Hello experts, I am doing volumetric studies where I am comparing the subcortical structures volumes among different experimental groups. I usually do two mprages on one subject in a single scan at two time-points. I run recon all on both mprages for a single subjects. To my surprise the volumes of same structure of a single subject calculated by freesurfer using two mprages are different.
I did longitudinal run using the two mprages from same subject, however then also the volumes show differences.
May you please advise me what to do. Thanks, Rashmi
Hi Rashmi
of course they are different - there is noise in the scans and motion and other sources of corruption! The amount of difference will depend on the structure and the quality of the data.
cheers Bruce On Thu, 14 Mar 2013, Rashmi Singh wrote:
Hello experts, I am doing volumetric studies where I am comparing the subcortical structures volumes among different experimental groups. I usually do two mprages on one subject in a single scan at two time-points. I run recon all on both mprages for a single subjects. To my surprise the volumes of same structure of a single subject calculated by freesurfer using two mprages are different.
I did longitudinal run using the two mprages from same subject, however then also the volumes show differences.
May you please advise me what to do. Thanks, Rashmi
Thank you Bruce. So what should I do. Shall I just take one of the mprage values or is it a good idea to get the average from two mprages for each structure. Can longitudinal run be helpful? Please suggest. Thank you! Rashmi
On 3/14/13 12:09 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Rashmi
of course they are different - there is noise in the scans and motion and other sources of corruption! The amount of difference will depend on the structure and the quality of the data.
cheers Bruce On Thu, 14 Mar 2013, Rashmi Singh wrote:
Hello experts, I am doing volumetric studies where I am comparing the subcortical structures volumes among different experimental groups. I usually do two mprages on one subject in a single scan at two time-points. I run recon all on both mprages for a single subjects. To my surprise the volumes of same structure of a single subject calculated by freesurfer using two mprages are different.
I did longitudinal run using the two mprages from same subject, however then also the volumes show differences.
May you please advise me what to do. Thanks, Rashmi
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.
yes, you should use the longitudinal stream for your analysis. You are probably better off picking the better mprage (i.e. less motion) and analyzing it at each timepoint
cheers Bruce
On Thu, 14 Mar 2013, Rashmi Singh wrote:
Thank you Bruce. So what should I do. Shall I just take one of the mprage values or is it a good idea to get the average from two mprages for each structure. Can longitudinal run be helpful? Please suggest. Thank you! Rashmi
On 3/14/13 12:09 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Rashmi
of course they are different - there is noise in the scans and motion and other sources of corruption! The amount of difference will depend on the structure and the quality of the data.
cheers Bruce On Thu, 14 Mar 2013, Rashmi Singh wrote:
Hello experts, I am doing volumetric studies where I am comparing the subcortical structures volumes among different experimental groups. I usually do two mprages on one subject in a single scan at two time-points. I run recon all on both mprages for a single subjects. To my surprise the volumes of same structure of a single subject calculated by freesurfer using two mprages are different.
I did longitudinal run using the two mprages from same subject, however then also the volumes show differences.
May you please advise me what to do. Thanks, Rashmi
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.
Ok I have done that. I did run longitudinal run using each mprage as an individual timepoint. So this way I got the longitudinal run stat output for both time points. So do you suggest I average them out or take the result of the output from one of the long run. Or are you suggesting that I take the volumes from the base run output. This seems so simple, am I complicating it? Sorry if I am not understanding you! Please advise. Rashmi
On 3/14/13 12:15 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
yes, you should use the longitudinal stream for your analysis. You are probably better off picking the better mprage (i.e. less motion) and analyzing it at each timepoint
cheers Bruce
On Thu, 14 Mar 2013, Rashmi Singh wrote:
Thank you Bruce. So what should I do. Shall I just take one of the mprage values or is it a good idea to get the average from two mprages for each structure. Can longitudinal run be helpful? Please suggest. Thank you! Rashmi
On 3/14/13 12:09 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Rashmi
of course they are different - there is noise in the scans and motion and other sources of corruption! The amount of difference will depend on the structure and the quality of the data.
cheers Bruce On Thu, 14 Mar 2013, Rashmi Singh wrote:
Hello experts, I am doing volumetric studies where I am comparing the subcortical structures volumes among different experimental groups. I usually do two mprages on one subject in a single scan at two time-points. I run recon all on both mprages for a single subjects. To my surprise the volumes of same structure of a single subject calculated by freesurfer using two mprages are different.
I did longitudinal run using the two mprages from same subject, however then also the volumes show differences.
May you please advise me what to do. Thanks, Rashmi
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.
what is your goal? If it is to detect longitidinal change I would advise take the best mprage at each timepoint and run it through cross-sectional then longitudinal analysis Bruce On Thu, 14 Mar 2013, Rashmi Singh wrote:
Ok I have done that. I did run longitudinal run using each mprage as an individual timepoint. So this way I got the longitudinal run stat output for both time points. So do you suggest I average them out or take the result of the output from one of the long run. Or are you suggesting that I take the volumes from the base run output. This seems so simple, am I complicating it? Sorry if I am not understanding you! Please advise. Rashmi
On 3/14/13 12:15 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
yes, you should use the longitudinal stream for your analysis. You are probably better off picking the better mprage (i.e. less motion) and analyzing it at each timepoint
cheers Bruce
On Thu, 14 Mar 2013, Rashmi Singh wrote:
Thank you Bruce. So what should I do. Shall I just take one of the mprage values or is it a good idea to get the average from two mprages for each structure. Can longitudinal run be helpful? Please suggest. Thank you! Rashmi
On 3/14/13 12:09 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Rashmi
of course they are different - there is noise in the scans and motion and other sources of corruption! The amount of difference will depend on the structure and the quality of the data.
cheers Bruce On Thu, 14 Mar 2013, Rashmi Singh wrote:
Hello experts, I am doing volumetric studies where I am comparing the subcortical structures volumes among different experimental groups. I usually do two mprages on one subject in a single scan at two time-points. I run recon all on both mprages for a single subjects. To my surprise the volumes of same structure of a single subject calculated by freesurfer using two mprages are different.
I did longitudinal run using the two mprages from same subject, however then also the volumes show differences.
May you please advise me what to do. Thanks, Rashmi
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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Rashmi Singh