RE: [Freesurfer] Configure Overlay Display for >2 Colors
Hi Bruce, Thanks for your quick reply. I tried fine-tuning the offset and the midpoint. I guess what I would like to have happen is to have a couple more colors come out beyond the blue-to-light blue range for the thinning. If I could get some greens in there too, that would make the picture much more descriptive to look at. Thanks for your help! Regards, Jeff Sadino > Date: Mon, 2 Mar 2009 17:28:08 -0500 > From: fis...@nmr.mgh.harvard.edu > To: jsad...@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Configure Overlay Display for >2 Colors > > Hi Jeff, > > have you tried setting the offset in the configure functional overlay > panel to be around the middle of your range (-1.5 or so I guess)? > > cheers, > Bruce > On Mon, 2 > Mar 2009, Jeff Sadino wrote: > > > > > Hello Surfers, > > I have an overlay file with values ranging from -4.63 (n=138477) to 1.34 > > (n=25365). I would like to display this data with more than the two colors > > of the Green/Red, Heat, Blue/Red, or complex Color Scales in the Configure > > Overlay dialog. So far, no luck, even with toying with the min, max, mid, > > and piecewise options every way I can think of. Is there some way to get a > > fuller color spectrum on my overlay? > > > > Thank you, > > Jeff Sadino > > > > _ > > Hotmail® is up to 70% faster. Now good news travels really fast. > > http://windowslive.com/online/hotmail?ocid=TXT_TAGLM_WL_HM_70faster_032009 _ Express your personality in color! Preview and select themes for Hotmail®. http://www.windowslive-hotmail.com/LearnMore/personalize.aspx?ocid=TXT_MSGTX_WL_HM_express_032009#colortheme___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Problem while fixing the Surface Topology
Hi Pradeep, sounds like a bug. Can you overlay the surface defect segmentations and see what defect #3 is? If you edit it a bit this will probably go away. If you tar and gzip the subject dir and send it to us we'll take a look You can also try the alternative (newer) topology correction and see if it works properly. Look at the recon-all help for how to run it cheers Bruce On Mon, 2 Mar 2009, Pradeep Reddy Ramana wrote: Hello FS Team, I had a question recently regarding an error encountered in the freesurfer recon-all. I believe error is the result of: mris_fix_topology -mgz -sphere qsphere.nofix -ga FirstOrderPoly lh CORRECTING DEFECT 3 (vertices=10731, convex hull=2557) normal vector of length zero at vertex 90051 with 0 faces vertex 90051 has 0 face No such file or directory recon-all exited with ERRORS I will appreciate very much if you can suggest a possible fix or a rerun with some set of flags etc. The partial log and a previous post by somebody else is here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg09492.html Thanks, Pradeep ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Problem while fixing the Surface Topology
Hello FS Team, I had a question recently regarding an error encountered in the freesurfer recon-all. I believe error is the result of: mris_fix_topology -mgz -sphere qsphere.nofix -ga FirstOrderPoly lh CORRECTING DEFECT 3 (vertices=10731, convex hull=2557) normal vector of length zero at vertex 90051 with 0 faces vertex 90051 has 0 face No such file or directory recon-all exited with ERRORS I will appreciate very much if you can suggest a possible fix or a rerun with some set of flags etc. The partial log and a previous post by somebody else is here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg09492.html Thanks, Pradeep -- Pradeep Kumar Reddy. Raamana PhD Student - Biomedical Engg. Medical Image Analysis Lab, Simon Fraser University, Burnaby BC - V5A1S6 - Canada. Work : +1 778 782 5509 "What is written without effort is, in general, read without pleasure." - Samuel Johnson ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Configure Overlay Display for >2 Colors
Hi Jeff, have you tried setting the offset in the configure functional overlay panel to be around the middle of your range (-1.5 or so I guess)? cheers, Bruce On Mon, 2 Mar 2009, Jeff Sadino wrote: Hello Surfers, I have an overlay file with values ranging from -4.63 (n=138477) to 1.34 (n=25365). I would like to display this data with more than the two colors of the Green/Red, Heat, Blue/Red, or complex Color Scales in the Configure Overlay dialog. So far, no luck, even with toying with the min, max, mid, and piecewise options every way I can think of. Is there some way to get a fuller color spectrum on my overlay? Thank you, Jeff Sadino _ Hotmail® is up to 70% faster. Now good news travels really fast. http://windowslive.com/online/hotmail?ocid=TXT_TAGLM_WL_HM_70faster_032009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Configure Overlay Display for >2 Colors
Hello Surfers, I have an overlay file with values ranging from -4.63 (n=138477) to 1.34 (n=25365). I would like to display this data with more than the two colors of the Green/Red, Heat, Blue/Red, or complex Color Scales in the Configure Overlay dialog. So far, no luck, even with toying with the min, max, mid, and piecewise options every way I can think of. Is there some way to get a fuller color spectrum on my overlay? Thank you, Jeff Sadino _ Hotmail® is up to 70% faster. Now good news travels really fast. http://windowslive.com/online/hotmail?ocid=TXT_TAGLM_WL_HM_70faster_032009___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all with MT images?
Many thanks for your e-mail, Bruce. I've tried and it gives an out of memory error. Perhaps it's because there's not enough contrast. I'll try that. Many thanks, Lucia > Hi Lucia, > > we've never tried, but certainly give it a shot. You would want to apply > an MT subtraction that enhances gray/white contrast though. > > cheers, > Bruce > On Mon, 2 Mar > 2009, Lucia Garrido wrote: > >> Dear Freesurfers, >> >> I was wondering whether it would be possible to run recon-all with MT >> images? My final aim is to compare cortical thickness between two >> groups. >> I've done this with T1 weighted images, but was wondering whether i >> could >> also do with MT images. Segmentation in SPM worked really well on these >> images. >> >> Thank you very much. >> >> Best wishes, >> >> Lucia >> >> ___ >> 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] recon-all with MT images?
Hi Lucia, we've never tried, but certainly give it a shot. You would want to apply an MT subtraction that enhances gray/white contrast though. cheers, Bruce On Mon, 2 Mar 2009, Lucia Garrido wrote: Dear Freesurfers, I was wondering whether it would be possible to run recon-all with MT images? My final aim is to compare cortical thickness between two groups. I've done this with T1 weighted images, but was wondering whether i could also do with MT images. Segmentation in SPM worked really well on these images. Thank you very much. Best wishes, Lucia ___ 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] microparcellation
Jose, mris_make_face_parcellation is here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc for three of the supported platforms. Nick On Mon, 2009-03-02 at 13:23 -0500, Bruce Fischl wrote: > Hi Jose, > > this looks pretty much correct. We have another utility, called > mris_make_face_parcellation that can be used to generate parcellation units > of mostly uniform area over the surface of the cortex. If you tell us your > hardware/software environment we can give you a beta. > > cheers, > Bruce > > > On Mon, 2 Mar 2009, Jose Luis Cantero > Lorente wrote: > > > Dear Freesurfers, > > > > We are trying to subdivide the cortical surface of our average subject into > > a set of small and compact regions of similar area. Please have a look to > > the attached file (taken from Hagmann et al. (2008) in PLoS Biol) to have a > > better idea what I would like to get. We tried it hard by using different > > strategies, but results were not as expected. Could anybody give me some > > insights about how to approach this problem by using Freesurfer or Matlab > > code? > > > > Thank you very much in advance. > > > > Best, > > Jose > > > > --- > > Jose Luis Cantero, Ph.D. > > Laboratory of Functional Neuroscience > > Department of Physiology, Anatomy, and Cellular Biology > > University Pablo de Olavide > > Ctra. de Utrera, Km.1 > > 41013 - Sevilla > > - Spain - > > > > Phone: +34 954 977433 > > Fax: +34 954 349151 > > Email: jlcan...@upo.es > > http://www.upo.es/neuroaging/es/ > > > ___ > 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] recon-all with MT images?
Dear Freesurfers, I was wondering whether it would be possible to run recon-all with MT images? My final aim is to compare cortical thickness between two groups. I've done this with T1 weighted images, but was wondering whether i could also do with MT images. Segmentation in SPM worked really well on these images. Thank you very much. Best wishes, Lucia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] microparcellation
Hi Jose, this looks pretty much correct. We have another utility, called mris_make_face_parcellation that can be used to generate parcellation units of mostly uniform area over the surface of the cortex. If you tell us your hardware/software environment we can give you a beta. cheers, Bruce On Mon, 2 Mar 2009, Jose Luis Cantero Lorente wrote: Dear Freesurfers, We are trying to subdivide the cortical surface of our average subject into a set of small and compact regions of similar area. Please have a look to the attached file (taken from Hagmann et al. (2008) in PLoS Biol) to have a better idea what I would like to get. We tried it hard by using different strategies, but results were not as expected. Could anybody give me some insights about how to approach this problem by using Freesurfer or Matlab code? Thank you very much in advance. Best, Jose --- Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cellular Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcan...@upo.es http://www.upo.es/neuroaging/es/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] clusterwise correction for multiple comparisons
Thank you for your help. As regards to the display, I am using the command that is found in the mri_glmfit-sim documentation. Even with that command I don't see the display as it is shown in the documentation. In addition to showing the clusters (all of them), the display also shows what looks like cortical parcellations. I would just like to know why our picture isn't matching what is shown in the documentation even when we are following the docu. steps. If an attached picture will help, please let me know and I can attach one. Thanks, Devdutta On 2/24/09, Douglas N Greve wrote: > > It is for the whole brain. Not sure what you display command is, but > mri_surfcluster will save all clusters in the cwp map. You can then set the > tksurfer threshold to exclude the ones below your target sig level. > > doug > > Devdutta W wrote: > >> Hi, >> In the mri_glmfit-sim command, when it does a "clusterwise correction" is >> it correcting across the whole brain? In other words, does the term >> "clusterwise" mean that it is only correcting within that cluster or is it >> correcting across the whole brain, cluster-by-cluster (instead of, say, >> voxel-by-voxel)? >> >> While doing this analysis, (after displaying the .annot file in tksurfer >> as stated in the documentation), I noticed that our display did not match >> what was shown in the docs. In the documentation, the picture we are >> supposed to see only displays the clusters (all clusters, regardless of the >> significance). Ours displayed cortical parcellations in addition to the >> clusters. This may just be a display issue and the analysis might still be >> correct, but I just want to be sure. Has anyone else encountered this? >> >> Thanks for any light anyone can shed on these questions. >> >> Devdutta >> >> >> >> >> >> ___ >> 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: [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
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: [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?
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
[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
[Freesurfer] ¿write_annotation?
Dear FS team, I used read_annotation(lh.aparca.annot) for obtaining [vertexs, label, colortable]. After that, I have modified these variables and would like to write a new annotation file. Is there the function "write_annotation" (or something similar)? Thanks in advance. Best, Rafa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
