Volumetric Group Analysis: asegstats2tbale result to plot a z-score map for the segmentation
Hello, FS experts:
I have a question for visualizing statistical analysis asegstats2tbale result into a map like what we have done in qdec, which uses the thickness information, so if i want to use the volume information of the different segmentation volume, and after doing z-score for two groups, how can I visualize it into a z map???
For example, for the volumetric group analysis, I compute the z-scores for the different subcortical volumes between these two group, how do i visualize the result in sphere???
Really need your help
Any help will be appreciated
Hao
This is a tricky thing to do. I've created a matlab file to help, which you can get from here:
https://gate.nmr.mgh.harvard.edu/safelinks/greve/annotval2surfoverlay.m
Look at the help for an example on how to use it. You will have to specify the list of ROI names and the corresponding list of values that you want each ROI to be filled with. See the example
On 12/6/16 9:57 AM, Hao wen wrote:
Hello, FS experts:
I have a question for visualizing statistical analysis asegstats2tbale result into a map like what we have done in qdec, which uses the thickness information, so if i want to use the volume information of the different segmentation volume, and after doing z-score for two groups, how can I visualize it into a z map???
For example, for the volumetric group analysis, I compute the z-scores for the different subcortical volumes between these two group, how do i visualize the result in sphere???
Really need your help
Any help will be appreciated
Hao
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks very much, I will try to look at that:)
Perfect FS,hahah
________________________________ De : freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Douglas Greve greve@nmr.mgh.harvard.edu Envoyé : mardi 6 décembre 2016 17:51 À : freesurfer@nmr.mgh.harvard.edu Objet : Re: [Freesurfer] Volumetric Group Analysis: asegstats2tbale result to plot a z-score map for the segmentation
This is a tricky thing to do. I've created a matlab file to help, which you can get from here:
https://gate.nmr.mgh.harvard.edu/safelinks/greve/annotval2surfoverlay.m
Look at the help for an example on how to use it. You will have to specify the list of ROI names and the corresponding list of values that you want each ROI to be filled with. See the example
On 12/6/16 9:57 AM, Hao wen wrote:
Hello, FS experts:
I have a question for visualizing statistical analysis asegstats2tbale result into a map like what we have done in qdec, which uses the thickness information, so if i want to use the volume information of the different segmentation volume, and after doing z-score for two groups, how can I visualize it into a z map???
For example, for the volumetric group analysis, I compute the z-scores for the different subcortical volumes between these two group, how do i visualize the result in sphere???
Really need your help
Any help will be appreciated
Hao
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello, I checked your script, I think this is to map the aparc.annot, I have already done that, what I want is to map the aseg.annot subcortical segmentation like what we can do for aparc, so do you have any idea?? Thanks in advance
________________________________ De : Hao wen Envoyé : mardi 6 décembre 2016 18:18 À : freesurfer@nmr.mgh.harvard.edu Objet : RE: [Freesurfer] Volumetric Group Analysis: asegstats2tbale result to plot a z-score map for the segmentation
Thanks very much, I will try to look at that:)
Perfect FS,hahah
________________________________ De : freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Douglas Greve greve@nmr.mgh.harvard.edu Envoyé : mardi 6 décembre 2016 17:51 À : freesurfer@nmr.mgh.harvard.edu Objet : Re: [Freesurfer] Volumetric Group Analysis: asegstats2tbale result to plot a z-score map for the segmentation
This is a tricky thing to do. I've created a matlab file to help, which you can get from here:
https://gate.nmr.mgh.harvard.edu/safelinks/greve/annotval2surfoverlay.m
Look at the help for an example on how to use it. You will have to specify the list of ROI names and the corresponding list of values that you want each ROI to be filled with. See the example
On 12/6/16 9:57 AM, Hao wen wrote:
Hello, FS experts:
I have a question for visualizing statistical analysis asegstats2tbale result into a map like what we have done in qdec, which uses the thickness information, so if i want to use the volume information of the different segmentation volume, and after doing z-score for two groups, how can I visualize it into a z map???
For example, for the volumetric group analysis, I compute the z-scores for the different subcortical volumes between these two group, how do i visualize the result in sphere???
Really need your help
Any help will be appreciated
Hao
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
That is a little easier. In matlab you can
seg = MRIread('youseg.mgz');
out = seg;
out.vol = zeros(size(out.vol));
ind = find(seg.vol == segno);
out.vol(ind) = valueforsegno;
MRIwrite(out,'out.mgz');
On 12/06/2016 05:04 PM, Hao wen wrote:
Hello, I checked your script, I think this is to map the aparc.annot, I have already done that, what I want is to map the aseg.annot subcortical segmentation like what we can do for aparc, so do you have any idea?? Thanks in advance
*De :* Hao wen *Envoyé :* mardi 6 décembre 2016 18:18 *À :* freesurfer@nmr.mgh.harvard.edu *Objet :* RE: [Freesurfer] Volumetric Group Analysis: asegstats2tbale result to plot a z-score map for the segmentation
Thanks very much, I will try to look at that:)
Perfect FS,hahah
*De :* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Douglas Greve greve@nmr.mgh.harvard.edu *Envoyé :* mardi 6 décembre 2016 17:51 *À :* freesurfer@nmr.mgh.harvard.edu *Objet :* Re: [Freesurfer] Volumetric Group Analysis: asegstats2tbale result to plot a z-score map for the segmentation
This is a tricky thing to do. I've created a matlab file to help, which you can get from here:
https://gate.nmr.mgh.harvard.edu/safelinks/greve/annotval2surfoverlay.m
Look at the help for an example on how to use it. You will have to specify the list of ROI names and the corresponding list of values that you want each ROI to be filled with. See the example
On 12/6/16 9:57 AM, Hao wen wrote:
Hello, FS experts:
I have a question for visualizing statistical analysis asegstats2tbale result into a map like what we have done in qdec, which uses the thickness information, so if i want to use the volume information of the different segmentation volume, and after doing z-score for two groups, how can I visualize it into a z map???
For example, for the volumetric group analysis, I compute the z-scores for the different subcortical volumes between these two group, how do i visualize the result in sphere???
Really need your help
Any help will be appreciated
Hao
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks for your advice,
After I got 'out.mgz', I know for aparc.annot, pysurfer use tksurfer to visualize the map, but for aseg.annot, because it is volume_based analysis, I want to have some thing like this, which has been down in freeview to display the segmentation output of recon-alll output:
[cid:43761105-d3db-43de-ad35-74ac853603b0]
But the different colors for the subcortical regions will be the correspondent z-value for two groups, so what do you think if we can make it by tksurfer, tkmedit or freeview?? Thanks very much ________________________________ De : freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Douglas N Greve greve@nmr.mgh.harvard.edu Envoyé : mardi 6 décembre 2016 23:21 À : freesurfer@nmr.mgh.harvard.edu Objet : Re: [Freesurfer] Volumetric Group Analysis: asegstats2tbale result to plot a z-score map for the segmentation
That is a little easier. In matlab you can
seg = MRIread('youseg.mgz');
out = seg;
out.vol = zeros(size(out.vol));
ind = find(seg.vol == segno);
out.vol(ind) = valueforsegno;
MRIwrite(out,'out.mgz');
On 12/06/2016 05:04 PM, Hao wen wrote:
Hello, I checked your script, I think this is to map the aparc.annot, I have already done that, what I want is to map the aseg.annot subcortical segmentation like what we can do for aparc, so do you have any idea?? Thanks in advance
*De :* Hao wen *Envoyé :* mardi 6 décembre 2016 18:18 *À :* freesurfer@nmr.mgh.harvard.edu *Objet :* RE: [Freesurfer] Volumetric Group Analysis: asegstats2tbale result to plot a z-score map for the segmentation
Thanks very much, I will try to look at that:)
Perfect FS,hahah
*De :* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Douglas Greve greve@nmr.mgh.harvard.edu *Envoyé :* mardi 6 décembre 2016 17:51 *À :* freesurfer@nmr.mgh.harvard.edu *Objet :* Re: [Freesurfer] Volumetric Group Analysis: asegstats2tbale result to plot a z-score map for the segmentation
This is a tricky thing to do. I've created a matlab file to help, which you can get from here:
https://gate.nmr.mgh.harvard.edu/safelinks/greve/annotval2surfoverlay.m
Look at the help for an example on how to use it. You will have to specify the list of ROI names and the corresponding list of values that you want each ROI to be filled with. See the example
On 12/6/16 9:57 AM, Hao wen wrote:
Hello, FS experts:
I have a question for visualizing statistical analysis asegstats2tbale result into a map like what we have done in qdec, which uses the thickness information, so if i want to use the volume information of the different segmentation volume, and after doing z-score for two groups, how can I visualize it into a z map???
For example, for the volumetric group analysis, I compute the z-scores for the different subcortical volumes between these two group, how do i visualize the result in sphere???
Really need your help
Any help will be appreciated
Hao
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer Info Page - Harvard Universityhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives. A searchable archive which of messages PRIOR to March 2004 is at ...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer Info Page - Harvard Universityhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives. A searchable archive which of messages PRIOR to March 2004 is at ...
-- 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 FileDrop v2.0 - Martinos Center for Biomedical Imaginghttps://gate.nmr.mgh.harvard.edu/filedrop2 gate.nmr.mgh.harvard.edu Filedrop is for sending files work-related files up to 2GiB; For files over 2GiB, please use the Accellion File Transfer from Partners; Filedrop is not a secure ...
www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Martinos Center File Drophttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html www.nmr.mgh.harvard.edu 11/15/2012 -- There is a new version of Filedrop. Please help us test it https://gate.nmr.mgh.harvard.edu/filedrop2/ Welcome to the Martinos Center file drop area.
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________ Freesurfer mailing list 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.
use tkmedit or freeview
On 12/07/2016 07:43 AM, Hao wen wrote:
Thanks for your advice,
After I got 'out.mgz', I know for aparc.annot, pysurfer use tksurfer to visualize the map, but for aseg.annot, because it is volume_based analysis, I want to have some thing like this, which has been down in freeview to display the segmentation output of recon-alll output:
But the different colors for the subcortical regions will be the correspondent z-value for two groups, so what do you think if we can make it by tksurfer, tkmedit or freeview?? Thanks very much
*De :* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Douglas N Greve greve@nmr.mgh.harvard.edu *Envoyé :* mardi 6 décembre 2016 23:21 *À :* freesurfer@nmr.mgh.harvard.edu *Objet :* Re: [Freesurfer] Volumetric Group Analysis: asegstats2tbale result to plot a z-score map for the segmentation That is a little easier. In matlab you can
seg = MRIread('youseg.mgz');
out = seg;
out.vol = zeros(size(out.vol));
ind = find(seg.vol == segno);
out.vol(ind) = valueforsegno;
MRIwrite(out,'out.mgz');
On 12/06/2016 05:04 PM, Hao wen wrote:
Hello, I checked your script, I think this is to map the aparc.annot, I have already done that, what I want is to map the aseg.annot subcortical segmentation like what we can do for aparc, so do you have any idea?? Thanks in advance
*De :* Hao wen *Envoyé :* mardi 6 décembre 2016 18:18 *À :* freesurfer@nmr.mgh.harvard.edu *Objet :* RE: [Freesurfer] Volumetric Group Analysis: asegstats2tbale result to plot a z-score map for the segmentation
Thanks very much, I will try to look at that:)
Perfect FS,hahah
*De :* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Douglas Greve greve@nmr.mgh.harvard.edu *Envoyé :* mardi 6 décembre 2016 17:51 *À :* freesurfer@nmr.mgh.harvard.edu *Objet :* Re: [Freesurfer] Volumetric Group Analysis: asegstats2tbale result to plot a z-score map for the segmentation
This is a tricky thing to do. I've created a matlab file to help, which you can get from here:
https://gate.nmr.mgh.harvard.edu/safelinks/greve/annotval2surfoverlay.m
Look at the help for an example on how to use it. You will have to specify the list of ROI names and the corresponding list of values that you want each ROI to be filled with. See the example
On 12/6/16 9:57 AM, Hao wen wrote:
Hello, FS experts:
I have a question for visualizing statistical analysis asegstats2tbale result into a map like what we have done in qdec, which uses the thickness information, so if i want to use the volume information of the different segmentation volume, and after doing z-score for two groups, how can I visualize it into a z map???
For example, for the volumetric group analysis, I compute the z-scores for the different subcortical volumes between these two group, how do i visualize the result in sphere???
Really need your help
Any help will be appreciated
Hao
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer Info Page - Harvard University https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives. A searchable archive which of messages PRIOR to March 2004 is at ...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer Info Page - Harvard University https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives. A searchable archive which of messages PRIOR to March 2004 is at ...
-- 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 https://gate.nmr.mgh.harvard.edu/filedrop2 FileDrop v2.0 - Martinos Center for Biomedical Imaging https://gate.nmr.mgh.harvard.edu/filedrop2 gate.nmr.mgh.harvard.edu Filedrop is for sending files work-related files up to 2GiB; For files over 2GiB, please use the Accellion File Transfer from Partners; Filedrop is not a secure ...
www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Martinos Center File Drop http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html www.nmr.mgh.harvard.edu 11/15/2012 -- There is a new version of Filedrop. Please help us test it https://gate.nmr.mgh.harvard.edu/filedrop2/ Welcome to the Martinos Center file drop area.
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list 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
freesurfer@nmr.mgh.harvard.edu
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Douglas Greve -
Douglas N Greve
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Hao wen