Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Re: [Freesurfer] Freesurfer Digest, Vol 102, Issue 10
by Linda Douw 13 Aug '12

13 Aug '12

Hi Doug, I first parcellate fsaverage5 using ico4 (all my functional data are morphed to fsaverage5 surface): mris_make_face_parcellation /fsaverage5/rh.inflated $FREESURFER_HOME/lib/bem/ic4.tri rh.ico4.annot Then I extract the waveforms using mri_segstats mri_segstats --i rh.functional.nii.gz --avgwf rh_ico4.txt --annot fsaverage5c rh ico4 --sum ico4_rh.sum Hope this clarifies the problem! Linda > ------------------------------ > > Message: 25 > Date: Fri, 10 Aug 2012 11:18:38 -0400 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] ico4 parcellation and mri_segstats > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <5025264E.3030801(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > what are your command lines? > doug > > On 08/09/2012 01:21 PM, Linda Douw wrote: >> Dear Freesurfers, >> >> I'm trying to extract the average waveforms from all 2562 ROIs in an >> annotation constructed using mris_make_face_parcellation with ico4. >> However, I get only 2460 waveforms after doing mri_segstats, and the >> summary files show that several ROIs are 'skipped' for some reason. Am I >> missing something? >> >> Thanks, >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > ------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > End of Freesurfer Digest, Vol 102, Issue 10 > ******************************************* > > >

2 1

polar angle analysis with clockwise- and counterclockwise-rotating wedges
by Thomas Janssens 13 Aug '12

13 Aug '12

Hi, I am currently analyzing some retinotopy data. For the polar angle stimulus we had both clockwise and counterclockwise stimuli. Both of them started at the top of the screen (12 o'clock), each run includes 4 full cycles and ends with the last wedge slightly before/after 12o'clock. We have created seperate paradigm files (direction pos / direction neg) for the clockwise and counterclockwise runs and followed the steps as indicated by the "FsFastIndividualRetinotopyAnalysis". However, when we run the Freesurfer retinotopy analysis on the whole data set, the polar angle is very noisy. When we run the same analysis separately for the clockwise and counterclockwise runs separately, the results look much better. Could anyone tell me what I am doing wrong? Thanks! Thomas

2 6

Re: [Freesurfer] memory corruption when performing mri_segstats
by Douglas N Greve 13 Aug '12

13 Aug '12

Hi Wenjing, I don't know what is happening either . Can you tar up the aparc+aseg.nii.gz and filtered_func_data.nii.gz file can send them to me on our file drop? www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> thanks doug On 08/13/2012 04:59 AM, Wenjing Li wrote: > Dear Doug, > > Sorry for the late response. Thanks for your quick reply. > Same errors happened for all of my data. There is an empty output > file. I don't know what's going on. > > All the best, > Wenjing > > On 9 August 2012 23:07, Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Does this happen on all of your data sets or just this one? Did it > create the output file? If so, does it have anything in it? > doug > > > On 08/09/2012 07:14 AM, Wenjing Li wrote: > > Hi Freesurfer experts, > > I want to extract time courses according to: > > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-July/015091.html > > Previous steps work fine, but memory corruption happened when > I perform the command line (I have a 12 GB memory): > > mri_segstats --seg SUBID.feat/reg/freesurfer/aparc+aseg.nii.gz > --in SUBID.feat/filtered_func_data.nii.gz --avgwf file.dat > > > I pasted the errors below: > > $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ > cwd > cmdline mri_segstats --seg > /mnt/workspace/subid.feat/reg/freesurfer/aparc+aseg.nii.gz > --in /mnt/workspace/subid.feat/filtered_func_data.nii.gz > --avgwf /mnt/workspace/subid.feat/file.dat > > sysname Linux > hostname fmri-Canlab > machine x86_64 > user wenjing > Loading /mnt/workspace/subid.feat/reg/freesurfer/aparc+aseg.nii.gz > Loading /mnt/workspace/subid.feat/filtered_func_data.nii.gz > Voxel Volume is 70.3125 mm^3 > > Generating list of segmentation ids > Found 109 segmentations > Computing statistics for each segmentation > 0 0 96808 6.80682e+06 > 1 2 3101 218039 <tel:3101%20%20218039> > 2 4 59 4148.44 > 3 5 3 210.938 > > 4 7 152 10687.5 <tel:7%20%20%20%20152%20%2010687.5> > 5 8 816 57375 > 6 10 116 8156.25 > 7 11 62 4359.38 > 8 12 114 8015.63 > 9 13 26 1828.13 > 10 14 13 914.063 > 11 15 30 2109.38 > > 12 16 257 18070.3 > 13 17 75 5273.44 > 14 18 31 2179.69 > 15 24 19 1335.94 > 16 26 11 773.438 > 17 28 60 4218.75 > 18 31 12 843.75 > 19 41 3163 222399 > > 20 43 37 2601.56 > 21 44 3 210.938 > 22 46 155 10898.4 > 23 47 789 55476.6 > 24 49 110 7734.38 > 25 50 65 4570.31 > 26 51 105 7382.82 <tel:51%20%20%20%20105%20%207382.82> > 27 52 24 1687.5 > > 28 53 75 5273.44 > 29 54 26 1828.13 > 30 58 9 632.813 > 31 60 59 4148.44 > 32 63 17 1195.31 > 33 77 19 1335.94 > 34 251 12 843.75 > 35 252 5 351.563 > > 36 253 5 351.563 > 37 254 6 421.875 > 38 255 15 1054.69 > 39 1000 38 2671.88 > 40 1001 57 4007.81 > 41 1002 34 2390.63 > 42 1003 121 8507.82 > 43 1005 43 3023.44 > > 44 1006 24 1687.5 > 45 1007 157 11039.1 > 46 1008 263 18492.2 > 47 1009 170 11953.1 > 48 1010 35 2460.94 > 49 1011 170 11953.1 > 50 1012 123 8648.44 > 51 1013 121 8507.82 > > 52 1014 74 5203.13 > 53 1015 265 18632.8 > 54 1016 38 2671.88 > 55 1017 55 3867.19 > 56 1018 64 4500 > 57 1019 33 2320.31 > 58 1020 61 4289.06 > 59 1021 33 2320.31 > > 60 1022 201 14132.8 > 61 1023 49 3445.31 > 62 1024 236 16593.8 > 63 1025 189 13289.1 > 64 1026 32 2250 > 65 1027 256 18000 > 66 1028 379 26648.4 > 67 1029 214 15046.9 > > 68 1030 205 14414.1 > 69 1031 205 14414.1 > 70 1032 13 914.063 > 71 1033 29 2039.06 > 72 1034 21 1476.56 > 73 1035 104 7312.5 > 74 2000 37 2601.56 > 75 2001 58 4078.13 > > 76 2002 24 1687.5 > 77 2003 120 8437.5 > 78 2005 46 3234.38 > 79 2006 33 2320.31 > 80 2007 147 10335.9 > 81 2008 314 22078.1 > 82 2009 190 13359.4 > 83 2010 40 2812.5 > > 84 2011 195 13710.9 > 85 2012 112 7875 > 86 2013 111 7804.69 > 87 2014 54 3796.88 > 88 2015 215 15117.2 > 89 2016 39 2742.19 > 90 2017 59 4148.44 > 91 2018 63 4429.69 > > 92 2019 39 2742.19 > 93 2020 79 5554.69 > 94 2021 38 2671.88 > 95 2022 189 13289.1 > 96 2023 55 3867.19 > 97 2024 211 14835.9 > 98 2025 153 10757.8 > 99 2026 35 2460.94 > > 100 2027 264 <tel:100%20%20%202027%20%20%20%20264> 18562.5 > 101 2028 369 <tel:101%20%20%202028%20%20%20%20369> 25945.3 > 102 2029 225 <tel:102%20%20%202029%20%20%20%20225> 15820.3 > 103 2030 221 <tel:103%20%20%202030%20%20%20%20221> 15539.1 > 104 2031 202 <tel:104%20%20%202031%20%20%20%20202> 14203.1 > 105 2032 13 914.063 > 106 2033 35 2460.94 > 107 2034 17 1195.31 > > 108 2035 110 <tel:108%20%20%202035%20%20%20%20110> 7734.38 > > Reporting on 109 segmentations > Computing spatial average of each frame > 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 > 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 > > 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 > 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 > 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 > 100101102103104105106107108 > > Writing to /mnt/workspace/subid.feat/file.dat > *** glibc detected *** mri_segstats: malloc(): memory > corruption: 0x34775428 *** > ======= Backtrace: ========= > /lib32/libc.so.6(+0x6c231)[0xf750d231] > /lib32/libc.so.6(+0x6f065)[0xf7510065] > > /lib32/libc.so.6(__libc_malloc+0x5c)[0xf7511c6c] > /lib32/libc.so.6(+0x5d01f)[0xf74fe01f] > /lib32/libc.so.6(fopen64+0x2c)[0xf750068c] > mri_segstats(vfprintf+0x3e9e)[0x80526d6] > /lib32/libc.so.6(__libc_start_main+0xe6)[0xf74b7bd6] > > mri_segstats(__gxx_personality_v0+0x1c9)[0x804f791] > ======= Memory map: ======== > 08048000-087f2000 r-xp 00000000 00:00 0 > 087f2000-2e568000 rwxp 00000000 00:00 0 > 2f1d4000-347b2000 rwxp 00000000 00:00 0 > [heap] > > f7300000-f7321000 rwxp 00000000 00:00 0 > f7321000-f7400000 ---p 00000000 00:00 0 > f7435000-f7469000 rwxp 00000000 00:00 0 > f7469000-f7473000 r-xp 00000000 08:01 522410 > /lib32/libnss_files-2.11.1.so > <http://libnss_files-2.11.1.so> <http://libnss_files-2.11.1.so> > > f7473000-f7474000 r-xp 00009000 08:01 522410 > /lib32/libnss_files-2.11.1.so > <http://libnss_files-2.11.1.so> <http://libnss_files-2.11.1.so> > f7474000-f7475000 rwxp 0000a000 08:01 522410 > /lib32/libnss_files-2.11.1.so > <http://libnss_files-2.11.1.so> <http://libnss_files-2.11.1.so> > > f7475000-f747d000 r-xp 00000000 08:01 522412 > /lib32/libnss_nis-2.11.1.so > <http://libnss_nis-2.11.1.so> <http://libnss_nis-2.11.1.so> > f747d000-f747e000 r-xp 00007000 08:01 522412 > /lib32/libnss_nis-2.11.1.so > <http://libnss_nis-2.11.1.so> <http://libnss_nis-2.11.1.so> > > f747e000-f747f000 rwxp 00008000 08:01 522412 > /lib32/libnss_nis-2.11.1.so > <http://libnss_nis-2.11.1.so> <http://libnss_nis-2.11.1.so> > > f749f000-f74a1000 rwxp 00000000 00:00 0 > f74a1000-f75f4000 r-xp 00000000 08:01 522401 > /lib32/libc-2.11.1.so <http://libc-2.11.1.so> > <http://libc-2.11.1.so> > > f75f4000-f75f5000 ---p 00153000 08:01 522401 > /lib32/libc-2.11.1.so <http://libc-2.11.1.so> > <http://libc-2.11.1.so> > f75f5000-f75f7000 r-xp 00153000 08:01 522401 > /lib32/libc-2.11.1.so <http://libc-2.11.1.so> > <http://libc-2.11.1.so> > > f75f7000-f75f8000 rwxp 00155000 08:01 522401 > /lib32/libc-2.11.1.so <http://libc-2.11.1.so> > <http://libc-2.11.1.so> > > f75f8000-f75fb000 rwxp 00000000 00:00 0 > f75fb000-f7618000 r-xp 00000000 08:07 262399 > /usr/lib32/libgcc_s.so.1 > > f7618000-f7619000 r-xp 0001c000 08:07 262399 > /usr/lib32/libgcc_s.so.1 > f7619000-f761a000 rwxp 0001d000 08:07 262399 > /usr/lib32/libgcc_s.so.1 > f761a000-f763e000 r-xp 00000000 08:01 522405 > /lib32/libm-2.11.1.so <http://libm-2.11.1.so> > <http://libm-2.11.1.so> > > f763e000-f763f000 r-xp 00023000 08:01 522405 > /lib32/libm-2.11.1.so <http://libm-2.11.1.so> > <http://libm-2.11.1.so> > f763f000-f7640000 rwxp 00024000 08:01 522405 > /lib32/libm-2.11.1.so <http://libm-2.11.1.so> > <http://libm-2.11.1.so> > > > f7640000-f7729000 r-xp 00000000 08:07 271130 > /usr/lib32/libstdc++.so.6.0.13 > f7729000-f772d000 r-xp 000e9000 08:07 271130 > /usr/lib32/libstdc++.so.6.0.13 > f772d000-f772e000 rwxp 000ed000 08:07 271130 > /usr/lib32/libstdc++.so.6.0.13 > > f772e000-f7735000 rwxp 00000000 00:00 0 > f7735000-f774a000 r-xp 00000000 08:01 522415 > /lib32/libpthread-2.11.1.so > <http://libpthread-2.11.1.so> <http://libpthread-2.11.1.so> > f774a000-f774b000 r-xp 00014000 08:01 522415 > /lib32/libpthread-2.11.1.so > <http://libpthread-2.11.1.so> <http://libpthread-2.11.1.so> > > f774b000-f774c000 rwxp 00015000 08:01 522415 > /lib32/libpthread-2.11.1.so > <http://libpthread-2.11.1.so> <http://libpthread-2.11.1.so> > > f774c000-f774e000 rwxp 00000000 00:00 0 > f774e000-f7750000 r-xp 00000000 08:01 522404 > /lib32/libdl-2.11.1.so <http://libdl-2.11.1.so> > <http://libdl-2.11.1.so> > > f7750000-f7751000 r-xp 00001000 08:01 522404 > /lib32/libdl-2.11.1.so <http://libdl-2.11.1.so> > <http://libdl-2.11.1.so> > f7751000-f7752000 rwxp 00002000 08:01 522404 > /lib32/libdl-2.11.1.so <http://libdl-2.11.1.so> > <http://libdl-2.11.1.so> > > > f7752000-f7753000 rwxp 00000000 00:00 0 > f7753000-f775c000 r-xp 00000000 08:01 522403 > /lib32/libcrypt-2.11.1.so > <http://libcrypt-2.11.1.so> <http://libcrypt-2.11.1.so> > f775c000-f775d000 r-xp 00008000 08:01 522403 > /lib32/libcrypt-2.11.1.so > <http://libcrypt-2.11.1.so> <http://libcrypt-2.11.1.so> > > f775d000-f775e000 rwxp 00009000 08:01 522403 > /lib32/libcrypt-2.11.1.so > <http://libcrypt-2.11.1.so> <http://libcrypt-2.11.1.so> > > f775e000-f7785000 rwxp 00000000 00:00 0 > f7785000-f7798000 r-xp 00000000 08:07 262397 > /usr/lib32/libz.so.1.2.3.3 > > f7798000-f7799000 r-xp 00012000 08:07 262397 > /usr/lib32/libz.so.1.2.3.3 > f7799000-f779a000 rwxp 00013000 08:07 262397 > /usr/lib32/libz.so.1.2.3.3 > f779a000-f77ad000 r-xp 00000000 08:01 522407 > /lib32/libnsl-2.11.1.so <http://libnsl-2.11.1.so> > <http://libnsl-2.11.1.so> > > f77ad000-f77ae000 r-xp 00012000 08:01 522407 > /lib32/libnsl-2.11.1.so <http://libnsl-2.11.1.so> > <http://libnsl-2.11.1.so> > f77ae000-f77af000 rwxp 00013000 08:01 522407 > /lib32/libnsl-2.11.1.so <http://libnsl-2.11.1.so> > <http://libnsl-2.11.1.so> > > > f77af000-f77b1000 rwxp 00000000 00:00 0 > f77b1000-f77b7000 r-xp 00000000 08:01 522408 > /lib32/libnss_compat-2.11.1.so > <http://libnss_compat-2.11.1.so> <http://libnss_compat-2.11.1.so> > f77b7000-f77b8000 r-xp 00006000 08:01 522408 > /lib32/libnss_compat-2.11.1.so > <http://libnss_compat-2.11.1.so> <http://libnss_compat-2.11.1.so> > > f77b8000-f77b9000 rwxp 00007000 08:01 522408 > /lib32/libnss_compat-2.11.1.so > <http://libnss_compat-2.11.1.so> <http://libnss_compat-2.11.1.so> > > f77b9000-f77bc000 rwxp 00000000 00:00 0 > f77bc000-f77d8000 r-xp 00000000 08:01 522398 > /lib32/ld-2.11.1.so <http://ld-2.11.1.so> > <http://ld-2.11.1.so> > > f77d8000-f77d9000 r-xp 0001b000 08:01 522398 > /lib32/ld-2.11.1.so <http://ld-2.11.1.so> > <http://ld-2.11.1.so> > f77d9000-f77da000 rwxp 0001c000 08:01 522398 > /lib32/ld-2.11.1.so <http://ld-2.11.1.so> > <http://ld-2.11.1.so> > > > f77da000-f77db000 r-xp 00000000 00:00 0 > [vdso] > ffdf0000-ffe06000 rwxp 00000000 00:00 0 > [stack] > Aborted > > Is this a memory or library problem? > > > Looking forward to your reply. > > All the best, > Wenjing > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > 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. > > > > > -- > Wenjing Li > Key Lab of Complex Systems and Intelligent Science, > Institute of Automation, Chinese Academy of Sciences(CASIA) > Beijing, 100190,P.R.CHINA -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

1 0

mri_annotation2label problem
by mnd12＠nmr.mgh.harvard.edu 13 Aug '12

13 Aug '12

Hello, I'm attempting to use a custom parcellation scheme (Lausanne2008) on fsaverage5. The gcs files I'm using can be found here: https://github.com/LTS5/cmp/tree/master/cmp/data/colortable_and_gcs/my_atla… The problem I'm getting is when I run mri_annotation2label using the annotation files I create using these gcs files and lh.sphere.reg I noticed that some of the labels are not being extracted, as seen in the first few lines of output copy/pasted here: 0 820 /autofs/cluster/neuromind/matt/fsaverage5/FSaverage5/tp1/FREESURFER/label/regenerated_lh_500/lh.unknown.label LabelWrite: saving to /autofs/cluster/neuromind/matt/fsaverage5/FSaverage5/tp1/FREESURFER/label/regenerated_lh_500/lh.unknown.label 4 190 /autofs/cluster/neuromind/matt/fsaverage5/FSaverage5/tp1/FREESURFER/label/regenerated_lh_500/lh.corpuscallosum.label LabelWrite: saving to /autofs/cluster/neuromind/matt/fsaverage5/FSaverage5/tp1/FREESURFER/label/regenerated_lh_500/lh.corpuscallosum.label 6 30 /autofs/cluster/neuromind/matt/fsaverage5/FSaverage5/tp1/FREESURFER/label/regenerated_lh_500/lh.entorhinal_1.label LabelWrite: saving to /autofs/cluster/neuromind/matt/fsaverage5/FSaverage5/tp1/FREESURFER/label/regenerated_lh_500/lh.entorhinal_1.label so it appears to skip labels 1,2,3 and 5. Interestingly this problem is only occurring when I use the gcs files named P1_16 P17_28 P29_36. Also, I'm able to successfully use this parcellation scheme on other subjects and with fsaverage, just not fsaverage5. Any help would be greatly appreciated! Thanks in advance, Matt DeSalvo

2 1

3d Gaussian filter on volume
by John Papaioannou 13 Aug '12

13 Aug '12

Hi, I can run a 3d Gaussian spacial filter on a T1.mgz image using matlab functions, but I was wondering if there isn't already a freesurfer script that does the same (with a FWHM input). John ___ John Papaioannou Medical Imaging Sciences Digital Mammography, CAD Mammography Department of Radiology Biological Sciences Division The University of Chicago 5841 South Maryland Avenue Chicago, Illinois 60637 773.834.5104 voice 773.702.0371 fax

3 2

mris_fix_topology stops with two T1-s
by Garikoitz Lerma Usabiaga 13 Aug '12

13 Aug '12

Hi FS experts, I've run recon-all -i file -s subject -qcache -measure thickness -all to: - 18 subjects, session 1 T1 - same 18 subjects, session 2 T1 and everything went well. Then I copied the <subject_id_session>/mri/orig/001.mgz-s to <subject_id>/mri/orig/001.mgz and 002.mgz, and run the same command again: recon-all -s <subject_id> -qcache -measure thickness -all Half of the subjects are failing when trying to correct the topology. Please find below the outputs of two of the subjects. Should I use the -i and the original files instead of the already created 001.mgz files? What should I check in order to avoid this error or what should I do in order to correct it? thank you very much, Gari ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.44 2010/05/27 23:37:16 nicks Exp $ $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ before topology correction, eno=-956 (nv=167898, nf=337708, ne=506562, g=479) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations marking ambiguous vertices... 127705 ambiguous faces found in tessellation segmenting defects... 125 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 6 into 1 -merging segment 9 into 1 -merging segment 21 into 1 -merging segment 24 into 1 -merging segment 26 into 1 -merging segment 29 into 1 -merging segment 44 into 1 -merging segment 56 into 1 -merging segment 2 into 1 -merging segment 65 into 1 -merging segment 67 into 1 -merging segment 71 into 1 -merging segment 4 into 1 -merging segment 12 into 1 -merging segment 34 into 18 -merging segment 30 into 19 -merging segment 38 into 35 -merging segment 61 into 47 -merging segment 107 into 106 -merging segment 115 into 113 105 defects to be corrected 0 vertices coincident reading input surface /home/BCBL/glerma/freesurfer/subjects/BERTSO/B_16/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -7.9838 (-3.9919) -vertex loglikelihood: -5.7349 (-2.8674) -normal dot loglikelihood: -3.5106 (-3.5106) -quad curv loglikelihood: -6.1770 (-3.0885) Total Loglikelihood : -23.4063 CORRECTING DEFECT 0 (vertices=23, convex hull=21) After retessellation of defect 0, euler #=-32 (96640,274187,177515) : difference with theory (-102) = -70 CORRECTING DEFECT 1 (vertices=44927, convex hull=14482) Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.44 2010/05/27 23:37:16 nicks Exp $ $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ before topology correction, eno=-600 (nv=159708, nf=320616, ne=480924, g=301) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 8 iterations marking ambiguous vertices... 115040 ambiguous faces found in tessellation segmenting defects... 96 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 16 into 0 -merging segment 39 into 0 -merging segment 48 into 0 -merging segment 22 into 21 -merging segment 38 into 34 -merging segment 42 into 37 -merging segment 70 into 69 89 defects to be corrected 0 vertices coincident reading input surface /home/BCBL/glerma/freesurfer/subjects/BERTSO/B_11b/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -7.9998 (-3.9999) -vertex loglikelihood: -5.5541 (-2.7771) -normal dot loglikelihood: -3.5423 (-3.5423) -quad curv loglikelihood: -6.1041 (-3.0520) Total Loglikelihood : -23.2003 CORRECTING DEFECT 0 (vertices=41794, convex hull=12626)

2 5

Displaying cortical thickness changes in volume images
by Rajagopalan, Venkateswaran 13 Aug '12

13 Aug '12

Dear All, I would like to display my cortical thickness chnages from longitudinal runs on my original T1-w volume images. I am wondering whether this is possible if so can anyone tell how I can do this. Thanks in advance Venkat =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2010). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

2 1

(no subject)
by Hugh Pemberton 12 Aug '12

12 Aug '12

Hi, How can I get sulcal depth measurements from Freesurfer? Cheers, Hugh

4 3

Averaging overlays/labels across subjects
by raij＠nmr.mgh.harvard.edu 12 Aug '12

12 Aug '12

Dear Surfers, I have (non-fMRI) .w format surface overlays/labels, computed at the smoothwm surface in each individual subject, in 25 subjects. FS5.1 recon-all has been run for all T1 images. I already managed to convert all individual surface overlays into the surface space of one of the subjects (or fsaverage) using mri_surf2surf, and in the process also converted the format from .w to .mgh (as I understand .w is pretty much legacy). Now, I would just need to compute an average across these overlays. I would greatly appreciate any suggestions which FS tools to use for this. Thank you in advance! (In case it matters, the overlays are E-field estimates, with a numerical value given for each vertex point. Also each overlay has only one time point.) Bests, Tommi --- Tommi Raij, MD, PhD MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.

2 1

Re: [Freesurfer] Tracula question
by Anastasia Yendiki 10 Aug '12

10 Aug '12

Hi Natalia - This is an error that will occur if lowb_brain_mask does not exist. The command that generates lowb_brain_mask is "bet" - can you find that line in the log file and run it directly on the command line and see if you get an error? On a separate note, have you opted to use a DWI mask instead of an anatomical mask by setting usemaskanat = 0? If not, then it may be that it's trying to use the DWI mask b/c it can't find the anatomicals, in which case I'd check if SUBJECTS_DIR has been set properly and a freesurfer recon of the same subject exists there. But this is a separate issue than the DWI mask not being generated. Hope this helps, a.y On Fri, 10 Aug 2012, Natalia Sánchez wrote: > The required files were not generated. > > the error occurs at > > rh.slft_PP_roi2.flt.nii.gz --bmask/Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dlabel/mni/lowb_brain > _mask.flt.nii.gz --fa/Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dmri/mni/dtifit_FA.fl > t.nii.gz --ncpts 5 --trunc --debug > ERROR: fio_pushd: > /Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dlabel/mni > ERROR: Must specify brain mask volume for output subject > > does the brain mask have to be input manually in the configuration file, or > is this part of the pre-processing? since I set the bet thr to 0.23 in the > config file i thought the brain mask was also created during the > preprocessing stage. Attached is my log file. > > I am familiar with FSL but I am using Free surfer since i think automating > the entire process, including tracking is a great advantage, but I'm just > starting to get the hang of it > > Thanks! > > > > -- Natalia Sánchez > PhD Candidate > Departments of Biomedical Engineering & > Physical Therapy and Human Movement Sciences Northwestern University > 645 North Michigan Ave, Suite 1100 > Chicago, IL 60611 > > > > > On Fri, Aug 10, 2012 at 4:28 PM, Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > dtifit_FA.fl > t.nii.gz > > > >

1 0

Jump to page: