Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30087 discussions

example in mris_label2annot's help
by Carl Anderson 25 Mar '14

25 Mar '14

Dear list, I tried runing the example in mris_label2annot's help: mris_label2annot --s bert --h lh --ctab aparc.annot.ctab --a myaparc --l lh.unknown.label --l lh.bankssts.label --l lh.caudalanteriorcingulate.label --nhits nhits.mgh got the following result: ERROR: cannot find or read aparc.annot.ctab aparc.annot.ctab is in bert and here is my setup: -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSL_DIR /usr/local/fsl could this be a bash vs tcsh problem as I am using bash? -- <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>> Carl M. Anderson, Ph.D. (mail stop 204) Assistant Professor of Psychiatry, Harvard Medical School & The Neuroimaging Center, McLean Hospital 115 Mill St. Belmont, MA 02478 Ph: 617-855-2972; Fax: 617-855-2770 e-mail: remfract(a)gmail.com; carl_anderson(a)hms.harvard.edu <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>

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Re: [Freesurfer] glmfit with correlated covariates
by L. Schweren 25 Mar '14

25 Mar '14

Dear FreeSurfer experts, Thank you for your fast reply. We are extracting cortical thickness values for statistical sub-analyses in SPSS (due to corrections required with regard to family relatedness within the data); therefore we want to be a 100% certain that the statistical model we use in SPSS is identical to the model used by mri_glmfit. Can you confirm that, out of the multiple linear regression types listed below, mri_glmfit makes use of the Direct (or Standard) regression model? Type Characteristics Direct (or Standard) . All IVs are entered simultaneously Hierarchical . IVs are entered in steps, i.e., some before others . Interpret: R2 change, F change Forward . The software enters IVs one by one until there are no more significant IVs to be entered Backward . The software removes IVs one to one until there are no more non-significant IVs to removed Stepwise . A combination of Forward and Backward MLR Thank you again for your help, Best wishes, Lizanne Date: Wed, 12 Mar 2014 11:04:00 -0400 From: Douglas Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] glmfit with correlated covariates To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <53207760.8010809(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset="iso-8859-1" It is just a standard multiple regression analysis where all regressors are fit simultaneously. One weight does not include that of another weight. doug On 3/12/14 5:16 AM, L. Schweren wrote: > > Dear FreeSurfer experts, > > I am attempting to disentangle the effects of different features of > pharmacological treatment on cortical thickness. > > I am running glmfit from the commandline, with multiple covariates > (a.o. Z_Age, Z_TreatmentDuration and Z_StartAge) in the fsgd-file. > These covariates are correlated up to approximately 0.6 , which to my > understanding is not ideal yet not inducing collinearity. Running > glmfit, I do not get any errors such as ill-designed matrix or so. > > My question regards the way the different regression weights are > calculated in each voxel. If I test the variance in CT of voxel A > explained by for example TreatmentDuration, and part of the variance > in voxel A is explained by both TreatmentDuration and StartAge, will > the regression weigth of TreatmentDuration than include the part that > is also explained by StartAge? Or are all other covariates first > "regressed out" of the variance, such that the variable I test can > only explain the variance that was not explained by any of the other > covariates? > > Thank you very much, your help is very much appreciated! > > Best wishes, > > Lizanne > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

4 5

Percent signal change after resampling and combining FEAT analyses
by Manuel Spitschan 25 Mar '14

25 Mar '14

Dear FreeSurfer experts, I've performed a few first-level analyses of BOLD data with FSL, and have followed the instructions on the FS Wiki (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslGroupFeat) to sample the COPEs of each run to a common surface (fsaverage) and run a fixed-effects analyses using 'mri_glmfit' across the runs. The resulting gamma.mgh contains the COPEs per vertex across the runs. How would I find out the appropriate scaling factor and the baseline image to calculate percent signal change per vertex following these analysis steps? Any help would be appreciated. Thanks in advance, Manuel Spitschan

2 1

thickness for "subcortical structures"
by Francesco Puccettone 25 Mar '14

25 Mar '14

Hello, I've read that cortical thickness analyses are limited to the cortex and cannot be used to examine subcortical grey matter. But does "subcortical grey matter" refer to deep gray matter structures such as the hippocampus, the basal ganglia or the nucleus accumbens - all of which are still technically part of the "cerebral cortex" - or does it in fact refer to gray matter nuclei surrounded by white matter, for which it would not be possible to model a white & a pial surface? Thank you! Francesco

3 3

FSAverage headmodel composition.
by Игорь Васильевич Изъюров 25 Mar '14

25 Mar '14

Hi all, Could you tell me about the gender composition of FSAverage head model? All the information about it is that it consits of 40 subjects of different ages. Best, Igor.

2 2

Can we use both -use-gpu and -openmp options in recon-all?
by Tran, Kevin (NIH/NIMH) [C] 25 Mar '14

25 Mar '14

Hi, I have posted a question about the error while using recon-all command with -use–gpu option on a CentOS 6 machine a while back. CUDA Error in file 'mriconvolve_cuda.cu' on line 945 : unload of CUDA runtime fa iled. Abort (core dumped) ERROR: mri_ca_register with non-zero status 134 The problem apparently came from this command mri_ca_register_cuda -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /opt/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.m3z We are wondering if it was OK to change the recon-all script so that we would enable OpenMP for this mri_ca_register command but use GPU for the rest of recon-all script? That is, we would replace line 2273 in recon-all from if($UseCuda) set cmd = (mri_ca_register_cuda) To if($UseCuda) set cmd = (mri_ca_register) So, with the –openmp option, this command will run with multiple cores. By not using GPU for this command, we can avoid the CUDA Error message. However, we are wondering if it's OK that we combined both -use–gnu and –openmp? Could you help us out? -- Kevin Tran, Contractor UNIX System Administrator The National Institutes of Health NIMH, Laboratory of Brain and Cognition 10 Center Drive, Room 4C215 Bethesda MD 20892-1366 kevintran(a)mail.nih.gov

2 1

Discrepancy between volume generated by aparcstats2table and mri_segstats
by Corinna Bauer 25 Mar '14

25 Mar '14

Hello all, I have noticed a discrepancy in the volumes generated by aparcstats2table and mri_segstats using aparc+aseg. Which is correct? I am using version 5.3. Thanks, Corinna

2 1

Mean Diffusivity
by Rotem Saar 25 Mar '14

25 Mar '14

Hi Doug, Thanks for your help. I got the attached output for the MD calculation - do you know if these are reasonable results ? how come the values of the corpus-callosum so different ? CC results - # ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range 35 251 449 449.0 CC_Posterior 5.9866 7.7511 0.0000 16.0000 16.0000 36 252 237 237.0 CC_Mid_Posterior 183.9494 785.5627 0.0000 5001.0000 5001.0000 37 253 174 174.0 CC_Central 1587.2874 2217.3154 0.0000 5002.0000 5002.0000 38 254 210 210.0 CC_Mid_Anterior 1338.9333 1656.6611 0.0000 5002.0000 5002.0000 39 255 401 401.0 CC_Anterior 1340.8704 920.4716 0.0000 3028.0000 3028.0000 All results- # ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range 1 0 16263767 16263767.0 Unknown 105.0203 555.8546 0.0000 5002.0000 5002.0000 2 4 1429 1429.0 Left-Lateral-Ventricle 1205.2814 1696.0261 0.0000 5001.0000 5001.0000 3 5 61 61.0 Left-Inf-Lat-Vent 1651.1803 1050.3809 0.0000 5001.0000 5001.0000 4 7 8733 8733.0 Left-Cerebellum-White-Matter 303.9889 692.3320 0.0000 3013.0000 3013.0000 5 8 35697 35697.0 Left-Cerebellum-Cortex 328.1487 800.4635 0.0000 3016.0000 3016.0000 6 10 5586 5586.0 Left-Thalamus-Proper 776.9293 1738.6683 0.0000 5001.0000 5001.0000 7 11 2003 2003.0 Left-Caudate 3098.6599 2212.4736 0.0000 5001.0000 5001.0000 8 12 4464 4464.0 Left-Putamen 3184.5918 1929.2238 0.0000 5001.0000 5001.0000 9 13 726 726.0 Left-Pallidum 3507.9766 2168.7949 4.0000 5001.0000 4997.0000 10 14 57 57.0 3rd-Ventricle 1272.3158 2118.5652 0.0000 5001.0000 5001.0000 11 15 747 747.0 4th-Ventricle 39.2918 136.0397 0.0000 1013.0000 1013.0000 12 16 15338 15338.0 Brain-Stem 887.5380 1201.0325 0.0000 5002.0000 5002.0000 13 17 2316 2316.0 Left-Hippocampus 2519.1814 2068.5225 0.0000 5001.0000 5001.0000 14 18 937 937.0 Left-Amygdala 3112.2273 1532.0126 0.0000 5001.0000 5001.0000 15 24 243 243.0 CSF 139.6379 706.3411 0.0000 5002.0000 5002.0000 16 26 431 431.0 Left-Accumbens-area 2903.3179 548.7380 1023.0000 5001.0000 3978.0000 17 28 1892 1892.0 Left-VentralDC 1104.6935 1975.9153 0.0000 5001.0000 5001.0000 18 30 18 18.0 Left-vessel 2812.7778 646.7617 1035.0000 3035.0000 2000.0000 19 31 264 264.0 Left-choroid-plexus 740.3864 1035.1217 0.0000 5001.0000 5001.0000 20 43 1486 1486.0 Right-Lateral-Ventricle 1163.9320 1678.3546 0.0000 5002.0000 5002.0000 21 44 66 66.0 Right-Inf-Lat-Vent 4869.5908 335.7767 4031.0000 5002.0000 971.0000 22 46 9063 9063.0 Right-Cerebellum-White-Matter 528.6555 1037.6643 0.0000 4013.0000 4013.0000 23 47 32805 32805.0 Right-Cerebellum-Cortex 348.7231 902.4393 0.0000 4013.0000 4013.0000 24 49 5262 5262.0 Right-Thalamus-Proper 625.0261 1578.8838 0.0000 5002.0000 5002.0000 25 50 2143 2143.0 Right-Caudate 2655.9062 1884.6532 0.0000 5002.0000 5002.0000 26 51 4344 4344.0 Right-Putamen 4297.2183 1264.8182 43.0000 5002.0000 4959.0000 27 52 921 921.0 Right-Pallidum 2260.4006 2455.9590 43.0000 5002.0000 4959.0000 28 53 2515 2515.0 Right-Hippocampus 2451.9885 2322.6428 0.0000 5002.0000 5002.0000 29 54 1121 1121.0 Right-Amygdala 3649.0322 2089.6423 43.0000 5002.0000 4959.0000 30 58 341 341.0 Right-Accumbens-area 2160.9326 1494.9885 0.0000 4023.0000 4023.0000 31 60 2309 2309.0 Right-VentralDC 856.0403 1765.5569 0.0000 5002.0000 5002.0000 32 62 17 17.0 Right-vessel 4945.1177 234.5327 4035.0000 5002.0000 967.0000 33 63 195 195.0 Right-choroid-plexus 1060.4257 1698.5687 0.0000 5002.0000 5002.0000 34 85 17 17.0 Optic-Chiasm 374.4706 610.2134 0.0000 2023.0000 2023.0000 35 251 449 449.0 CC_Posterior 5.9866 7.7511 0.0000 16.0000 16.0000 36 252 237 237.0 CC_Mid_Posterior 183.9494 785.5627 0.0000 5001.0000 5001.0000 37 253 174 174.0 CC_Central 1587.2874 2217.3154 0.0000 5002.0000 5002.0000 38 254 210 210.0 CC_Mid_Anterior 1338.9333 1656.6611 0.0000 5002.0000 5002.0000 39 255 401 401.0 CC_Anterior 1340.8704 920.4716 0.0000 3028.0000 3028.0000 40 1000 24 24.0 ctx-lh-unknown 5001.0000 -nan 5001.0000 5001.0000 0.0000 41 1001 854 854.0 ctx-lh-bankssts 218.2401 534.4711 0.0000 3009.0000 3009.0000 42 1002 421 421.0 ctx-lh-caudalanteriorcingulate 2067.9407 1589.9967 0.0000 5001.0000 5001.0000 43 1003 3160 3160.0 ctx-lh-caudalmiddlefrontal 1924.0532 1171.6512 0.0000 5001.0000 5001.0000 44 1005 497 497.0 ctx-lh-cuneus 0.0000 0.0000 0.0000 0.0000 0.0000 45 1006 618 618.0 ctx-lh-entorhinal 3607.0874 1856.6394 0.0000 5001.0000 5001.0000 46 1007 3182 3182.0 ctx-lh-fusiform 1484.3463 1486.4078 0.0000 5001.0000 5001.0000 47 1008 4949 4949.0 ctx-lh-inferiorparietal 6.5112 80.7200 0.0000 1007.0000 1007.0000 48 1009 3357 3357.0 ctx-lh-inferiortemporal 823.0471 1069.3124 0.0000 3031.0000 3031.0000 49 1010 876 876.0 ctx-lh-isthmuscingulate 7.8413 7.7702 0.0000 16.0000 16.0000 50 1011 2523 2523.0 ctx-lh-lateraloccipital 0.2029 1.2581 0.0000 8.0000 8.0000 51 1012 2879 2879.0 ctx-lh-lateralorbitofrontal 1774.3990 1452.4291 0.0000 5001.0000 5001.0000 52 1013 1962 1962.0 ctx-lh-lingual 6.9760 5.2759 0.0000 47.0000 47.0000 53 1014 1714 1714.0 ctx-lh-medialorbitofrontal 1330.5485 1269.4579 0.0000 5001.0000 5001.0000 54 1015 4145 4145.0 ctx-lh-middletemporal 851.2019 1035.8433 0.0000 3031.0000 3031.0000 55 1016 811 811.0 ctx-lh-parahippocampal 1237.8545 1632.6826 0.0000 5001.0000 5001.0000 56 1017 1031 1031.0 ctx-lh-paracentral 163.8759 464.2348 0.0000 3014.0000 3014.0000 57 1018 1511 1511.0 ctx-lh-parsopercularis 1511.6346 1118.9261 0.0000 3027.0000 3027.0000 58 1019 793 793.0 ctx-lh-parsorbitalis 308.1538 665.0723 0.0000 3024.0000 3024.0000 59 1020 1487 1487.0 ctx-lh-parstriangularis 1024.8049 1068.4369 0.0000 5001.0000 5001.0000 60 1021 362 362.0 ctx-lh-pericalcarine 0.1768 1.6749 0.0000 16.0000 16.0000 61 1022 2404 2404.0 ctx-lh-postcentral 230.2013 565.3003 0.0000 3030.0000 3030.0000 62 1023 837 837.0 ctx-lh-posteriorcingulate 365.9355 763.2245 0.0000 3026.0000 3026.0000 63 1024 5058 5058.0 ctx-lh-precentral 697.4423 964.1465 0.0000 3030.0000 3030.0000 64 1025 2900 2900.0 ctx-lh-precuneus 0.3721 2.4073 0.0000 16.0000 16.0000 65 1026 968 968.0 ctx-lh-rostralanteriorcingulate 1851.4866 1085.8788 0.0000 3028.0000 3028.0000 66 1027 5944 5944.0 ctx-lh-rostralmiddlefrontal 637.7747 985.5963 0.0000 3028.0000 3028.0000 67 1028 9845 9845.0 ctx-lh-superiorfrontal 1617.2528 1355.0308 0.0000 5001.0000 5001.0000 68 1029 3901 3901.0 ctx-lh-superiorparietal 45.0510 249.0687 0.0000 3007.0000 3007.0000 69 1030 5179 5179.0 ctx-lh-superiortemporal 1407.5188 1191.6757 0.0000 5001.0000 5001.0000 70 1031 4343 4343.0 ctx-lh-supramarginal 492.8904 936.2776 0.0000 3033.0000 3033.0000 71 1032 202 202.0 ctx-lh-frontalpole 0.0000 0.0000 0.0000 0.0000 0.0000 72 1033 1041 1041.0 ctx-lh-temporalpole 2141.6599 1133.5350 0.0000 5001.0000 5001.0000 73 1034 372 372.0 ctx-lh-transversetemporal 1850.0807 1024.5981 0.0000 5001.0000 5001.0000 74 1035 2899 2899.0 ctx-lh-insula 2277.8611 1366.0648 0.0000 5001.0000 5001.0000 75 2000 138 138.0 ctx-rh-unknown 4081.4709 1066.3595 43.0000 5002.0000 4959.0000 76 2001 751 751.0 ctx-rh-bankssts 2120.9041 1563.7277 0.0000 4015.0000 4015.0000 77 2002 856 856.0 ctx-rh-caudalanteriorcingulate 1341.9065 1345.1031 0.0000 5002.0000 5002.0000 78 2003 2573 2573.0 ctx-rh-caudalmiddlefrontal 3033.8103 1231.6836 0.0000 5002.0000 5002.0000 79 2005 524 524.0 ctx-rh-cuneus 0.0000 0.0000 0.0000 0.0000 0.0000 80 2006 410 410.0 ctx-rh-entorhinal 4432.1440 723.8027 43.0000 5002.0000 4959.0000 81 2007 3196 3196.0 ctx-rh-fusiform 2248.0046 1983.5382 0.0000 5002.0000 5002.0000 82 2008 5482 5482.0 ctx-rh-inferiorparietal 47.2470 342.8887 0.0000 4009.0000 4009.0000 83 2009 3422 3422.0 ctx-rh-inferiortemporal 2445.4734 1710.7948 0.0000 5002.0000 5002.0000 84 2010 799 799.0 ctx-rh-isthmuscingulate 11.3517 13.3818 0.0000 46.0000 46.0000 85 2011 2898 2898.0 ctx-rh-lateraloccipital 1.3623 7.8864 0.0000 47.0000 47.0000 86 2012 2711 2711.0 ctx-rh-lateralorbitofrontal 2557.2144 1550.0718 0.0000 5002.0000 5002.0000 87 2013 2155 2155.0 ctx-rh-lingual 36.0097 129.2816 0.0000 2007.0000 2007.0000 88 2014 2138 2138.0 ctx-rh-medialorbitofrontal 657.1188 977.1573 0.0000 4028.0000 4028.0000 89 2015 4142 4142.0 ctx-rh-middletemporal 1941.5190 1535.4354 0.0000 4031.0000 4031.0000 90 2016 700 700.0 ctx-rh-parahippocampal 2320.7200 1722.3994 0.0000 5002.0000 5002.0000 91 2017 1416 1416.0 ctx-rh-paracentral 1129.2288 1324.3389 0.0000 4014.0000 4014.0000 92 2018 1076 1076.0 ctx-rh-parsopercularis 2799.9099 1442.7355 0.0000 5002.0000 5002.0000 93 2019 795 795.0 ctx-rh-parsorbitalis 938.1031 1388.8167 0.0000 4024.0000 4024.0000 94 2020 1307 1307.0 ctx-rh-parstriangularis 1947.5524 1547.6558 0.0000 4028.0000 4028.0000 95 2021 414 414.0 ctx-rh-pericalcarine 0.0000 0.0000 0.0000 0.0000 0.0000 96 2022 2549 2549.0 ctx-rh-postcentral 1229.1384 1388.3079 0.0000 4034.0000 4034.0000 97 2023 901 901.0 ctx-rh-posteriorcingulate 522.5083 1161.7966 0.0000 5002.0000 5002.0000 98 2024 4605 4605.0 ctx-rh-precentral 1467.4482 1491.9133 0.0000 4035.0000 4035.0000 99 2025 3024 3024.0 ctx-rh-precuneus 1.0999 4.9147 0.0000 46.0000 46.0000 100 2026 924 924.0 ctx-rh-rostralanteriorcingulate 651.9740 888.0228 0.0000 4028.0000 4028.0000 101 2027 6470 6470.0 ctx-rh-rostralmiddlefrontal 1012.6683 1376.5038 0.0000 4028.0000 4028.0000 102 2028 9798 9798.0 ctx-rh-superiorfrontal 2197.2322 1592.8611 0.0000 5002.0000 5002.0000 103 2029 3746 3746.0 ctx-rh-superiorparietal 175.9952 667.3113 0.0000 4033.0000 4033.0000 104 2030 5304 5304.0 ctx-rh-superiortemporal 2633.3694 1327.8750 0.0000 5002.0000 5002.0000 105 2031 3576 3576.0 ctx-rh-supramarginal 1440.6700 1530.0399 0.0000 5002.0000 5002.0000 106 2032 325 325.0 ctx-rh-frontalpole 0.0000 0.0000 0.0000 0.0000 0.0000 107 2033 603 603.0 ctx-rh-temporalpole 3632.8491 978.0482 0.0000 5002.0000 5002.0000 108 2034 163 163.0 ctx-rh-transversetemporal 2137.0061 1348.5909 0.0000 4035.0000 4035.0000 109 2035 2857 2857.0 ctx-rh-insula 3450.0242 1476.4425 0.0000 5002.0000 5002.0000 110 3001 885 885.0 wm-lh-bankssts 221.4158 647.5278 0.0000 3009.0000 3009.0000 111 3002 1179 1179.0 wm-lh-caudalanteriorcingulate 1693.7269 1835.8118 0.0000 5001.0000 5001.0000 112 3003 4161 4161.0 wm-lh-caudalmiddlefrontal 1699.8068 1099.4926 0.0000 5001.0000 5001.0000 113 3005 480 480.0 wm-lh-cuneus 0.0000 0.0000 0.0000 0.0000 0.0000 114 3006 82 82.0 wm-lh-entorhinal 3762.0854 1140.0966 4.0000 5001.0000 4997.0000 115 3007 2578 2578.0 wm-lh-fusiform 1215.8875 1372.1278 0.0000 5001.0000 5001.0000 116 3008 4617 4617.0 wm-lh-inferiorparietal 22.2378 160.6620 0.0000 3007.0000 3007.0000 117 3009 1812 1812.0 wm-lh-inferiortemporal 1031.3306 1193.7415 0.0000 3031.0000 3031.0000 118 3010 2032 2032.0 wm-lh-isthmuscingulate 16.1855 97.1478 0.0000 1016.0000 1016.0000 119 3011 2997 2997.0 wm-lh-lateraloccipital 0.3363 1.6057 0.0000 8.0000 8.0000 120 3012 3063 3063.0 wm-lh-lateralorbitofrontal 2151.0332 1257.6028 0.0000 5001.0000 5001.0000 121 3013 2399 2399.0 wm-lh-lingual 9.0196 57.9046 0.0000 1007.0000 1007.0000 122 3014 1000 1000.0 wm-lh-medialorbitofrontal 1279.4041 1197.7087 0.0000 5001.0000 5001.0000 123 3015 1061 1061.0 wm-lh-middletemporal 1541.8662 1267.1495 0.0000 3031.0000 3031.0000 124 3016 485 485.0 wm-lh-parahippocampal 1200.3381 1504.2911 0.0000 5001.0000 5001.0000 125 3017 1419 1419.0 wm-lh-paracentral 153.4567 402.2811 0.0000 3012.0000 3012.0000 126 3018 1642 1642.0 wm-lh-parsopercularis 1965.9324 1107.3256 0.0000 3035.0000 3035.0000 127 3019 223 223.0 wm-lh-parsorbitalis 612.5202 779.3184 0.0000 3024.0000 3024.0000 128 3020 1630 1630.0 wm-lh-parstriangularis 2005.0251 1242.6742 0.0000 5001.0000 5001.0000 129 3021 1200 1200.0 wm-lh-pericalcarine 0.2133 1.7157 0.0000 16.0000 16.0000 130 3022 3343 3343.0 wm-lh-postcentral 884.3278 996.7158 0.0000 3033.0000 3033.0000 131 3023 2369 2369.0 wm-lh-posteriorcingulate 586.1232 1373.9506 0.0000 5001.0000 5001.0000 132 3024 6878 6878.0 wm-lh-precentral 795.6331 948.9272 0.0000 3035.0000 3035.0000 133 3025 3369 3369.0 wm-lh-precuneus 0.0427 0.8260 0.0000 16.0000 16.0000 134 3026 1423 1423.0 wm-lh-rostralanteriorcingulate 2465.6416 931.6223 0.0000 3028.0000 3028.0000 135 3027 5509 5509.0 wm-lh-rostralmiddlefrontal 1474.4030 1228.9650 0.0000 5001.0000 5001.0000 136 3028 10076 10076.0 wm-lh-superiorfrontal 2539.9971 1525.0880 0.0000 5001.0000 5001.0000 137 3029 5391 5391.0 wm-lh-superiorparietal 149.2150 477.9887 0.0000 3033.0000 3033.0000 138 3030 3330 3330.0 wm-lh-superiortemporal 1719.6111 1152.3683 0.0000 5001.0000 5001.0000 139 3031 4393 4393.0 wm-lh-supramarginal 1512.4888 1253.5046 0.0000 3033.0000 3033.0000 140 3032 9 9.0 wm-lh-frontalpole 0.0000 0.0000 0.0000 0.0000 0.0000 141 3033 136 136.0 wm-lh-temporalpole 1872.0515 1192.4773 0.0000 3031.0000 3031.0000 142 3034 327 327.0 wm-lh-transversetemporal 2253.0886 1308.4039 5.0000 5001.0000 4996.0000 143 3035 3806 3806.0 wm-lh-insula 1893.2344 1842.3096 0.0000 5001.0000 5001.0000 144 4001 1055 1055.0 wm-rh-bankssts 2382.6738 1306.7096 0.0000 4016.0000 4016.0000 145 4002 1626 1626.0 wm-rh-caudalanteriorcingulate 2365.9939 1754.4871 0.0000 5002.0000 5002.0000 146 4003 3274 3274.0 wm-rh-caudalmiddlefrontal 2900.4553 1251.0457 0.0000 5002.0000 5002.0000 147 4005 462 462.0 wm-rh-cuneus 0.0000 0.0000 0.0000 0.0000 0.0000 148 4006 106 106.0 wm-rh-entorhinal 3299.4058 1537.5352 43.0000 5002.0000 4959.0000 149 4007 2257 2257.0 wm-rh-fusiform 1534.2335 1856.6631 0.0000 5002.0000 5002.0000 150 4008 4279 4279.0 wm-rh-inferiorparietal 298.4765 778.5995 0.0000 4009.0000 4009.0000 151 4009 1746 1746.0 wm-rh-inferiortemporal 2093.4932 1636.5851 0.0000 5002.0000 5002.0000 152 4010 1740 1740.0 wm-rh-isthmuscingulate 38.8356 243.3854 0.0000 2016.0000 2016.0000 153 4011 2606 2606.0 wm-rh-lateraloccipital 0.3427 3.9993 0.0000 47.0000 47.0000 154 4012 2949 2949.0 wm-rh-lateralorbitofrontal 2979.5647 1360.8296 0.0000 5002.0000 5002.0000 155 4013 2344 2344.0 wm-rh-lingual 69.8114 372.1888 0.0000 4007.0000 4007.0000 156 4014 1302 1302.0 wm-rh-medialorbitofrontal 2224.4915 1450.4080 0.0000 4028.0000 4028.0000 157 4015 1691 1691.0 wm-rh-middletemporal 2155.5742 1632.5012 0.0000 5002.0000 5002.0000 158 4016 414 414.0 wm-rh-parahippocampal 2000.5846 1798.7676 0.0000 5002.0000 5002.0000 159 4017 2204 2204.0 wm-rh-paracentral 1233.0594 1383.9352 0.0000 4014.0000 4014.0000 160 4018 1397 1397.0 wm-rh-parsopercularis 3697.2634 1052.3094 0.0000 5002.0000 5002.0000 161 4019 349 349.0 wm-rh-parsorbitalis 1171.5272 1165.5026 0.0000 4003.0000 4003.0000 162 4020 1450 1450.0 wm-rh-parstriangularis 2595.8911 1333.6057 0.0000 5002.0000 5002.0000 163 4021 1072 1072.0 wm-rh-pericalcarine 0.0000 0.0000 0.0000 0.0000 0.0000 164 4022 3537 3537.0 wm-rh-postcentral 1828.3132 1400.6344 0.0000 4035.0000 4035.0000 165 4023 2235 2235.0 wm-rh-posteriorcingulate 674.7817 1563.4506 0.0000 5002.0000 5002.0000 166 4024 6263 6263.0 wm-rh-precentral 1554.2966 1416.0610 0.0000 4035.0000 4035.0000 167 4025 3400 3400.0 wm-rh-precuneus 17.1824 184.4637 0.0000 2007.0000 2007.0000 168 4026 1047 1047.0 wm-rh-rostralanteriorcingulate 1860.3477 1164.7131 0.0000 4028.0000 4028.0000 169 4027 5332 5332.0 wm-rh-rostralmiddlefrontal 2273.0229 1726.8505 0.0000 5002.0000 5002.0000 170 4028 9343 9343.0 wm-rh-superiorfrontal 3128.9961 1617.0729 0.0000 5002.0000 5002.0000 171 4029 5015 5015.0 wm-rh-superiorparietal 700.2903 1143.9926 0.0000 4033.0000 4033.0000 172 4030 2331 2331.0 wm-rh-superiortemporal 3029.0220 1305.0964 0.0000 5002.0000 5002.0000 173 4031 4879 4879.0 wm-rh-supramarginal 2473.6401 1590.3677 0.0000 5002.0000 5002.0000 174 4032 64 64.0 wm-rh-frontalpole 0.0000 0.0000 0.0000 0.0000 0.0000 175 4033 149 149.0 wm-rh-temporalpole 2900.0806 1074.6902 0.0000 4031.0000 4031.0000 176 4034 197 197.0 wm-rh-transversetemporal 2931.1321 1435.5095 0.0000 5002.0000 5002.0000 177 4035 3833 3833.0 wm-rh-insula 2861.4229 2209.4307 41.0000 5002.0000 4961.0000 178 5001 17178 17178.0 Left-UnsegmentedWhiteMatter 1464.7604 1875.4178 0.0000 5001.0000 5001.0000 179 5002 18204 18204.0 Right-UnsegmentedWhiteMatter 1945.1401 2139.9580 0.0000 5002.0000 5002.0000 Thanks Rotem I would use step 3 for the wmparc instead of vol2vol. you need both --seg and --seg-erode --seg-erode 1 --seg /usr/local/freesurfer/ subjects/Anatomy0981/mri/wmparc2diff.mgz doug On 03/20/2014 04:43 AM, Rotem Saar wrote: > Hi Doug, > > Thanks you for directing me to my mistake in step 3 (see below new cmd > line in step 3). What I did is the following - > > 1) dt_recon --i > /usr/local/freesurfer/subjects/Anatomy0981/DTI/I160.dcm --s > Anatomy0981 --o /usr/local/freesurfer/subjects/Anatomy0981/DTI --b > /usr/local/freesurfer/subjects/Anatomy0981/DTI/bvals.bval > /usr/local/freesurfer/subjects/Anatomy0981/DTI/bvecs.bvec > > 2) mri_vol2vol --mov > /usr/local/freesurfer/subjects/Anatomy0981/DTI/lowb.nii --targ > /usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc.mgz --inv > --interp nearest --o > /usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc2diff.mgz --reg > /usr/local/freesurfer/subjects/Anatomy0981/DTI/register.dat --no-save-reg > > 3) mri_label2vol --seg > /usr/local/freesurfer/subjects/Anatomy0981/mri/aparc+aseg.mgz --temp > /usr/local/freesurfer/subjects/Anatomy0981/mri/aparc+aseg.mgz --reg > /usr/local/freesurfer/subjects/Anatomy0981/DTI/register.dat --o > /usr/local/freesurfer/subjects/Anatomy0981/mri/forMD.bshort > > it created many *.bshort files > > My qs: > 1) Should I repeat step 3 with the wmparc.mgz or is it not necessary ? > 2) How do I plot all MD values like I did before for FA values ? > trying to use - > > mri_segstats --seg-erode 1 > /usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc2diff.mgz --ctab > $FREESURFER_HOME/FreeSurferColorLUT.txt --i > /usr/local/freesurfer/subjects/Anatomy0981/DTI/fa-masked.mgz --sum > /usr/local/freesurfer/subjects/Anatomy0981/stats/all_stats_MD-masked > > always end with the same message - it wants a segmentation volume but > nothing works ("unknown")... I used aseg.mgz for example and other > options - nada. However, If I omit the "-erode 1" it reports the > table, but for FA values. What do I need to change in step 3 and how > can I fix the last step ? > > Thank you for your help > > Rotem Rotem Saar-Ashkenazy Department of Brain and Cognitive Science Ben Gurion University of the Negev Beer-Sheva 84105 Israel

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Re: [Freesurfer] major lobes
by Juranek, Jenifer 25 Mar '14

25 Mar '14

Hi Doug, I recently saw your solution to a reported problem with grabbing StrictLobes WM & GM (posted on the Freesurfer forum 12/04/2013; thread title= major lobes). I have successfully grabbed the StrictLobes WM, but I am having trouble with the GM. According to the forum (posted 12/04/2013), the solution that worked was a link (you provided) to download a new binary for mri_annotation2label from the following location:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_… However, this link appears to be broken now that I am attempting to utilize your fix on my RHEL6 workstation. I checked the download site , but there is no new version of Freesurfer since May 2013. Any chance you could provide a link to the new binary for mri_annotation2label you had made available back in Dec 2013? Many Thanks, Jenifer Juranek

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Request for feedback on challenges/hurdles to using/learning Nipype
by Satrajit Ghosh 25 Mar '14

25 Mar '14

hi all, we are looking for feedback on learning/using/installing Nipype - any challenge or hurdle that may have derailed you, wasted your time, left you wanting a photon torpedo, etc.,. we are in the process of re-architecting components of Nipype and feedback would help a lot. please post/discuss at: http://neurostars.org/p/73/ cheers, satra

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