[Freesurfer] aparc-stats wth curv-file as input?
Dear FS-Team, I have mapped some PET-data on the corresponding subject's cortical surface. Is it possible to get some statistics from the resulting curv-file using the FS-parcellation as ROIs? Thanks in advance, Florian begin:vcard fn:Florian Gerstl n:Gerstl;Florian org:Medical University of Vienna, Austria;Department of Biomedical Engineering and Physics adr:;;Lazarettgasse 14;Vienna;;1090;Austria email;internet:florian.ger...@meduniwien.ac.at title:MR Center of Excellence tel;work:+43-1-40400-6465 tel;fax:+43-1-40400-7631 version:2.1 end:vcard ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] aparc-stats wth curv-file as input?
sure, once you have it sampled on the surface you can treat it like a thickness study (unless you have a timecourse, in which case it would be like an fMRI study). cheers, Bruce On Mon, 2 Mar 2009, Florian Gerstl wrote: Dear FS-Team, I have mapped some PET-data on the corresponding subject's cortical surface. Is it possible to get some statistics from the resulting curv-file using the FS-parcellation as ROIs? Thanks in advance, Florian ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] aparc-stats wth curv-file as input?
Thanks for your quick reply! However, when I cast the mris_anatomical_stats command with the "-log" flag the program seems to crash. That's not really a concern for me as I can still use the -f flag to obtain a results-file (no problems there) and I'm not sure whether this is a problem only with our computers but since it is reproducible I thought I'd bring it to your attention.. below I have pasted the command I used with the resulting errors cheers, Florian mris_anatomical_stats -log out.log -a aparc -f pet.lh.curv s05 lh outputting results to out.log... computing statistics for each annotation in aparc. reading volume /fsubjects/o05/mri/wm.mgz... reading input surface /fsubjects/o05/surf/lh.white... reading input pial surface /fsubjects/o05/surf/lh.pial... reading input white surface /fsubjects/o05/surf/lh.white... reading colortable from annotation file... colortable with 35 entries read (originally /space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt) *** glibc detected *** mris_anatomical_stats: double free or corruption (!prev): 0x046135d0 *** === Backtrace: = /lib/libc.so.6[0x7f3fb9ffe08a] /lib/libc.so.6(cfree+0x8c)[0x7f3fba001c1c] /lib/libc.so.6(fclose+0x14c)[0x7f3fb9fecdac] mris_anatomical_stats(vfprintf+0x23f7)[0x4079f7] /lib/libc.so.6(__libc_start_main+0xf4)[0x7f3fb9fa81c4] mris_anatomical_stats(__gxx_personality_v0+0xfa)[0x40626a] === Memory map: 0040-00785000 r-xp 00:1b 1949331435 /progs/freesurfer/bin/mris_anatomical_stats 00884000-008de000 rw-p 00384000 00:1b 1949331435 /progs/freesurfer/bin/mris_anatomical_stats 008de000-07ac rw-p 008de000 00:00 0 [heap] 7f3fb000-7f3fb0021000 rw-p 7f3fb000 00:00 0 7f3fb0021000-7f3fb400 ---p 7f3fb0021000 00:00 0 7f3fb577e000-7f3fb5794000 r-xp 09:02 4026756148 /lib/libnsl-2.7.so 7f3fb5794000-7f3fb5993000 ---p 00016000 09:02 4026756148 /lib/libnsl-2.7.so 7f3fb5993000-7f3fb5995000 rw-p 00015000 09:02 4026756148 /lib/libnsl-2.7.so 7f3fb5995000-7f3fb5997000 rw-p 7f3fb5995000 00:00 0 7f3fb5997000-7f3fb59a1000 r-xp 09:02 4026756153 /lib/libnss_nis-2.7.so 7f3fb59a1000-7f3fb5ba ---p a000 09:02 4026756153 /lib/libnss_nis-2.7.so 7f3fb5ba-7f3fb5ba2000 rw-p 9000 09:02 4026756153 /lib/libnss_nis-2.7.so 7f3fb5ba2000-7f3fb5bac000 r-xp 09:02 4026756151 /lib/libnss_files-2.7.so 7f3fb5bac000-7f3fb5dac000 ---p a000 09:02 4026756151 /lib/libnss_files-2.7.so 7f3fb5dac000-7f3fb5dae000 rw-p a000 09:02 4026756151 /lib/libnss_files-2.7.so 7f3fb5dae000-7f3fb9f8a000 rw-p 7f3fb5dae000 00:00 0 7f3fb9f8a000-7f3fba0e2000 r-xp 09:02 4026756142 /lib/libc-2.7.so 7f3fba0e2000-7f3fba2e2000 ---p 00158000 09:02 4026756142 /lib/libc-2.7.so 7f3fba2e2000-7f3fba2e5000 r--p 00158000 09:02 4026756142 /lib/libc-2.7.so 7f3fba2e5000-7f3fba2e7000 rw-p 0015b000 09:02 4026756142 /lib/libc-2.7.so 7f3fba2e7000-7f3fba2ec000 rw-p 7f3fba2e7000 00:00 0 7f3fba2ec000-7f3fba2f9000 r-xp 09:02 4026532161 /lib/libgcc_s.so.1 7f3fba2f9000-7f3fba4f9000 ---p d000 09:02 4026532161 /lib/libgcc_s.so.1 7f3fba4f9000-7f3fba4fa000 rw-p d000 09:02 4026532161 /lib/libgcc_s.so.1 7f3fba4fa000-7f3fba57a000 r-xp 09:02 4026756146 /lib/libm-2.7.so 7f3fba57a000-7f3fba779000 ---p 0008 09:02 4026756146 /lib/libm-2.7.so 7f3fba779000-7f3fba77b000 rw-p 0007f000 09:02 4026756146 /lib/libm-2.7.so 7f3fba77b000-7f3fba86a000 r-xp 09:02 268435746 /usr/lib/libstdc++.so.6.0.9 7f3fba86a000-7f3fbaa6a000 ---p 000ef000 09:02 268435746 /usr/lib/libstdc++.so.6.0.9 7f3fbaa6a000-7f3fbaa7 r--p 000ef000 09:02 268435746 /usr/lib/libstdc++.so.6.0.9 7f3fbaa7-7f3fbaa73000 rw-p 000f5000 09:02 268435746 /usr/lib/libstdc++.so.6.0.9 7f3fbaa73000-7f3fbaa86000 rw-p 7f3fbaa73000 00:00 0 7f3fbaa86000-7f3fbaa9c000 r-xp 09:02 4026756156 /lib/libpthread-2.7.so 7f3fbaa9c000-7f3fbac9c000 ---p 00016000 09:02 4026756156 /lib/libpthread-2.7.so 7f3fbac9c000-7f3fbac9e000 rw-p 00016000 09:02 4026756156 /lib/libpthread-2.7.so 7f3fbac9e000-7f3fbaca2000 rw-p 7f3fbac9e000 00:00 0 7f3fbaca2000-7f3fbaca4000 r-xp 09:02 4026756145 /lib/libdl-2.7.so 7f3fbaca4000-7f3fbaea4000 ---p 2000 09:02 4026756145 /lib/libdl-2.7.so 7f3fbaea4000-7f3fbaea6000 rw-p 2000 09:02 4026756145 /lib/libdl-2.7.so 7f3fbaea6000-7f3fbaeaf000 r-xp 09:02 4026756144 /lib/libcrypt-2.7.so 7f3fbaeaf000-7f3fbb0ae000 ---p 9000 09:02 4026
Re: [Freesurfer] aparc-stats wth curv-file as input?
Florian Gerstl wrote: Thanks for your quick reply! However, when I cast the mris_anatomical_stats command with the "-log" You might also try 'mris_curvature_stats'. It gives mostly the same stats that 'mris_anatomical_stats' (and some additional ones geared to curvature-type files): $>mris_curvature_stats If you have the ROI in a FS label file: $>mris_curvature_stats -l will limit the stats analysis only to the . If you just want simple stats (mean, std, etc), you can also try: $>mris_calc stats Cheers -=R -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Analysis-bugs] Re: [Freesurfer] aparc-stats wth curv-file as input?
what version of freesurfer is being used? type freesurfer --version and send us the last line. we may have fixed this in an earlier version. On Mon, 2009-03-02 at 16:43 +0100, Florian Gerstl wrote: > Thanks for your quick reply! > However, when I cast the mris_anatomical_stats command with the "-log" > flag the program seems to crash. That's not really a concern for me as I > can still use the -f flag to obtain a results-file (no problems there) > and I'm not sure whether this is a problem only with our computers but > since it is reproducible I thought I'd bring it to your attention.. > > below I have pasted the command I used with the resulting errors > > cheers, > Florian > > > > mris_anatomical_stats -log out.log -a aparc -f pet.lh.curv s05 lh > > > > outputting results to out.log... > computing statistics for each annotation in aparc. > reading volume /fsubjects/o05/mri/wm.mgz... > reading input surface /fsubjects/o05/surf/lh.white... > reading input pial surface /fsubjects/o05/surf/lh.pial... > reading input white surface /fsubjects/o05/surf/lh.white... > reading colortable from annotation file... > colortable with 35 entries read (originally > /space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt) > *** glibc detected *** mris_anatomical_stats: double free or corruption > (!prev): 0x046135d0 *** > === Backtrace: = > /lib/libc.so.6[0x7f3fb9ffe08a] > /lib/libc.so.6(cfree+0x8c)[0x7f3fba001c1c] > /lib/libc.so.6(fclose+0x14c)[0x7f3fb9fecdac] > mris_anatomical_stats(vfprintf+0x23f7)[0x4079f7] > /lib/libc.so.6(__libc_start_main+0xf4)[0x7f3fb9fa81c4] > mris_anatomical_stats(__gxx_personality_v0+0xfa)[0x40626a] > === Memory map: > 0040-00785000 r-xp 00:1b 1949331435 > /progs/freesurfer/bin/mris_anatomical_stats > 00884000-008de000 rw-p 00384000 00:1b 1949331435 > /progs/freesurfer/bin/mris_anatomical_stats > 008de000-07ac rw-p 008de000 00:00 0 > [heap] > 7f3fb000-7f3fb0021000 rw-p 7f3fb000 00:00 0 > 7f3fb0021000-7f3fb400 ---p 7f3fb0021000 00:00 0 > 7f3fb577e000-7f3fb5794000 r-xp 09:02 4026756148 > /lib/libnsl-2.7.so > 7f3fb5794000-7f3fb5993000 ---p 00016000 09:02 4026756148 > /lib/libnsl-2.7.so > 7f3fb5993000-7f3fb5995000 rw-p 00015000 09:02 4026756148 > /lib/libnsl-2.7.so > 7f3fb5995000-7f3fb5997000 rw-p 7f3fb5995000 00:00 0 > 7f3fb5997000-7f3fb59a1000 r-xp 09:02 4026756153 > /lib/libnss_nis-2.7.so > 7f3fb59a1000-7f3fb5ba ---p a000 09:02 4026756153 > /lib/libnss_nis-2.7.so > 7f3fb5ba-7f3fb5ba2000 rw-p 9000 09:02 4026756153 > /lib/libnss_nis-2.7.so > 7f3fb5ba2000-7f3fb5bac000 r-xp 09:02 4026756151 > /lib/libnss_files-2.7.so > 7f3fb5bac000-7f3fb5dac000 ---p a000 09:02 4026756151 > /lib/libnss_files-2.7.so > 7f3fb5dac000-7f3fb5dae000 rw-p a000 09:02 4026756151 > /lib/libnss_files-2.7.so > 7f3fb5dae000-7f3fb9f8a000 rw-p 7f3fb5dae000 00:00 0 > 7f3fb9f8a000-7f3fba0e2000 r-xp 09:02 4026756142 > /lib/libc-2.7.so > 7f3fba0e2000-7f3fba2e2000 ---p 00158000 09:02 4026756142 > /lib/libc-2.7.so > 7f3fba2e2000-7f3fba2e5000 r--p 00158000 09:02 4026756142 > /lib/libc-2.7.so > 7f3fba2e5000-7f3fba2e7000 rw-p 0015b000 09:02 4026756142 > /lib/libc-2.7.so > 7f3fba2e7000-7f3fba2ec000 rw-p 7f3fba2e7000 00:00 0 > 7f3fba2ec000-7f3fba2f9000 r-xp 09:02 4026532161 > /lib/libgcc_s.so.1 > 7f3fba2f9000-7f3fba4f9000 ---p d000 09:02 4026532161 > /lib/libgcc_s.so.1 > 7f3fba4f9000-7f3fba4fa000 rw-p d000 09:02 4026532161 > /lib/libgcc_s.so.1 > 7f3fba4fa000-7f3fba57a000 r-xp 09:02 4026756146 > /lib/libm-2.7.so > 7f3fba57a000-7f3fba779000 ---p 0008 09:02 4026756146 > /lib/libm-2.7.so > 7f3fba779000-7f3fba77b000 rw-p 0007f000 09:02 4026756146 > /lib/libm-2.7.so > 7f3fba77b000-7f3fba86a000 r-xp 09:02 268435746 > /usr/lib/libstdc++.so.6.0.9 > 7f3fba86a000-7f3fbaa6a000 ---p 000ef000 09:02 268435746 > /usr/lib/libstdc++.so.6.0.9 > 7f3fbaa6a000-7f3fbaa7 r--p 000ef000 09:02 268435746 > /usr/lib/libstdc++.so.6.0.9 > 7f3fbaa7-7f3fbaa73000 rw-p 000f5000 09:02 268435746 > /usr/lib/libstdc++.so.6.0.9 > 7f3fbaa73000-7f3fbaa86000 rw-p 7f3fbaa73000 00:00 0 > 7f3fbaa86000-7f3fbaa9c000 r-xp 09:02 4026756156 > /lib/libpthread-2.7.so > 7f3fbaa9c000-7f3fbac9c000 ---p 00016000 09:02 4026756156 > /lib/libpthread-2.7.so > 7f3fbac9c000-7f3fbac9e000 rw-p 00016000 09:02 4026756156 > /lib/libpthread-2.7.so > 7f3fbac9e000-7f3fbaca2000 rw-p 7f3fbac9e000 00:00 0 > 7f3fbaca
Re: [Analysis-bugs] Re: [Freesurfer] aparc-stats wth curv-file as input?
freesurfer --version produces the following output (last 2 lines): You are running this version of FreeSurfer: freesurfer-Linux-centos4_x86_64-stable-pub-v4.2.0 Actually, I thought I had a pretty recent version... Kind regards Florian Nick Schmansky wrote: > what version of freesurfer is being used? > > type freesurfer --version and send us the last line. we may have > fixed this in an earlier version. > > On Mon, 2009-03-02 at 16:43 +0100, Florian Gerstl wrote: > >> Thanks for your quick reply! >> However, when I cast the mris_anatomical_stats command with the "-log" >> flag the program seems to crash. That's not really a concern for me as I >> can still use the -f flag to obtain a results-file (no problems there) >> and I'm not sure whether this is a problem only with our computers but >> since it is reproducible I thought I'd bring it to your attention.. >> >> below I have pasted the command I used with the resulting errors >> >> cheers, >> Florian >> >> >> >> mris_anatomical_stats -log out.log -a aparc -f pet.lh.curv s05 lh >> >> >> >> outputting results to out.log... >> computing statistics for each annotation in aparc. >> reading volume /fsubjects/o05/mri/wm.mgz... >> reading input surface /fsubjects/o05/surf/lh.white... >> reading input pial surface /fsubjects/o05/surf/lh.pial... >> reading input white surface /fsubjects/o05/surf/lh.white... >> reading colortable from annotation file... >> colortable with 35 entries read (originally >> /space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt) >> *** glibc detected *** mris_anatomical_stats: double free or corruption >> (!prev): 0x046135d0 *** >> === Backtrace: = >> /lib/libc.so.6[0x7f3fb9ffe08a] >> /lib/libc.so.6(cfree+0x8c)[0x7f3fba001c1c] >> /lib/libc.so.6(fclose+0x14c)[0x7f3fb9fecdac] >> mris_anatomical_stats(vfprintf+0x23f7)[0x4079f7] >> /lib/libc.so.6(__libc_start_main+0xf4)[0x7f3fb9fa81c4] >> mris_anatomical_stats(__gxx_personality_v0+0xfa)[0x40626a] >> === Memory map: >> 0040-00785000 r-xp 00:1b 1949331435 >> /progs/freesurfer/bin/mris_anatomical_stats >> 00884000-008de000 rw-p 00384000 00:1b 1949331435 >> /progs/freesurfer/bin/mris_anatomical_stats >> 008de000-07ac rw-p 008de000 00:00 0 >> [heap] >> 7f3fb000-7f3fb0021000 rw-p 7f3fb000 00:00 0 >> 7f3fb0021000-7f3fb400 ---p 7f3fb0021000 00:00 0 >> 7f3fb577e000-7f3fb5794000 r-xp 09:02 4026756148 >> /lib/libnsl-2.7.so >> 7f3fb5794000-7f3fb5993000 ---p 00016000 09:02 4026756148 >> /lib/libnsl-2.7.so >> 7f3fb5993000-7f3fb5995000 rw-p 00015000 09:02 4026756148 >> /lib/libnsl-2.7.so >> 7f3fb5995000-7f3fb5997000 rw-p 7f3fb5995000 00:00 0 >> 7f3fb5997000-7f3fb59a1000 r-xp 09:02 4026756153 >> /lib/libnss_nis-2.7.so >> 7f3fb59a1000-7f3fb5ba ---p a000 09:02 4026756153 >> /lib/libnss_nis-2.7.so >> 7f3fb5ba-7f3fb5ba2000 rw-p 9000 09:02 4026756153 >> /lib/libnss_nis-2.7.so >> 7f3fb5ba2000-7f3fb5bac000 r-xp 09:02 4026756151 >> /lib/libnss_files-2.7.so >> 7f3fb5bac000-7f3fb5dac000 ---p a000 09:02 4026756151 >> /lib/libnss_files-2.7.so >> 7f3fb5dac000-7f3fb5dae000 rw-p a000 09:02 4026756151 >> /lib/libnss_files-2.7.so >> 7f3fb5dae000-7f3fb9f8a000 rw-p 7f3fb5dae000 00:00 0 >> 7f3fb9f8a000-7f3fba0e2000 r-xp 09:02 4026756142 >> /lib/libc-2.7.so >> 7f3fba0e2000-7f3fba2e2000 ---p 00158000 09:02 4026756142 >> /lib/libc-2.7.so >> 7f3fba2e2000-7f3fba2e5000 r--p 00158000 09:02 4026756142 >> /lib/libc-2.7.so >> 7f3fba2e5000-7f3fba2e7000 rw-p 0015b000 09:02 4026756142 >> /lib/libc-2.7.so >> 7f3fba2e7000-7f3fba2ec000 rw-p 7f3fba2e7000 00:00 0 >> 7f3fba2ec000-7f3fba2f9000 r-xp 09:02 4026532161 >> /lib/libgcc_s.so.1 >> 7f3fba2f9000-7f3fba4f9000 ---p d000 09:02 4026532161 >> /lib/libgcc_s.so.1 >> 7f3fba4f9000-7f3fba4fa000 rw-p d000 09:02 4026532161 >> /lib/libgcc_s.so.1 >> 7f3fba4fa000-7f3fba57a000 r-xp 09:02 4026756146 >> /lib/libm-2.7.so >> 7f3fba57a000-7f3fba779000 ---p 0008 09:02 4026756146 >> /lib/libm-2.7.so >> 7f3fba779000-7f3fba77b000 rw-p 0007f000 09:02 4026756146 >> /lib/libm-2.7.so >> 7f3fba77b000-7f3fba86a000 r-xp 09:02 268435746 >> /usr/lib/libstdc++.so.6.0.9 >> 7f3fba86a000-7f3fbaa6a000 ---p 000ef000 09:02 268435746 >> /usr/lib/libstdc++.so.6.0.9 >> 7f3fbaa6a000-7f3fbaa7 r--p 000ef000 09:02 268435746 >> /usr/lib/libstdc++.so.6.0.9 >> 7f3fbaa7-7f3fbaa73000 rw-p 000f5000 09:02 268435746 >> /usr/lib/libstdc++.so.6.0.9 >> 7f3fbaa73000-7f3fbaa86000 rw-p 7f3fbaa73000
