sorry, I'm going to defer to Doug on surf2surf On Wed, 6 May 2020, Ian Hardingham wrote:
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Thanks Bruce.
So a reminder I'm calling:
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
I'm assuming that means the "input surface" is /usr/local/freesurfer/subjects/fsaverage/surf/lh.white, and here's the mris_info for that, but bear in mind that I don't know for sure from that line that that's what is being used.
SURFACE INFO ======================================== type : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE num vertices: 163842 num faces : 327680 num strips : 0 surface area: 65417 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195470 group avg surface area: 82220 ctr : (-31.9282, -18.8144, 16.3699) vertex locs : surfaceRAS talairch.xfm: 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; surfaceRAS to talaraiched surfaceRAS: 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; talairached surfaceRAS to surfaceRAS: 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Volume Geometry (vg) volume geometry: extent : (256, 256, 256) voxel : ( 1.0000, 1.0000, 1.0000) x_(ras) : (-1.0000, 0.0000, 0.0000) y_(ras) : ( 0.0000, 0.0000, -1.0000) z_(ras) : ( 0.0000, 1.0000, 0.0000) c_(ras) : ( 0.0000, 0.0000, 0.0000) file : ../mri/orig.mgz Volume Geometry vox2ras -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; Volume Geometry vox2ras-tkr -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; mris_info creationtime 2020/05/06-14:31:38-GMT sysname Linux hostname ryzen-cumnor machine x86_64 surfacefile /usr/local/freesurfer/subjects/fsaverage/surf/lh.white hemicode 0 talairach_flag 0 rescale 0.000000 nvertices 163842 nfaces 327680 total_area 65416.984375 group_avg_surf_area 82219.960938 group_avg_vtxarea_loaded 1 avgvtxarea 0.399269 avgvtxdist 0.721953 stdvtxdist 0.195470 vtx0xyz -36.806278 -18.292723 64.461525
On 06/05/2020 15:23, Bruce Fischl wrote: hmm, that is not an icosahedral surface, which should have 160K vertices. Can you check your input surface? You'll also need to fix your freeview problem, but someone else will have to help you with that On Wed, 6 May 2020, 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 : ( 1.0000, 1.0000, 1.0000) x_(ras) : (-0.9990, -0.0436, 0.0000) y_(ras) : (-0.0436, 0.9990, 0.0000) z_(ras) : ( 0.0000, 0.0000, 1.0000) c_(ras) : (-0.5431, 8.9290, -17.0723) file : /media/ian/bronson/subject/T1_nifti.nii.gz Volume Geometry vox2ras -0.99905 -0.04362 0.00000 92.25847; -0.04362 0.99905 0.00000 -99.12585; 0.00000 0.00000 1.00000 -145.07230; 0.00000 0.00000 0.00000 1.00000; Volume Geometry vox2ras-tkr -1.00000 0.00000 0.00000 88.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 112.00000; 0.00000 0.00000 0.00000 1.00000; 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 0.000000 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 am trying to convert the "fsaverage" subject's surface coordinates to my own subject's surface space. FSaverage's lh.white file is 5898808 bytes: 5898808 Apr 11 2013 /usr/local/freesurfer/subjects/fsaverage/surf/lh.white After converting with this command: 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 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.freesur
fer.io.read_geometry Best, Tim On May 5, 2020 at 7:59 PM "Douglas N. Greve" <dgreve@mgh.harvard.edu> 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 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 _______________________________________________ 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 -- 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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