Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30129 discussions

Talaraich problem
by Calabrese Massimiliano 22 Mar '05

22 Mar '05

Hi all I have a problem ( computer crash) during talairach program in recon-all -stage1 , does this mean that There is a problem with MINC installation or the MINC program? Is this the software to compute the Talairach transform? I had to do again the installation of freesurfer and it is possible that my MINC installation is not correct. The problem seems to be in mritotal -verbose -debug -clobber -protocol icmb orig/orig.mnc transforms/talairach.xfm at this point the linux freeze If I run stage1 without talairach there are no problems. Thanks a lot for any advice Massimiliano Calabrese NIB, NINDS, NIH.

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correcting bad euler numbers
by Goldman, Aaron (NIH/NIMH) 22 Mar '05

22 Mar '05

Hi. After doing stage 1-4 with all the manual edits, I have a fair number of surfaces that came out with an euler number of 1 instead of 2. However, looking at the inflated surfaces, I don't see any obvious defects. In situations like this, what would be the most efficient way to locate the problem area and fix it? Thanks, -Aaron- Aaron L. Goldman Post-Bacc IRTA Genes, Cognition and Psychosis Program, NIMH Building 10, Room 3C108 Phone: (301) 435-0944 Email: <mailto:aarong@mail.nih.gov> aarong(a)mail.nih.gov

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new tcl and tk
by Xander Meadow 22 Mar '05

22 Mar '05

Hi, I'm running Freesurfer on RedHat Enterprise linux stations and we recently updated to version 4 of RedHat. Doing that updated our libtcl and libtk libraries to libtcl8.4.so and libtk8.4.so. Our problem arises because freesurfer is still looking for version 8.3 of both libraries. Is there a settings file where I can make this change? Or, am I behind in my version of freesurfer? I thought I'd stayed up to date, but I could easily be mistaken. Thanks so much. -Xander

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Parcellation IV
by Wan Park 22 Mar '05

22 Mar '05

Thanks Xiao Han! I worked finally! Cheers (see below) Now I have this question: I see there is a lot of regions. How do each region correspond to specific color in the visualization? Thanks a lot! Wan total white matter volume = 533145 mm^3 table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard error (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 2955 1803 6322 3.453 +- 0.875 0.204 0.080 71.570 9.042 G_parietal_inferior-Angular_part 3572 2241 6032 2.691 +- 0.894 0.192 0.060 59.096 9.520 S_intraparietal-and_Parietal_transverse 2379 1388 3665 2.599 +- 0.657 0.190 0.060 58.310 6.513 G_parietal_superior 1269 713 1901 2.621 +- 1.066 0.208 0.087 33.729 5.435 G_occipital_middle 824 464 1105 2.449 +- 1.013 0.159 0.057 14.657 1.930 S_occipital_superior_and_transversalis 5746 3588 9688 2.721 +- 0.785 0.153 0.043 60.049 8.714 S_temporal_superior 3950 2272 5219 2.285 +- 0.617 0.183 0.060 74.201 8.967 G_precentral 3509 1947 5172 2.636 +- 0.791 0.193 0.078 291.730 9.736 G_postcentral 4558 2846 6608 2.321 +- 0.553 0.170 0.043 54.653 7.641 S_central 3180 1931 5328 2.757 +- 0.611 0.147 0.037 30.201 4.109 S_postcentral 2393 1395 2388 1.717 +- 0.559 0.225 0.074 58.455 7.835 G_paracentral 465 248 684 2.720 +- 0.584 0.138 0.040 5.397 1.079 S_intermedius_primus-Jensen 2626 1508 3646 2.381 +- 0.738 0.158 0.047 37.750 4.537 G_precuneus 2486 1441 3440 2.371 +- 0.824 0.214 0.088 68.986 9.620 Pole_occipital 1150 831 1277 1.559 +- 0.531 0.201 0.059 13.629 3.664 G_occipital_superior 1045 613 1346 2.158 +- 0.733 0.191 0.069 20.900 2.763 G_occipital_inferior 2403 1278 3600 2.793 +- 0.657 0.182 0.067 52.261 6.180 G_temporal_middle 1531 921 2238 2.456 +- 0.524 0.197 0.055 26.134 2.962 S_precentral-Superior-part 1747 926 2300 2.469 +- 0.746 0.165 0.065 26.462 4.279 G_parietal_inferior-Supramarginal_part 788 441 1023 2.287 +- 0.956 0.205 0.097 16.175 3.575 S_occipital_middle_and_Lunatus 1694 924 1989 2.253 +- 0.946 0.204 0.087 47.149 7.090 G_cuneus 301 118 243 2.046 +- 0.736 0.140 0.059 4.324 0.713 S_occipital_inferior 770 453 1140 2.513 +- 0.520 0.162 0.041 8.611 1.256 S_occipital_anterior 8169 4643 9060 1.971 +- 0.606 0.185 0.061 142.550 19.432 G_frontal_superior 806 483 904 1.868 +- 0.652 0.170 0.054 11.111 1.823 S_cingulate-Marginalis_part 761 454 869 1.961 +- 0.665 0.145 0.037 7.589 0.992 S_subparietal 2634 1496 3645 2.456 +- 0.629 0.205 0.076 62.685 6.930 G_temporal_inferior 385 173 500 2.845 +- 0.535 0.133 0.041 4.932 0.410 G_temp_sup-Planum_tempolale 946 577 1356 2.365 +- 0.443 0.172 0.040 9.745 1.653 S_temporal_inferior 2556 1766 2644 1.539 +- 0.548 0.174 0.045 35.471 6.396 S_parieto_occipital 1608 945 2243 2.355 +- 0.613 0.154 0.035 12.523 2.516 Lat_Fissure-post_sgt 2976 1816 4799 2.656 +- 0.539 0.209 0.061 67.117 7.108 G_occipit-temp_lat-Or_fusiform 91 42 56 1.341 +- 0.194 0.141 0.026 0.851 0.105 S_paracentral 2519 1720 3436 2.049 +- 1.045 0.152 0.040 26.893 5.123 S_calcarine 365 212 345 1.644 +- 0.419 0.128 0.015 2.299 0.248 S_collateral_transverse_post 1247 714 1541 2.183 +- 0.494 0.165 0.036 12.002 2.265 S_occipito-temporal_lateral 3489 2058 3863 1.885 +- 0.594 0.175 0.049 48.747 6.589 S_cingulate-Main_part 1792 1174 2649 2.327 +- 1.109 0.179 0.041 38.026 2.807 G_occipit-temp_med-Lingual_part 1340 746 1715 2.317 +- 0.546 0.177 0.061 22.078 3.527 G_temp_sup-Lateral_aspect 3040 1843 3431 1.874 +- 0.487 0.147 0.031 28.439 3.845 S_frontal_superior 1638 893 2173 2.380 +- 0.695 0.159 0.045 24.985 3.034 G_cingulate-Main_part 637 336 867 2.556 +- 0.682 0.171 0.064 14.747 1.730 G_subcentral 214 102 226 2.234 +- 0.679 0.080 0.017 0.636 0.115 S_subcentral_post 1509 817 2192 2.657 +- 0.733 0.162 0.058 26.524 3.281 G_temp_sup-G_temp_transv_and_interm_S 811 432 1032 2.336 +- 0.799 0.143 0.041 10.138 1.131 S_pericallosal 1438 720 1688 2.373 +- 0.619 0.127 0.050 16.264 2.842 G_temp_sup-Planum_polare 1561 943 2367 2.519 +- 0.422 0.151 0.040 15.352 2.301 S_occipito-temporal_medial_and_S_Lingual 324 179 458 2.554 +- 0.547 0.142 0.030 2.692 0.407 S_temporal_transverse 2501 1428 3976 2.759 +- 0.632 0.189 0.064 51.645 5.402 G_frontal_middle 1838 1103 2580 2.352 +- 0.577 0.137 0.033 16.472 2.179 S_precentral-Inferior-part 1465 878 1891 2.281 +- 0.919 0.162 0.034 22.944 2.086 Corpus_callosum 1869 1067 2386 2.221 +- 0.616 0.162 0.046 19.322 3.634 S_circular_insula_inferior 1542 925 1887 2.019 +- 0.616 0.153 0.037 14.490 2.201 S_circular_insula_superior 620 297 514 1.822 +- 0.563 0.136 0.035 5.491 0.970 G_insular_long 125 67 179 2.627 +- 0.384 0.182 0.041 1.293 0.295 S_subcentral_ant 1126 623 1797 2.751 +- 0.840 0.201 0.091 27.892 3.360 G_frontal_inf-Opercular_part 22 3 6 2.114 +- 0.520 0.016 0.003 0.017 0.001 S_central_insula 1526 892 1823 2.055 +- 0.564 0.151 0.033 16.765 1.989 S_frontal_inferior 154 100 100 1.014 +- 0.401 0.170 0.030 2.377 0.311 G_cingulate-Isthmus 1101 659 1437 2.197 +- 0.487 0.145 0.030 9.574 1.225 S_collateral_transverse_ant 9783 5994 14723 2.464 +- 0.678 0.169 0.053 146.050 22.466 Medial_wall 609 347 534 1.588 +- 0.504 0.171 0.039 6.182 1.180 G_insular_short 1950 1162 2269 1.976 +- 0.512 0.155 0.036 20.872 2.707 S_frontal_middle 2142 1215 3287 2.720 +- 0.600 0.159 0.042 28.728 3.325 G_occipit-temp_med-Parahippocampal_part 310 187 305 1.653 +- 0.432 0.163 0.028 2.810 0.416 Lat_Fissure-ant_sgt-ramus_vertical 494 285 413 1.465 +- 0.372 0.194 0.054 7.790 1.015 S_circular_insula_anterior 1236 616 1408 2.334 +- 0.607 0.150 0.058 20.536 3.161 Pole_temporal 708 341 714 2.147 +- 0.669 0.150 0.058 12.349 1.376 G_frontal_inf-Triangular_part 204 107 146 1.415 +- 0.418 0.134 0.023 1.496 0.247 Lat_Fissure-ant_sgt-ramus_horizontal 357 194 354 1.958 +- 0.632 0.126 0.024 2.739 0.341 S_orbital_lateral 359 172 355 2.047 +- 0.863 0.136 0.036 3.476 0.458 G_frontal_inf-Orbital_part 111 52 111 2.118 +- 0.400 0.117 0.019 0.665 0.106 S_transverse_frontopolar 1842 979 1604 1.697 +- 0.602 0.141 0.034 16.881 2.657 G_orbital 1129 774 1026 1.316 +- 0.250 0.161 0.035 9.832 1.784 S_orbital-H_shapped 8 1 3 1.951 +- 0.187 0.035 0.004 0.008 0.002 S_intracingulate 164 87 188 2.121 +- 0.423 0.162 0.054 2.308 0.243 S_frontomarginal 694 360 870 2.434 +- 0.484 0.160 0.066 14.935 1.792 G_transverse_frontopolar 279 138 262 2.008 +- 0.469 0.132 0.033 2.265 0.478 G_frontomarginal 244 119 228 1.988 +- 0.678 0.124 0.043 2.159 0.438 S_suborbital 348 204 339 1.614 +- 0.405 0.151 0.038 3.816 0.537 S_orbital_medial-Or_olfactory 374 201 336 1.636 +- 0.466 0.149 0.039 3.158 0.567 G_rectus 127 47 119 2.493 +- 0.826 0.111 0.035 0.737 0.225 G_subcallosal [ogden:freesurfer_package/freesurfer/subjects] wpark%

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Surface crossing
by Keyma Prince 22 Mar '05

22 Mar '05

Hello, In the attached image the pial surface and the wm mater surface are crossing. Can you let me know if this should be fixed or if it will have an effect on the parcellation steps? The whole volume is located at /space/engram/10/users/rk_fmri_struc/Y15_102304_STRUC. -Keyma Keyma Prince Massachusetts Institute of Technology Department of Brain and Cognitive Sciences NE20-392 Cambridge, MA 02139

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FW: [Freesurfer] thickness measures
by Kirk, Gregory 21 Mar '05

21 Mar '05

-----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Kirk, Gregory Sent: Tuesday, March 15, 2005 1:49 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: RE: [Freesurfer] thickness measures Hi I would like to know if anyone has much experience doing pediatrics with freesurfer. I was able to get what look like good results from a 2 year old and a 16 year old, the surfaces look good with only automated topology fixing. An 8 year old needs a lot of manual work. The +- on the cortical thickness was .8 and .9, I don't know if that is larger than usual or not, for averge of a hemisphere. Greg. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Parcellation II
by Wan Park 21 Mar '05

21 Mar '05

cheers! i did exactly the same thing with another brain but this time i obtained this which looks much better: (i am sending this again in a smaller size to avoid the mediator) i guess this is correct. now, how can i use this areas to calculate the gray matter volume of these "standard areas"? thanks! wan

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Parcellation
by Wan Park 21 Mar '05

21 Mar '05

Hello, I need to parcellate the brain in "standard areas" (eg. prefrontal, occipital, temporal, etc.). I have a MAC and I did the parcellation with the new binaries that Kevin Teich sent me. What I have is a multicolor brain painted in tiny pieces. Is this correct? What I am interested is to calculate the gray matter volume (with mris_anatimical_stats) of some "standard areas". How can I do this? Thank you very much! Wan

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recon-all -stage1 sharpen_volume
by Michele Perry 18 Mar '05

18 Mar '05

When I run recon-all -stage1 -subjid <subjectID>, it exits after the following: --------------------------------------------- Nu Intensity Correction Fri Mar 18 17:19:49 PST 2005 mri_convert orig nu0.mnc mri_convert orig nu0.mnc reading from orig... TR=2730.00, TE=3.31, TI=1000.00, flip angle=7.00 i_ras = (-1, 0, 0) j_ras = (0, -0, -1) k_ras = (0, 1, -0) writing to nu0.mnc... nu_correct -clobber nu0.mnc nu1.mnc [mperry@ip06:<SUBJECTS_DIR>/<subjectID>/mri/] [2005-03-18 17:19:59] running: /usr/pubsw/packages/mni/1.2/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /usr/tmp/nu_correct_31180/ nu0.mnc nu1.imp Can't locate MNI/Startup.pm in @INC (@INC contains: /usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl /usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 .) at /usr/pubsw/packages/mni/1.2/bin/sharpen_volume line 33. BEGIN failed--compilation aborted at /usr/pubsw/packages/mni/1.2/bin/sharpen_volume line 33. nu_estimate_np_and_em: crashed while running sharpen_volume (termination status=512) nu_correct: crashed while running nu_estimate_np_and_em (termination status=512) ERROR: nu_correct ------------------------------------------ Filesystem 1K-blocks Used Available Use% Mounted on 693727244 310617732 347870136 48% ------------------------------------------ recon-all exited with errors at Fri Mar 18 17:19:59 PST 2005 vi /usr/pubsw/packages/mni/1.2/bin/sharpen_volume line 33 is: use MNI::Startup qw(nocputimes); That's the first line after all the initial comments. Any advice? Michele

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nu_correct problem
by Michele Perry 16 Mar '05

16 Mar '05

I'm having problems with recon-all. It used to work but recently, every time I've used it, I get a nu_correct error. I don't think we have had any freesurfer upgrades since the last time recon-all worked. Here's the log. Anyone know what's wrong? ip07:mperry[12] setenv SUBJECTS_DIR <path/to/subjects/dirs> ip07:mperry[13] setenv FUNCTIONALS_DIR <path/to/subjects/dirs> ip07:mperry[14] recon-all -stage1 -subjid subject_ID ######################################## program versions used $Id: recon-all-nmr,v 1.50 2004/08/31 18:05:08 tosa Exp $ $Id: mri_motion_correct2,v 1.8 2004/10/04 22:52:12 greve Exp $ mri_convert --version $ $Header: /software/source/minc/cvsroot/minc/progs/rawtominc/rawtominc.c,v 6.12 2 003/11/14 16:52:24 stever Exp $ minctracc.c $Header: /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 96.5.2.1 2003/07/05 01:58:08 stever Exp $ $Header: /software/source/minc/cvsroot/minc/progs/mincresample/mincresample.c,v 6.12 2003/09/18 15:01:33 bert Exp $ $Header: /software/source/minc/cvsroot/minc/progs/mincaverage/mincaverage.c,v 6. 4 2001/04/24 13:38:42 neelin Exp $ $Id: talairach2,v 1.7 2004/08/31 18:07:37 tosa Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.11.2.1 2003/11/17 06:01:15 stever Exp $ # $Id: nu_estimate.in,v 1.1 2003/04/16 14:29:34 bert Exp $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ ####################################### INFO: SUBJECTS_DIR is <path/to/subjects/dirs> --------------------------------------------- MotionCor Tue Mar 15 16:03:21 PST 2005 <path/to/subjects/dirs>/<subject_ID>/mri/orig mri_motion_correct2 -o . -i 001 -i 002 tmpdir is ./tmp-mri_motion_correct2-23141 -------------------------------------------------------------- mri_motion_correct2 logfile is ./mri_motion_correct2.log -------------------------------------------------------------- ----------------------------------------- Converting 001 Tue Mar 15 16:03:21 PST 2005 mri_convert 001 <path/to/subjects/dirs>/<subject_ID>/mri/orig/tmp-mri_mo tion_correct2-23141/cor-1.mnc reading from 001... TR=2730.00, TE=3.31, TI=1000.00, flip angle=7.00 i_ras = (-1, 0, 0) j_ras = (0, -0, -1) k_ras = (0, 1, -0) writing to <path/to/subjects/dirs>/<subject_ID>/mri/orig/tmp-mri_motion_ correct2-23141/cor-1.mnc... ----------------------------------------- Converting 002 Tue Mar 15 16:03:29 PST 2005 mri_convert 002 <path/to/subjects/dirs>/<subject_ID>/mri/orig/tmp-mri_mo tion_correct2-23141/cor-2.mnc reading from 002... TR=2730.00, TE=3.31, TI=1000.00, flip angle=7.00 i_ras = (-1, 0, 0) j_ras = (0, -0, -1) k_ras = (0, 1, -0) writing to <path/to/subjects/dirs>/<subject_ID>/mri/orig/tmp-mri_motion_ correct2-23141/cor-2.mnc... ----------------------------------------- Motion Correcting <path/to/subjects/dirs>/<subject_ID>/mri/orig/tmp-mri_ motion_correct2-23141/cor-2.mnc Tue Mar 15 16:03:36 PST 2005 COG of v1: 2.191772 14.916920 -47.842663 COG of v2: 2.203371 14.932534 -47.776924 [trans] = 0.011599 0.015615 0.065739 Initial objective function val = 0.01807109 Final objective function value = 0.00892547 ----------------------------------------- Resampling <path/to/subjects/dirs>/<subject_ID>/mri/orig/tmp-mri_motion_ correct2-23141/cor-2.mnc Tue Mar 15 16:04:30 PST 2005 Transforming slices:............................................................ ................................................................................ ................................................................................ ....................................Done ----------------------------------------- Averaging Tue Mar 15 16:04:37 PST 2005 Processing:..................................................................... ................................................................................ ................................................................................ ...........................Done ----------------------------------------- Converting Average to output Tue Mar 15 16:04:41 PST 2005 mri_convert <path/to/subjects/dirs>/<subject_ID>/mri/orig/tmp-mri_motion _correct2-23141/avgvol.mnc . -tr 2730 -te 3.31 -TI 1000 -flip_angle 0.122173 reading from <path/to/subjects/dirs>/<subject_ID>/mri/orig/tmp-mri_motio n_correct2-23141/avgvol.mnc... TR=0.00, 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) Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions writing to .... Started at: Tue Mar 15 16:03:21 PST 2005 Ended at: Tue Mar 15 16:04:46 PST 2005 mri_motion_correct2: done --------------------------------------------- Nu Intensity Correction Tue Mar 15 16:04:46 PST 2005 mri_convert orig nu0.mnc mri_convert orig nu0.mnc reading from orig... TR=2730.00, TE=3.31, TI=1000.00, flip angle=7.00 i_ras = (-1, 0, 0) j_ras = (0, -0, -1) k_ras = (0, 1, -0) writing to nu0.mnc... nu_correct -clobber nu0.mnc nu1.mnc [mperry@ip07:<path/to/subjects/dirs>/<subject_ID>/mri/] [2005-03-15 16:0 4:54] running: /usr/pubsw/packages/mni/1.2/bin/nu_estimate_np_and_em -parzen -log -sharpen 0. 15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -d istance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /usr/tmp/nu_correct_2326 4/ nu0.mnc nu1.imp spawn: exec of sharpen_volume failed: No such file or directory nu_estimate_np_and_em: crashed while running sharpen_volume (termination status= 65280) nu_correct: crashed while running nu_estimate_np_and_em (termination status=6528 0) ERROR: nu_correct ------------------------------------------ Filesystem 1K-blocks Used Available Use% Mounted on 693727248 307742336 350745536 47% /space/aliens/1 ------------------------------------------ recon-all exited with errors at Tue Mar 15 16:04:55 PST 2005

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