/03/2013 11:55 PM, jh kim wrote:
Dear Doug and experts
I've analyzed structural changes of the subcortical GM by using both VBM (DARTEL in SPM8) and subcortical volumemetric measurement using FreeSurfer 5.1. While there is no significant volumetric difference between the groups in VBM (corrected p<0.05), FS results showed that some subcortical GM had significant volume reductions in patients relative to controls (MANCOVA controlling for the effect of ICV, age, gender, followed by Bonferroni correction). One of the referees raised the question regarding this discrepancy between the VBM and FS findings. How can I cope with it?
Thank you in advance for your help.
Kim
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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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.
The FS segmentation is a combined segmentation and registration to an atlas space. This is probabilistic in that the atlas is built from 40 subjects and uses intensity, location, and neighborhood priors. I think VBM is using unified segementation which performs intensity normalization, segmentation, and registration simultaneously also using a probabilistic atlas. VBM segments GM/WM/CSF whereas FS segments various GM and ventricular structures as well as WM. VBM is a voxelwise analysis which is registered to an atlas, modulated, and spatially smoothed, all of which will have strong effects on the results. Maybe a VBM expert on the list can chime in with more info.
doug
On 11/05/2013 08:08 PM, jh kim wrote:
Dear Drs. Bruce and Doug Thanks for the valuable comments.
Discrepancy between FS and VBM lies in putamen and hippocampus. Would you please briefly comment regarding segmentation method of above structures in FS? I'm just wondering whether segmentation of grey matter in FS is largely different from that of VBM? Sorry for bothering you again with my silly question.
Thanks. Kim
2013/11/5 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
Hi Kim, the answer is both easy and difficult. The easy answer is that they are completely different methods and will often give inconsistent results. I'm not sure what answer the reviewer will accept, and you might need to post the same question to the VBM and DARTEL crews. In your VBM analysis, I assume that you used modulation (ie, you were looking at volume and not "GM density")? VBM performs a voxel by voxel comparison and you probably smoothed by 10mm or so. Either of those could have washed out the effect. Certainly a reasonable response is that the FS analysis is for the entire ROI and and the VBM is voxelwise. Hope that help.s doug On 11/03/2013 11:55 PM, jh kim wrote: > Dear Doug and experts > > I've analyzed structural changes of the subcortical GM by using both > VBM (DARTEL in SPM8) and subcortical volumemetric measurement using > FreeSurfer 5.1. While there is no significant volumetric difference > between the groups in VBM (corrected p<0.05), FS results showed that > some subcortical GM had significant volume reductions in patients > relative to controls (MANCOVA controlling for the effect of ICV, age, > gender, followed by Bonferroni correction). > One of the referees raised the question regarding this discrepancy > between the VBM and FS findings. > How can I cope with it? > > Thank you in advance for your help. > > Kim > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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
Dear Doug
Thank you so much. Your comment would be of great help to me.
Kim
2013/11/7 Douglas N Greve greve@nmr.mgh.harvard.edu
The FS segmentation is a combined segmentation and registration to an atlas space. This is probabilistic in that the atlas is built from 40 subjects and uses intensity, location, and neighborhood priors. I think VBM is using unified segementation which performs intensity normalization, segmentation, and registration simultaneously also using a probabilistic atlas. VBM segments GM/WM/CSF whereas FS segments various GM and ventricular structures as well as WM. VBM is a voxelwise analysis which is registered to an atlas, modulated, and spatially smoothed, all of which will have strong effects on the results. Maybe a VBM expert on the list can chime in with more info.
doug
On 11/05/2013 08:08 PM, jh kim wrote:
Dear Drs. Bruce and Doug Thanks for the valuable comments.
Discrepancy between FS and VBM lies in putamen and hippocampus. Would you please briefly comment regarding segmentation method of above structures in FS? I'm just wondering whether segmentation of grey matter in FS is largely different from that of VBM? Sorry for bothering you again with my silly question.
Thanks. Kim
2013/11/5 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
Hi Kim, the answer is both easy and difficult. The easy answer isthat
they are completely different methods and will often giveinconsistent
results. I'm not sure what answer the reviewer will accept, and you might need to post the same question to the VBM and DARTEL crews. In your VBM analysis, I assume that you used modulation (ie, you were looking at volume and not "GM density")? VBM performs a voxel byvoxel
comparison and you probably smoothed by 10mm or so. Either of those could have washed out the effect. Certainly a reasonable response is that the FS analysis is for the entire ROI and and the VBM is voxelwise. Hope that help.s doug On 11/03/2013 11:55 PM, jh kim wrote: > Dear Doug and experts > > I've analyzed structural changes of the subcortical GM by usingboth
> VBM (DARTEL in SPM8) and subcortical volumemetric measurement using > FreeSurfer 5.1. While there is no significant volumetric difference > between the groups in VBM (corrected p<0.05), FS results showedthat
> some subcortical GM had significant volume reductions in patients > relative to controls (MANCOVA controlling for the effect of ICV, age, > gender, followed by Bonferroni correction). > One of the referees raised the question regarding this discrepancy > between the VBM and FS findings. > How can I cope with it? > > Thank you in advance for your help. > > Kim > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas N Greve -
jh kim