[Freesurfer] ctx-lh-corpuscallosum
External Email - Use Caution Hi Freesurfers. There is a "ctx-lh/rh-corpuscallosum" label in Freesurfer, but the Corpus Callosum is not considered to be in the cortex. Can you explain precisely what this label refers to? Thanks, Ian ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Recon-all 5.3.0 failing and I can't see the error message
External Email - Use Caution Here you go Doug, thanks. docker@7d97b79d7546:/execute/freesurfer2016/mri$ mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz /execute/freesurfer2016/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz nIters 1 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux 7d97b79d7546 5.3.0-59-generic #53~18.04.1-Ubuntu SMP Thu Jun 4 14:58:26 UTC 2020 x86_64 GNU/Linux Tue Jun 30 12:13:22 UTC 2020 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.835 /execute/freesurfer2016/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.835/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.835/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=7.92, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.835/nu0.mnc... Iteration 1 Tue Jun 30 12:13:23 UTC 2020 nu_correct -clobber ./tmp.mri_nu_correct.mni.835/nu0.mnc ./tmp.mri_nu_correct.mni.835/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.835/0/ -iterations 1000 -distance 50 Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 165. nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280) ERROR: nu_correct On 29/06/2020 15:50, Douglas N. Greve wrote: Not sure. Can you run this cd /execute/freesurfer2016/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz and send the terminal output? On 6/29/2020 7:01 AM, Ian wrote: External Email - Use Caution I have attached the log - is there any chance you could tell me what the problem is? Thanks, Ian -- ___ 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 -- *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] Recon-all 5.3.0 failing and I can't see the error message
External Email - Use Caution I have attached the log - is there any chance you could tell me what the problem is? Thanks, Ian -- Mon Jun 29 10:53:22 UTC 2020 /execute/freesurfer2016 /usr/local/freesurfer/bin/recon-all -all -subjid ./freesurfer2016 subjid freesurfer2016 setenv SUBJECTS_DIR /execute FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux 7d97b79d7546 5.3.0-59-generic #53~18.04.1-Ubuntu SMP Thu Jun 4 14:58:26 UTC 2020 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize8192 kbytes coredumpsize unlimited memoryuseunlimited vmemoryuse unlimited descriptors 1048576 memorylocked 16384 kbytes maxproc unlimited maxlocks unlimited maxsignal63578 maxmessage 819200 maxnice 0 maxrtprio0 maxrttimeunlimited totalusedfree shared buff/cache available Mem: 16390764 6474076 212720 304968 9703968 9295408 Swap: 2097148 818176 1278972 program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/06/29-10:53:23-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: docker Machine: 7d97b79d7546 Platform: Linux PlatformVersion: 5.3.0-59-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/06/29-10:53:23-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: docker Machine: 7d97b79d7546 Platform: Linux PlatformVersion: 5.3.0-59-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/06/29-10:53:23-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: docker Machine: 7d97b79d7546 Platform: Linux PlatformVersion: 5.3.0-59-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/06/29-10:53:23-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: docker Machine: 7d97b79d7546 Platform: Linux PlatformVersion: 5.3.0-59-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/06/29-10:53:23-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: docker Machine: 7d97b79d7546 Platform: Linux PlatformVersion: 5.3.0-59-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/06/29-10:53:23-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: docker Machine: 7d97b79d7546 Platform: Linux PlatformVersion: 5.3.0-59-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/06/29-10:53:23-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: docker Machine: 7d97b79d7546 Platform: Linux PlatformVersion: 5.3.0-59-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/06/29-10:53:23-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: docker Machine: 7d97b79d7546 Platform: Linux PlatformVersion: 5.3.0-59-generic CompilerName: GCC CompilerVersion: 40400 === NUMBER OF OPENMP THREADS = 1 === ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2020/06/29-10:53:23-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: docker Machine: 7d97b79d7546 Platform: Linux PlatformVersion: 5.3.0-59-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info
[Freesurfer] Freesurfer 5.3.0 recon-all failure
External Email - Use Caution Hey guys. I have need to run recon-all from freesurfer 5.3.0. When I do I get this error: INFO: SUBJECTS_DIR is /execute Actual FREESURFER_HOME /usr/local/freesurfer Linux ca9b4aef337a 5.3.0-59-generic #53~18.04.1-Ubuntu SMP Thu Jun 4 14:58:26 UTC 2020 x86_64 GNU/Linux Can't locate MNI/Startup.pm in @INC (you may need to install the MNI::Startup module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.28.1 /usr/local/share/perl/5.28.1 /usr/lib/x86_64-linux-gnu/perl5/5.28 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.28 /usr/share/perl/5.28 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at /usr/local/freesurfer/mni/bin/nu_correct line 37. BEGIN failed--compilation aborted at /usr/local/freesurfer/mni/bin/nu_correct line 37. Could you advise please? Thanks, Ian -- *Ian Hardingham* ___ 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 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
[Freesurfer] Ventricular location
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
Re: [Freesurfer] Get Freesurfer versions 4 and 5
External Email - Use Caution Sorry, found them, never mind! On 18/05/2020 12:26, Ian wrote: External Email - Use Caution Hi freesurfers, Is it possible to download freesurfer versions 4 and 5? Thanks, Ian -- *Ian Hardingham* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- *Ian Hardingham* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Get Freesurfer versions 4 and 5
External Email - Use Caution Hi freesurfers, Is it possible to download freesurfer versions 4 and 5? Thanks, Ian -- *Ian Hardingham* ___ 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
[Freesurfer] Which subject does recon-all register surfaces to?
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
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 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
Re: [Freesurfer] Get Atlas surfaces in subject space
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
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
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 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
Re: [Freesurfer] Get Atlas surfaces in subject space
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.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
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
___
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 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] Get Atlas surfaces in subject space
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] 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] 8 Gb of ram
External Email - Use Caution Hey guys. I'm running Freesurfer on an AWS EC2 instance, in a docker container (t3.large specifically.) Would you expect 8Gb of ram to *always* be enough to run recon-all on a 280x280x240 T1 image? The instance is running Ubuntu; the container image is based on Ubuntu; and nothing else is being explicitly run on the instance while recon-all is running. Thanks, Ian -- *Ian Hardingham* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] recon-all-failure with file links
External Email - Use Caution Oops, looks like the files didn't attach. Here are links to the logs: https://obd-public.s3.eu-west-2.amazonaws.com/recon-all-standard_out_log.log https://obd-public.s3.eu-west-2.amazonaws.com/recon-all-status.log https://obd-public.s3.eu-west-2.amazonaws.com/recon-all.log Hi all. I have a T1 scan which I run through recon-all with: recon-all -all -parallel -subjid freesurfer (after mksubjdirs etc) On my office machine, recon-all completes successfully. On a cloud machine (16GB of ram), it fails after about 4 hours. I have attached the logs - the only immediate error I can see is "Cannot find rh.white.H". Any advice would be much appreciated, thank you. Ian -- *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] 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
[Freesurfer] hippocampal subfield segmentation input mask?
External Email - Use Caution Dear FreeSurfer list, I'm wondering if there is any way to input different starting segmentations for the hippocampus into the hippocampal subfield segmentation? We've got a hippocampus specific segmentation algorithm which we'd like to try as input to see if it provides a better starting point than whole brain labels. Are there any other inputs we'd need? Best wishes, Ian Malone -- Research Associate Dementia Research Centre Queen Square Institute of Neurology UCL London WC1N 3BG ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Nonisotropic PSF in mri_gtmpvc
Hello, Is there a way to specify a nonisotropic PSF when using mri_gtmpvc? I have reason to believe there are differences between the axial and transverse resolutions of the PET scanner in my study and would like to incorporate them if possible. Thanks, Ian Kennedy ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] generating new surface
Dear Freesurfers, I need to generate a surface which lies halfway between the wm/gm border and the pial surface so that I can then import it in matlab using read_surf.m to get the vertex coordinates and faces for the surface that, as I said, would not be the pial surface, but defined at half cortical thickness. I looked at mri_vol2surf --help, and its option --projfrac 0.5 seemed to be what I wanted, but I don't know how to call mri_vol2surf for the specific needs I have. Also, mri_vol2surf produces an overlay mappable onto a surface and not a surface per se, so maybe what I am looking for lies elsewhere. Any help would be highly appreciated!! ian ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] public MRI dataset, alzheimer's and controls, MIRIAD
Dear FreeSurfer users, We are happy to announce the release of a new publicly available dataset of volumetric brain MRI of Alzheimer's patients and age-matched controls: MIRIAD (Minimal Interval Resonance Imaging in Alzheimer's Disease). MIRIAD complements existing datasets such as ADNI by providing a high number of scans for each subject over a range of intervals from 2 weeks up to 2 years and back-to-back scans, enabling reproducibility, symmetry and transitivity assessment of longitudinal measures. You can find further information and download links at http://miriad.drc.ion.ucl.ac.uk/, and an accompanying publication providing an overview of the study and previous publications at http://dx.doi.org/10.1016/j.neuroimage.2012.12.044 (Malone et al., NeuroImage Vol 70, P33–36) Registration is required so we can assess impact and notify users of any updates. Please take the time to read the Data Use Agreement at https://www.ucl.ac.uk/drc/research/miriad/Database. Instructions for downloading the entire dataset and demographic and psychology data can be found at https://www.ucl.ac.uk/drc/research/miriad/Downloading. The release of this data was made possible through the support of the UK Alzheimer's Society and the kind permission of the original study participants and funders. Full acknowledgements can be found at https://www.ucl.ac.uk/drc/research/miriad/Acknowledgements. Best wishes for your future research, Ian Malone Dementia Research Centre, UCL Institute of Neurology MIRIAD Team: Dementia Research Centre, UCL Institute of Neurology, UK Centre for Medical Image Computing, UCL, UK NMR Research Unit, UCL Institute of Neurology, UK Wellcome Trust Centre for Neuroimaging, UCL Institute of Neurology, UK ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Thresholding using FDR
Hello, When thresholding significance using FDR for one of my overlays, I noticed that a rate of .1 and .05 give me the same minimum and maximum threshold values. At both levels, there were no voxels of significance. Does this mean that freesurfer will not continue to update max and min values when nothing is significant? Thanks, Ian ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] DODS Overlay
Hello, If I were to run a DODS -- say, an F-test looking for group differences and interactions in thickness among drug users vs non- users, dependents vs abusers, and drug use in the last month vs no use in the last month -- how would I visualize the results? I assume there's no intelligible way to make an overlay out of interactions, unless you look at the F-test output one contrast at a time (e.g., what areas show a significant interaction in thickness between dependents vs abusers and use in the last month?). Take care, Ian Carroll ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] freesurfer 5.1 error: MPR2MNI305_TARGET: Undefined variable
Hi Thanks guys for the reply, I have fixed this now. ian -Original Message- From: dgw [mailto:dgwake...@gmail.com] Sent: 07 March 2012 19:55 To: Nick Schmansky Cc: Ian Charest; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] freesurfer 5.1 error: MPR2MNI305_TARGET: Undefined variable Hi Ian, This is a bug in the CBU's freesurfer wrappers written at the CBU site and not a FreeSurfer bug. Ask them to look into fixing it. Basically, the wrapper doesn't transfer all the variables necessary for FreeSurfer to run properly. The only work around for you at the moment would be to run it locally i.e. not use the CBU's wrappers. D Nick Schmansky wrote: are there other mni tools installed? are the variables from the different freesurfer installs getting mixed? n. On Wed, 2012-03-07 at 19:01 +, Ian Charest wrote: Hi again More on this note: Using the previous stable version 4.3.0 that I have installed here, I have absolutely no problem in running the same process. ian From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Ian Charest Sent: 07 March 2012 18:09 To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] freesurfer 5.1 error: MPR2MNI305_TARGET: Undefined variable Hi When running recon-all I get the following error: ERROR: mpr2mni305 failed, see transforms/talairach_avi.log I called recon-all like so: recon-all -i /imaging/ic01/mridata/subject01/structurals/subject01.MR.SEQUENCE.001 4.0001.2011.12.16.57.613319.8231038.IMA -all -subjid subject01 I checked the talairach_avi.log file (see the full report below), and the mistake happens at the call to mpr2mni305 MPR2MNI305_TARGET: Undefined variable. I searched the mailing list for similar errors and saw a similar post here: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011- May/01844 5.html but in this user’s case there seemed to be a problem with the MPRAGE image itself (the brain seemed “squashed”) I checked the dimensions of my orig.mgz and they are ok (1x1x1). I had a look at my orig.mgz in tkmedit and all seems fine. Any Idea what could be going wrong? Best Wishes Ian Charest == talairach_avi.log: /imaging/ic01/subjects/subject01/mri /imaging/local/software/freesurfer/5.1.0/i686//bin/talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ Linux l34 2.6.9-89.0.25.ELsmp #1 SMP Mon Apr 19 06:05:15 EDT 2010 i686 i686 i386 GNU/Linux Wed Mar 7 16:56:30 GMT 2012 /imaging/local/software/freesurfer/5.1.0/i686/bin_original/mri_conver t orig.mgz talsrcimg.img $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from orig.mgz... TR=2300.00, TE=2.96, TI=900.00, flip angle=9.00 i_ras = (-1, 4.65661e-08, -4.09782e-08) j_ras = (-2.23517e-08, -3.72529e-09, -1) k_ras = (3.81842e-08, 1, -6.98492e-10) writing to talsrcimg.img... Analyze Output Matrix -1.000 -0.000 0.000 132.161; 0.000 -0.000 1.000 -103.886; -0.000 -1.000 -0.000 97.205; 0.000 0.000 0.000 1.000; INFO: set hdr.hist.orient to -1 mpr2mni305 talsrcimg Wed Mar 7 16:56:34 GMT 2012 /imaging/local/software/freesurfer/5.1.0/i686/bin_original/mpr2mni305 talsrcimg $Id: mpr2mni305,v 1.4 2009/06/03 16:01:38 nicks Exp $ MPR2MNI305_TARGET: Undefined variable. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] freesurfer 5.1 error: MPR2MNI305_TARGET: Undefined variable
Hi When running recon-all I get the following error: ERROR: mpr2mni305 failed, see transforms/talairach_avi.log I called recon-all like so: recon-all -i /imaging/ic01/mridata/subject01/structurals/subject01.MR.SEQUENCE.0014.0001.2011.12.16.57.613319.8231038.IMA -all -subjid subject01 I checked the talairach_avi.log file (see the full report below), and the mistake happens at the call to mpr2mni305 MPR2MNI305_TARGET: Undefined variable. I searched the mailing list for similar errors and saw a similar post here: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-May/018445.htmlhttps://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2011-May/018445.html but in this user's case there seemed to be a problem with the MPRAGE image itself (the brain seemed squashed) I checked the dimensions of my orig.mgz and they are ok (1x1x1). I had a look at my orig.mgz in tkmedit and all seems fine. Any Idea what could be going wrong? Best Wishes Ian Charest == talairach_avi.log: /imaging/ic01/subjects/subject01/mri /imaging/local/software/freesurfer/5.1.0/i686//bin/talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ Linux l34 2.6.9-89.0.25.ELsmp #1 SMP Mon Apr 19 06:05:15 EDT 2010 i686 i686 i386 GNU/Linux Wed Mar 7 16:56:30 GMT 2012 /imaging/local/software/freesurfer/5.1.0/i686/bin_original/mri_convert orig.mgz talsrcimg.img $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from orig.mgz... TR=2300.00, TE=2.96, TI=900.00, flip angle=9.00 i_ras = (-1, 4.65661e-08, -4.09782e-08) j_ras = (-2.23517e-08, -3.72529e-09, -1) k_ras = (3.81842e-08, 1, -6.98492e-10) writing to talsrcimg.img... Analyze Output Matrix -1.000 -0.000 0.000 132.161; 0.000 -0.000 1.000 -103.886; -0.000 -1.000 -0.000 97.205; 0.000 0.000 0.000 1.000; INFO: set hdr.hist.orient to -1 mpr2mni305 talsrcimg Wed Mar 7 16:56:34 GMT 2012 /imaging/local/software/freesurfer/5.1.0/i686/bin_original/mpr2mni305 talsrcimg $Id: mpr2mni305,v 1.4 2009/06/03 16:01:38 nicks Exp $ MPR2MNI305_TARGET: Undefined variable. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] freesurfer 5.1 error: MPR2MNI305_TARGET: Undefined variable
Hi again More on this note: Using the previous stable version 4.3.0 that I have installed here, I have absolutely no problem in running the same process. ian From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Ian Charest Sent: 07 March 2012 18:09 To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] freesurfer 5.1 error: MPR2MNI305_TARGET: Undefined variable Hi When running recon-all I get the following error: ERROR: mpr2mni305 failed, see transforms/talairach_avi.log I called recon-all like so: recon-all -i /imaging/ic01/mridata/subject01/structurals/subject01.MR.SEQUENCE.0014.0001.2011.12.16.57.613319.8231038.IMA -all -subjid subject01 I checked the talairach_avi.log file (see the full report below), and the mistake happens at the call to mpr2mni305 MPR2MNI305_TARGET: Undefined variable. I searched the mailing list for similar errors and saw a similar post here: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-May/018445.htmlhttps://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2011-May/018445.html but in this user's case there seemed to be a problem with the MPRAGE image itself (the brain seemed squashed) I checked the dimensions of my orig.mgz and they are ok (1x1x1). I had a look at my orig.mgz in tkmedit and all seems fine. Any Idea what could be going wrong? Best Wishes Ian Charest == talairach_avi.log: /imaging/ic01/subjects/subject01/mri /imaging/local/software/freesurfer/5.1.0/i686//bin/talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ Linux l34 2.6.9-89.0.25.ELsmp #1 SMP Mon Apr 19 06:05:15 EDT 2010 i686 i686 i386 GNU/Linux Wed Mar 7 16:56:30 GMT 2012 /imaging/local/software/freesurfer/5.1.0/i686/bin_original/mri_convert orig.mgz talsrcimg.img $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from orig.mgz... TR=2300.00, TE=2.96, TI=900.00, flip angle=9.00 i_ras = (-1, 4.65661e-08, -4.09782e-08) j_ras = (-2.23517e-08, -3.72529e-09, -1) k_ras = (3.81842e-08, 1, -6.98492e-10) writing to talsrcimg.img... Analyze Output Matrix -1.000 -0.000 0.000 132.161; 0.000 -0.000 1.000 -103.886; -0.000 -1.000 -0.000 97.205; 0.000 0.000 0.000 1.000; INFO: set hdr.hist.orient to -1 mpr2mni305 talsrcimg Wed Mar 7 16:56:34 GMT 2012 /imaging/local/software/freesurfer/5.1.0/i686/bin_original/mpr2mni305 talsrcimg $Id: mpr2mni305,v 1.4 2009/06/03 16:01:38 nicks Exp $ MPR2MNI305_TARGET: Undefined variable. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] FreeSurfer Ubuntu 11.10
Hi Brian I had to change the terminal config for it to use tcsh. I think Ubuntu now uses The Debian Almquist shell (dash) and I have had problems running freesurfer from it. install tcsh using aptitude and then in the preferences of your terminal (Edit profile preferences) in the tab title and command click on run custom command instead of my shell and type /bin/tcsh as your custom command. You can also set up some environment variables by editing the .tcshrc found in your home directory. gedit ~/.tcshrc and add a modified version of this code according to where your freesurfer install is and where your subject directory lies... alias freesurfer 'setenv FREESURFER_HOME /usr/local/freesurfer; setenv SUBJECTS_DIR ~/subjects; source $FREESURFER_HOME/SetUpFreeSurfer.csh' now if you close your terminal and open a new one, freesurfer should work. Hope it helps Ian From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of James, Brian [brian.ja...@nbrhc.on.ca] Sent: 30 December 2011 20:40 To: martijnsteenw...@gmail.com Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FreeSurfer Ubuntu 11.10 That is what I did…my path is /usr/local/freesurfer However, mine doesn’t seem to work. Brian. From: Martijn Steenwijk [mailto:martijnsteenw...@gmail.com] Sent: December-30-11 2:37 PM To: James, Brian Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] FreeSurfer Ubuntu 11.10 Just untarring the .tar.gz in /usr/local like documented here (http://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall) works like a charm on Ubuntu 11.10. Best, Martijn Van: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens James, Brian Verzonden: vrijdag 30 december 2011 21:13 Aan: freesurfer@nmr.mgh.harvard.edu Onderwerp: [Freesurfer] FreeSurfer Ubuntu 11.10 Hi Everyone, I thought I would try installing FreeSurfer on Ubuntu because I was having so many issues trying to install Octave on CentOS. On the bright side, Ubuntu can download Octave directly from the repository. The downside is when I test my freesurfer install with tkmedit bert orig,mgz, I get the following error: /usr/local/freesurfer/tktools/tksurfer.bin: Exec format error. Binary file not executable. Is there is something additional I need to install because it is on Ubuntu? Brian James Technical Applications Analyst North Bay Regional Health Centrehttp://www.nbrhc.on.ca/ (705) 474-8600 x2611 The information contained in this electronic transmission is intended for the person(s) or entity to whom it is addressed. Delivery of this message to any person other than the intended recipient(s) is not intended in any way to waive confidentiality. This material may contain confidential or personal information which may be subject to the provisions of Ontario's Personal Health Information Protection Act. Any review, retransmission, dissemination or other use of this information by entities other than the intended recipient is prohibited. If you receive this in error, please contact the sender and delete the material immediately. L'information contenue dans ce message électronique est destinée uniquement au destinataire ou aux destinataires visés. La transmission de ce message à une personne autre que son destinataire ou ses destinataires visés ne supprime en rien l'obligation d'en respecter la confidentialité. Ce message peut contenir des renseignements de nature confidentielle ou personnelle qui pourraient être soumis aux dispositions de la Loi de 2004 sur la protection des renseignements personnels sur la santé. L'examen, la retransmission, la diffusion et toute autre utilisation de l'information contenue dans ce message par des personnes autres que le destinataire ou les destinataires visés sont interdits. Si vous recevez ce message par erreur, veuillez le supprimer immédiatement et en avertir l'expéditeur. The information contained in this electronic transmission is intended for the person(s) or entity to whom it is addressed. Delivery of this message to any person other than the intended recipient(s) is not intended in any way to waive confidentiality. This material may contain confidential or personal information which may be subject to the provisions of Ontario's Personal Health Information Protection Act. Any review, retransmission, dissemination or other use of this information by entities other than the intended recipient is prohibited. If you receive this in error, please contact the sender and delete the material immediately. L'information contenue dans ce message électronique est destinée uniquement au destinataire ou aux destinataires visés. La transmission de ce message à une personne autre que son destinataire ou ses destinataires visés ne supprime en rien l'obligation d'en respecter la confidentialité. Ce message peut contenir des
[Freesurfer] Probabilistic V1 labels to volume
Hi There was a post recently on the mailing list about exporting Probabilistic V1 labels to a volume. I have applied the probabilistic mapping of an individual subject and now have the lh.v1.prob.label I would like to convert this label as a volume, and the function mri_label2vol is a little bit confusing. One important thing here is that I don't want the created volume to be binary. but rather to keep the probabilities of a voxel being on V1. I have tried mri_label2vol --label lh.v1.prob.label --subject $SUBJECT --o lh.v1.prob.label I don't understand why I one should need a register.dat file here or even a template file, as I want to generate a volume in RAS space, from a label which I would think is also in RAS space. As for the template file, should it be orig.mgz? Any suggestions here would be appreciated! Regards Ian Charest ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] recommende pc and cuda
Richard G. Edgar wrote: On Tue, 2011-04-05 at 11:23 +0200, Knut J Bjuland wrote: Will a Tesla C2050 or another good CPU be able to reduce the running time from 20-24 hr to less time like for instance 8hr or below that time. On the standard test case we use here, a full recon-all run takes 8 hours on a 3.2 GHz Nehalem core, and about 4 hours 20 mins when using the Tesla C2050. Would I be right in concluding that a 4-core Nehalem (e.g. i7) has more throughput than the C2050 then? -- imalone ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] recommende pc and cuda
On 05/04/11 16:55, Richard G. Edgar wrote: On Tue, 2011-04-05 at 16:30 +0100, Ian Malone wrote: Richard G. Edgar wrote: On the standard test case we use here, a full recon-all run takes 8 hours on a 3.2 GHz Nehalem core, and about 4 hours 20 mins when using the Tesla C2050. Would I be right in concluding that a 4-core Nehalem (e.g. i7) has more throughput than the C2050 then? Yes, but less than having 3 CPU jobs, and one GPU one. I did test once, and there isn't much penalty to running one recon-all job per core on a Nehalem system. Right now, the CPU still does most of the work in the recon-all stream - it's something of a game of Amdahl's Law Wac-A-Mole. You could always try starting 4 GPU jobs at once I've not done the testing, but a C2050 would probably have enough RAM, and in any given recon-all run, the GPU does spend a lot of time idle. Hence, it would end up being divvied up between the four jobs. Thanks, that's interesting to know. -- imalone ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_convert failure
The file is the right size, however further investigation shows that vox_offset in the .hdr file was (incorrectly) non-zero; equal to 1, so mri_convert is correct in skipping one byte at the start. Sorry for the fuss. Ian Douglas N Greve wrote: Can you verify that the file is the right size? Ian Malone wrote: Hi, I'm finding that mri_convert produces a read error when trying to convert some short analyze files to mgz, invoked as the following: mri_convert -it analyze -i `pwd`/reslice/00125-003-1.img -o reslice/mni.mgz The output contains (the dimensions shown are correct): ERROR: premature end of file ERROR: Success (0) frame = 0, slice = 219, k=219, row = 155 nread = 171, nexpected = 172 fname = height = 156 width = 172 depth = 220 and: analyzeRead2(): error reading from file reslice/00125-003-1.img The file in question is 11806080 bytes. Using strace I can see that when the .img file is opened 1 byte is read from it before reading in blocks of 1024, and a final read of 383 bytes. Trying another short file (which works) this initial 1 byte read does not happen. Is this is bug? I can provide the files in question if needed. Build stamp: freesurfer-Linux-rh9-stable-pub-v4.0.3 Kernel info: Linux 2.6.21.5-smp i686 Thanks, Ian Malone ___ 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] mri_label2vol aliasing problem
Hi, I'm trying to use mri_label2voxel to produce an image of a segmented region in the original image voxel space and am seeing black lines through the output region, these are oriented parallel to the voxel axes. In the attached image you can see three of them: two parallel horizontal lines and one vertical one just cutting through the right hand side of the region. This appears to be some kind of aliasing artefact; if I move all the labels by adding 0.2 to each of the location values in the labels file then the lines are shifted to different voxels (not the immediately adjacent ones). Using the 1mm^3 voxel registered volume as the template does not show this problem, neither does viewing the label overlaid on orig.mgz in tkmedit. Is there anything I can adjust to avoid this while still outputting a volume in the original image dimensions? Thanks, Ian Malone inline: mri_label2vol_aliasing.png___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_convert failure
Hi, I'm finding that mri_convert produces a read error when trying to convert some short analyze files to mgz, invoked as the following: mri_convert -it analyze -i `pwd`/reslice/00125-003-1.img -o reslice/mni.mgz The output contains (the dimensions shown are correct): ERROR: premature end of file ERROR: Success (0) frame = 0, slice = 219, k=219, row = 155 nread = 171, nexpected = 172 fname = height = 156 width = 172 depth = 220 and: analyzeRead2(): error reading from file reslice/00125-003-1.img The file in question is 11806080 bytes. Using strace I can see that when the .img file is opened 1 byte is read from it before reading in blocks of 1024, and a final read of 383 bytes. Trying another short file (which works) this initial 1 byte read does not happen. Is this is bug? I can provide the files in question if needed. Build stamp: freesurfer-Linux-rh9-stable-pub-v4.0.3 Kernel info: Linux 2.6.21.5-smp i686 Thanks, Ian Malone ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
