Re: [Freesurfer] Ventricular location
External Email - Use Caution Perfect, thanks Tim. On 17/06/2020 10:50, Tim Schäfer wrote: > External Email - Use Caution > > To find the code, look at FreeSurferColorLUT.txt, e.g., you may be interested > in a subset of these: > >grep -i vent $FREESURFER_HOME/FreeSurferColorLUT.txt > > The last 4 values on each line make up a color code (RGBA, in range 0-255 per > channel). The first value is the region code, used in a segmentation file. > > So the voxels with intensity 14 in the file /mri/aseg.mgz should > belong to the 3rd ventricle. > > I hope that is what you were asking? > > Tim > >> On June 17, 2020 at 11:41 AM Ian Hardingham wrote: >> >> >> External Email - Use Caution >> >> Are the ventricles currently in V6 Surf directory as a set of vertices, >> or a labelled list of voxels, or anything like that? >> >> Ian >> >> On 16/06/2020 13:39, Ian wrote: >>> External Email - Use Caution >>> >>> Hi Freesurfers. >>> >>> I'm looking to find the center of the various Ventricles. Are they >>> included in the freesurfer segmentation images with a specific code? >>> >>> If not, what approach would you use? >>> >>> Thanks, >>> Ian >>> >>> -- >>> >>> *Ian Hardingham* >>> >>> >>> >>> ___ >>> 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
Re: [Freesurfer] Ventricular location
External Email - Use Caution Are the ventricles currently in V6 Surf directory as a set of vertices, or a labelled list of voxels, or anything like that? Ian On 16/06/2020 13:39, Ian wrote: External Email - Use Caution Hi Freesurfers. I'm looking to find the center of the various Ventricles. Are they included in the freesurfer segmentation images with a specific code? If not, what approach would you use? Thanks, Ian -- *Ian Hardingham* ___ 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
Re: [Freesurfer] Ventricular location
External Email - Use Caution Hi Doug, just an FYI that I think this requires extra recon-all files that are only output by v7 ? ./mri_segcentroids --i freesurfer/surf --o results.txt error: corRead(): can't open file freesurfer/surf/COR-.info On 16/06/2020 15:44, Douglas N. Greve wrote: Yes, I put a linux version here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_segcentroids On 6/16/2020 10:32 AM, Ian Hardingham wrote: External Email - Use Caution Is this only in FSL 7 Doug? I can't find it in 6. On 16/06/2020 14:59, Douglas N. Greve wrote: Try mri_segcentroids. Run it with --help to get docs On 6/16/2020 8:39 AM, Ian wrote: External Email - Use Caution Hi Freesurfers. I'm looking to find the center of the various Ventricles. Are they included in the freesurfer segmentation images with a specific code? If not, what approach would you use? Thanks, Ian -- *Ian Hardingham* ___ 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
Re: [Freesurfer] Ventricular location
External Email - Use Caution Thank you so much Doug. Ian On 16/06/2020 15:44, Douglas N. Greve wrote: Yes, I put a linux version here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_segcentroids On 6/16/2020 10:32 AM, Ian Hardingham wrote: External Email - Use Caution Is this only in FSL 7 Doug? I can't find it in 6. On 16/06/2020 14:59, Douglas N. Greve wrote: Try mri_segcentroids. Run it with --help to get docs On 6/16/2020 8:39 AM, Ian wrote: External Email - Use Caution Hi Freesurfers. I'm looking to find the center of the various Ventricles. Are they included in the freesurfer segmentation images with a specific code? If not, what approach would you use? Thanks, Ian -- *Ian Hardingham* ___ 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
Re: [Freesurfer] Ventricular location
External Email - Use Caution Is this only in FSL 7 Doug? I can't find it in 6. On 16/06/2020 14:59, Douglas N. Greve wrote: Try mri_segcentroids. Run it with --help to get docs On 6/16/2020 8:39 AM, Ian wrote: External Email - Use Caution Hi Freesurfers. I'm looking to find the center of the various Ventricles. Are they included in the freesurfer segmentation images with a specific code? If not, what approach would you use? Thanks, Ian -- *Ian Hardingham* ___ 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
Re: [Freesurfer] Which subject does recon-all register surfaces to?
External Email - Use Caution Thanks Bruce. On 13/05/2020 15:41, Bruce Fischl wrote: Hi Ian we don't register to an individual subject - we register to a probabilistic atlas compiled from many subjects. The fsaverage subjects were also generated from that data so they are in register, but the actual atlas is a .tif file that you can find as the target of mris_register in your recon-all.log file cheers Bruce On Wed, 13 May 2020, Ian wrote: External Email - Use Caution Hi guys. After recon-all, the /surf/?h.sphere.reg file implies a registration has been performed to an "average" subject on a sphere. Can you please tell me which subject this is? Is it SUBJECTS_DIR/fsaverage? If so, what is SUBJECTS_DIR/fsaverage/lh.sphere.reg a registration to? If not, where can I find the subject that recon-all registers to? Thanks, Ian -- Ian Hardingham ___ 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
Re: [Freesurfer] Get Atlas surfaces in subject space
External Email - Use Caution Thanks for the reply Doug. I'm looking for the same number of verts as the *subject* - maybe it's as simple as I should be registering the subjects *to* the FS average subject? But the problem is that I want the points in subject space, not average space. So if I have five subjects - I would like the same number of points for each one, which I thought I would get by registering the average to each of them... On 11/05/2020 18:56, Douglas N. Greve wrote: Ian, it seems like you want two different things. When you run mri_surf2surf, it gives you an output that has the same number of vertices as the target which would allow you to do the one-to-one comparison that you want to do. But at the same time, there seems to be a problem with having the same number of vertices. I'm still confused as to what you want to do. If you want to do a one-to-one comparison, then you've got to change the number of vertices, unless I'm missing something. On 5/11/2020 9:38 AM, Ian wrote: External Email - Use Caution Thanks Tim. I'd like a set of points on the surface to compare across subjects, where there are the same number of points for each subject and they're roughly in the same "physiological position" on each subject. So again, if on my atlas I have a point which is at the top of the ctx-rh-fusiform sulcus, I'd like that point to be registered to the top of the ctx-rh-fusiform sulcus in my subjects. On 11/05/2020 13:49, Tim Schäfer wrote: External Email - Use Caution The registration registers the meshes, but it does not alter the number of vertices in them. There is no 1-to-1 correspondence between the vertices of the 2 meshes. May I ask why you need this? What do you want to achieve? Tim On May 11, 2020 at 2:11 PM Ian wrote: External Email - Use Caution I'm just going to try this again, but this time with a different command: mris_apply_reg --src-xyz /usr/local/freesurfer/subjects/fsaverage/surf/lh.white --trg /home/ian/lh_reg.white --streg /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg /obd-fs/proc/my_subject/freesurfer/surf/lh.sphere.reg" This gives me the same issue - fsaverage/surf/lh.white has 300k+ points in it, and the output of this command has fewer than half that. I do not understand what kind of registration would reduce the number of points. What is the relationship between the first point in --src_xyz file and the first point in the output registered file? If I halved the number of points in the input, would I expect the output to be half the size? Or less? I'm sure there's a simple explanation that I don't have my head around just yet - thank you for your patience. Ian On 07/05/2020 22:45, Douglas N. Greve wrote: Isn't that what you got from the mri_surf2surf command? On 5/7/2020 3:08 PM, Ian Hardingham wrote: ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- *Ian Hardingham* Chief Technology Officer signature_873986710 ian.harding...@oxfordbraindiagnostics.com <mailto:terry.poll...@oxfordbraindiagnostics.com> +44 (0)7789 770555 Oxford Centre for Innovation | New Road | Oxford | OX1 1BY Oxford Brain Diagnostics Ltd is a company registered in England and Wales | Company No. 11703979 | VAT No. 321 3026 62 ___ 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
Re: [Freesurfer] Get Atlas surfaces in subject space
External Email - Use Caution I don't see how it's possible I got a comparable list of points when the input was in the order of 300k verts, and the ouput was 180k verts - I would need the number of output verts to be exactly the same as the number of input verts. On 07/05/2020 22:45, Douglas N. Greve wrote: Isn't that what you got from the mri_surf2surf command? On 5/7/2020 3:08 PM, Ian Hardingham wrote: External Email - Use Caution Thanks Doug - yes, I'd like the vertex coordinates in the same format as the local subject surface files are in. On 07/05/2020 19:02, Douglas N. Greve wrote: It comes down to how you want to define "roughly in the same place". Does this mean an affine (12dof) transform? And what information do you want? An XYZ coordinate? On 5/7/2020 11:06 AM, Ian Hardingham wrote: External Email - Use Caution I'd like to get a set of points to compare across several brains, so that the nth point in brain A is in roughly the same place as the nth point in brain B - so I'd like to have an agreed upon set of vertices (the source brain's vertices) translated to positions on the target brain (which may well not be vertices in the target geometry.) On 07/05/2020 15:59, Douglas N. Greve wrote: I don't understand. What is the difference between the target brain and the target subject's vertices? On 5/7/2020 2:17 AM, Ian Hardingham wrote: External Email - Use Caution Ok, thanks Doug, but I'm looking to get the positions of the source vertexes on the target brain, not the target subject's vertices... On 06/05/2020 23:07, Douglas N. Greve wrote: That looks like it could be right. It has 102,020 vertices, which should be the number of vertices in the target subject (and is in the typical range for an individual subject) On 5/6/2020 10:21 AM, Ian Hardingham wrote: External Email - Use Caution FSLInfo attached, thanks Bruce. When trying to run freeview I get "freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory" - do I need to add /usr/local/freesurfer/lib/* to path or something along those lines? SURFACE INFO type : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE num vertices: 102020 num faces : 204036 num strips : 0 surface area: 65520.5 AvgVtxArea 0.642232 AvgVtxDist 0.940503 StdVtxDist 0.417776 ctr : (-31.9056, -18.8197, 16.3545) vertex locs : surfaceRAS Volume Geometry (vg) volume geometry: extent : (176, 224, 256) voxel : ( 1., 1., 1.) x_(ras) : (-0.9990, -0.0436, 0.) y_(ras) : (-0.0436, 0.9990, 0.) z_(ras) : ( 0., 0., 1.) c_(ras) : (-0.5431, 8.9290, -17.0723) file : /media/ian/bronson/subject/T1_nifti.nii.gz Volume Geometry vox2ras -0.99905 -0.04362 0.0 92.25847; -0.04362 0.99905 0.0 -99.12585; 0.0 0.0 1.0 -145.07230; 0.0 0.0 0.0 1.0; Volume Geometry vox2ras-tkr -1.0 0.0 0.0 88.0; 0.0 0.0 1.0 -128.0; 0.0 -1.0 0.0 112.0; 0.0 0.0 0.0 1.0; cmd[0]: mris_remove_intersection ../surf/lh.orig ../surf/lh.orig ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:14:53-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_remove_intersection.c,v 1.6 2011/03/02 00:04:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[1]: mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs T1_MDEFT_BONANN lh ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:14:56-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[2]: mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:18:33-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[3]: mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:18:36-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[4]: mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:20:12-GMT BuildTimeStamp: May 13 2013
Re: [Freesurfer] Get Atlas surfaces in subject space
External Email - Use Caution Thanks Doug - yes, I'd like the vertex coordinates in the same format as the local subject surface files are in. On 07/05/2020 19:02, Douglas N. Greve wrote: It comes down to how you want to define "roughly in the same place". Does this mean an affine (12dof) transform? And what information do you want? An XYZ coordinate? On 5/7/2020 11:06 AM, Ian Hardingham wrote: External Email - Use Caution I'd like to get a set of points to compare across several brains, so that the nth point in brain A is in roughly the same place as the nth point in brain B - so I'd like to have an agreed upon set of vertices (the source brain's vertices) translated to positions on the target brain (which may well not be vertices in the target geometry.) On 07/05/2020 15:59, Douglas N. Greve wrote: I don't understand. What is the difference between the target brain and the target subject's vertices? On 5/7/2020 2:17 AM, Ian Hardingham wrote: External Email - Use Caution Ok, thanks Doug, but I'm looking to get the positions of the source vertexes on the target brain, not the target subject's vertices... On 06/05/2020 23:07, Douglas N. Greve wrote: That looks like it could be right. It has 102,020 vertices, which should be the number of vertices in the target subject (and is in the typical range for an individual subject) On 5/6/2020 10:21 AM, Ian Hardingham wrote: External Email - Use Caution FSLInfo attached, thanks Bruce. When trying to run freeview I get "freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory" - do I need to add /usr/local/freesurfer/lib/* to path or something along those lines? SURFACE INFO type : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE num vertices: 102020 num faces : 204036 num strips : 0 surface area: 65520.5 AvgVtxArea 0.642232 AvgVtxDist 0.940503 StdVtxDist 0.417776 ctr : (-31.9056, -18.8197, 16.3545) vertex locs : surfaceRAS Volume Geometry (vg) volume geometry: extent : (176, 224, 256) voxel : ( 1., 1., 1.) x_(ras) : (-0.9990, -0.0436, 0.) y_(ras) : (-0.0436, 0.9990, 0.) z_(ras) : ( 0., 0., 1.) c_(ras) : (-0.5431, 8.9290, -17.0723) file : /media/ian/bronson/subject/T1_nifti.nii.gz Volume Geometry vox2ras -0.99905 -0.04362 0.0 92.25847; -0.04362 0.99905 0.0 -99.12585; 0.0 0.0 1.0 -145.07230; 0.0 0.0 0.0 1.0; Volume Geometry vox2ras-tkr -1.0 0.0 0.0 88.0; 0.0 0.0 1.0 -128.0; 0.0 -1.0 0.0 112.0; 0.0 0.0 0.0 1.0; cmd[0]: mris_remove_intersection ../surf/lh.orig ../surf/lh.orig ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:14:53-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_remove_intersection.c,v 1.6 2011/03/02 00:04:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[1]: mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs T1_MDEFT_BONANN lh ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:14:56-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[2]: mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:18:33-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[3]: mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:18:36-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[4]: mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:20:12-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[5]: mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/27-00:03:14-GMT BuildTimeStamp: M
Re: [Freesurfer] Get Atlas surfaces in subject space
External Email - Use Caution I'd like to get a set of points to compare across several brains, so that the nth point in brain A is in roughly the same place as the nth point in brain B - so I'd like to have an agreed upon set of vertices (the source brain's vertices) translated to positions on the target brain (which may well not be vertices in the target geometry.) On 07/05/2020 15:59, Douglas N. Greve wrote: I don't understand. What is the difference between the target brain and the target subject's vertices? On 5/7/2020 2:17 AM, Ian Hardingham wrote: External Email - Use Caution Ok, thanks Doug, but I'm looking to get the positions of the source vertexes on the target brain, not the target subject's vertices... On 06/05/2020 23:07, Douglas N. Greve wrote: That looks like it could be right. It has 102,020 vertices, which should be the number of vertices in the target subject (and is in the typical range for an individual subject) On 5/6/2020 10:21 AM, Ian Hardingham wrote: External Email - Use Caution FSLInfo attached, thanks Bruce. When trying to run freeview I get "freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory" - do I need to add /usr/local/freesurfer/lib/* to path or something along those lines? SURFACE INFO type : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE num vertices: 102020 num faces : 204036 num strips : 0 surface area: 65520.5 AvgVtxArea 0.642232 AvgVtxDist 0.940503 StdVtxDist 0.417776 ctr : (-31.9056, -18.8197, 16.3545) vertex locs : surfaceRAS Volume Geometry (vg) volume geometry: extent : (176, 224, 256) voxel : ( 1., 1., 1.) x_(ras) : (-0.9990, -0.0436, 0.) y_(ras) : (-0.0436, 0.9990, 0.) z_(ras) : ( 0., 0., 1.) c_(ras) : (-0.5431, 8.9290, -17.0723) file : /media/ian/bronson/subject/T1_nifti.nii.gz Volume Geometry vox2ras -0.99905 -0.04362 0.0 92.25847; -0.04362 0.99905 0.0 -99.12585; 0.0 0.0 1.0 -145.07230; 0.0 0.0 0.0 1.0; Volume Geometry vox2ras-tkr -1.0 0.0 0.0 88.0; 0.0 0.0 1.0 -128.0; 0.0 -1.0 0.0 112.0; 0.0 0.0 0.0 1.0; cmd[0]: mris_remove_intersection ../surf/lh.orig ../surf/lh.orig ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:14:53-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_remove_intersection.c,v 1.6 2011/03/02 00:04:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[1]: mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs T1_MDEFT_BONANN lh ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:14:56-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[2]: mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:18:33-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[3]: mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:18:36-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[4]: mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:20:12-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[5]: mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/27-00:03:14-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 mris_info creationtime 2020/05/06-14:18:48-GMT sysname Linux hostname ryzen-cumnor machine x86_64 surfacefile /home/ian/cdm_registered_test/registered_lh.white hemicode 1 talaira
Re: [Freesurfer] Get Atlas surfaces in subject space
External Email - Use Caution Ok, thanks Doug, but I'm looking to get the positions of the source vertexes on the target brain, not the target subject's vertices... On 06/05/2020 23:07, Douglas N. Greve wrote: That looks like it could be right. It has 102,020 vertices, which should be the number of vertices in the target subject (and is in the typical range for an individual subject) On 5/6/2020 10:21 AM, Ian Hardingham wrote: External Email - Use Caution FSLInfo attached, thanks Bruce. When trying to run freeview I get "freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory" - do I need to add /usr/local/freesurfer/lib/* to path or something along those lines? SURFACE INFO type : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE num vertices: 102020 num faces : 204036 num strips : 0 surface area: 65520.5 AvgVtxArea 0.642232 AvgVtxDist 0.940503 StdVtxDist 0.417776 ctr : (-31.9056, -18.8197, 16.3545) vertex locs : surfaceRAS Volume Geometry (vg) volume geometry: extent : (176, 224, 256) voxel : ( 1., 1., 1.) x_(ras) : (-0.9990, -0.0436, 0.) y_(ras) : (-0.0436, 0.9990, 0.) z_(ras) : ( 0., 0., 1.) c_(ras) : (-0.5431, 8.9290, -17.0723) file : /media/ian/bronson/subject/T1_nifti.nii.gz Volume Geometry vox2ras -0.99905 -0.04362 0.0 92.25847; -0.04362 0.99905 0.0 -99.12585; 0.0 0.0 1.0 -145.07230; 0.0 0.0 0.0 1.0; Volume Geometry vox2ras-tkr -1.0 0.0 0.0 88.0; 0.0 0.0 1.0 -128.0; 0.0 -1.0 0.0 112.0; 0.0 0.0 0.0 1.0; cmd[0]: mris_remove_intersection ../surf/lh.orig ../surf/lh.orig ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:14:53-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_remove_intersection.c,v 1.6 2011/03/02 00:04:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[1]: mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs T1_MDEFT_BONANN lh ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:14:56-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[2]: mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:18:33-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[3]: mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:18:36-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[4]: mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/26-23:20:12-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 cmd[5]: mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/27-00:03:14-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-23-generic CompilerName: GCC CompilerVersion: 30400 mris_info creationtime 2020/05/06-14:18:48-GMT sysname Linux hostname ryzen-cumnor machine x86_64 surfacefile /home/ian/cdm_registered_test/registered_lh.white hemicode 1 talairach_flag 0 rescale 0.00 nvertices 102020 nfaces 204036 total_area 65520.492188 group_avg_vtxarea_loaded 0 avgvtxarea 0.642232 avgvtxdist 0.940503 stdvtxdist 0.417776 vtx0xyz -8.576451 -101.319672 3.333434 On 06/05/2020 15:00, Bruce Fischl wrote: can you run mris_info on the output surfcae? And maybe send a freeview snapshot of it (in 3d rendering mode) On Wed, 6 May 2020, Ian wrote: External Email - Use Caution Thanks Tim and Doug. I have the files generating and loading properly now, but I'm not convinced it's giving the output I'm looking for. I
Re: [Freesurfer] Get Atlas surfaces in subject space
My newly registered lh.white file is half the size:
3316997 May 6 10:41 /home/ian/cdm_registered_test/registered_lh.white
(and appears to have half the vertices accordingly.)
So this must be incorrect, or at least not my intended purpose.
To try and be clear, I'm looking to get the position of every vertex
in fsaverage's surfaces "on" the surface of my subject's surfaces.
So if there's a vertex at the peak of a particular sulcii on
fsaverage, I'm looking to find where the peak of that sulcii is on my
subject.
Thanks,
Ian
On 06/05/2020 09:08, Tim Schäfer wrote:
External Email - Use Caution
Just a note: there should be no need to convert to gifti, nibabel
can read
the FreeSurer binary surface format directly with
`nibabel.freesurfer.io.read_geometry()`.
The docs are here:
https://nipy.org/nibabel/reference/nibabel.freesurfer.html#nibabel.freesurfer.io.read_geometry
Best,
Tim
On May 5, 2020 at 7:59 PM "Douglas N. Greve"
wrote:
You should load the surfaces in FV. If it load in FV ok but
nibable is
crashing, you should contact them.
On 5/5/2020 1:05 PM, Ian Hardingham wrote:
External Email - Use Caution
Thank you both.
I've made edits and these are the current commands:
mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz white
--trgsubject fs_target --tval-xyz {input_dir}/T1_nifti.nii.gz
--trgsurfval {output_dir}/registered_lh.white
mri_surf2surf --hemi rh --srcsubject fsaverage --sval-xyz white
--trgsubject fs_target --tval-xyz {input_dir}/T1_nifti.nii.gz
--trgsurfval {output_dir}/registered_rh.white
mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz pial
--trgsubject fs_target --tval-xyz {input_dir}/T1_nifti.nii.gz
--trgsurfval {output_dir}/registered_lh.pial
mri_surf2surf --hemi rh --srcsubject fsaverage --sval-xyz pial
--trgsubject fs_target --tval-xyz {input_dir}/T1_nifti.nii.gz
--trgsurfval {output_dir}/registered_rh.pial
These execute successfully and the file size looks about right, but
after using mris_convert to convert to Gifti format nibabel
crashes on
trying to load them - is there anything obviously wrong in my
commands?
I'll also take a look at mris_apply_reg.
On 05/05/2020 18:01, Douglas N. Greve wrote:
Don't specify a --trg_type. But add --tval-xyz
mris_apply_reg will do the same thing, but the interface might be a
little easier
On 5/5/2020 12:49 PM, Bruce Fischl wrote:
no definitely not "w" format, which we don't use for anything
anymore. YOu should use tval-xyz also I think
On Tue, 5 May 2020, Ian Hardingham wrote:
External Email - Use Caution
It would appear not, as I'm getting an error on my pial output
files but not
my white ones. Here are my commands:
mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz white
--trgsubject
fs_target --trgsurfval ./registered_lh.white --trg_type w
mri_surf2surf --hemi rh --srcsubject fsaverage --sval-xyz white
--trgsubject
fs_target --trgsurfval ./registered_rh.white --trg_type w
mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz pial
--trgsubject
fs_target --trgsurfval ./registered_lh.pial --trg_type w
mri_surf2surf --hemi rh --srcsubject fsaverage --sval-xyz pial
--trgsubject
fs_target --trgsurfval ./registered_rh.pial --trg_type w
The white calls output seems to be fine, but the pial ones
aren't. I
somewhat naively trued trg_type pial but that wasn't correct.
On 05/05/2020 17:33, Ian Hardingham wrote:
Thanks Bruce, extremely helpful.
Can I just check that the "w" format is what is used by
both
the
lh/rh.pial and the lh/rh.white files? I only ask
because my
surf2surf command outputs the exact output filename if
the end
is ".white", but if it's ".pial" it outputs ".pial.w",
which I
find a little curious.
Ian
On 05/05/2020 16:34, Bruce Fischl wrote:
yes, check out options like:
--sval-xyz
if you need further help though I'll have to defer to Doug
:)
Bruce
On Tue, 5 May 2020, Ian Hardingham wrote:
External Email - Use Caution
Bruce, I've read the docs on mri_surf2surf - I
wish to get surface files out
(again, lh.pial, rh.pial, lh.white, and
rh.white) rather than values for
something such as thickness - is there an
option for mri_surf2surf to allow
this?
On 05/05/2020 14:43, Bruce Fischl wrote:
Hi Ian
you can use mri_surf2surf to map
surfaces between subjects, but
our atlas isn't really a surface. You
can use the surfaces in
the fsaverage dir, but they are meant
for visualization and are
much smoother than individuals
Re: [Freesurfer] Get Atlas surfaces in subject space
External Email - Use Caution
Thank you both.
I've made edits and these are the current commands:
mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz white
--trgsubject fs_target --tval-xyz {input_dir}/T1_nifti.nii.gz
--trgsurfval {output_dir}/registered_lh.white
mri_surf2surf --hemi rh --srcsubject fsaverage --sval-xyz white
--trgsubject fs_target --tval-xyz {input_dir}/T1_nifti.nii.gz
--trgsurfval {output_dir}/registered_rh.white
mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz pial
--trgsubject fs_target --tval-xyz {input_dir}/T1_nifti.nii.gz
--trgsurfval {output_dir}/registered_lh.pial
mri_surf2surf --hemi rh --srcsubject fsaverage --sval-xyz pial
--trgsubject fs_target --tval-xyz {input_dir}/T1_nifti.nii.gz
--trgsurfval {output_dir}/registered_rh.pial
These execute successfully and the file size looks about right, but
after using mris_convert to convert to Gifti format nibabel crashes on
trying to load them - is there anything obviously wrong in my commands?
I'll also take a look at mris_apply_reg.
On 05/05/2020 18:01, Douglas N. Greve wrote:
Don't specify a --trg_type. But add --tval-xyz
mris_apply_reg will do the same thing, but the interface might be a
little easier
On 5/5/2020 12:49 PM, Bruce Fischl wrote:
no definitely not "w" format, which we don't use for anything
anymore. YOu should use tval-xyz also I think
On Tue, 5 May 2020, Ian Hardingham wrote:
External Email - Use Caution
It would appear not, as I'm getting an error on my pial output files
but not
my white ones. Here are my commands:
mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz white
--trgsubject
fs_target --trgsurfval ./registered_lh.white --trg_type w
mri_surf2surf --hemi rh --srcsubject fsaverage --sval-xyz white
--trgsubject
fs_target --trgsurfval ./registered_rh.white --trg_type w
mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz pial
--trgsubject
fs_target --trgsurfval ./registered_lh.pial --trg_type w
mri_surf2surf --hemi rh --srcsubject fsaverage --sval-xyz pial
--trgsubject
fs_target --trgsurfval ./registered_rh.pial --trg_type w
The white calls output seems to be fine, but the pial ones aren't. I
somewhat naively trued trg_type pial but that wasn't correct.
On 05/05/2020 17:33, Ian Hardingham wrote:
Thanks Bruce, extremely helpful.
Can I just check that the "w" format is what is used by both the
lh/rh.pial and the lh/rh.white files? I only ask because my
surf2surf command outputs the exact output filename if the end
is ".white", but if it's ".pial" it outputs ".pial.w", which I
find a little curious.
Ian
On 05/05/2020 16:34, Bruce Fischl wrote:
yes, check out options like:
--sval-xyz
if you need further help though I'll have to defer to Doug
:)
Bruce
On Tue, 5 May 2020, Ian Hardingham wrote:
External Email - Use Caution
Bruce, I've read the docs on mri_surf2surf - I
wish to get surface files out
(again, lh.pial, rh.pial, lh.white, and
rh.white) rather than values for
something such as thickness - is there an
option for mri_surf2surf to allow
this?
On 05/05/2020 14:43, Bruce Fischl wrote:
Hi Ian
you can use mri_surf2surf to map
surfaces between subjects, but
our atlas isn't really a surface. You
can use the surfaces in
the fsaverage dir, but they are meant
for visualization and are
much smoother than individuals
cheers
Bruce
On Tue, 5 May 2020, Ian wrote:
External Email - Use
Caution
Hi Freesurfers.
I have a subject S with recon-all
having been run on
it.
I have the subject-specific
surface files
/surf/lh.pial, rh.pial, lh.white,
and rh.white.
I would like an Atlas's lh.pial,
rh.pial, lh.white,
and rh.white in subject
space.
Any helpers on how to achieve
this?
Thanks,
Ian
--
Ian Hardingham
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Re: [Freesurfer] Get Atlas surfaces in subject space
External Email - Use Caution It would appear not, as I'm getting an error on my pial output files but not my white ones. Here are my commands: mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz white --trgsubject fs_target --trgsurfval ./registered_lh.white --trg_type w mri_surf2surf --hemi rh --srcsubject fsaverage --sval-xyz white --trgsubject fs_target --trgsurfval ./registered_rh.white --trg_type w mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz pial --trgsubject fs_target --trgsurfval ./registered_lh.pial --trg_type w mri_surf2surf --hemi rh --srcsubject fsaverage --sval-xyz pial --trgsubject fs_target --trgsurfval ./registered_rh.pial --trg_type w The white calls output seems to be fine, but the pial ones aren't. I somewhat naively trued trg_type pial but that wasn't correct. On 05/05/2020 17:33, Ian Hardingham wrote: Thanks Bruce, extremely helpful. Can I just check that the "w" format is what is used by both the lh/rh.pial and the lh/rh.white files? I only ask because my surf2surf command outputs the exact output filename if the end is ".white", but if it's ".pial" it outputs ".pial.w", which I find a little curious. Ian On 05/05/2020 16:34, Bruce Fischl wrote: yes, check out options like: --sval-xyz if you need further help though I'll have to defer to Doug :) Bruce On Tue, 5 May 2020, Ian Hardingham wrote: External Email - Use Caution Bruce, I've read the docs on mri_surf2surf - I wish to get surface files out (again, lh.pial, rh.pial, lh.white, and rh.white) rather than values for something such as thickness - is there an option for mri_surf2surf to allow this? On 05/05/2020 14:43, Bruce Fischl wrote: Hi Ian you can use mri_surf2surf to map surfaces between subjects, but our atlas isn't really a surface. You can use the surfaces in the fsaverage dir, but they are meant for visualization and are much smoother than individuals cheers Bruce On Tue, 5 May 2020, Ian wrote: External Email - Use Caution Hi Freesurfers. I have a subject S with recon-all having been run on it. I have the subject-specific surface files /surf/lh.pial, rh.pial, lh.white, and rh.white. I would like an Atlas's lh.pial, rh.pial, lh.white, and rh.white in subject space. Any helpers on how to achieve this? Thanks, Ian -- Ian Hardingham ___ 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
Re: [Freesurfer] Get Atlas surfaces in subject space
External Email - Use Caution Thanks Bruce, extremely helpful. Can I just check that the "w" format is what is used by both the lh/rh.pial and the lh/rh.white files? I only ask because my surf2surf command outputs the exact output filename if the end is ".white", but if it's ".pial" it outputs ".pial.w", which I find a little curious. Ian On 05/05/2020 16:34, Bruce Fischl wrote: yes, check out options like: --sval-xyz if you need further help though I'll have to defer to Doug :) Bruce On Tue, 5 May 2020, Ian Hardingham wrote: External Email - Use Caution Bruce, I've read the docs on mri_surf2surf - I wish to get surface files out (again, lh.pial, rh.pial, lh.white, and rh.white) rather than values for something such as thickness - is there an option for mri_surf2surf to allow this? On 05/05/2020 14:43, Bruce Fischl wrote: Hi Ian you can use mri_surf2surf to map surfaces between subjects, but our atlas isn't really a surface. You can use the surfaces in the fsaverage dir, but they are meant for visualization and are much smoother than individuals cheers Bruce On Tue, 5 May 2020, Ian wrote: External Email - Use Caution Hi Freesurfers. I have a subject S with recon-all having been run on it. I have the subject-specific surface files /surf/lh.pial, rh.pial, lh.white, and rh.white. I would like an Atlas's lh.pial, rh.pial, lh.white, and rh.white in subject space. Any helpers on how to achieve this? Thanks, Ian -- Ian Hardingham ___ 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
Re: [Freesurfer] Get Atlas surfaces in subject space
External Email - Use Caution Bruce, I've read the docs on mri_surf2surf - I wish to get surface files out (again, lh.pial, rh.pial, lh.white, and rh.white) rather than values for something such as thickness - is there an option for mri_surf2surf to allow this? On 05/05/2020 14:43, Bruce Fischl wrote: Hi Ian you can use mri_surf2surf to map surfaces between subjects, but our atlas isn't really a surface. You can use the surfaces in the fsaverage dir, but they are meant for visualization and are much smoother than individuals cheers Bruce On Tue, 5 May 2020, Ian wrote: External Email - Use Caution Hi Freesurfers. I have a subject S with recon-all having been run on it. I have the subject-specific surface files /surf/lh.pial, rh.pial, lh.white, and rh.white. I would like an Atlas's lh.pial, rh.pial, lh.white, and rh.white in subject space. Any helpers on how to achieve this? Thanks, Ian -- Ian Hardingham ___ 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] How is Total cortical gray matter volume calculated
External Email - Use Caution Morning Freesurfers. Can you describe how the FS stat Total cortical gray matter volume is calculated from the files in the freesurfer subject directory? Is there an mgz file where each voxel has an estimated percentage grey matter here as the value... or is the volume between the surfaces calculated somehow? Thanks, Ian ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] nu_correct: Command not found
External Email - Use Caution Hello all. I am attempting to run recon-all in a docker container. I have a set of commands to set up the system, and on my local machine (Ubuntu) it works fine. However on the docker container (also Ubuntu) I get nu_correct: Command not found. I imagine there is some software that is required that I haven't installed on the container image - does anyone have any idea what it might be? 1. I have run these commands: source /usr/local/freesurfer/SetUpFreeSurfer.sh export PATH=/usr/local/freesurfer/bin:PATH=/usr/local/freesurfer/mni/bin:$PATH 2. I have set FREESURFER_HOME Attached at the end is some output from both failing and successful runs. 3. nu_correct exists in freesurfer/mni/bin 4. Perl is present and correct on both systems. Thank you in advance, Ian FAILING OUTPUT: # #@# Talairach Thu Mar 28 14:12:31 UTC 2019 /subjects/FS_subj_001/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /subjects/FS_subj_001/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux 40ed7e79aa5d 4.15.0-46-generic #49-Ubuntu SMP Wed Feb 6 09:33:07 UTC 2019 x86_64 GNU/Linux Thu Mar 28 14:12:32 UTC 2019 nu_correct: Command not found. SUCCESSFUL OUTPUT: # #@# Talairach Thu Mar 28 14:33:45 GMT 2019 /home/ian/subjects/FS_subj_001/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /home/ian/subjects/FS_subj_001/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux ian-Sabre-17WV8 4.15.0-46-generic #49-Ubuntu SMP Wed Feb 6 09:33:07 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux Thu Mar 28 14:33:45 GMT 2019 Program nu_correct, built from: -- Ian Hardingham ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
