Does the cortex label have any holes in it and do the holes in your output correspond? Try it with out the --cortex flag. doug
ps. Please remember to send to the list and not to me directly. That way others can benefit from the exchange and the record goes into our mail archive.
On 05/09/2013 11:07 AM, Glen Lee wrote:
Hi Doug
See below for the command line that I used.
smoothK=4;
mri_surf2surf --hemi lh --s fsaverage_sym --fwhm ' ... num2str(smoothK) ' --cortex --sval ' Functional_dir Subj '/GLM/all_base-sym_R.mgh '...
On Wed, May 8, 2013 at 11:31 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Glen, can you give us more information about what you did? Eg, command line? doug On 5/8/13 8:53 PM, Glen Lee wrote:Hello freesurfer experts, I'm a newbie for freesurfer and would like to ask a naive question. I've just applied smoothing onto a single surface mgh file using mri_surf2surf (with fwhm ==4) and examined the values in the output map. As it turns out, values become 0 in a number of vertices after smoothing while those in many other vertices look normal (i.e., more or less similar to the values in the vertex of unsmoothed map). I'm not sure why this happened as smoothing average values locally within the kernel (4mm). Any helpful answers would be greatly appreciated. Glen p.s) fyi, the original EPI is a slap data covering only the temporal & occipital cortex. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.
Thanks Doug. I'll give it a try right away.
Glen
On Thu, May 9, 2013 at 11:28 AM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Does the cortex label have any holes in it and do the holes in your output correspond? Try it with out the --cortex flag. doug
ps. Please remember to send to the list and not to me directly. That way others can benefit from the exchange and the record goes into our mail archive.
On 05/09/2013 11:07 AM, Glen Lee wrote:
Hi Doug
See below for the command line that I used.
smoothK=4;
mri_surf2surf --hemi lh --s fsaverage_sym --fwhm ' ... num2str(smoothK) ' --cortex --sval ' Functional_dir Subj '/GLM/all_base-sym_R.mgh '...
On Wed, May 8, 2013 at 11:31 PM, Douglas Greve <greve@nmr.mgh.harvard.edu<mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>> wrote:
Hi Glen, can you give us more information about what you did? Eg, command line? doug On 5/8/13 8:53 PM, Glen Lee wrote:Hello freesurfer experts, I'm a newbie for freesurfer and would like to ask a naive question. I've just applied smoothing onto a single surface mgh file using mri_surf2surf (with fwhm ==4) and examined the values in the output map. As it turns out, values become 0 in a number of vertices after smoothing while those in many other vertices look normal (i.e., more or less similar to the values in the vertex of unsmoothed map). I'm not sure why this happened as smoothing average values locally within the kernel (4mm). Any helpful answers would be greatly appreciated. Glen p.s) fyi, the original EPI is a slap data covering only the temporal & occipital cortex. ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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.-- 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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
On Thu, May 9, 2013 at 11:28 AM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Does the cortex label have any holes in it and do the holes in your output correspond? Try it with out the --cortex flag. doug -> there was some improvement when I did smoothing after removed '-- cortex flag', such that the number of vertex with '0' was decreased from 35785 to 21898.
I piped in a slab EPI image (covering only temporal regions) to the freesurfer using mri_vol2surf function (see below for more details). I'm guessing this has caused some holes (i.e., zero-value vertices) in labels during 2D reconstruction? Or alternatively, do you see any problem in the command below?
mri_vol2surf --src ' Functional_dir Subj '/FUNCTIONAL/rabold' num2str(run) zero_digit num2str(TR) '.nii' ... ' --srcreg ~/DMPC/3D/data/' Subj '/ANATOMY_SPM/FS-register.dat --hemi rh --projfrac 0.5 --noreshape --o ~/DMPC/2D/data/' Subj '/MGH/rabold' num2str(run) zero_digit num2str(TR) '_R.mgh'];
command looks ok. Just using a slab would create 0s in a lot of places, but those 0s should get smoothed with other non 0s
On 05/09/2013 02:06 PM, Glen Lee wrote:
On Thu, May 9, 2013 at 11:28 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Does the cortex label have any holes in it and do the holes in your output correspond? Try it with out the --cortex flag. doug -> there was some improvement when I did smoothing after removed '-- cortex flag', such that the number of vertex with '0' was decreased from 35785 to 21898.I piped in a slab EPI image (covering only temporal regions) to the freesurfer using mri_vol2surf function (see below for more details). I'm guessing this has caused some holes (i.e., zero-value vertices) in labels during 2D reconstruction? Or alternatively, do you see any problem in the command below?
mri_vol2surf --src ' Functional_dir Subj '/FUNCTIONAL/rabold' num2str(run) zero_digit num2str(TR) '.nii' ... ' --srcreg ~/DMPC/3D/data/' Subj '/ANATOMY_SPM/FS-register.dat --hemi rh --projfrac 0.5 --noreshape --o ~/DMPC/2D/data/' Subj '/MGH/rabold' num2str(run) zero_digit num2str(TR) '_R.mgh'];
You are right, Doug. The number of zero-value vertices got reduced more and more when I increased the smoothing kernel size.
Thanks a lot for your help! -Glen
On Thu, May 9, 2013 at 3:29 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
command looks ok. Just using a slab would create 0s in a lot of places, but those 0s should get smoothed with other non 0s
On 05/09/2013 02:06 PM, Glen Lee wrote:
On Thu, May 9, 2013 at 11:28 AM, Douglas N Greve < greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu>> wrote:
Does the cortex label have any holes in it and do the holes in your output correspond? Try it with out the --cortex flag. doug -> there was some improvement when I did smoothing after removed '-- cortex flag', such that the number of vertex with '0' was decreased from 35785 to 21898.I piped in a slab EPI image (covering only temporal regions) to the freesurfer using mri_vol2surf function (see below for more details). I'm guessing this has caused some holes (i.e., zero-value vertices) in labels during 2D reconstruction? Or alternatively, do you see any problem in the command below?
mri_vol2surf --src ' Functional_dir Subj '/FUNCTIONAL/rabold' num2str(run) zero_digit num2str(TR) '.nii' ... ' --srcreg ~/DMPC/3D/data/' Subj '/ANATOMY_SPM/FS-register.dat --hemi rh --projfrac 0.5 --noreshape --o ~/DMPC/2D/data/' Subj '/MGH/rabold' num2str(run) zero_digit num2str(TR) '_R.mgh'];
-- 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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
Glen Lee