Dear FS folkers,
I am working on a functional probabilistic atlas. I find that some functional regions (particular along a big sulcus) show quite high probability value over a large sample, whereas the probability for some regions are quite lower. I think this disparity could be accounted for by the anatomical variation on each surface node that appears while surface-based registering individual surface to the average template that was provided by Freesurfer. For instance, the anatomical variation could be pretty small within a big sulcus (like central sulcus).
I assume that Freesurfer output a file which characterizes this type of anatomical variation. Could someone point me which file it is and how to use it to create a group-level measure in order to clear display somewhere has large variation. Thanks.
Best, Liang
Hi Liang
yes, that information is encoded in the .tif file that is the target of the registration. You can use mrisp_paint to copy a frame out of $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif
the tif file is 3 sets of triplets in different frames. The first is the mean of the measure, the second is the variance and the third is the degrees of freedom. The 3 triplets are for the curvature of the inflated surface, the sulc and mean curvature of the white surface.
cheers Bruce
On Thu, 13 Sep 2012, liang wang wrote:
Dear FS folkers, I am working on a functional probabilistic atlas. I find that some functional regions (particular along a big sulcus) show quite high probability value over a large sample, whereas the probability for some regions are quite lower. I think this disparity could be accounted for by the anatomical variation on each surface node that appears while surface-based registering individual surface to the average template that was provided by Freesurfer. For instance, the anatomical variation could be pretty small within a big sulcus (like central sulcus).
I assume that Freesurfer output a file which characterizes this type of anatomical variation. Could someone point me which file it is and how to use it to create a group-level measure in order to clear display somewhere has large variation. Thanks.
Best, Liang
-- Liang Wang, PhD Neuroscience of Attention and Perception Laboratory Princeton Neuroscience Institute Princeton University Princeton, NJ, 08540
Dear Bruce,
Thanks for pointing me those information. That .tif file includes the mean and variance for the population sample that was used in Freesurfer. I would like to get similar measures for our own subjects. I think I could use the surface file (like surf/?h.sulc) in each subject folder to compute the mean and variance, right? Is this file already in spherical template space? Thanks again.
Best, Liang
2012/9/14 Bruce Fischl fischl@nmr.mgh.harvard.edu
Hi Liang
yes, that information is encoded in the .tif file that is the target of the registration. You can use mrisp_paint to copy a frame out of $FREESURFER_HOME/average/?h.**average.curvature.filled.**buckner40.tif
the tif file is 3 sets of triplets in different frames. The first is the mean of the measure, the second is the variance and the third is the degrees of freedom. The 3 triplets are for the curvature of the inflated surface, the sulc and mean curvature of the white surface.
cheers Bruce
On Thu, 13 Sep 2012, liang wang wrote:
Dear FS folkers,
I am working on a functional probabilistic atlas. I find that some functional regions (particular along a big sulcus) show quite high probability value over a large sample, whereas the probability for some regions are quite lower. I think this disparity could be accounted for by the anatomical variation on each surface node that appears while surface-based registering individual surface to the average template that was provided by Freesurfer. For instance, the anatomical variation could be pretty small within a big sulcus (like central sulcus).
I assume that Freesurfer output a file which characterizes this type of anatomical variation. Could someone point me which file it is and how to use it to create a group-level measure in order to clear display somewhere has large variation. Thanks.
Best, Liang
-- Liang Wang, PhD Neuroscience of Attention and Perception Laboratory Princeton Neuroscience Institute Princeton University Princeton, NJ, 08540
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/**compliancelinehttp://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 can just run mris_preproc --meas curv --o stack.mgh ... This will give you a stack from which you can compute the mean and stddev mri_concat stack.mgh --mean --o stack.mean.mgh mri_concat stack.mgh --std --o stack.std.mgh
doug
On 09/14/2012 01:55 PM, liang wang wrote:
Dear Bruce,
Thanks for pointing me those information. That .tif file includes the mean and variance for the population sample that was used in Freesurfer. I would like to get similar measures for our own subjects. I think I could use the surface file (like surf/?h.sulc) in each subject folder to compute the mean and variance, right? Is this file already in spherical template space? Thanks again.
Best, Liang
2012/9/14 Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>
Hi Liang yes, that information is encoded in the .tif file that is the target of the registration. You can use mrisp_paint to copy a frame out of $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif the tif file is 3 sets of triplets in different frames. The first is the mean of the measure, the second is the variance and the third is the degrees of freedom. The 3 triplets are for the curvature of the inflated surface, the sulc and mean curvature of the white surface. cheers Bruce On Thu, 13 Sep 2012, liang wang wrote: Dear FS folkers, I am working on a functional probabilistic atlas. I find that some functional regions (particular along a big sulcus) show quite high probability value over a large sample, whereas the probability for some regions are quite lower. I think this disparity could be accounted for by the anatomical variation on each surface node that appears while surface-based registering individual surface to the average template that was provided by Freesurfer. For instance, the anatomical variation could be pretty small within a big sulcus (like central sulcus). I assume that Freesurfer output a file which characterizes this type of anatomical variation. Could someone point me which file it is and how to use it to create a group-level measure in order to clear display somewhere has large variation. Thanks. Best, Liang -- Liang Wang, PhD Neuroscience of Attention and Perception Laboratory Princeton Neuroscience Institute Princeton University Princeton, NJ, 08540 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.-- Liang Wang, PhD Neuroscience of Attention and Perception Laboratory Princeton Neuroscience Institute Princeton University Princeton, NJ, 08540
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
yes, you can use mris_make_template to generate these results (it's what we used to create the tif files in the first place) On Fri, 14 Sep 2012, liang wang wrote:
Dear Bruce, Thanks for pointing me those information. That .tif file includes the mean and variance for the population sample that was used in Freesurfer. I would like to get similar measures for our own subjects. I think I could use the surface file (like surf/?h.sulc) in each subject folder to compute the mean and variance, right? Is this file already in spherical template space? Thanks again.
Best, Liang
2012/9/14 Bruce Fischl fischl@nmr.mgh.harvard.edu Hi Liang
yes, that information is encoded in the .tif file that is the target of the registration. You can use mrisp_paint to copy a frame out of $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif the tif file is 3 sets of triplets in different frames. The first is the mean of the measure, the second is the variance and the third is the degrees of freedom. The 3 triplets are for the curvature of the inflated surface, the sulc and mean curvature of the white surface. cheers Bruce On Thu, 13 Sep 2012, liang wang wrote: Dear FS folkers, I am working on a functional probabilistic atlas. I find that some functional regions (particular along a big sulcus) show quite high probability value over a large sample, whereas the probability for some regions are quite lower. I think this disparity could be accounted for by the anatomical variation on each surface node that appears while surface-based registering individual surface to the average template that was provided by Freesurfer. For instance, the anatomical variation could be pretty small within a big sulcus (like central sulcus). I assume that Freesurfer output a file which characterizes this type of anatomical variation. Could someone point me which file it is and how to use it to create a group-level measure in order to clear display somewhere has large variation. Thanks. Best, Liang -- Liang Wang, PhD Neuroscience of Attention and Perception Laboratory Princeton Neuroscience Institute Princeton University Princeton, NJ, 08540The 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.
-- Liang Wang, PhD Neuroscience of Attention and Perception Laboratory Princeton Neuroscience Institute Princeton University Princeton, NJ, 08540
Thanks Bruce. one more question:
This is my command (5 subjects)
mris_make_template lh sphere.reg subj1 subj2 subj3 subj4 subj5 ./Temp5subj.tif
where I select sphere.reg as sphere surface. I assume 1) that the generated template Temp5subj.tif is in the Freesurfer buckner40 spherical space and 2) the mean and variance of the measure included in the new template are also in the buckner40 spherical space. Is that correct?
In addition, could you simply explain what's the difference between lh.curv and lh.sulc. Both files look similar and include negative and positive valude, except that lh.sulc seems to be smoothed. Thanks.
Best, Liang
2012/9/14 Bruce Fischl fischl@nmr.mgh.harvard.edu
yes, you can use mris_make_template to generate these results (it's what we used to create the tif files in the first place)
On Fri, 14 Sep 2012, liang wang wrote:
Dear Bruce,
Thanks for pointing me those information. That .tif file includes the mean and variance for the population sample that was used in Freesurfer. I would like to get similar measures for our own subjects. I think I could use the surface file (like surf/?h.sulc) in each subject folder to compute the mean and variance, right? Is this file already in spherical template space? Thanks again.
Best, Liang
2012/9/14 Bruce Fischl fischl@nmr.mgh.harvard.edu Hi Liang
yes, that information is encoded in the .tif file that is thetarget of the registration. You can use mrisp_paint to copy a frame out of $FREESURFER_HOME/average/?h.**average.curvature.filled.** buckner40.tif
the tif file is 3 sets of triplets in different frames. The first is the mean of the measure, the second is the variance and the third is the degrees of freedom. The 3 triplets are for the curvature of the inflated surface, the sulc and mean curvature of the white surface. cheers Bruce On Thu, 13 Sep 2012, liang wang wrote: Dear FS folkers, I am working on a functional probabilistic atlas. I find that some functional regions (particular along a big sulcus) show quite high probability value over a large sample, whereas the probability for some regions are quite lower. I think this disparity could be accounted for by the anatomical variation on each surface node that appears while surface-based registering individual surface to the average template that was provided by Freesurfer. For instance, the anatomical variation could be pretty small within a big sulcus (like central sulcus). I assume that Freesurfer output a file which characterizes this type of anatomical variation. Could someone point me which file it is and how to use it to create a group-level measure in order to clear display somewhere has large variation. Thanks. Best, Liang -- Liang Wang, PhD Neuroscience of Attention and Perception Laboratory Princeton Neuroscience Institute Princeton University Princeton, NJ, 08540The 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/**compliancelinehttp://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.
-- Liang Wang, PhD Neuroscience of Attention and Perception Laboratory Princeton Neuroscience Institute Princeton University Princeton, NJ, 08540
Hi Liang
the sulc is the integrated signed dot product of the movement vector with the surface normal during inflation. It reflects large scale geometry better than ?h.curv, which is the spatially smoothed mean curvature. If you are using sphere.reg you can probably specify -norot so it doesn't try to do rigid registration on the sphere (since they are already registered)
cheers Bruce
On Fri, 14 Sep 2012, liang wang wrote:
Thanks Bruce. one more question: This is my command (5 subjects)
mris_make_template lh sphere.reg subj1 subj2 subj3 subj4 subj5 ./Temp5subj.tif
where I select sphere.reg as sphere surface. I assume 1) that the generated template Temp5subj.tif is in the Freesurfer buckner40 spherical space and 2) the mean and variance of the measure included in the new template are also in the buckner40 spherical space. Is that correct?
In addition, could you simply explain what's the difference between lh.curv and lh.sulc. Both files look similar and include negative and positive valude, except that lh.sulc seems to be smoothed. Thanks.
Best, Liang
2012/9/14 Bruce Fischl fischl@nmr.mgh.harvard.edu yes, you can use mris_make_template to generate these results (it's what we used to create the tif files in the first place) On Fri, 14 Sep 2012, liang wang wrote:
Dear Bruce, Thanks for pointing me those information. That .tif file includes the mean and variance for the population sample that was used in Freesurfer. I would like to get similar measures for our own subjects. I think I could use the surface file (like surf/?h.sulc) in each subject folder to compute the mean and variance, right? Is this file already in spherical template space? Thanks again. Best, Liang 2012/9/14 Bruce Fischl <fischl@nmr.mgh.harvard.edu> Hi Liang yes, that information is encoded in the .tif file that is the target of the registration. You can use mrisp_paint to copy a frame out of $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif the tif file is 3 sets of triplets in different frames. The first is the mean of the measure, the second is the variance and the third is the degrees of freedom. The 3 triplets are for the curvature of the inflated surface, the sulc and mean curvature of the white surface. cheers Bruce On Thu, 13 Sep 2012, liang wang wrote: Dear FS folkers, I am working on a functional probabilistic atlas. I find that some functional regions (particular along a big sulcus) show quite high probability value over a large sample, whereas the probability for some regions are quite lower. I think this disparity could be accounted for by the anatomical variation on each surface node that appears while surface-based registering individual surface to the average template that was provided by Freesurfer. For instance, the anatomical variation could be pretty small within a big sulcus (like central sulcus). I assume that Freesurfer output a file which characterizes this type of anatomical variation. Could someone point me which file it is and how to use it to create a group-level measure in order to clear display somewhere has large variation. Thanks. Best, Liang -- Liang Wang, PhD Neuroscience of Attention and Perception Laboratory Princeton Neuroscience Institute Princeton University Princeton, NJ, 08540 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. -- Liang Wang, PhD Neuroscience of Attention and Perception Laboratory Princeton Neuroscience Institute Princeton University Princeton, NJ, 08540-- Liang Wang, PhD Neuroscience of Attention and Perception Laboratory Princeton Neuroscience Institute Princeton University Princeton, NJ, 08540
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas N Greve -
liang wang