Dear freesurfer experts,
Will you please let me know if it's possible to get one average mgz image file by concatenating the hippocampal volumes of different subjects using dev version? Since, I already have the hippocampal subfields mgz volume files, I intend to run the glmfit later on between two groups to get sig.mgh files.
Thanks and regards?
Sampada
Hi Sampada
can you elaborate a bit? What are you trying to achieve? Do you want an average hippocampus? Average maps of subfields? What hypothesis are you trying to test? The individual subject data is not resampled to a common coordinate system, so just averaging them as is won't produce anything interested.
cheers Bruce
On Sun, 10 Jul 2016, Dr Sampada Sinha wrote:
Dear freesurfer experts, Will you please let me know if it's possible to get one average mgz image file by concatenating the hippocampal volumes of different subjects using dev version? Since, I already have the hippocampal subfields mgz volume files, I intend to run the glmfit later on between two groups to get sig.mgh files.
Thanks and regards?
Sampada
-- Sampada Pre-doctoral student Department of Geriatric Mental Health (DGMH) King George Medical University Lucknow-226003 India
Dear Bruce,
Thanks for you for your response. I am trying to generate an average hippocampal volume and its correlation with HAM-D score in early and late onset depression (eod vs lod). One way I tried to do it was by binarizing and concatanating the hippocampal volumes and then run mri_glmfit. But, I am stuck at glm_fit and would be grateful if you can let me know how to proceed from here. How do I run the glm_fit between eod and lod patients? Secondly, after running glm_fit how do I calculate the significance from sig.mgh?
Appreciate all your help.
Thanks and regards,
Sampada
On Sun, Jul 10, 2016 at 7:15 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Sampada
can you elaborate a bit? What are you trying to achieve? Do you want an average hippocampus? Average maps of subfields? What hypothesis are you trying to test? The individual subject data is not resampled to a common coordinate system, so just averaging them as is won't produce anything interested.
cheers Bruce
On Sun, 10 Jul 2016, Dr Sampada Sinha wrote:
Dear freesurfer experts, Will you please let me know if it's possible to get one average mgz image file by concatenating the hippocampal volumes of different subjects using dev version? Since, I already have the hippocampal subfields mgz volume files, I intend to run the glmfit later on between two groups to get
sig.mgh
files.
Thanks and regards?
Sampada
-- Sampada Pre-doctoral student Department of Geriatric Mental Health (DGMH) King George Medical University Lucknow-226003 India
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Hi Sampada
why not just take the volume of the hippocampus from the aseg.stats? Why do you want an mgz? You just want one number per subject, right?
Bruce
On Tue, 12 Jul 2016, Dr Sampada Sinha wrote:
Dear Bruce,
Thanks for you for your response. I am trying to generate an average hippocampal volume and its correlation with HAM-D score in early and late onset depression (eod vs lod). One way I tried to do it was by binarizing and concatanating the hippocampal volumes and then run mri_glmfit. But, I am stuck at glm_fit and would be grateful if you can let me know how to proceed from here. How do I run the glm_fit between eod and lod patients? Secondly, after running glm_fit how do I calculate the significance from sig.mgh?
Appreciate all your help.
Thanks and regards,
Sampada
On Sun, Jul 10, 2016 at 7:15 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Sampada
can you elaborate a bit? What are you trying to achieve? Do you want an average hippocampus? Average maps of subfields? What hypothesis are you trying to test? The individual subject data is not resampled to a common coordinate system, so just averaging them as is won't produce anything interested. cheers Bruce On Sun, 10 Jul 2016, Dr Sampada Sinha wrote: > Dear freesurfer experts, > Will you please let me know if it's possible to get one average mgz image > file by concatenating the hippocampal volumes of different subjects using > dev version? Since, I already have the hippocampal subfields mgz volume > files, I intend to run the glmfit later on between two groups to get sig.mgh > files. > > Thanks and regards? > > Sampada > > > -- > Sampada > Pre-doctoral student > Department of Geriatric Mental Health (DGMH) > King George Medical University > Lucknow-226003 > India > > > > > > > > > > >
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-- Sampada Pre-doctoral student Department of Geriatric Mental Health (DGMH) King George Medical University Lucknow-226003 India
Dear Bruce, I am trying to generate the following picture (please see attached) for eod vs lod groups. Can you please tell me how to do this?
Thanks and regards,
Sampada
On Tue, Jul 12, 2016 at 6:44 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Sampada
why not just take the volume of the hippocampus from the aseg.stats? Why do you want an mgz? You just want one number per subject, right?
Bruce
On Tue, 12 Jul 2016, Dr Sampada Sinha wrote:
Dear Bruce,
Thanks for you for your response. I am trying to generate an average hippocampal volume and its correlation with HAM-D score in early and late onset depression (eod vs lod). One way I tried to do it was by binarizing and concatanating the hippocampal volumes and then run mri_glmfit. But, I am stuck at glm_fit and would be grateful if you can let me know how to proceed from here. How do I run the glm_fit between eod and lod patients? Secondly, after running glm_fit how do I calculate the significance from sig.mgh?
Appreciate all your help.
Thanks and regards,
Sampada
On Sun, Jul 10, 2016 at 7:15 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote: Hi Sampada
can you elaborate a bit? What are you trying to achieve? Do you want an average hippocampus? Average maps of subfields? What hypothesis are you trying to test? The individual subject data is not resampled to a common coordinate system, so just averaging them as is won't produce anything interested. cheers Bruce On Sun, 10 Jul 2016, Dr Sampada Sinha wrote: > Dear freesurfer experts, > Will you please let me know if it's possible to get one average mgz image > file by concatenating the hippocampal volumes of different subjects using > dev version? Since, I already have the hippocampal subfields mgz volume > files, I intend to run the glmfit later on between two groups to get sig.mgh > files. > > Thanks and regards? > > Sampada > > > -- > Sampada > Pre-doctoral student > Department of Geriatric Mental Health (DGMH) > King George Medical University > Lucknow-226003 > India > > > > > > > > > > >
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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.
-- Sampada Pre-doctoral student Department of Geriatric Mental Health (DGMH) King George Medical University Lucknow-226003 India
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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.
Try running make_average_volume. This will produce an aseg.mgz file with all the ROIs merged across all subjects
On 07/13/2016 07:10 AM, Dr Sampada Sinha wrote:
Dear Bruce, I am trying to generate the following picture (please see attached) for eod vs lod groups. Can you please tell me how to do this?
Thanks and regards,
Sampada
On Tue, Jul 12, 2016 at 6:44 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Sampada why not just take the volume of the hippocampus from the aseg.stats? Why do you want an mgz? You just want one number per subject, right? Bruce On Tue, 12 Jul 2016, Dr Sampada Sinha wrote: Dear Bruce, Thanks for you for your response. I am trying to generate an average hippocampal volume and its correlation with HAM-D score in early and late onset depression (eod vs lod). One way I tried to do it was by binarizing and concatanating the hippocampal volumes and then run mri_glmfit. But, I am stuck at glm_fit and would be grateful if you can let me know how to proceed from here. How do I run the glm_fit between eod and lod patients? Secondly, after running glm_fit how do I calculate the significance from sig.mgh? Appreciate all your help. Thanks and regards, Sampada On Sun, Jul 10, 2016 at 7:15 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Sampada can you elaborate a bit? What are you trying to achieve? Do you want an average hippocampus? Average maps of subfields? What hypothesis are you trying to test? The individual subject data is not resampled to a common coordinate system, so just averaging them as is won't produce anything interested. cheers Bruce On Sun, 10 Jul 2016, Dr Sampada Sinha wrote: > Dear freesurfer experts, > Will you please let me know if it's possible to get one average mgz image > file by concatenating the hippocampal volumes of different subjects using > dev version? Since, I already have the hippocampal subfields mgz volume > files, I intend to run the glmfit later on between two groups to get sig.mgh > files. > > Thanks and regards? > > Sampada > > > -- > Sampada > Pre-doctoral student > Department of Geriatric Mental Health (DGMH) > King George Medical University > Lucknow-226003 > India > > > > > > > > > > > _______________________________________________ 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. -- Sampada Pre-doctoral student Department of Geriatric Mental Health (DGMH) King George Medical University Lucknow-226003 India _______________________________________________ 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.-- Sampada Pre-doctoral student Department of Geriatric Mental Health (DGMH) King George Medical University Lucknow-226003 India
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