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Hello! I have a surface overlay that I want to extract the mean of the values within a label and export to a text file. How can I do that? I was looking into mris_anatomical_stats, but does mris_anatomical_stats let you tell it what file to pull the data from instead of just doing the standard extractions? Alternatively, I would be fine with just extracting all the values within the label and then finding the mean on my own. How could I extract all the values within the label and exporting to a text file?
Thanks, Sara Sims
look at mri_segstats. Run it with --help to get examples. Note that if your input volume has multiple frames, you can use --avgwf to get means of all the frames
On 4/19/2019 4:46 PM, Sims, Sara A (Campus) wrote:
External Email - Use Caution Hello! I have a surface overlay that I want to extract the mean of the values within a label and export to a text file. How can I do that? I was looking into mris_anatomical_stats, but does mris_anatomical_stats let you tell it what file to pull the data from instead of just doing the standard extractions? Alternatively, I would be fine with just extracting all the values within the label and then finding the mean on my own. How could I extract all the values within the label and exporting to a text file?
Thanks, Sara Sims
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Oh, I thought mri_segstats only took volumes. Can I feed it a surface with this flag: --surf-ctx-vol?
Sara Sims
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Saturday, April 20, 2019 at 12:07 PM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Extracting mean of values within a lable
look at mri_segstats. Run it with --help to get examples. Note that if your input volume has multiple frames, you can use --avgwf to get means of all the frames On 4/19/2019 4:46 PM, Sims, Sara A (Campus) wrote:
External Email - Use Caution Hello! I have a surface overlay that I want to extract the mean of the values within a label and export to a text file. How can I do that? I was looking into mris_anatomical_stats, but does mris_anatomical_stats let you tell it what file to pull the data from instead of just doing the standard extractions? Alternatively, I would be fine with just extracting all the values within the label and then finding the mean on my own. How could I extract all the values within the label and exporting to a text file?
Thanks, Sara Sims
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I think it is the --label flag. Run it with --help to see the docs
On 4/20/2019 10:16 PM, Sims, Sara A (Campus) wrote:
External Email - Use Caution Oh, I thought mri_segstats only took volumes. Can I feed it a surface with this flag: --surf-ctx-vol?
Sara Sims
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Saturday, April 20, 2019 at 12:07 PM To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Extracting mean of values within a lable
look at mri_segstats. Run it with --help to get examples. Note that if your input volume has multiple frames, you can use --avgwf to get means of all the frames On 4/19/2019 4:46 PM, Sims, Sara A (Campus) wrote:
External Email - Use Caution Hello! I have a surface overlay that I want to extract the mean of the values within a label and export to a text file. How can I do that? I was looking into mris_anatomical_stats, but does mris_anatomical_stats let you tell it what file to pull the data from instead of just doing the standard extractions? Alternatively, I would be fine with just extracting all the values within the label and then finding the mean on my own. How could I extract all the values within the label and exporting to a text file?
Thanks, Sara Sims
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Greve, Douglas N.,Ph.D. -
Sims, Sara A (Campus)