Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

mri_vol2surf or mri_cor2label
by Stephanie Rossi 09 Aug '12

09 Aug '12

Hi, I have seeds defined in fsl for individual subjects (nii.gz) and I would like to convert them to freesurfer labels for individual subjects. Which command would I have to use: mri_vol2surf or mri_cor2label? Thank you for your help! Best, Stephanie

2 3

memory corruption when performing mri_segstats
by Wenjing Li 09 Aug '12

09 Aug '12

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 2 4 59 4148.44 3 5 3 210.938 4 7 152 10687.5 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 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 18562.5 101 2028 369 25945.3 102 2029 225 15820.3 103 2030 221 15539.1 104 2031 202 14203.1 105 2032 13 914.063 106 2033 35 2460.94 107 2034 17 1195.31 108 2035 110 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 f7473000-f7474000 r-xp 00009000 08:01 522410 /lib32/libnss_files-2.11.1.so f7474000-f7475000 rwxp 0000a000 08:01 522410 /lib32/libnss_files-2.11.1.so f7475000-f747d000 r-xp 00000000 08:01 522412 /lib32/libnss_nis-2.11.1.so f747d000-f747e000 r-xp 00007000 08:01 522412 /lib32/libnss_nis-2.11.1.so f747e000-f747f000 rwxp 00008000 08:01 522412 /lib32/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 f75f4000-f75f5000 ---p 00153000 08:01 522401 /lib32/libc-2.11.1.so f75f5000-f75f7000 r-xp 00153000 08:01 522401 /lib32/libc-2.11.1.so f75f7000-f75f8000 rwxp 00155000 08:01 522401 /lib32/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 f763e000-f763f000 r-xp 00023000 08:01 522405 /lib32/libm-2.11.1.so f763f000-f7640000 rwxp 00024000 08:01 522405 /lib32/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 f774a000-f774b000 r-xp 00014000 08:01 522415 /lib32/libpthread-2.11.1.so f774b000-f774c000 rwxp 00015000 08:01 522415 /lib32/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 f7750000-f7751000 r-xp 00001000 08:01 522404 /lib32/libdl-2.11.1.so f7751000-f7752000 rwxp 00002000 08:01 522404 /lib32/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 f775c000-f775d000 r-xp 00008000 08:01 522403 /lib32/libcrypt-2.11.1.so f775d000-f775e000 rwxp 00009000 08:01 522403 /lib32/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 f77ad000-f77ae000 r-xp 00012000 08:01 522407 /lib32/libnsl-2.11.1.so f77ae000-f77af000 rwxp 00013000 08:01 522407 /lib32/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 f77b7000-f77b8000 r-xp 00006000 08:01 522408 /lib32/libnss_compat-2.11.1.so f77b8000-f77b9000 rwxp 00007000 08:01 522408 /lib32/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 f77d8000-f77d9000 r-xp 0001b000 08:01 522398 /lib32/ld-2.11.1.so f77d9000-f77da000 rwxp 0001c000 08:01 522398 /lib32/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 **

2 1

Creating and using an atlas from scratch
by Jeff Thompson 09 Aug '12

09 Aug '12

Hello, I'm trying to create a canine atlas to use in freesurfers recon-all pipeline. I want to be able to perform cortical thickness measurements. I have manually skull-stripped 10 beagle brains. I have used fsl's FLIRT and FNIRT to make an averaged image of these 10 brain images in nifti format. As an alternative I have also used mri_robust_template to create an average template .mgz file to replace the talairach atlas. Could someone tell me what else is needed to replace the standard atlas and templates in the recon-all pipeline for what I need? Also where to replace the standard atlas and template files to be able to run recon-all? Any help is much appreciated, Jeff Thompson

2 1

Re: [Freesurfer] mri_vol2surf or mri_cor2label
by Auer, Tibor 09 Aug '12

09 Aug '12

Hi, you should use mri_cor2label. Bests, Auer, Tibor M.D. Ph.D. Biomedizinische NMR Forschungs GmbH am Max-Planck Institut für Biophysikalische Chemie Am Fassberg 11 37077 Göttingen Germany Phone/Work: +49-(0)551-201-1725 Phone/Home: +49-(0)551-387-0076 Mobile: +49-(0)176-8012-7921 Mail: tauer(a)mpibpc.mpg.de -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Stephanie Rossi Sent: Thursday, August 09, 2012 7:04 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] mri_vol2surf or mri_cor2label Hi, I have seeds defined in fsl for individual subjects (nii.gz) and I would like to convert them to freesurfer labels for individual subjects. Which command would I have to use: mri_vol2surf or mri_cor2label? Thank you for your help! Best, Stephanie _______________________________________________ Freesurfer mailing list Freesurfer(a)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.

1 0

asking about seed/target ROIs in TRACULA
by Juke Cha 09 Aug '12

09 Aug '12

Hi, I'm wondering if I can get any information about ROIs being used in the global tractography procedure in TRACULA. I'm particularly interested in the uncinate fasciculus. I've searched for such information in the website and the article, to no avail. Thanks for your help! Best, Juke

2 1

Making Anatomical Mass for optical data
by Mark Fletcher 09 Aug '12

09 Aug '12

Dear FreeSurfer Developers, Currently we are trying to analyze our functional data (optical imaging) using ROI’s that are defined on the basis of FreeSurfer Segmentation. In order to do this, we need a 3 dimensional mask in which a particular region as identified by FreeSurfer is used as a mask for analyzing our functional data. How can we output from FreeSurfer what each voxel is classified as (hippocampus, etc.), or a mask having a value of 1 for each region, and a 0 for every other voxel. Also, what coordinate space would this be in? We would prefer either MNI or TAI (or a way to get into either space). Thanks you so much for your help. Sincerely, Mark Fletcher CNL Lab UIUC

2 1

Subcortical segmentations
by Jordan Pierce 08 Aug '12

08 Aug '12

Hi, I have a question about subcortical segmentations: there are a lot of places across subjects where the thalamus label seems to include white matter (images attached), am I right to think that this needs to corrected and is there any reason the program might do this so often? Thanks, Jordan Pierce

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Re: [Freesurfer] Freesurfer Digest, Vol 102, Issue 1
by Gibbard, Clare 08 Aug '12

08 Aug '12

Hi Doug, Thank you, that worked perfectly. Best wishes, Clare ________________________________________ Date: Tue, 31 Jul 2012 14:30:50 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Recon-all -qcache curvature error & recon-all make -all To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <5018245A.1050903(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Subject 20 is definitely out of synch, but the "make all" feature is not catching it. Try re-running this subject with -autorecon3 doug On 07/25/2012 11:45 AM, Gibbard, Clare wrote: > Hi Bruce, > > Thanks, I've attached the end of the recon-all.log file for one of the subjects (the whole thing was too large). This is what I get when I run recon-all -version: > $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ > > When I try to run recon-all -s subject_no -make all I don't think anything comes up in the log. I get this in the terminal window: > clare@clare-OptiPlex-990:~/subjects$ recon-all -s subject_20 -make all > Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 > Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 > Subject 'subject_20': make all > make: Nothing to be done for `all'. > clare@clare-OptiPlex-990:~/subjects$ > > Let me know if you need anything else. Thank you. > > Best wishes, > Clare > ________________________________________ > From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] > Sent: 25 July 2012 14:44 > To: Gibbard, Clare > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Recon-all -qcache curvature error& recon-all make -all > > Hi Clare > > can you send us the screen output and also what version you are running? > > thanks > Bruce > On > Wed, 25 Jul 2012, Gibbard, Clare wrote: > >> Hello, >> >> I have run several scans using recon-all -all -subjid subject_no -expert >> expert.opts where my expert.opts file changes the parameters for the >> mri_normalize step (this works well in my scans). I then had to edit a few >> of the scans by adding in more white matter and a few control points. I >> re-ran them to incorporate the edits using recon-all -s subject_no -make all >> -xopts-use. This worked well. >> >> I then ran recon-all -s subject_no -qcache ready for doing a group >> analysis. I got an error reading the curvature file in those subjects I had >> edited. I can see from the mailing list that others have had this error >> previously and ran recon-all -s subject_no -make all to fix it. I tried >> this, but I got a message saying that there was nothing to be done for all. >> >> Are you able to advise me on what I can try now? Do I need to go back a >> step? >> >> Thank you very much, >> Clare

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Re: [Freesurfer] contrast matrix
by Douglas N Greve 07 Aug '12

07 Aug '12

Hi Meng, in the case of a 2x2 interaction, the F test has only 1 dof in the numerator. This makes it the same as an unsigned t-test. The interaction in intercept is just the interaction regressing out gender and age (the first row of your matrix). The interaction in slope is the 2x2xage interaction regressing out the effect of gender (the 2nd row). doug On 08/06/2012 10:28 PM, Meng Li wrote: > Hi professor, > I know that if performing the Analysis of Variance (eg. 2*2 > interaction analysis), we should use the F-test, so I wonder the > reason why the contrast matrix of 4G0V > (http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G0V) use the t-test. > And if I want to know whether there is an interaction between > diagnosis and genotype regressing out the effect of gender and age (in > either intercept or slope ??) as previous emial mentioned, that is > using the F-test to detect the interaction, so whether I should use > the following matrix: > 0.25 0.25 -0.25 -0.25 -0.25 -0.25 0.25 0.25 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0.25 0.25 -0.25 -0.25 -0.25 -0.25 0.25 0.25 > Thanks, > Best wishes, > Meng > Date: Mon, 06 Aug 2012 10:01:22 -0400 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] contrast matrix > To: freesurfer(a)nmr.mgh.harvard.edu > Hi Meng, the first row is what you want. The second row tests for an > interaction between diagnosis, genotype, and age. > doug > On 08/04/2012 10:23 PM, Meng Li wrote: > > Hi Freesurfers, > > > > My experimental design includes 3 discrete factors and 1 continuous > > variables: > > > > Discrete factors: diagnosis with two levels (A, B); genotype with two > > levels (G, T); gender (F, M) > > > > Continuous variable: age > > > > So I can get 8 classes: AGF, AGM, ATF,ATM, BGF, BGM, BTF, BTM. Then I > > want to perform 2 (diagnosis)* 2(genotype) interaction analysis with > > regressing out the effect of gender and age. Is the following contrast > > matrix correct? > > > > 0.25 0.25 -0.25 -0.25 -0.25 -0.25 0.25 0.25 0 0 0 0 0 0 0 0 > > > > 0 0 0 0 0 0 0 00.25 0.25 -0.25 -0.25 -0.25 -0.25 0.25 0.25 > > > > Any help will be very appreciated. > > > > Best wishes, > > > > Meng > > > > > > > -- 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

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T1 space to DTI space
by Trietsch, Rayna 07 Aug '12

07 Aug '12

Hi, I am trying to go from T1 space to DTI space using fsl_rigid_register to co-register the T1 image to the b0 image. fsl_rigd_register gives me a matrix outputted as a .fslmat file. If I multiple that matrix by a matrix of the coordinates of my head points from tkmedit than I should get the coordinates which I can input into TrackVis but I get coordinates which are out of the xyz range of the image in TrackVis. Any ideas on what could be going wrong or another approach? Thanks! ~Rayna~

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