Re: [Freesurfer] Question about ?h.sulc and ?h.curv
Thanks, Bruce and Matt. bestJingDate: Wed, 8 Feb 2012 11:53:44 -0500 From: fis...@nmr.mgh.harvard.edu To: m...@ma-tea.com CC: freesurfer@nmr.mgh.harvard.edu; mj_com...@hotmail.com Subject: Re: [Freesurfer] Question about ?h.sulc and ?h.curv oops, thanks Matt Bruce On Wed, 8 Feb 2012, Matt Glasser wrote: > I think Bruce meant: > > "the ?h.sulc is the integrated dot > product of the movement vector with the surface normal during inflation." > > Peace, > > Matt. > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent: Wednesday, February 08, 2012 10:48 AM > To: Jing Ming > Cc: Freesurfer > Subject: Re: [Freesurfer] Question about ?h.sulc and ?h.curv > > They are computed from the ?h.white surface. The ?h.curv is the > spatially smoothed mean curvature, and the ?h.curv is the integrated dot > product of the movement vector with the surface normal during inflation. > Therefore the curv is a local differential measure that will highlight > small scale structure, while the sulc is insensitive to small local > geometry and highlights larger scale structure (e.g. was the point deep > even though it was folded out) > > On > Tue, 7 Feb 2012, Jing Ming wrote: > >> Hi surfers: >> >>I have a two questions. >> >> 1) how does freesurfer calculate ?h.sulc file and ?h.curv. Are they > calculated after gray/white/csf segmentation? Are they calculate based on > gray/white boundary? >> So, difference between ?h.sulc or ?h.curv will directly come from white > matter change, right? >> >> 2) what's the difference between ?h.sulc and ?h.curv? In terms of sulcal > structure, does ?h.sulc indicate sulcal depth and ?h.curv somehow indicate > sulcal width? >> To me, from the display, ?h.sulc seems a smoothed version of ?h.curv. From > some reference, I know .sulc is also called average convexity, so is the > convexity for >> each vertex averaged within a small region or is it averaged through the > whole hemisphere brain surface? >> >>Thanks much for your help! >> >> Best >> Jing >> >> > > > > ___ 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 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] Question about ?h.sulc and ?h.curv
Hi surfers: I have a two questions. 1) how does freesurfer calculate ?h.sulc file and ?h.curv. Are they calculated after gray/white/csf segmentation? Are they calculate based on gray/white boundary? So, difference between ?h.sulc or ?h.curv will directly come from white matter change, right? 2) what's the difference between ?h.sulc and ?h.curv? In terms of sulcal structure, does ?h.sulc indicate sulcal depth and ?h.curv somehow indicate sulcal width? To me, from the display, ?h.sulc seems a smoothed version of ?h.curv. From some reference, I know .sulc is also called average convexity, so is the convexity for each vertex averaged within a small region or is it averaged through the whole hemisphere brain surface?Thanks much for your help! BestJing___ 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.
Re: [Freesurfer] manual editting problem
Thanks Bruce. Jing > Date: Fri, 16 Sep 2011 08:38:55 -0400 > From: fis...@nmr.mgh.harvard.edu > To: k...@nmr.mgh.harvard.edu > CC: s...@nmr.mgh.harvard.edu; jennifer_g_gold...@rush.edu; vy_d...@rush.edu; > freesurfer@nmr.mgh.harvard.edu; mj_com...@hotmail.com > Subject: Re: [Freesurfer] manual editting problem > > p.s. you also have topological defects there, which you can tell as the > orig (green) surface doesn't follow the voxels in the wm.mgz. The > interventions Khoa suggests should help this as well. If you are missing > that much wm you probably want to use control points. > > cheers > Bruce > > > > On Thu, 15 Sep 2011, k...@nmr.mgh.harvard.edu > wrote: > > > Hi Jing, > > > > You have some white matter voxels missing in the wm.mgz for the rh. You > > can add some wm to that volume using the edit tool or you can also try > > control points. If you are adding wm, make sure you select the aux volume > > on the brush info toolbox. Fill in wm voxels for all slices. Control > > points would help with extending the pial surf on the lh. > > > > -Khoa > > > >> > >> Hi Bruce and Sita: > >> > >> Thanks for your relay. And Here are the images. > >> > >> Jing > >> > >> > >> > >> From: Jing Ming [mj_com...@hotmail.com] > >> > >> Sent: Thursday, September 15, 2011 7:31 PM > >> > >> To: Vy Dinh > >> > >> Subject: FW: [Freesurfer] manual editting problem > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >>> CC: mj_com...@hotmail.com; jennifer_g_gold...@rush.edu; vyd...@rush.edu; > >>> freesurfer@nmr.mgh.harvard.edu > >> > >>> From: fis...@nmr.mgh.harvard.edu > >> > >>> Subject: Re: [Freesurfer] manual editting problem > >> > >>> Date: Thu, 15 Sep 2011 20:07:41 -0400 > >> > >>> To: s...@nmr.mgh.harvard.edu > >> > >>> > >> > >>> Can you send an image? > >> > >>> > >> > >>> > >> > >>> > >> > >>> On Sep 15, 2011, at 6:38 PM, Sita Kakunoori > >>> wrote: > >> > >>> > >> > >>>> > >> > >>>> How does the wm.mgz look. Correcting the white surface will correct > >>> the > >> > >>>> pial surface as well. > >> > >>>> > >> > >>>> Sita. > >> > >>>> > >> > >>>> > >> > >>>> On Thu, 15 Sep 2011, Jing Ming wrote: > >> > >>>> > >> > >>>>> > >> > >>>>> Hi Surfers: > >> > >>>>> We have been coming > >> > >>>>> across several gray matter regions that are not included within the > >>> pial > >> > >>>>> surface (red line) when it should be (e.g., very anterior parts of > >>> the > >> > >>>>> temporal lobe). From my understanding of similar posts on the forum, > >>> it > >> > >>>>> seems that there isn't a way to add this region to the pial surface > >>> so > >> > >>>>> that the missing brain matter is included. We have tried using the > >>> clone > >> > >>>>> tool to fill in this region, as per the tutorial and have > >>> experimented > >> > >>>>> with this tool using the tutorial data. I followed the steps in the > >> > >>>>> tutorial but could not observe any changes when the middle button was > >> > >>>>> selected. Does anyone have any ideas on how to troubleshoot this > >> > >>>>> issue? Can someone please explain to me why this is not possible? > >>> Also > >> > >>>>> how does Freesurfer determine what regions to include within the pial > >> > >>>>> surface? If there is a way that has been developed recently, please > >> > >>>>> enlighten me. > >> > >>>>> > >> > >>>>> -Jing > >> > >>>> ___ > >> > >>>> Freesurfer mailing list > >> > >>>> Freesurfer@nmr.mgh.harvard.edu > >> > >>>>
Re: [Freesurfer] manual editting problem
Thanks much Khoa. Jing > Date: Thu, 15 Sep 2011 22:00:39 -0400 > From: k...@nmr.mgh.harvard.edu > To: mj_com...@hotmail.com > CC: s...@nmr.mgh.harvard.edu; jennifer_g_gold...@rush.edu; vy_d...@rush.edu; > freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] manual editting problem > > Hi Jing, > > You have some white matter voxels missing in the wm.mgz for the rh. You > can add some wm to that volume using the edit tool or you can also try > control points. If you are adding wm, make sure you select the aux volume > on the brush info toolbox. Fill in wm voxels for all slices. Control > points would help with extending the pial surf on the lh. > > -Khoa > > > > > Hi Bruce and Sita: > > > > Thanks for your relay. And Here are the images. > > > > Jing > > > > > > > > From: Jing Ming [mj_com...@hotmail.com] > > > > Sent: Thursday, September 15, 2011 7:31 PM > > > > To: Vy Dinh > > > > Subject: FW: [Freesurfer] manual editting problem > > > > > > > > > > > > > > > > > > > > > >> CC: mj_com...@hotmail.com; jennifer_g_gold...@rush.edu; vyd...@rush.edu; > >> freesurfer@nmr.mgh.harvard.edu > > > >> From: fis...@nmr.mgh.harvard.edu > > > >> Subject: Re: [Freesurfer] manual editting problem > > > >> Date: Thu, 15 Sep 2011 20:07:41 -0400 > > > >> To: s...@nmr.mgh.harvard.edu > > > >> > > > >> Can you send an image? > > > >> > > > >> > > > >> > > > >> On Sep 15, 2011, at 6:38 PM, Sita Kakunoori > >> wrote: > > > >> > > > >> > > > > >> > How does the wm.mgz look. Correcting the white surface will correct > >> the > > > >> > pial surface as well. > > > >> > > > > >> > Sita. > > > >> > > > > >> > > > > >> > On Thu, 15 Sep 2011, Jing Ming wrote: > > > >> > > > > >> >> > > > >> >> Hi Surfers: > > > >> >> We have been coming > > > >> >> across several gray matter regions that are not included within the > >> pial > > > >> >> surface (red line) when it should be (e.g., very anterior parts of > >> the > > > >> >> temporal lobe). From my understanding of similar posts on the forum, > >> it > > > >> >> seems that there isn't a way to add this region to the pial surface > >> so > > > >> >> that the missing brain matter is included. We have tried using the > >> clone > > > >> >> tool to fill in this region, as per the tutorial and have > >> experimented > > > >> >> with this tool using the tutorial data. I followed the steps in the > > > >> >> tutorial but could not observe any changes when the middle button was > > > >> >> selected. Does anyone have any ideas on how to troubleshoot this > > > >> >> issue? Can someone please explain to me why this is not possible? > >> Also > > > >> >> how does Freesurfer determine what regions to include within the pial > > > >> >> surface? If there is a way that has been developed recently, please > > > >> >> enlighten me. > > > >> >> > > > >> >> -Jing > > > >> > ___ > > > >> > 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 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 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] manual editting problem
Hi Surfers: We have been coming across several gray matter regions that are not included within the pial surface (red line) when it should be (e.g., very anterior parts of the temporal lobe). From my understanding of similar posts on the forum, it seems that there isn't a way to add this region to the pial surface so that the missing brain matter is included. We have tried using the clone tool to fill in this region, as per the tutorial and have experimented with this tool using the tutorial data. I followed the steps in the tutorial but could not observe any changes when the middle button was selected. Does anyone have any ideas on how to troubleshoot this issue? Can someone please explain to me why this is not possible? Also how does Freesurfer determine what regions to include within the pial surface? If there is a way that has been developed recently, please enlighten me. -Jing ___ 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] about mri_vol2surf
Hi Surfers: I am using mri_vol2surf to project fMRI result into the fsaverage surface. And the fMRI result may contain some subcortical regions, so, I wonder mri_vol2surf will automatically get rid of the subcortical region and only map cortical area into surface right? Is there any material about the mapping algorithm of mri_vol2surf? Thanks much! Jing ___ 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] multimodality registration problem
Hi surfers: I would like to project some fMRI data into fsaverage surface. And the fMRI result is registered into AFNI template, which is talariach template. I wonder how can I register this fMRI result into fsaverage template. The mri_vol2surf need a register.dat, between moving data and anatomical data, and requires this anatomaical data processed by freesurfer. So, that means, I need to run recon-all to AFNI talariach template? Thanks much for your help! Jing ___ 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] register.dat in mri_vol2surf
Hi surfers: I want to project PET data from a group of subjects in the native space into fsaverage surface. It seems I should use mri_vol2surf. And here I am asked to input register.dat for --srcreg argument. I wonder which register.dat should I use, the register matrix between subject volume data with the fsaverage template? or subject PET with their T1? And how to generate this register.dat. Thanks very much for your help! Jing ___ 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] problem of mri_vol2surf
Hi surfers: I was trying to convert a volume dataset from PET to fs surface template. The command I used is the following: mri_vol2surf --src pet2t1.mgz --srcreg register.dat --hemi rh --o ./sig-rh.mgh --out_type mgh --float2int round --trgsubject ico --icoorder 7 The output file here is .mgh format. I also tried paint format. However, I was not able overlay the surface file (.mgh or .w) using freesufer. Is there anythign wrong with the command line? Here is the the output log: ** IcoOrder = 7, nIcoVtxs = 163842 srcvol = pet2t1.mgz srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh trgsubject = ico surfreg = sphere.reg interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Reading surface /project/ADNI/PET/127_S_1210X1a_63646/127_S_1210X1a_63646/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 0 0 0 vol2surf_linear: nhits = 152282/152282 Done mapping volume to surface Number of source voxels hit = 94326 Reading source surface registration /project/ADNI/PET/127_S_1210X1a_63646/127_S_1210X1a_63646/surf/rh.sphere.reg Done loading source registration surface Reading icosahedron, order = 7, radius = 100 Reading icosahedron /pkg/brainmap/freesurfer/lib/bem/ic7.tri Done loading target registration surface Mapping Surfaces (127_S_1210X1a_63646 -> ico) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (152282) Reverse Loop had 34160 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 Done mapping surfaces nSrc121 = 116454, nSrcLost = 0, nSrcMulti = 35828, MnSrcMultiHits = 2.2761 nTrg121 = 138122, nTrgMulti = 25720, MnTrgMultiHits = 2.32815 Reshaping 6 (nvertices = 163842) Writing to ./sig-rh.mgh Dim: 27307 1 6 ** Thanks Jing Ming Northwestern University ___ 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.
