Hi Bruce and Doug,

Thanks so much for the advice.

I think I'll try to hack something together since I have to perform this step for numerous subjects.

One quick question - is the order of the vertices preserved between the pial curv and spherical curv ascii files?

Thanks again,

John

On 11/9/15 8:04 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:

there used to be something built into tksurfer to do soap bubble smoothing. You can try smooth_vals_spare from the tcl prompt. I think it depends on setting the fixedval field in the vertex struct to 1 for the stationary points of the soap bubble. You can first read in a file that is 1 for the fixed points and zero elsewhere then call fix_nonzero_vals. Then load the vals you want and try the soap bubble. It's pretty old code and hasn't been used in ages though, so it is likely to have problems.

I guess writing a stand-alone soap bubble would be pretty trivial, so if you find this doesn't work and this is important to you let us know and I'll add it to our to-do list.

cheers Bruce

On Mon, 9 Nov 2015, Douglas N Greve wrote:

...

Sounds like you are trying to do soap bubble interpolation (?). I don't think we have a binary for that. Maybe Bruce knows of one. You could hack something together, with smoothing (mri_surf2surf), creating binary masks (mris_binarize), and masking (mri_mask), and basic math operations (fscalc).

On 11/09/2015 02:07 PM, Gardus III, John D wrote:

...

Hello all,

I'm in the process of mapping some non-FreeSurfer derived outcomes to a curv file containing the vertices of the pial surface mesh. I have values at roughly 100 vertices, leaving some 37000 with 'nan'.

I then run an intra-subject surf2surf command in an attempt to interpolate between vertices for which I have values. The problem is that the NaNs pull the existing values down, resulting in a smearing/dilution of my outcomes.

Is there any way to interpolate and make the intervening vertices purely a function of nearby vertices for which values exist?

Thanks,

John

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as long as it is the same subject/hemi, then yes On Tue, 10 Nov 2015, Gardus III, John D wrote:

Hi Bruce and Doug,

Thanks so much for the advice.

I think I'll try to hack something together since I have to perform this step for numerous subjects.

One quick question - is the order of the vertices preserved between the pial curv and spherical curv ascii files?

Thanks again,

John

On 11/9/15 8:04 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:

...

there used to be something built into tksurfer to do soap bubble smoothing. You can try smooth_vals_spare from the tcl prompt. I think it depends on setting the fixedval field in the vertex struct to 1 for the stationary points of the soap bubble. You can first read in a file that is 1 for the fixed points and zero elsewhere then call fix_nonzero_vals. Then load the vals you want and try the soap bubble. It's pretty old code and hasn't been used in ages though, so it is likely to have problems.

I guess writing a stand-alone soap bubble would be pretty trivial, so if you find this doesn't work and this is important to you let us know and I'll add it to our to-do list.

cheers Bruce

On Mon, 9 Nov 2015, Douglas N Greve wrote:

...

Sounds like you are trying to do soap bubble interpolation (?). I don't think we have a binary for that. Maybe Bruce knows of one. You could hack something together, with smoothing (mri_surf2surf), creating binary masks (mris_binarize), and masking (mri_mask), and basic math operations (fscalc).

On 11/09/2015 02:07 PM, Gardus III, John D wrote:

...

Hello all,

I'm in the process of mapping some non-FreeSurfer derived outcomes to a curv file containing the vertices of the pial surface mesh. I have values at roughly 100 vertices, leaving some 37000 with 'nan'.

I then run an intra-subject surf2surf command in an attempt to interpolate between vertices for which I have values. The problem is that the NaNs pull the existing values down, resulting in a smearing/dilution of my outcomes.

Is there any way to interpolate and make the intervening vertices purely a function of nearby vertices for which values exist?

Thanks,

John

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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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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.

This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by e-mail and destroy all copies of the original.

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