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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:
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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:
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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:
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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 : ( 1.0000, 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.freesurfe... >>>>> >>>>> >>>>> 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 >> >> _______________________________________________ >> 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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