Re: [Freesurfer] recon-all error
External Email - Use Caution Dear Bruce I have used FileDrop to upload the file to your email address (fis...@nmr.mgh.harvard.edu). I hope that you can take the time to help us solve the problem. Thank you in advance. cheers yu junjie -- Original -- From: "Bruce Fischl"; Date: Wed, Apr 24, 2019 09:52 PM To: "Freesurfer support list"; Subject: Re: [Freesurfer] recon-all error hmmm, how long did you let it run? I've never seen this before. Can you upload your subject to our ftp site? cheers Bruce On Wed, 24 Apr 2019, 1013364183 wrote: > > External Email - Use Caution > > Dear freesurfer > We run the recon-all command of freesurfer, but when it runs to the > randomSeed 0 step below, it > will not run anymore, that is, the running terminal has been stuck in the > following statement for > more than 10 days.We want to ask why this happens? How should we solve this > problem? > The running statement is as follows: > only generating white matter surface > using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline > not using aparc to prevent surfaces crossing the midline > INFO: assuming MGZ format for volumes. > using brain.finalsurfs as T1 volume... > $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ > $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ > reading volume > /fileserver/projects/Nian/EDSR_20181118_1/result/freesurfer/neck-stripping187547/mri/filled.mgz... > reading > volume/fileserver/projects/Nian/EDSR_20181118_1/result/freesurfer/neck-stripping187547/mri/brain.finalsur > fs.mgz... > reading > volume/fileserver/projects/Nian/EDSR_20181118_1/result/freesurfer/neck-stripping187547/mri/../mri/aseg.pr > esurf.mgz... > reading volume > /fileserver/projects/Nian/EDSR_20181118_1/result/freesurfer/neck-stripping187547/mri/wm.mgz... > 1792 bright wm thresholded. > 583658 bright non-wm voxels segmented. > reading original surface position from > /fileserver/projects/Nian/EDSR_20181118_1/result/freesurfer/neck-stripping187547/surf/lh.orig... > computing class statistics... > border white:318655 voxels (1.90%) > border gray 363634 voxels (2.17%) > WM (109.0): 109.3 +- 4.5 [70.0 --> 110.0] > GM (109.0) : 101.3 +- 17.8 [30.0 --> 110.0] > setting MIN_GRAY_AT_WHITE_BORDER to 92.2 (was 70) > setting MAX_BORDER_WHITE to 114.5 (was 105) > setting MIN_BORDER_WHITE to 110.0 (was 85) > setting MAX_CSF to 35.0 (was 40) > setting MAX_GRAY to 105.5 (was 95) > setting MAX_GRAY_AT_CSF_BORDER to 60.0 (was 75) > setting MIN_GRAY_AT_CSF_BORDER to 56.6 (was 40) > repositioning cortical surface to gray/white boundary > smoothing T1 volume with sigma = 2.000 > vertex spacing 0.26 +- 0.11 (0.00-->2.25) (max @ vno 28887 --> 31618) > face area > > ___ 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] recon-all error
External Email - Use Caution Dear freesurfer We run the recon-all command of freesurfer, but when it runs to the randomSeed 0 step below, it will not run anymore, that is, the running terminal has been stuck in the following statement for more than 10 days.We want to ask why this happens? How should we solve this problem? The running statement is as follows: only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /fileserver/projects/Nian/EDSR_20181118_1/result/freesurfer/neck-stripping187547/mri/filled.mgz... reading volume /fileserver/projects/Nian/EDSR_20181118_1/result/freesurfer/neck-stripping187547/mri/brain.finalsurfs.mgz... reading volume /fileserver/projects/Nian/EDSR_20181118_1/result/freesurfer/neck-stripping187547/mri/../mri/aseg.presurf.mgz... reading volume /fileserver/projects/Nian/EDSR_20181118_1/result/freesurfer/neck-stripping187547/mri/wm.mgz... 1792 bright wm thresholded. 583658 bright non-wm voxels segmented. reading original surface position from /fileserver/projects/Nian/EDSR_20181118_1/result/freesurfer/neck-stripping187547/surf/lh.orig... computing class statistics... border white:318655 voxels (1.90%) border gray 363634 voxels (2.17%) WM (109.0): 109.3 +- 4.5 [70.0 --> 110.0] GM (109.0) : 101.3 +- 17.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 92.2 (was 70) setting MAX_BORDER_WHITE to 114.5 (was 105) setting MIN_BORDER_WHITE to 110.0 (was 85) setting MAX_CSF to 35.0 (was 40) setting MAX_GRAY to 105.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 60.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 56.6 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.26 +- 0.11 (0.00-->2.25) (max @ vno 28887 --> 31618) face area___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] trilinear interpolation
External Email - Use Caution Dear Bruce, Hello, we used mri_convert ?Cvs [] ?CI [] ?Co[] ?Crt interpolate to perform the trilinear interpolation on the image, and also used the trilinear interpolation in the torch to process the image. We found the result obtained by the interpolation method in freesurfer is better than the result obtained by the trilinear interpolation method in the torch. Does the freesurfer perform other operations when performing the trilinear interpolation on the image? What is the principle? Thank you! yours yujunjie___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] fdr correction problem
External Email - Use Caution Dear Bruce?? I have fdr correction for sig.mgh obtained by mri_glmfit, but the corrected graphs are all 0. Why is this, the instructions and the running results are as follows: mri_fdr --fdr .05 --i lh2.gender_age.glmdir/group2/sig.mgh lh2.gender_age.glmdir/mask.mgh 2.mgh $Id: mri_fdr.c,v 1.2 2016/01/07 22:23:57 greve Exp $ cwd /usr/local/freesurfer/subjects cmdline mri_fdr --fdr .05 --i lh2.gender_age.glmdir/group2/sig.mgh lh2.gender_age.glmdir/mask.mgh 2.mgh sysname Linux hostname xiaorn machine x86_64 user xiaorn fdr 0.05 ninputs 1 MRIfdr2vwth: np = 149953, nv = 163842 MRIfdr2vwth: vwth = 0.03, log10(vwhth) = 5.583609 voxel-wise-threshold 5.5836093010 Writing to 2.mgh mri_fdr done yours yujunjie___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] fdr correction problem
External Email - Use Caution Dear Bruce?? I have fdr correction for sig.mgh obtained by mri_glmfit, but the corrected graphs are all 0. Why is this, the instructions and the running results are as follows: mri_fdr --fdr .05 --i lh2.gender_age.glmdir/group2/sig.mgh lh2.gender_age.glmdir/mask.mgh 2.mgh $Id: mri_fdr.c,v 1.2 2016/01/07 22:23:57 greve Exp $ cwd /usr/local/freesurfer/subjects cmdline mri_fdr --fdr .05 --i lh2.gender_age.glmdir/group2/sig.mgh lh2.gender_age.glmdir/mask.mgh 2.mgh sysname Linux hostname xiaorn machine x86_64 user xiaorn fdr 0.05 ninputs 1 MRIfdr2vwth: np = 149953, nv = 163842 MRIfdr2vwth: vwth = 0.03, log10(vwhth) = 5.583609 voxel-wise-threshold 5.5836093010 Writing to 2.mgh mri_fdr done yours yujunjie___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] ???????????? ?????? Calculated thickness
External Email - Use Caution Dear Tim, I have used chmod to give this file permission. I want to know because this instruction is no longer available? yours yujunjie ------ ??: "ts+ml" : 2018??12??9??(??) 1:15 ??: "Freesurfer support list"; : Re: [Freesurfer]?? ?? Calculated thickness External Email - Use Caution Just to be sure, could you also post the output of the following command: who am i; ls -ld /usr/local/freesurfer/subjects/groupstudy/ I suspect that you do not have write access to /usr/local/. Unless you are running FreeSurfer as root (which you definitely should not do), you should not be allowed to write into /usr/. I suggest you try changing the output directory to some place where definitely have write access. You could do something like this: mkdir ~/groupstudy/ mris_surface_stats -nsmooth 60 -surf_name $SUBJECTS_DIR/1001/surf/lh.white -out_name ~/groupstudy/lh_std_10.mgh -absmean ~/groupstudy/lh_absmean_10.mgh -mean ~/groupstudy/lh_mean_10.mgh -absstd ~/groupstudy/lh_absstd_10.mgh /usr/local/freesurfer/subjects/1001/surf/lh.thickness_diff.mgh Best, Tim > On December 8, 2018 at 2:08 PM 1013364183 wrote: > > > External Email - Use Caution > > Dear Bruce, > I run the following command: > > mris_surface_stats -nsmooth 60 -surf_name $SUBJECTS_DIR/1001/surf/lh.white > -out_name $SUBJECTS_DIR/groupstudy/lh_std_10.mgh -absmean > $SUBJECTS_DIR/groupstudy/lh_absmean_10.mgh -mean > $SUBJECTS_DIR/groupstudy/lh_mean_10. Mgh -absstd > $SUBJECTS_DIR/groupstudy/lh_absstd_10.mgh > /usr/local/freesurfer/subjects/1001/surf/lh.thickness_diff.mgh > > > The results are as follows: > Perform 60 steps of smoothing of input data > Using /usr/local/freesurfer/subjects/groupstudy/lh_std_10.mgh as output file > Using /usr/local/freesurfer/subjects/groupstudy/lh_absmean_10.mgh as output > file for abs-mean > Using /usr/local/freesurfer/subjects/groupstudy/lh_mean_10.mgh as output file > for mean > Using /usr/local/freesurfer/subjects/groupstudy/lh_absstd_10.mgh as output > file for std-of-abs-mean > Reading /usr/local/freesurfer/subjects/1001/surf/lh.thickness_diff.mgh... > Smooth input data by 60 steps > Stats over surface (318651 vertices): mean = 0.0888528, std = 0.334772, > absmean = 0.23932, absstd = 0.250386 > > > > But I did not get the generated mgh file.Is this what is the reason? > > > > yours yujunjie > > > > -- -- > ??: "Bruce Fischl"; > : 2018??12??8??(??) 1:16 > ??: "Freesurfer support list"; > > : Re: [Freesurfer] ?? Calculated thickness > > > > Hi yujunjie > > in general if you want our help you have to give us more information. We > need for example the full command line you ran and the full output of it > (in text, not a screen shot!) > > cheers > Bruce > On Sat, 8 Dec 2018, 1013364183 wrote: > > > > > External Email - Use Caution > > > > The problem is in the fourth step of ThicknessRepeatibility - > > mris_surface_stats > > > > > > -- -- > > ??: "Bruce Fischl"; > > : 2018??12??8??(??) 0:57 > > ??: "Freesurfer support list"; > > : Re: [Freesurfer] Calculated thickness > > > > Hi yujunjie > > > > you can use mris_distance_transform -vol to compute a volumetric map of > > distances to the surface if that is what you want. > > > > cheers > > Bruce > > On Fri, 7 Dec 2018, > > 1013364183 wrote: > > > > > > > > External Email - Use Caution > > > > > > Dear FS?? > > > I now have two different surfaces, the two surfaces have intersecting > > > parts, I want to calculate > > > their signed distance, what should I do?I want to calculate the thick std > > > and mean mgh files > > through > > > mris_surface_stats, but there is no output. What is the reason? > > > > > > yours yujunjie > > > > > > > > ___ > > 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 -- Tim 0176 84273709 ___ 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] ?????? ?????? Calculated thickness
External Email - Use Caution Dear Bruce, I run the following command: mris_surface_stats -nsmooth 60 -surf_name $SUBJECTS_DIR/1001/surf/lh.white -out_name $SUBJECTS_DIR/groupstudy/lh_std_10.mgh -absmean $SUBJECTS_DIR/groupstudy/lh_absmean_10.mgh -mean $SUBJECTS_DIR/groupstudy/lh_mean_10. Mgh -absstd $SUBJECTS_DIR/groupstudy/lh_absstd_10.mgh /usr/local/freesurfer/subjects/1001/surf/lh.thickness_diff.mgh The results are as follows: Perform 60 steps of smoothing of input data Using /usr/local/freesurfer/subjects/groupstudy/lh_std_10.mgh as output file Using /usr/local/freesurfer/subjects/groupstudy/lh_absmean_10.mgh as output file for abs-mean Using /usr/local/freesurfer/subjects/groupstudy/lh_mean_10.mgh as output file for mean Using /usr/local/freesurfer/subjects/groupstudy/lh_absstd_10.mgh as output file for std-of-abs-mean Reading /usr/local/freesurfer/subjects/1001/surf/lh.thickness_diff.mgh... Smooth input data by 60 steps Stats over surface (318651 vertices): mean = 0.0888528, std = 0.334772, absmean = 0.23932, absstd = 0.250386 But I did not get the generated mgh file.Is this what is the reason? yours yujunjie -- -- ??: "Bruce Fischl"; : 2018??12??8??(??) 1:16 ??: "Freesurfer support list"; : Re: [Freesurfer] ?? Calculated thickness Hi yujunjie in general if you want our help you have to give us more information. We need for example the full command line you ran and the full output of it (in text, not a screen shot!) cheers Bruce On Sat, 8 Dec 2018, 1013364183 wrote: > > External Email - Use Caution > > The problem is in the fourth step of ThicknessRepeatibility - > mris_surface_stats > > > -- -- > ??: "Bruce Fischl"; > : 2018??12??8??(??) 0:57 > ??: "Freesurfer support list"; > : Re: [Freesurfer] Calculated thickness > > Hi yujunjie > > you can use mris_distance_transform -vol to compute a volumetric map of > distances to the surface if that is what you want. > > cheers > Bruce > On Fri, 7 Dec 2018, > 1013364183 wrote: > > > > > External Email - Use Caution > > > > Dear FS?? > > I now have two different surfaces, the two surfaces have intersecting > > parts, I want to calculate > > their signed distance, what should I do?I want to calculate the thick std > > and mean mgh files > through > > mris_surface_stats, but there is no output. What is the reason? > > > > yours yujunjie > > > > > ___ > 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
[Freesurfer] gray intensity
External Email - Use Caution Dear Bruce, I want to get the percent gray-white contrast((white-gray)/(white + gray).100%) and gray intensity sampled at 30% cortical depth. What should I do? yours yujunjie___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] ?????? Calculated thickness
External Email - Use Caution The problem is in the fourth step of ThicknessRepeatibility - mris_surface_stats -- -- ??: "Bruce Fischl"; : 2018??12??8??(??) 0:57 ??: "Freesurfer support list"; : Re: [Freesurfer] Calculated thickness Hi yujunjie you can use mris_distance_transform -vol to compute a volumetric map of distances to the surface if that is what you want. cheers Bruce On Fri, 7 Dec 2018, 1013364183 wrote: > > External Email - Use Caution > > Dear FS?? > I now have two different surfaces, the two surfaces have intersecting > parts, I want to calculate > their signed distance, what should I do?I want to calculate the thick std and > mean mgh files through > mris_surface_stats, but there is no output. What is the reason? > > yours yujunjie > > ___ 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] ?????? Calculated thickness
External Email - Use Caution Dear Bruce, I want to implement ThicknessRepeatibility, but I can't get the output mgh file in the last step. What is the reason? http://ftp.nmr.mgh.harvard.edu/fswiki/ThicknessRepeatibility yu'jun'jie -- -- ??: "Bruce Fischl"; : 2018??12??8??(??) 0:57 ??: "Freesurfer support list"; : Re: [Freesurfer] Calculated thickness Hi yujunjie you can use mris_distance_transform -vol to compute a volumetric map of distances to the surface if that is what you want. cheers Bruce On Fri, 7 Dec 2018, 1013364183 wrote: > > External Email - Use Caution > > Dear FS?? > I now have two different surfaces, the two surfaces have intersecting > parts, I want to calculate > their signed distance, what should I do?I want to calculate the thick std and > mean mgh files through > mris_surface_stats, but there is no output. What is the reason? > > yours yujunjie > > ___ 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] Calculated thickness
External Email - Use Caution Dear FS?? I now have two different surfaces, the two surfaces have intersecting parts, I want to calculate their signed distance, what should I do?I want to calculate the thick std and mean mgh files through mris_surface_stats, but there is no output. What is the reason? yours yujunjie___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Surface displacement
External Email - Use Caution Dear Bruce, We resample the surface of the high resolution image to the low resolution image surface, then compare the surface of the original image to the resampled surface to calculate his surface displacement. What should we do? -- Original -- From: "Bruce Fischl"; Date: Mon, Dec 3, 2018 11:49 PM To: "Freesurfer support list"; Subject: Re: [Freesurfer] Surface displacement Hi yujunjie you need to give us more information than this. cheers Bruce On Mon, 3 Dec 2018, 1013364183 wrote: > > External Email - Use Caution > > Dear FS, > We want to calculate the displacement of different surfaces, what should we > do? > > yours yujunjie > > ___ 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] Surface displacement
External Email - Use Caution Dear FS, We want to calculate the displacement of different surfaces, what should we do? yours yujunjie___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] ?????? ?????? ?????? ?????? Triangular mesh samplingproblem
External Email - Use Caution Dear Bruce, Thank you very much for your help. yours yujunjie -- -- ??: "Bruce Fischl"; : 2018??12??2??(??) 0:28 ??: "Freesurfer support list"; : "Jonathan Polimeni"; : Re: [Freesurfer] ?? ?? ?? Triangular mesh samplingproblem Hi yujunjie I included him in the previous (and this) email cheers Bruce On Sun, 2 Dec 2018, 1013364183 wrote: > > External Email - Use Caution > > Dear Bruce, > How should I contact Jon (ccd)?Can mri_surf2surf really implement Figure > 2(a)? > > yours yujunjie > > > -- -- > ??: "Bruce Fischl"; > : 2018??12??2??(??) 0:07 > ??: "Freesurfer support list";"Jonathan > Polimeni"; > : Re: [Freesurfer] ?? ?? Triangular mesh sampling problem > > hmm, maybe Jon (ccd) can help? > > Bruce > On Sat, 1 Dec 2018, 1013364183 wrote: > > > > > External Email - Use Caution > > > > Dear Bruce, > > I use mri_surf2surf to map lh.thickness from high resolution to low > > resolution, and vice versa, > > can this statement implement the operation of Figure 2(a)? > > > > yours yujunjie > > > > -- -- > > ??: "Bruce Fischl"; > > : 2018??11??29??(??) 11:46 > > ??: "Freesurfer support list"; > > : Re: [Freesurfer] ?? Triangular mesh sampling problem > > > > Hi yujunjie > > > > there is source code in mrishash.c and mrisurf.c for this kind of thing, > > e.g. MHTfindClosestVertex. We don't have any complete code that will do > > exactly what you want though, so you will have to poke around in the source > > yourself I'm afraid. > > > > cheers > > Bruce > > > > > > On > > Thu, 29 Nov 2018, 1013364183 wrote: > > > > > > > > External Email - Use Caution > > > > > > Dear Bruce, > > > I want to do the following, which source code should we use, and if so, > > > can you send me a > > > connection? > > > We now have high and low resolution images, we want to resample each > > > triangular surface mesh > > > generated from low-resolution data onto the corresponding triangular > > > surface mesh generated from > > > high-resolution data and vice versa as follows: For every vertex in a > > > low-resolution surface > mesh > > we > > > found the closest point on the high-resolution surface mesh (which > > > typically fell within a > > triangle > > > face of the mesh), and defined a point at that location on the > > > high-resolution surface mesh > > > (subsequently referred to as ??sparse?? meshes).What should we do to use > > > freesurfer to do the > > above? > > > > > > Thank you in advance > > > look forward to your reply > > > yours yujunjie > > > -- -- > > > ??: "Bruce Fischl"; > > > : 2018??11??7??(??) 2:42 > > > ??: "Freesurfer support list"; > > > : Re: [Freesurfer] Triangular mesh sampling problem > > > > > > Hi yujunjie > > > > > > we have code interenally that will do what you are asking, but no binary, > > > sorry. You could download our source code and try to write your own, > > > although it will be a bit of a project. > > > > > > cheers > > > Bruce > > > On Tue, 6 Nov 2018, 1013364183 > > > wrote: > > > > > > > > > > > External Email - Use Caution > > > > > > > > Dear FS > > > > We now have high and low resolution images, we want to resample each > > > > triangular surface mesh > > > > generated from low-resolution data onto the corresponding triangular > > > > surface mesh generated > from > > > > high-resolution data and vice versa as follows: For every vertex in a > > > > low-resolution surface > > mesh > > > we > > > > found the closest point on the high-resolution surface mesh (which > > > > typically fell within a > > > triangle > > > > face of the mesh), and defined a point at that location on the > > > > high-resolution surface mesh
[Freesurfer] ?????? ?????? ?????? Triangular mesh sampling problem
External Email - Use Caution Dear Bruce, How should I contact Jon (ccd)?Can mri_surf2surf really implement Figure 2(a)? yours yujunjie -- -- ??: "Bruce Fischl"; : 2018??12??2??(??) 0:07 ??: "Freesurfer support list";"Jonathan Polimeni"; : Re: [Freesurfer] ?? ?? Triangular mesh sampling problem hmm, maybe Jon (ccd) can help? Bruce On Sat, 1 Dec 2018, 1013364183 wrote: > > External Email - Use Caution > > Dear Bruce, > I use mri_surf2surf to map lh.thickness from high resolution to low > resolution, and vice versa, > can this statement implement the operation of Figure 2(a)? > > yours yujunjie > > -- -- > ??: "Bruce Fischl"; > : 2018??11??29??(??) 11:46 > ??: "Freesurfer support list"; > : Re: [Freesurfer] ?? Triangular mesh sampling problem > > Hi yujunjie > > there is source code in mrishash.c and mrisurf.c for this kind of thing, > e.g. MHTfindClosestVertex. We don't have any complete code that will do > exactly what you want though, so you will have to poke around in the source > yourself I'm afraid. > > cheers > Bruce > > > On > Thu, 29 Nov 2018, 1013364183 wrote: > > > > > External Email - Use Caution > > > > Dear Bruce, > > I want to do the following, which source code should we use, and if so, > > can you send me a > > connection? > > We now have high and low resolution images, we want to resample each > > triangular surface mesh > > generated from low-resolution data onto the corresponding triangular > > surface mesh generated from > > high-resolution data and vice versa as follows: For every vertex in a > > low-resolution surface mesh > we > > found the closest point on the high-resolution surface mesh (which > > typically fell within a > triangle > > face of the mesh), and defined a point at that location on the > > high-resolution surface mesh > > (subsequently referred to as ??sparse?? meshes).What should we do to use > > freesurfer to do the > above? > > > > Thank you in advance > > look forward to your reply > > yours yujunjie > > -- -- > > ??: "Bruce Fischl"; > > : 2018??11??7??(??) 2:42 > > ??: "Freesurfer support list"; > > : Re: [Freesurfer] Triangular mesh sampling problem > > > > Hi yujunjie > > > > we have code interenally that will do what you are asking, but no binary, > > sorry. You could download our source code and try to write your own, > > although it will be a bit of a project. > > > > cheers > > Bruce > > On Tue, 6 Nov 2018, 1013364183 > > wrote: > > > > > > > > External Email - Use Caution > > > > > > Dear FS > > > We now have high and low resolution images, we want to resample each > > > triangular surface mesh > > > generated from low-resolution data onto the corresponding triangular > > > surface mesh generated from > > > high-resolution data and vice versa as follows: For every vertex in a > > > low-resolution surface > mesh > > we > > > found the closest point on the high-resolution surface mesh (which > > > typically fell within a > > triangle > > > face of the mesh), and defined a point at that location on the > > > high-resolution surface mesh > > > (subsequently referred to as ??sparse?? meshes).What should we do to use > > > freesurfer to do the > > above? > > > > > > Thanks in advance > > > > > > yours yujunjie > > > > > > > > ___ > > 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___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] ?????? ?????? Triangular mesh sampling problem
External Email - Use Caution Dear Bruce, I use mri_surf2surf to map lh.thickness from high resolution to low resolution, and vice versa, can this statement implement the operation of Figure 2(a)? yours yujunjie -- -- ??: "Bruce Fischl"; : 2018??11??29??(??) 11:46 ??: "Freesurfer support list"; : Re: [Freesurfer] ?? Triangular mesh sampling problem Hi yujunjie there is source code in mrishash.c and mrisurf.c for this kind of thing, e.g. MHTfindClosestVertex. We don't have any complete code that will do exactly what you want though, so you will have to poke around in the source yourself I'm afraid. cheers Bruce On Thu, 29 Nov 2018, 1013364183 wrote: > > External Email - Use Caution > > Dear Bruce, > I want to do the following, which source code should we use, and if so, can > you send me a > connection? > We now have high and low resolution images, we want to resample each > triangular surface mesh > generated from low-resolution data onto the corresponding triangular surface > mesh generated from > high-resolution data and vice versa as follows: For every vertex in a > low-resolution surface mesh we > found the closest point on the high-resolution surface mesh (which typically > fell within a triangle > face of the mesh), and defined a point at that location on the > high-resolution surface mesh > (subsequently referred to as ??sparse?? meshes).What should we do to use > freesurfer to do the above? > > Thank you in advance > look forward to your reply > yours yujunjie > -- -- > ??: "Bruce Fischl"; > : 2018??11??7??(??) 2:42 > ??: "Freesurfer support list"; > : Re: [Freesurfer] Triangular mesh sampling problem > > Hi yujunjie > > we have code interenally that will do what you are asking, but no binary, > sorry. You could download our source code and try to write your own, > although it will be a bit of a project. > > cheers > Bruce > On Tue, 6 Nov 2018, 1013364183 > wrote: > > > > > External Email - Use Caution > > > > Dear FS > > We now have high and low resolution images, we want to resample each > > triangular surface mesh > > generated from low-resolution data onto the corresponding triangular > > surface mesh generated from > > high-resolution data and vice versa as follows: For every vertex in a > > low-resolution surface mesh > we > > found the closest point on the high-resolution surface mesh (which > > typically fell within a > triangle > > face of the mesh), and defined a point at that location on the > > high-resolution surface mesh > > (subsequently referred to as ??sparse?? meshes).What should we do to use > > freesurfer to do the > above? > > > > Thanks in advance > > > > yours yujunjie > > > > > ___ > 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
[Freesurfer] ?????? ?????? ?????? Triangular mesh sampling problem
External Email - Use Caution Dear Bruce, I want to know if mri_surf2surf can map high resolution meshes to low resolution meshes or low resolution meshes to high resolution meshes. If so, what should be done specifically. Thanks in advance yours yujunjie -- -- ??: "Bruce Fischl"; : 2018??11??30??(??) 0:24 ??: "Freesurfer support list"; : Re: [Freesurfer] ?? ?? Triangular mesh sampling problem yes, sorry, I can't think of a way to do it with existing binaries (maybe someone else can?). The only alternative I can think of is to use the various fsaverage meshes instead of the subject meshes. Then the "projection" becomes trivial as the lower res meshes are just the first N vertices in the higher res ones. cheers Bruce On Fri, 30 Nov 2018, 1013364183 wrote: > > External Email - Use Caution > > Dear Bruce, >Thank you very much for your reply, I will try the method you said. But I > still want to confirm that the > operation in the implementation diagram (attached) must change the source > code? > > Thanks in advance > yours yujunjie > -- -- > ??: "Bruce Fischl"; > : 2018??11??29??(??) 11:46 > ??: "Freesurfer support list"; > : Re: [Freesurfer] ?? Triangular mesh sampling problem > > Hi yujunjie > > there is source code in mrishash.c and mrisurf.c for this kind of thing, > e.g. MHTfindClosestVertex. We don't have any complete code that will do > exactly what you want though, so you will have to poke around in the source > yourself I'm afraid. > > cheers > Bruce > > > On > Thu, 29 Nov 2018, 1013364183 wrote: > > > > > External Email - Use Caution > > > > Dear Bruce, > > I want to do the following, which source code should we use, and if so, > > can you send me a > > connection? > > We now have high and low resolution images, we want to resample each > > triangular surface mesh > > generated from low-resolution data onto the corresponding triangular > > surface mesh generated from > > high-resolution data and vice versa as follows: For every vertex in a > > low-resolution surface mesh we > > found the closest point on the high-resolution surface mesh (which > > typically fell within a triangle > > face of the mesh), and defined a point at that location on the > > high-resolution surface mesh > > (subsequently referred to as ??sparse?? meshes).What should we do to use > > freesurfer to do the above? > > > > Thank you in advance > > look forward to your reply > > yours yujunjie > > -- -- > > ??: "Bruce Fischl"; > > : 2018??11??7??(??) 2:42 > > ??: "Freesurfer support list"; > > ????: Re: [Freesurfer] Triangular mesh sampling problem > > > > Hi yujunjie > > > > we have code interenally that will do what you are asking, but no binary, > > sorry. You could download our source code and try to write your own, > > although it will be a bit of a project. > > > > cheers > > Bruce > > On Tue, 6 Nov 2018, 1013364183 > > wrote: > > > > > > > > External Email - Use Caution > > > > > > Dear FS > > > We now have high and low resolution images, we want to resample each > > > triangular surface mesh > > > generated from low-resolution data onto the corresponding triangular > > > surface mesh generated from > > > high-resolution data and vice versa as follows: For every vertex in a > > > low-resolution surface mesh > > we > > > found the closest point on the high-resolution surface mesh (which > > > typically fell within a > > triangle > > > face of the mesh), and defined a point at that location on the > > > high-resolution surface mesh > > > (subsequently referred to as ??sparse?? meshes).What should we do to use > > > freesurfer to do the > > above? > > > > > > Thanks in advance > > > > > > yours yujunjie > > > > > > > > ___ > > 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___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] ?????? Triangular mesh sampling problem
External Email - Use Caution Dear Bruce, I want to do the following, which source code should we use, and if so, can you send me a connection? We now have high and low resolution images, we want to resample each triangular surface mesh generated from low-resolution data onto the corresponding triangular surface mesh generated from high-resolution data and vice versa as follows: For every vertex in a low-resolution surface mesh we found the closest point on the high-resolution surface mesh (which typically fell within a triangle face of the mesh), and defined a point at that location on the high-resolution surface mesh (subsequently referred to as ??sparse?? meshes).What should we do to use freesurfer to do the above? Thank you in advance look forward to your reply yours yujunjie -- -- ??: "Bruce Fischl"; : 2018??11??7??(??) 2:42 ??: "Freesurfer support list"; : Re: [Freesurfer] Triangular mesh sampling problem Hi yujunjie we have code interenally that will do what you are asking, but no binary, sorry. You could download our source code and try to write your own, although it will be a bit of a project. cheers Bruce On Tue, 6 Nov 2018, 1013364183 wrote: > > External Email - Use Caution > > Dear FS > We now have high and low resolution images, we want to resample each > triangular surface mesh > generated from low-resolution data onto the corresponding triangular surface > mesh generated from > high-resolution data and vice versa as follows: For every vertex in a > low-resolution surface mesh we > found the closest point on the high-resolution surface mesh (which typically > fell within a triangle > face of the mesh), and defined a point at that location on the > high-resolution surface mesh > (subsequently referred to as ??sparse?? meshes).What should we do to use > freesurfer to do the above? > > Thanks in advance > > yours yujunjie > > ___ 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] ?????? ?????? ?????? Recon-all run error
External Email - Use Caution Dear Bruce, I am sorry to let you wait so long, I have some troubles in transferring the data set, but it has been solved. Now I have sent the data set to ftp. I hope you can take the time to help us deal with the data set. We have already Running this data set for a long time but did not get results, the name of the data set is data_Yujunjie.zip,. The run command and the expert file are in the attachment. Express your heartfelt thanks again?? yours yujunjie -- -- ??: "Bruce Fischl"; : 2018??11??18??(??) 11:15 ??: "Freesurfer support list"; : Re: [Freesurfer] ?? ?? Recon-all run error Instructions on how you can upload tarred and gzipped files here: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange On Sun, 18 Nov 2018, 1013364183 wrote: > > External Email - Use Caution > > Dear Bruce, > I am very sorry to bother you. We are currently experimenting with > freesurfer, but I have > encountered a lot of problems during the experiment. We have three > resolutions of data, the skull of > medium-resolution data can't be removed (neck can't be removed), and with > high-resolution data, it > will report memory transfer errors. You said before that we can submit data > sets to you, how should > we provide you with data sets? > > Thanks in advance > yours yujunjie > > -- -- > ??: "Bruce Fischl"; > : 2018??11??7??(??) 2:42 > ??: "Freesurfer support list"; > : Re: [Freesurfer] ?? Recon-all run error > > does it occur if you run it outside of recon-all? Do you have enough free > ram? If so, you can filedrop us the dataset and we can try to replicate and > fit ix. > > On Tue, 6 Nov 2018, 1013364183 wrote: > > > > > External Email - Use Caution > > > > Dear Bruce, > > I found the error location in the recon-all.log folder. Here is the place > > where it went wrong??I > > don't think it's the reason for insufficient memory.. > > ''mri_convert.bin: putget.c:322: fill_NC_var: Assertion `chunksz % 4 == > > 0' failed.'' > > This data is ok when we run with versions prior to freesurfer 6.0. But > > after we run the 6.0 > > version and set the expert file, this error will occur.Do I need to step > > through the instructions > to > > see the problem? How should this error be solved? > > > > Thanks in advance > > > > yours yujunjie > > > > -- -- > > ??: "Bruce Fischl"; > > : 2018??11??6??(??) 9:40 > > ??: "Freesurfer support list"; > > : Re: [Freesurfer] Recon-all run error > > > > that certainly looks like something is running out of ram. Can you run > > the command that failed directly on the command line and see if it works? > > Was anything else running on the machine at the time? We do report total > > and free memory at the start of the recon in the recon-all.log file > > > > cheers > > Bruce > > On Tue, > > 6 Nov 2018, 1013364183 wrote: > > > > > > > > External Email - Use Caution > > > > > > Dear FS, > > > When we run ??recon-all?? with a 5GB high-resolution image, core dumped > > > appears when the > > mri_convert > > > command is executed. The specific errors are as follows: > > > /opt/el7/pkgs/freesurfer/freesurfer_6.0/bin/mri_convert: line 3: 29235 > > > Aborted (core dumped) > > > mri_convert.bin "$@" > > > ERROR: converting to minc > > > We want to know if our high resolution image is too large for freesurfer > > > to handle, or our > > computer > > > memory (64GB running memory) is limited. > > > > > > Thanks a lot in advance! > > > yours sincerely, > > > yu junjie > > > > > > > > > > > ___ > > 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 expert.opts Description: Binary data recon-all.txt Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] ?????? ?????? ?????? Recon-all run error
External Email - Use Caution Dear Bruce, Thank you very much for your reply, I will submit our data set as soon as possible. yours yujunjie -- -- ??: "Bruce Fischl"; : 2018??11??18??(??) 11:15 ??: "Freesurfer support list"; : Re: [Freesurfer] ?? ?? Recon-all run error Instructions on how you can upload tarred and gzipped files here: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange On Sun, 18 Nov 2018, 1013364183 wrote: > > External Email - Use Caution > > Dear Bruce, > I am very sorry to bother you. We are currently experimenting with > freesurfer, but I have > encountered a lot of problems during the experiment. We have three > resolutions of data, the skull of > medium-resolution data can't be removed (neck can't be removed), and with > high-resolution data, it > will report memory transfer errors. You said before that we can submit data > sets to you, how should > we provide you with data sets? > > Thanks in advance > yours yujunjie > > -- -- > ??: "Bruce Fischl"; > : 2018??11??7??(??) 2:42 > ??: "Freesurfer support list"; > : Re: [Freesurfer] ?? Recon-all run error > > does it occur if you run it outside of recon-all? Do you have enough free > ram? If so, you can filedrop us the dataset and we can try to replicate and > fit ix. > > On Tue, 6 Nov 2018, 1013364183 wrote: > > > > > External Email - Use Caution > > > > Dear Bruce, > > I found the error location in the recon-all.log folder. Here is the place > > where it went wrong??I > > don't think it's the reason for insufficient memory.. > > ''mri_convert.bin: putget.c:322: fill_NC_var: Assertion `chunksz % 4 == > > 0' failed.'' > > This data is ok when we run with versions prior to freesurfer 6.0. But > > after we run the 6.0 > > version and set the expert file, this error will occur.Do I need to step > > through the instructions > to > > see the problem? How should this error be solved? > > > > Thanks in advance > > > > yours yujunjie > > > > -- -- > > ??: "Bruce Fischl"; > > : 2018??11??6??(??) 9:40 > > ??: "Freesurfer support list"; > > : Re: [Freesurfer] Recon-all run error > > > > that certainly looks like something is running out of ram. Can you run > > the command that failed directly on the command line and see if it works? > > Was anything else running on the machine at the time? We do report total > > and free memory at the start of the recon in the recon-all.log file > > > > cheers > > Bruce > > On Tue, > > 6 Nov 2018, 1013364183 wrote: > > > > > > > > External Email - Use Caution > > > > > > Dear FS, > > > When we run ??recon-all?? with a 5GB high-resolution image, core dumped > > > appears when the > > mri_convert > > > command is executed. The specific errors are as follows: > > > /opt/el7/pkgs/freesurfer/freesurfer_6.0/bin/mri_convert: line 3: 29235 > > > Aborted (core dumped) > > > mri_convert.bin "$@" > > > ERROR: converting to minc > > > We want to know if our high resolution image is too large for freesurfer > > > to handle, or our > > computer > > > memory (64GB running memory) is limited. > > > > > > Thanks a lot in advance! > > > yours sincerely, > > > yu junjie > > > > > > > > > > > ___ > > 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___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] ?????? ?????? Recon-all run error
External Email - Use Caution Dear Bruce, I am very sorry to bother you. We are currently experimenting with freesurfer, but I have encountered a lot of problems during the experiment. We have three resolutions of data, the skull of medium-resolution data can't be removed (neck can't be removed), and with high-resolution data, it will report memory transfer errors. You said before that we can submit data sets to you, how should we provide you with data sets? Thanks in advance yours yujunjie -- -- ??: "Bruce Fischl"; : 2018??11??7??(??) 2:42 ??: "Freesurfer support list"; : Re: [Freesurfer] ?? Recon-all run error does it occur if you run it outside of recon-all? Do you have enough free ram? If so, you can filedrop us the dataset and we can try to replicate and fit ix. On Tue, 6 Nov 2018, 1013364183 wrote: > > External Email - Use Caution > > Dear Bruce, > I found the error location in the recon-all.log folder. Here is the place > where it went wrong??I > don't think it's the reason for insufficient memory.. > ''mri_convert.bin: putget.c:322: fill_NC_var: Assertion `chunksz % 4 == 0' > failed.'' > This data is ok when we run with versions prior to freesurfer 6.0. But > after we run the 6.0 > version and set the expert file, this error will occur.Do I need to step > through the instructions to > see the problem? How should this error be solved? > > Thanks in advance > > yours yujunjie > > -- -- > ??: "Bruce Fischl"; > : 2018??11??6??(??) 9:40 > ??: "Freesurfer support list"; > : Re: [Freesurfer] Recon-all run error > > that certainly looks like something is running out of ram. Can you run > the command that failed directly on the command line and see if it works? > Was anything else running on the machine at the time? We do report total > and free memory at the start of the recon in the recon-all.log file > > cheers > Bruce > On Tue, > 6 Nov 2018, 1013364183 wrote: > > > > > External Email - Use Caution > > > > Dear FS, > > When we run ??recon-all?? with a 5GB high-resolution image, core dumped > > appears when the > mri_convert > > command is executed. The specific errors are as follows: > > /opt/el7/pkgs/freesurfer/freesurfer_6.0/bin/mri_convert: line 3: 29235 > > Aborted (core dumped) > > mri_convert.bin "$@" > > ERROR: converting to minc > > We want to know if our high resolution image is too large for freesurfer to > > handle, or our > computer > > memory (64GB running memory) is limited. > > > > Thanks a lot in advance! > > yours sincerely, > > yu junjie > > > > > > > ___ > 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
[Freesurfer] ?????? ?????? ?????? Recon-all run error
External Email - Use Caution Dear Greve, Thank you very much for your reply.Where is the tutorial for checking for and fixing defects? Is it the link below? http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFixV6.0 yours yujunjie -- -- ??: "Greve, Douglas N.,Ph.D."; : 2018??11??15??(??) 5:12 ??: "freesurfer@nmr.mgh.harvard.edu"; : Re: [Freesurfer]?? ?? Recon-all run error It looks like you might have a very big defect. Probably there is a bit of skull or cerebellum still attached. Follow the tutorial for checking for and fixing defects. On 11/14/2018 02:59 AM, 1013364183 wrote: > > External Email - Use Caution > > Dear Bruce Fischl, > I am very sorry that I have not reply to you last week. > Our data has been running for a few weeks, but the computer did not > react. There is a log file in the attachment. We want to ask that > could you help us run the data? We will send you a set of data > firstly(We still have two sets of data). If you can help us run our > high resolution data, we will be very grateful. And can we write your > name in the acknowledgments section? Our tutor is now at Boston > Children's Hospital (BCH). If possible, she would like to consult you > in person. > The download link is: > https://drive.google.com/file/d/1_5tYKHipNOTFe96p4BOMc1kbNPK1O93W/view?usp=drive_web > https://drive.google.com/file/d/12TZ0_J_njiZju9PDyvwxnHIiDe8D5SOA/view?usp=drive_web > > Looking forward to your reply. > Thanks in advance > > yours yujunjie > -- -- > *??:* "Bruce Fischl"; > *:* 2018??11??7??(??) 2:42 > *??:* "Freesurfer support list"; > *:* Re: [Freesurfer] ?? Recon-all run error > > does it occur if you run it outside of recon-all? Do you have enough free > ram? If so, you can filedrop us the dataset and we can try to > replicate and > fit ix. > > On Tue, 6 Nov 2018, 1013364183 wrote: > > > > > External Email - Use Caution > > > > Dear Bruce, > > I found the error location in the recon-all.log folder. Here is > the place where it went wrong??I > > don't think it's the reason for insufficient memory.. > > ''mri_convert.bin: putget.c:322: fill_NC_var: Assertion `chunksz % > 4 == 0' failed.'' > > This data is ok when we run with versions prior to freesurfer 6.0. > But after we run the 6.0 > > version and set the expert file, this error will occur.Do I need to > step through the instructions to > > see the problem? How should this error be solved? > > > > Thanks in advance > > > > yours yujunjie > > > > -- -- > > ??: "Bruce Fischl"; > > : 2018??11??6??(??) 9:40 > > ??: "Freesurfer support list"; > > : Re: [Freesurfer] Recon-all run error > > > > that certainly looks like something is running out of ram. Can you run > > the command that failed directly on the command line and see if it > works? > > Was anything else running on the machine at the time? We do report total > > and free memory at the start of the recon in the recon-all.log file > > > > cheers > > Bruce > > On Tue, > > 6 Nov 2018, 1013364183 wrote: > > > > > > > > External Email - Use Caution > > > > > > Dear FS, > > > When we run ??recon-all?? with a 5GB high-resolution image, core > dumped appears when the > > mri_convert > > > command is executed. The specific errors are as follows: > > > /opt/el7/pkgs/freesurfer/freesurfer_6.0/bin/mri_convert: line 3: > 29235 Aborted (core dumped) > > > mri_convert.bin "$@" > > > ERROR: converting to minc > > > We want to know if our high resolution image is too large for > freesurfer to handle, or our > > computer > > > memory (64GB running memory) is limited. > > > > > > Thanks a lot in advance! > > > yours sincerely, > > > yu junjie > > > > > > > > > > > ___ > > 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 ___ 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] ?????? multi-threaded question
External Email - Use Caution Dear Bruce, Thank you very much for your reply. I have not been able to find -openmp option.How should we set this parameter? Can you give me a link? yours yujunjie -- -- ??: "Bruce Fischl"; : 2018??11??17??(??) 11:03 ??: "Freesurfer support list"; : Re: [Freesurfer] multi-threaded question Yes, use the -openmp option in recon-all Cheers Bruce On Nov 16, 2018, at 9:52 PM, 1013364183 wrote: External Email - Use Caution Dear FS, I would like to ask if freesurfer can run multi-threaded. If so, can you give us some guidance on this? Thanks in advance yours yujunjie ___ 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] multi-threaded question
External Email - Use Caution Dear FS, I would like to ask if freesurfer can run multi-threaded. If so, can you give us some guidance on this? Thanks in advance yours yujunjie___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] 回复： 回复： Recon-all run error
External Email - Use Caution
Dear fsbuild,
Thank you very much for your help, I will try to enter this line of
statements and then run high-resolution data, but I did not find the putget.c
file, is it under the installation of freesurfer file, or a system file.
yours yujunjie
-- 原始邮件 --
发件人: "fsbuild";
发送时间: 2018年11月6日(星期二) 中午11:50
收件人: "freesurfer";
主题: Re: [Freesurfer]回复： Recon-all run error
External Email - Use Caution
Hello Yujunjie, Bruce,
This file in the packages archive, ./netcdf_3_6_0_p1/putget.c, has an
assertion at line 322 that looks like the failure. I don't know this code,
but something is going wrong trying to fill the buffer, e.g., maybe it works
for smaller images but not for larger images ? It could be that older version
of freesurfer used a different version of netcdf. I've attached a screenshot
of the code.
You could try setting all the soft limits for the shell to be unlimited, e.g.,
in bash,
$ ulimit -c unlimited
1013364183
November 5, 2018 at 21:22 via Postbox
External Email - Use Caution
Dear Bruce,
I found the error location in the recon-all.log folder. Here is the place
where it went wrong，I don't think it's the reason for insufficient memory..
''mri_convert.bin: putget.c:322: fill_NC_var: Assertion `chunksz % 4 == 0'
failed.''
This data is ok when we run with versions prior to freesurfer 6.0. But
after we run the 6.0 version and set the expert file, this error will occur.Do
I need to step through the instructions to see the problem? How should this
error be solved?
Thanks in advance
yours yujunjie___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Triangular mesh sampling problem
External Email - Use Caution Dear FS We now have high and low resolution images, we want to resample each triangular surface mesh generated from low-resolution data onto the corresponding triangular surface mesh generated from high-resolution data and vice versa as follows: For every vertex in a low-resolution surface mesh we found the closest point on the high-resolution surface mesh (which typically fell within a triangle face of the mesh), and defined a point at that location on the high-resolution surface mesh (subsequently referred to as ??sparse?? meshes).What should we do to use freesurfer to do the above? Thanks in advance yours yujunjie___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] ?????? Recon-all run error
External Email - Use Caution Dear Bruce, I found the error location in the recon-all.log folder. Here is the place where it went wrong??I don't think it's the reason for insufficient memory.. ''mri_convert.bin: putget.c:322: fill_NC_var: Assertion `chunksz % 4 == 0' failed.'' This data is ok when we run with versions prior to freesurfer 6.0. But after we run the 6.0 version and set the expert file, this error will occur.Do I need to step through the instructions to see the problem? How should this error be solved? Thanks in advance yours yujunjie -- -- ??: "Bruce Fischl"; : 2018??11??6??(??) 9:40 ??: "Freesurfer support list"; : Re: [Freesurfer] Recon-all run error that certainly looks like something is running out of ram. Can you run the command that failed directly on the command line and see if it works? Was anything else running on the machine at the time? We do report total and free memory at the start of the recon in the recon-all.log file cheers Bruce On Tue, 6 Nov 2018, 1013364183 wrote: > > External Email - Use Caution > > Dear FS, > When we run ??recon-all?? with a 5GB high-resolution image, core dumped > appears when the mri_convert > command is executed. The specific errors are as follows: > /opt/el7/pkgs/freesurfer/freesurfer_6.0/bin/mri_convert: line 3: 29235 > Aborted (core dumped) > mri_convert.bin "$@" > ERROR: converting to minc > We want to know if our high resolution image is too large for freesurfer to > handle, or our computer > memory (64GB running memory) is limited. > > Thanks a lot in advance! > yours sincerely, > yu junjie > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Recon-all run error
External Email - Use Caution Dear FS, When we run ??recon-all?? with a 5GB high-resolution image, core dumped appears when the mri_convert command is executed. The specific errors are as follows: /opt/el7/pkgs/freesurfer/freesurfer_6.0/bin/mri_convert: line 3: 29235 Aborted (core dumped) mri_convert.bin "$@" ERROR: converting to minc We want to know if our high resolution image is too large for freesurfer to handle, or our computer memory (64GB running memory) is limited. Thanks a lot in advance! yours sincerely, yu junjie___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
