Freesurfer

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30089 discussions

mri_convert downsample then resample shifts image upward one voxel
by Joshua Lee 10 Aug '12

10 Aug '12

I used mri_convert to resample my norm.mgz to 0.25 mm iso nii.gz, and then again back up to 1mm isotropic space. The resultant image shifted up a voxel from the original converted straght to nii.gz. This points to the resampling procedure, and not the conversion to different file format. Suggestions? Note: I wanted to hand trace the hippocampus in the norm.mgz, and upsampled the norm.mgz to trace on. I traced it, and then downsampled to 1mm to compare with Freesurfer segmentation, but found it shifted. Josh

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Re. QDEC results
by Gibbard, Clare 10 Aug '12

10 Aug '12

Hi Doug, Thanks for your quick response - that all makes sense now. Best wishes, Clare ------------------------------ Message: 13 Date: Fri, 10 Aug 2012 10:19:43 +0000 From: "Gibbard, Clare" <c.gibbard(a)ucl.ac.uk> Subject: [Freesurfer] QDEC results To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <D2ACCCB2F2AEDD40865D0836BF8D33B6224C82C9(a)DB3PRD0104MB131.eurprd01.prod.exchangelabs.com> Content-Type: text/plain; charset="iso-8859-1" Hello, I went on the FS course in Amsterdam recently. I have run a QDEC analysis to see whether cortical thickness differs between my two groups. I have two questions: 1. I put in the lh_bankssts_thickness as my continuous variable. The display outputs results for whether average thickness differs between my groups. The significant clusters appear in areas which are far away from the lh_bankssts. Is this correct? Does the design somehow look at overall cortical thickness in the lh even though I have only specified the lh_bankssts? 2. I can't see the button for controlling for multiple comparisons. From the wiki I believe this is supposed to appear under a scalar heading, but I can't see it. Do I need to add something in order to do this? Thank you very much. Best wishes, Clare ---------------- Message: 21 Date: Fri, 10 Aug 2012 11:03:52 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] QDEC results To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <502522D8.2080307(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Clare, On 08/10/2012 06:19 AM, Gibbard, Clare wrote: > Hello, > > I went on the FS course in Amsterdam recently. I have run a QDEC > analysis to see whether cortical thickness differs between my two > groups. I have two questions: > > 1. I put in the lh_bankssts_thickness as my continuous variable. The > display outputs results for whether average thickness differs between > my groups. The significant clusters appear in areas which are far > away from the lh_bankssts. Is this correct? Does the design somehow > look at overall cortical thickness in the lh even though I have only > specified the lh_bankssts? I think it is correct. You are not confining the analysis to bankssts. You are basically using bankssts as a nuisance variable. > > 2. I can't see the button for controlling for multiple comparisons. > From the wiki I believe this is supposed to appear under a scalar > heading, but I can't see it. Do I need to add something in order to > do this? You should not need anything else. Are you on the "Display" tab? It should be under the "Clusters" area. doug

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ico4 parcellation and mri_segstats
by Linda Douw 10 Aug '12

10 Aug '12

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, -- Linda Douw, Ph.D. Research fellow Department of Radiology Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School 149 13th Street Charlestown, MA 02129

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Talairach registration
by Alexandra Tanner 10 Aug '12

10 Aug '12

Hi Doug, I'm currently looking into doing surface edits on past data and I heard someone mention that one should never scale the brain when editing the talairach registration. I was wondering if this was true, or if it's okay to scale the brain so long as you check the scaling in all 3 dimensions after doing so. Any input would be great! Thanks, Alex

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QDEC results
by Gibbard, Clare 10 Aug '12

10 Aug '12

Hello, I went on the FS course in Amsterdam recently. I have run a QDEC analysis to see whether cortical thickness differs between my two groups. I have two questions: 1. I put in the lh_bankssts_thickness as my continuous variable. The display outputs results for whether average thickness differs between my groups. The significant clusters appear in areas which are far away from the lh_bankssts. Is this correct? Does the design somehow look at overall cortical thickness in the lh even though I have only specified the lh_bankssts? 2. I can't see the button for controlling for multiple comparisons. From the wiki I believe this is supposed to appear under a scalar heading, but I can't see it. Do I need to add something in order to do this? Thank you very much. Best wishes, Clare ----------- Clare Gibbard PhD Student Imaging & BioPhysics Unit 4th Floor Institute of Child Health 30 Guilford Street London WC1N 1EH Tel. 020 7905 2192 Email: c.gibbard(a)ucl.ac.uk

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unable to download ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol
by Knut J Bjuland 10 Aug '12

10 Aug '12

HI I am unable to download ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol. Could you pleas add the file back. Knut J

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Freesurfer 5.2 or new trac_all
by Knut J Bjuland 10 Aug '12

10 Aug '12

When will FreeSurfer 5.2 be release. Is is possible to download the news version of trac-all and fsl_sub and use them in FreeSurfer 5. since I am using fsl 4.1.9. Knut Jørgen

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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

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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 **

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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

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