Dear FS experts, I have SUV maps for subjects within two groups. I moved these SUV maps into surface then I concatenated the images in the order of two groups then I used the compiled file in a glm analysis to check the difference between the two groups.
I aim to use V1 Atlas to derive the SUV values from the BA labels. I am not sure how to utilize these labels in such analysis. In this context I have two questions:
1. Can these label be converted to ROIs similar to the ROIs derived from wmpar.mgz using the command mri_binarize?
2. in WIKI it was mentioned that the command "recon-all -s subjid -label_v1" output the stat values for every BA label. How can I derive similar stats from the SUV maps in the compiled file.
Thanks in advance John
Hi John
if you have run recon-all you should have a bunch of ex vivo BA labels in the label dir.
cheers Bruce On Wed, 13 Sep 2017, John Anderson wrote:
Dear FS experts, I have SUV maps for subjects within two groups. I moved these SUV maps into surface then I concatenated the images in the order of two groups then I used the compiled file in a glm analysis to check the difference between the two groups.
I aim to use V1 Atlas to derive the SUV values from the BA labels. I am not sure how to utilize these labels in such analysis. In this context I have two questions:
- Can these label be converted to ROIs similar to the ROIs derived from wmpar.mgz using the command
mri_binarize?
- in WIKI it was mentioned that the command "recon-all -s subjid -label_v1" output the stat values
for every BA label. How can I derive similar stats from the SUV maps in the compiled file.
Thanks in advance John
Thank you Dr Bruce, The stat values for every BA are generated using the command mris_anatomical_stats. I found this command in the stats file for one of the BAs. In this stats file I see values for gray matter volume, thickness ,... etc.
If I move SUV map or FA map to surface using the command mri_vol2surf. Then how can I generate the SUV and FA values from the BA labels similar to what the command mris_anatomical_stats does?
-------- Original Message -------- Subject: Re: [Freesurfer] BA Labels Local Time: September 13, 2017 2:57 PM UTC Time: September 13, 2017 6:57 PM From: fischl@nmr.mgh.harvard.edu To: John Anderson John.anderso@protonmail.com, Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Hi John
if you have run recon-all you should have a bunch of ex vivo BA labels in the label dir.
cheers Bruce On Wed, 13 Sep 2017, John Anderson wrote:
Dear FS experts, I have SUV maps for subjects within two groups. I moved these SUV maps into surface then I concatenated the images in the order of two groups then I used the compiled file in a glm analysis to check the difference between the two groups.
I aim to use V1 Atlas to derive the SUV values from the BA labels. I am not sure how to utilize these labels in such analysis. In this context I have two questions:
- Can these label be converted to ROIs similar to the ROIs derived from wmpar.mgz using the command
mri_binarize?
- in WIKI it was mentioned that the command "recon-all -s subjid -label_v1" output the stat values
for every BA label. How can I derive similar stats from the SUV maps in the compiled file.
Thanks in advance John
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.
you should be able to use mris_anatomical_stats I believe
cheers Bruce On Wed, 13 Sep 2017, John Anderson wrote:
Thank you Dr Bruce, The stat values for every BA are generated using the command mris_anatomical_stats. I found this command in the stats file for one of the BAs. In this stats file I see values for gray matter volume, thickness ,... etc.
If I move SUV map or FA map to surface using the command mri_vol2surf. Then how can I generate the SUV and FA values from the BA labels similar to what the command mris_anatomical_stats does?
-------- Original Message --------Subject: Re: [Freesurfer] BA Labels Local Time: September 13, 2017 2:57 PM UTC Time: September 13, 2017 6:57 PM From: fischl@nmr.mgh.harvard.edu To: John Anderson John.anderso@protonmail.com, Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Hi John
if you have run recon-all you should have a bunch of ex vivo BA labels in the label dir.
cheers Bruce On Wed, 13 Sep 2017, John Anderson wrote:
Dear FS experts, I have SUV maps for subjects within two groups. I moved these SUV maps into surface then I concatenated the images in the order of two groups then I used the compiled file in a glm
analysis
to check the difference between the two groups.
I aim to use V1 Atlas to derive the SUV values from the BA labels. I am not sure how to
utilize
these labels in such analysis. In this context I have two questions:
- Can these label be converted to ROIs similar to the ROIs derived from wmpar.mgz using the
command
mri_binarize?
- in WIKI it was mentioned that the command "recon-all -s subjid -label_v1" output the stat
values
for every BA label. How can I derive similar stats from the SUV maps in the compiled file.
Thanks in advance John
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.
It seems that this command doesn't accept input files. Are there any commands in Freesurfer that can do similar job?
-------- Original Message -------- Subject: Re: [Freesurfer] BA Labels Local Time: September 13, 2017 3:11 PM UTC Time: September 13, 2017 7:11 PM From: fischl@nmr.mgh.harvard.edu To: John Anderson John.anderso@protonmail.com Freesurfer support list freesurfer@nmr.mgh.harvard.edu
you should be able to use mris_anatomical_stats I believe
cheers Bruce On Wed, 13 Sep 2017, John Anderson wrote:
Thank you Dr Bruce, The stat values for every BA are generated using the command mris_anatomical_stats. I found this command in the stats file for one of the BAs. In this stats file I see values for gray matter volume, thickness ,... etc.
If I move SUV map or FA map to surface using the command mri_vol2surf. Then how can I generate the SUV and FA values from the BA labels similar to what the command mris_anatomical_stats does?
-------- Original Message -------- Subject: Re: [Freesurfer] BA Labels Local Time: September 13, 2017 2:57 PM UTC Time: September 13, 2017 6:57 PM From: fischl@nmr.mgh.harvard.edu To: John Anderson John.anderso@protonmail.com, Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Hi John
if you have run recon-all you should have a bunch of ex vivo BA labels in the label dir.
cheers Bruce On Wed, 13 Sep 2017, John Anderson wrote:
Dear FS experts, I have SUV maps for subjects within two groups. I moved these SUV maps into surface then I concatenated the images in the order of two groups then I used the compiled file in a glm
analysis
to check the difference between the two groups.
I aim to use V1 Atlas to derive the SUV values from the BA labels. I am not sure how to
utilize
these labels in such analysis. In this context I have two questions:
- Can these label be converted to ROIs similar to the ROIs derived from wmpar.mgz using the
command
mri_binarize?
- in WIKI it was mentioned that the command "recon-all -s subjid -label_v1" output the stat
values
for every BA label. How can I derive similar stats from the SUV maps in the compiled file.
Thanks in advance John
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.
mri_segstats with the --slabel option
On 09/13/2017 03:14 PM, John Anderson wrote:
It seems that this command doesn't accept input files. Are there any commands in Freesurfer that can do similar job?
-------- Original Message -------- Subject: Re: [Freesurfer] BA Labels Local Time: September 13, 2017 3:11 PM UTC Time: September 13, 2017 7:11 PM From: fischl@nmr.mgh.harvard.edu To: John Anderson John.anderso@protonmail.com Freesurfer support list freesurfer@nmr.mgh.harvard.edu
you should be able to use mris_anatomical_stats I believe
cheers Bruce On Wed, 13 Sep 2017, John Anderson wrote:
Thank you Dr Bruce, The stat values for every BA are generated using the command
mris_anatomical_stats. I found this
command in the stats file for one of the BAs. In this stats file I see values for gray matter volume, thickness
,... etc.
If I move SUV map or FA map to surface using the command
mri_vol2surf. Then how can I generate the
SUV and FA values from the BA labels similar to what the
command mris_anatomical_stats does?
-------- Original Message -------- Subject: Re: [Freesurfer] BA Labels Local Time: September 13, 2017 2:57 PM UTC Time: September 13, 2017 6:57 PM From: fischl@nmr.mgh.harvard.edu To: John Anderson John.anderso@protonmail.com, Freesurfer support
list
freesurfer@nmr.mgh.harvard.edu
Hi John
if you have run recon-all you should have a bunch of ex vivo BA
labels in
the label dir.
cheers Bruce On Wed, 13 Sep 2017, John Anderson wrote:
Dear FS experts, I have SUV maps for subjects within two groups. I moved these SUV
maps into surface then I
concatenated the images in the order of two groups then I used
the compiled file in a glm
analysis
to check the difference between the two groups.
I aim to use V1 Atlas to derive the SUV values from the BA
labels. I am not sure how to
utilize
these labels in such analysis. In this context I have two questions:
- Can these label be converted to ROIs similar to the ROIs
derived from wmpar.mgz using the
command
mri_binarize?
- in WIKI it was mentioned that the command "recon-all -s subjid
-label_v1" output the stat
values
for every BA label. How can I derive similar stats from the SUV
maps in the compiled file.
Thanks in advance John
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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