I am doing volumetric studies where instead of using ICV, I use total brain volume as a co-variate. This is why I need total brain volume measurements. Do you suggest that its not a good idea to use mri-binarize of brain.mgz for calculating it? Earlier freesurfer experts had suggeted me to use this option. Rashmi _______________________ ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Friday, September 13, 2013 9:09 AM To: Rashmi Singh Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] recon all question
what do you want to do with the brain volume? Are you really after ICV/TIV? We use the det. of the jacobian of the tal xform as per Randy Buckner, and for it we have compared to actual ICV volumes derived from T2 volumes and manual stripping
For the FLAIR, we usually get a T2-space based FLAIR that is also 1mm isotropic. Once you are done with recon-all, you run it again with the switch -FLAIRpial <path to flair volume> and it will do a post-hoc surface deformation to avoid dura.
cheers Bruce
On Fri, 13 Sep 2013, Rashmi Singh wrote:
Thank you Bruce ! mri_binarize was suggested to me by the freesurfer group, so now I am a
little concerned when you say that this has not been assessed for accuracy. May you suggest how otherwise do you get the total brain volume ( which you suggest is more accurate), as this measurement is not present in the freesurfer output stat files.
May you please elaborate a little more the steps of using T2-FlAIR for
recon all or suggest me where I can find the detail information ( may be on the website). While scanning we do collect T2-FLAIR that is linked with T1 for each subject. Is that what you mean by get a T2-FLAIR? Also, what is a -T2Flair swicht?
Sorry, with a background of molecular biology and being a novice in image
analysis, it really takes me time and lots of effort to understand imaging and its analysis. Your guidance is appreciated.
Thanks,
Rashmi ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Friday, September 13, 2013 8:46 AM To: Rashmi Singh Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] recon all question
- I don't think I know anyone who has done this, and we haven't assessed
it for accuracy.
- The best thing to do is get a T2-FLAIR and run it with the -T2Flair
switch after recon-all is done. This does a great job avoiding dura
cheers Bruce
On Fri, 13 Sep 2013, Rashmi Singh wrote:
Hey Bruce, I have two more questions.
- I was suggested to use mri_binarize with brain.mgz to get the total
brain volume. Is there any reference that I can cite regarding use of mri_binarize to calculate total brain volume.
2)I learnt that using T2 weighted image along with T1 weighted image
from the same scanning session generates a good contrast and gives better segmentation/parcellation outputs using FreeSurfer.
May the FreeSurfer experts guide me through this.
Thanks, Rashmi ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, September 12, 2013 5:27 PM To: Rashmi Singh Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon all question
Hi Rashmi
putting them in the orig folder with those numbers will get recon-all to do motion correction and averaging.
cheers Bruce On Thu, 12 Sep 2013, Rashmi Singh wrote:
Hello Freesurfer experts, I am doing volumetrics study. During the scan we get 2-3 mprage per scan for a subject. While running the FreeSurfer, if I want to use the three mprages
for
that subject as an input file, may I just keep the three mgz files (001.mgz, 002 .mgz and 003.mgz) in the orig folder and run the simple
recon
all command :=Recon-all -s (subject file name) -all or do I need to
have
some additional l flags so that recon all command will use the three
T1
images to get one output file? 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
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Hi, A reasonable definition of TBV would be TotalGrayVol + CorticalWhiteMatterVol from the aseg.stats file.
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 63110 Email: mharms@wustl.edu
On 9/13/13 9:18 AM, "Rashmi Singh" rsingh@laureateinstitute.org wrote:
I am doing volumetric studies where instead of using ICV, I use total brain volume as a co-variate. This is why I need total brain volume measurements. Do you suggest that its not a good idea to use mri-binarize of brain.mgz for calculating it? Earlier freesurfer experts had suggeted me to use this option. Rashmi _______________________ ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Friday, September 13, 2013 9:09 AM To: Rashmi Singh Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] recon all question
what do you want to do with the brain volume? Are you really after ICV/TIV? We use the det. of the jacobian of the tal xform as per Randy Buckner, and for it we have compared to actual ICV volumes derived from T2 volumes and manual stripping
For the FLAIR, we usually get a T2-space based FLAIR that is also 1mm isotropic. Once you are done with recon-all, you run it again with the switch -FLAIRpial <path to flair volume> and it will do a post-hoc surface deformation to avoid dura.
cheers Bruce
On Fri, 13 Sep 2013, Rashmi Singh wrote:
Thank you Bruce ! mri_binarize was suggested to me by the freesurfer group, so now I am a
little concerned when you say that this has not been assessed for accuracy. May you suggest how otherwise do you get the total brain volume ( which you suggest is more accurate), as this measurement is not present in the freesurfer output stat files.
May you please elaborate a little more the steps of using T2-FlAIR for
recon all or suggest me where I can find the detail information ( may be on the website). While scanning we do collect T2-FLAIR that is linked with T1 for each subject. Is that what you mean by get a T2-FLAIR? Also, what is a -T2Flair swicht?
Sorry, with a background of molecular biology and being a novice in image
analysis, it really takes me time and lots of effort to understand imaging and its analysis. Your guidance is appreciated.
Thanks,
Rashmi ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Friday, September 13, 2013 8:46 AM To: Rashmi Singh Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] recon all question
- I don't think I know anyone who has done this, and we haven't
assessed it for accuracy.
- The best thing to do is get a T2-FLAIR and run it with the -T2Flair
switch after recon-all is done. This does a great job avoiding dura
cheers Bruce
On Fri, 13 Sep 2013, Rashmi Singh wrote:
Hey Bruce, I have two more questions.
- I was suggested to use mri_binarize with brain.mgz to get the total
brain volume. Is there any reference that I can cite regarding use of mri_binarize to calculate total brain volume.
2)I learnt that using T2 weighted image along with T1 weighted image
from the same scanning session generates a good contrast and gives better segmentation/parcellation outputs using FreeSurfer.
May the FreeSurfer experts guide me through this.
Thanks, Rashmi ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, September 12, 2013 5:27 PM To: Rashmi Singh Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon all question
Hi Rashmi
putting them in the orig folder with those numbers will get recon-all to do motion correction and averaging.
cheers Bruce On Thu, 12 Sep 2013, Rashmi Singh wrote:
Hello Freesurfer experts, I am doing volumetrics study. During the scan we get 2-3 mprage per scan for a subject. While running the FreeSurfer, if I want to use the three mprages
for
that subject as an input file, may I just keep the three mgz files (001.mgz, 002 .mgz and 003.mgz) in the orig folder and run the simple
recon
all command :=Recon-all -s (subject file name) -all or do I need to
have
some additional l flags so that recon all command will use the three
T1
images to get one output file? 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.
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.
Hi Rashmi, You can find an explanation of the various measures we offer here: https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats
Allison
On Fri, 13 Sep 2013, Rashmi Singh wrote:
I am doing volumetric studies where instead of using ICV, I use total brain volume as a co-variate. This is why I need total brain volume measurements. Do you suggest that its not a good idea to use mri-binarize of brain.mgz for calculating it? Earlier freesurfer experts had suggeted me to use this option. Rashmi _______________________ ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Friday, September 13, 2013 9:09 AM To: Rashmi Singh Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] recon all question
what do you want to do with the brain volume? Are you really after ICV/TIV? We use the det. of the jacobian of the tal xform as per Randy Buckner, and for it we have compared to actual ICV volumes derived from T2 volumes and manual stripping
For the FLAIR, we usually get a T2-space based FLAIR that is also 1mm isotropic. Once you are done with recon-all, you run it again with the switch -FLAIRpial <path to flair volume> and it will do a post-hoc surface deformation to avoid dura.
cheers Bruce
On Fri, 13 Sep 2013, Rashmi Singh wrote:
Thank you Bruce ! mri_binarize was suggested to me by the freesurfer group, so now I am a
little concerned when you say that this has not been assessed for accuracy. May you suggest how otherwise do you get the total brain volume ( which you suggest is more accurate), as this measurement is not present in the freesurfer output stat files.
May you please elaborate a little more the steps of using T2-FlAIR for
recon all or suggest me where I can find the detail information ( may be on the website). While scanning we do collect T2-FLAIR that is linked with T1 for each subject. Is that what you mean by get a T2-FLAIR? Also, what is a -T2Flair swicht?
Sorry, with a background of molecular biology and being a novice in image
analysis, it really takes me time and lots of effort to understand imaging and its analysis. Your guidance is appreciated.
Thanks,
Rashmi ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Friday, September 13, 2013 8:46 AM To: Rashmi Singh Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] recon all question
- I don't think I know anyone who has done this, and we haven't assessed
it for accuracy.
- The best thing to do is get a T2-FLAIR and run it with the -T2Flair
switch after recon-all is done. This does a great job avoiding dura
cheers Bruce
On Fri, 13 Sep 2013, Rashmi Singh wrote:
Hey Bruce, I have two more questions.
- I was suggested to use mri_binarize with brain.mgz to get the total
brain volume. Is there any reference that I can cite regarding use of mri_binarize to calculate total brain volume.
2)I learnt that using T2 weighted image along with T1 weighted image
from the same scanning session generates a good contrast and gives better segmentation/parcellation outputs using FreeSurfer.
May the FreeSurfer experts guide me through this.
Thanks, Rashmi ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, September 12, 2013 5:27 PM To: Rashmi Singh Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon all question
Hi Rashmi
putting them in the orig folder with those numbers will get recon-all to do motion correction and averaging.
cheers Bruce On Thu, 12 Sep 2013, Rashmi Singh wrote:
Hello Freesurfer experts, I am doing volumetrics study. During the scan we get 2-3 mprage per scan for a subject. While running the FreeSurfer, if I want to use the three mprages
for
that subject as an input file, may I just keep the three mgz files (001.mgz, 002 .mgz and 003.mgz) in the orig folder and run the simple
recon
all command :=Recon-all -s (subject file name) -all or do I need to
have
some additional l flags so that recon all command will use the three
T1
images to get one output file? 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Allison Stevens -
Harms, Michael -
Rashmi Singh