Freesurfer December 2013

freesurfer@nmr.mgh.harvard.edu

107 participants
197 discussions

Re: [Freesurfer] qdec analysis with 2 covariates
by Douglas N Greve 10 Dec '13

10 Dec '13

Is there a cache.mri_glmfit-sim.log in the output folder? Can you send it to me? Also, please remember to post to the list. thanks! doug On 12/10/2013 02:30 PM, Jon Wieser wrote: > FS version 5.3 > > ----- Original Message ----- > From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> > To: "Jon Wieser" <wieser(a)uwm.edu>, Freesurfer(a)nmr.mgh.harvard.edu > Sent: Tuesday, December 10, 2013 1:05:26 PM > Subject: Re: [Freesurfer] qdec analysis with 2 covariates > > > hmmm, it should be there. What version of FS are you using? > > > > On 12/10/2013 12:57 PM, Jon Wieser wrote: >> i was getting the values for the command terminal, when I press the "find clusters and GOTo Max" button on the qdec GUI. >> there is no file named cache.th20.abs.y.dat or something similar. i did a "find" command to list all the *abs*.dat files in the directory >> >> qdec/MTA_ADHD_MJ/lh-Diff-MJnonuser-MJuser-Intercept-thickness/mc-z.abs.th13.pdf.dat >> qdec/MTA_ADHD_MJ/lh-X-ADHD-MJ_group-Intercept-thickness/mc-z.abs.th20.pdf.dat >> qdec/Untitled/lh-Avg-thickness-Age-Cor/mc-z.abs.th13.pdf.dat >> qdec/Untitled/lh-Avg-thickness-Gender-Cor/mc-z.abs.th13.pdf.dat >> qdec/Untitled/lh-Diff-ADHD-nonADHD-Intercept-thickness/mc-z.abs.th13.pdf.dat >> qdec/Untitled/lh-Diff-MJnonuser-MJuser-Intercept-thickness/mc-z.abs.th13.pdf.dat >> qdec/Untitled/lh-X-ADHD-MJ_group-Intercept-thickness/mc-z.abs.th13.pdf.dat >> >> >> >> >> these files contain: >> >> # CSD PDF/CDF >> # simtype null-z >> # anattype surface fsaverage lh >> # FixGroupSubjectArea 1 >> # merged 0 >> # contrast NA >> # seed 1271277527 >> # thresh 1.300000 >> # threshsign 0.000000 >> # searchspace 74612.965197 >> # nullfwhm 15.000000 >> # varfwhm -1.000000 >> # nrepetitions 10000 >> # NOTE: nreps and nrepetitions are both valid for volume data. >> # NOTE: nreps is invalid (-1) for surface data to assure. >> # NOTE: backwards INcompatibility. >> # $Id: volcluster.c,v 1.50.2.1 2011/03/28 15:32:36 greve Exp $ >> # nreps -1 >> # FixSurfClusterArea 1 >> # $Id: surfcluster.c,v 1.26.2.2 2011/11/10 16:01:11 greve Exp $ >> # nbins 100 >> # BinNo MaxClustBin MaxClustPDF MaxClustCDF GRFCDF MaxSigBin MaxSigPDF MaxSigCDF >> 0 204.826004 0.000500 0.999500 0.998289 2.456050 0.000500 0.999500 >> 1 220.348267 0.001800 0.997700 0.996805 2.811329 0.008100 0.991400 >> 2 235.870529 0.004300 0.993400 0.994388 3.166609 0.022200 0.969200 >> 3 251.392792 0.007100 0.986300 0.990673 3.521888 0.030300 0.938900 >> 4 266.915039 0.015600 0.970700 0.985251 3.877167 0.028900 0.910000 >> 5 282.437317 0.017500 0.953200 0.977702 4.232447 0.022600 0.887400 >> 6 297.959595 0.021400 0.931800 0.967628 4.587726 0.015200 0.872200 >> 7 313.481842 0.033600 0.898200 0.954689 4.943005 0.012300 0.859900 >> 8 329.004089 0.036100 0.862100 0.938634 5.298285 0.009800 0.850100 >> 9 344.526367 0.038000 0.824100 0.919325 5.653563 0.007300 0.842800 >> 10 360.048645 0.042500 0.781600 0.896747 6.008843 0.009200 0.833600 >> 11 375.570892 0.050000 0.731600 0.871009 6.364122 0.006900 0.826700 >> 12 391.093140 0.043400 0.688200 0.842332 6.719401 0.007100 0.819600 >> 13 406.615417 0.047300 0.640900 0.811034 7.074681 0.005500 0.814100 >> 14 422.137695 0.050700 0.590200 0.777508 7.429960 0.005500 0.808600 >> 15 437.659943 0.047400 0.542800 0.742195 7.785239 0.005200 0.803400 >> 16 453.182190 0.044100 0.498700 0.705560 8.140518 0.004900 0.798500 >> 17 468.704468 0.042700 0.456000 0.668070 8.495798 0.005100 0.793400 >> 18 484.226746 0.040600 0.415400 0.630176 8.851077 0.006100 0.787300 >> 19 499.748962 0.034900 0.380500 0.592300 9.206356 0.004800 0.782500 >> 20 515.271240 0.032200 0.348300 0.554820 9.561636 0.003600 0.778900 >> 21 530.793518 0.031400 0.316900 0.518067 9.916915 0.003400 0.775500 >> 22 546.315796 0.032400 0.284500 0.482320 10.272194 0.004000 0.771500 >> 23 561.838013 0.023800 0.260700 0.447809 10.627474 0.004800 0.766700 >> 24 577.360291 0.026100 0.234600 0.414711 10.982753 0.004500 0.762200 >> 25 592.882568 0.022700 0.211900 0.383160 11.338033 0.003300 0.758900 >> 26 608.404846 0.017500 0.194400 0.353244 11.693312 0.003100 0.755800 >> 27 623.927063 0.018200 0.176200 0.325018 12.048591 0.003700 0.752100 >> 28 639.449341 0.017400 0.158800 0.298504 12.403871 0.003800 0.748300 >> 29 654.971619 0.014900 0.143900 0.273697 12.759150 0.004400 0.743900 >> 30 670.493896 0.014200 0.129700 0.250569 13.114429 0.003700 0.740200 >> 31 686.016113 0.014300 0.115400 0.229078 13.469708 0.002800 0.737400 >> 32 701.538391 0.013100 0.102300 0.209165 13.824987 0.003800 0.733600 >> 33 717.060669 0.011700 0.090600 0.190763 14.180266 0.003700 0.729900 >> 34 732.582947 0.008500 0.082100 0.173798 14.535546 0.002900 0.727000 >> 35 748.105164 0.008400 0.073700 0.158191 14.890825 0.003200 0.723800 >> 36 763.627441 0.006800 0.066900 0.143861 15.246104 0.003300 0.720500 >> 37 779.149719 0.007100 0.059800 0.130727 15.601384 0.004600 0.715900 >> 38 794.671936 0.007200 0.052600 0.118707 15.956663 0.000000 0.715900 >> 39 810.194214 0.005400 0.047200 0.107723 16.311943 0.000000 0.715900 >> 40 825.716492 0.005400 0.041800 0.097698 16.667221 0.000000 0.715900 >> 41 841.238770 0.004800 0.037000 0.088559 17.022501 0.000000 0.715900 >> 42 856.761047 0.004600 0.032400 0.080237 17.377781 0.000000 0.715900 >> 43 872.283264 0.003200 0.029200 0.072665 17.733059 0.000000 0.715900 >> 44 887.805542 0.003400 0.025800 0.065783 18.088339 0.000000 0.715900 >> 45 903.327820 0.002200 0.023600 0.059531 18.443619 0.000000 0.715900 >> 46 918.850037 0.002600 0.021000 0.053855 18.798897 0.000000 0.715900 >> 47 934.372314 0.002200 0.018800 0.048707 19.154179 0.000000 0.715900 >> 48 949.894592 0.001900 0.016900 0.044040 19.509457 0.000000 0.715900 >> 49 965.416870 0.002200 0.014700 0.039810 19.864735 0.000000 0.715900 >> 50 980.939148 0.000700 0.014000 0.035979 20.220016 0.000000 0.715900 >> 51 996.461365 0.002100 0.011900 0.032510 20.575294 0.000000 0.715900 >> 52 1011.983643 0.000800 0.011100 0.029371 20.930573 0.000000 0.715900 >> 53 1027.505981 0.000800 0.010300 0.026530 21.285854 0.000000 0.715900 >> 54 1043.028198 0.001000 0.009300 0.023961 21.641132 0.000000 0.715900 >> 55 1058.550415 0.001000 0.008300 0.021638 21.996410 0.000000 0.715900 >> 56 1074.072754 0.000900 0.007400 0.019538 22.351692 0.000000 0.715900 >> 57 1089.594971 0.000900 0.006500 0.017640 22.706970 0.000000 0.715900 >> 58 1105.117310 0.000800 0.005700 0.015925 23.062248 0.000000 0.715900 >> 59 1120.639526 0.000100 0.005600 0.014375 23.417530 0.000000 0.715900 >> 60 1136.161743 0.000300 0.005300 0.012975 23.772808 0.000000 0.715900 >> 61 1151.684082 0.000800 0.004500 0.011711 24.128086 0.000000 0.715900 >> 62 1167.206299 0.000400 0.004100 0.010569 24.483368 0.000000 0.715900 >> 63 1182.728516 0.000200 0.003900 0.009538 24.838646 0.000000 0.715900 >> 64 1198.250854 0.000200 0.003700 0.008607 25.193924 0.000000 0.715900 >> 65 1213.773071 0.000300 0.003400 0.007767 25.549206 0.000000 0.715900 >> 66 1229.295410 0.000400 0.003000 0.007008 25.904484 0.000000 0.715900 >> 67 1244.817627 0.000400 0.002600 0.006323 26.259762 0.000000 0.715900 >> 68 1260.339966 0.000300 0.002300 0.005705 26.615044 0.000000 0.715900 >> 69 1275.862183 0.000400 0.001900 0.005147 26.970322 0.000000 0.715900 >> 70 1291.384399 0.000100 0.001800 0.004644 27.325600 0.000000 0.715900 >> 71 1306.906738 0.000000 0.001800 0.004190 27.680882 0.000000 0.715900 >> 72 1322.428955 0.000400 0.001400 0.003780 28.036160 0.000000 0.715900 >> 73 1337.951172 0.000100 0.001300 0.003410 28.391438 0.000000 0.715900 >> 74 1353.473511 0.000100 0.001200 0.003076 28.746719 0.000000 0.715900 >> 75 1368.995728 0.000100 0.001100 0.002775 29.101997 0.000000 0.715900 >> 76 1384.517944 0.000100 0.001000 0.002503 29.457275 0.000000 0.715900 >> 77 1400.040283 0.000300 0.000700 0.002258 29.812557 0.000000 0.715900 >> 78 1415.562500 0.000100 0.000600 0.002037 30.167835 0.000000 0.715900 >> 79 1431.084839 0.000000 0.000600 0.001838 30.523113 0.000000 0.715900 >> 80 1446.607056 0.000100 0.000500 0.001658 30.878395 0.000000 0.715900 >> 81 1462.129272 0.000200 0.000300 0.001495 31.233673 0.000000 0.715900 >> 82 1477.651611 0.000000 0.000300 0.001349 31.588951 0.000000 0.715900 >> 83 1493.173828 0.000200 0.000100 0.001217 31.944233 0.000000 0.715900 >> 84 1508.696167 0.000000 0.000100 0.001098 32.299511 0.000000 0.715900 >> 85 1524.218384 0.000000 0.000100 0.000990 32.654789 0.000000 0.715900 >> 86 1539.740601 0.000000 0.000100 0.000893 33.010071 0.000000 0.715900 >> 87 1555.262939 0.000000 0.000100 0.000805 33.365349 0.000000 0.715900 >> 88 1570.785156 0.000000 0.000100 0.000727 33.720627 0.000000 0.715900 >> 89 1586.307373 0.000000 0.000100 0.000655 34.075909 0.000000 0.715900 >> 90 1601.829712 0.000000 0.000100 0.000591 34.431187 0.000000 0.715900 >> 91 1617.351929 0.000000 0.000100 0.000533 34.786469 0.000000 0.715900 >> 92 1632.874146 0.000000 0.000100 0.000481 35.141747 0.000000 0.715900 >> 93 1648.396484 0.000000 0.000100 0.000434 35.497025 0.000000 0.715900 >> 94 1663.918701 0.000000 0.000100 0.000391 35.852306 0.000000 0.715900 >> 95 1679.441040 0.000000 0.000100 0.000353 36.207584 0.000000 0.715900 >> 96 1694.963257 0.000000 0.000100 0.000318 36.562862 0.000000 0.715900 >> 97 1710.485474 0.000000 0.000100 0.000287 36.918144 0.000000 0.715900 >> 98 1726.007812 0.000000 0.000100 0.000259 37.273422 0.000000 0.715900 >> 99 1741.530029 0.000100 -0.000000 0.000234 37.628700 0.715900 0.000000 >> >> ----- Original Message ----- >> From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >> To: "Jon Wieser" <wieser(a)uwm.edu> >> Cc: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu> >> Sent: Monday, December 9, 2013 5:02:41 PM >> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >> >> which file did you look in? It should have a name like >> cache.th20.abs.y.ocn.dat >> >> On 12/09/2013 05:09 PM, Jon Wieser wrote: >>> I found data for the average thickness all subjects for each cluster, but I haven't found the individual subject's thickness for each cluster. can you direct me to that data? >>> Jon >>> ----- Original Message ----- >>> From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>> To: "Jon Wieser" <wieser(a)uwm.edu> >>> Cc: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu> >>> Sent: Monday, December 9, 2013 2:15:39 PM >>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>> >>> It is in one of the output files. Look for the .dat file in >>> mri_glmfit-sim --help >>> >>> On 12/09/2013 03:01 PM, Jon Wieser wrote: >>>> thanks doug, >>>> >>>> We've run a 2x2 analysis for thickness in Qdec and want the get the average thickness value for each cluster, for each subject. >>>> How can i get a table of thickness data , for feach subject in the analysis >>>> Jon >>>> >>>> ----- Original Message ----- >>>> From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>> To: freesurfer(a)nmr.mgh.harvard.edu >>>> Sent: Monday, December 9, 2013 1:48:15 PM >>>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>>> >>>> >>>> Hi Jon, QDEC does not currently allow more than one covariates of >>>> interest. You will have to use the command-line stream (ie, >>>> mris_preproc, mri_surf2surf, mri_glmfit, mri_glmfit-sim) >>>> >>>> doug >>>> >>>> >>>> On 12/05/2013 02:57 PM, Jon Wieser wrote: >>>>> HI freesurfer experts >>>>> >>>>> I want to do an analysis in qdec with 2 groups(ADHD, and Marijuana usage) and 2 covariates(age and gender) to study the effect of these factors on cortical thickness. I can only select a covariate in the qdec gui. is there a way to select both covariates in the qdec GUI? >>>>> Thanks >>>>> Jon >>>>> -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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T1 FLASH parameters for cortical thickness analyses
by Ritobrato Datta 10 Dec '13

10 Dec '13

Hi All, I have collected T1 3D FLASH on a subject and here are some details of the sequence, Manufacturer = SIEMENS StudyDescription = Neuro_3T^brain_3t SeriesDescription = Axial Global FLASH FA27 ManufacturersModelName = Verio ReferencedImageSequence = 1.2.840.10008.5.1.4.1.1.4\1.3.12.2.1107.5.2.36.40156.30000013112219461598300005978\1.2.840.10008.5.1.4.1.1.4\1.3.12.2.1107.5.2.36.40156.30000013112219461598300005980\1.2.840.10008.5.1.4.1.1.4\1.3.12.2.1107.5.2.36.40156.30000013112219461598300005979 ScanningSequence = GR SequenceVariant = SP ScanOptions = SAT1 MRAcquisitionType = 3D SequenceName = *fl3d1 SliceThickness = 1 RepetitionTime = 20 EchoTime = 5 InversionTime = - NumberofAverages = 1 ImagingFrequency = 123.200338 ImagedNucleus = 1H EchoNumbers = 1 MagneticFieldStrength = 3 NumberofPhaseEncodingSteps = 192 EchoTrainLength = 1 PercentSampling = 100 PercentPhaseFieldofView = 75 PixelBandwidth = 179 DeviceSerialNumber = 40156 SoftwareVersions = syngo MR B17 ProtocolName = Axial Global FLASH FA27 TransmitCoilName = Body AcquisitionMatrix = 0\256\192\0 In-planePhaseEncodingDirection = ROW FlipAngle = 27 VariableFlipAngleFlag = N SAR = 0.19411263 My questions are the following - 1) Can I get reliable cortical thickness estimates using a T1 3D FLASH sequence at 3T Siemens TRIO ? 2) Which version of freesurfer is recommended ? 3) One reason, I collected T1 FLASH is I want to get whole brain volume and brain parenchymal fraction in Multiple sclerosis patients. But if freesurfer prefers MPRAGES over FLASH for cortical thickness, I am wondering how reliable are the standard MPRAGE sequences for calculation of whole brain volume and brain parenchymal fractions ? 4) I ran the recon on the FLASH using freesurfer 5.3 and it looks very decent but has anyone tested and optimized the parameters for the T1 FLASH sequence for cortical thickness estimations ? 5) If you can share your opinion and experiences in this topic and maybe point me to some references using flash and freesurfer for cortical thickness, that will be very helpful. Best Ri

2 3

Re: [Freesurfer] multiple frames error message for recon-all
by Chan, Noel Yan-Ki,Ph.D. 10 Dec '13

10 Dec '13

Thanks Bruce. I checked, it is multi-echo mprage, it's just when I unpack it, it didn't automatically generate the RMS. so can you walk me through when to do the mri-average-sqr? So I just type the command: unpacksdcmdir -src /cluster/archive/304/siemens/Skyra-45407-20130822-092226-174000 -targ . -scanonly unpacklogpre Then it gives me: Tue Dec 10 14:56:36 EST 2013 Log File is ./unpack.log INFO: Logfile is ./unpack.log SkipMoCo 0 Scanning source directory ... INFO: summary file is ./dicomdir.sumfile INFO: status file is ./parse.status Scanning directory Tue Dec 10 14:56:36 EST 2013 mri_parse_sdcmdir --sortbyrun --d /cluster/archive/304/siemens/Skyra-45407-20130822-092226-174000 --o ./dicomdir.sumfile --status ./parse.status 0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38 40 42 44 46 48 50 52 54 56 58 60 62 64 66 68 70 72 74 76 78 80 82 84 86 88 90 92 94 96 98 100 Done scanning Tue Dec 10 14:58:48 EST 2013 ------------------------------------------ 1 localizer ok 256 256 3 1 MR.1.3.12.2.1107.5.2.19.45407.2013082209234488137601798 2 localizer ok 256 256 3 1 MR.1.3.12.2.1107.5.2.19.45407.2013082209234486217101797 3 AAHead_Scout ok 160 160 128 1 MR.1.3.12.2.1107.5.2.19.45407.2013082209242568708801865 4 AAHead_Scout ok 162 162 5 1 MR.1.3.12.2.1107.5.2.19.45407.2013082209243010322103111 5 AAHead_Scout ok 162 162 3 1 MR.1.3.12.2.1107.5.2.19.45407.2013082209243010400603115 6 AAHead_Scout ok 162 162 3 1 MR.1.3.12.2.1107.5.2.19.45407.2013082209243010456303118 7 MEMPRAGE_tfl_mgh_multiecho_1mm_iso ok 256 256 176 4 MR.1.3.12.2.1107.5.2.19.45407.2013082209321083146803580 8 fMRI_resting_state ok 72 72 47 124 MR.1.3.12.2.1107.5.2.19.45407.2013082209330867404606382 How do I create the RMS? Thanks, Noel --- Noel Yanki Chan, PhD Department of Psychiatry Neuroscience Laboratory of Sara Lazar, PhD Harvard Medical School Massachusetts General Hospital Building 120, 2nd avenue, Suite 103 Charlestown, MA 02129 Tel: 617-643-5078 (lab) 607-229-7096 (cell) On Dec 10, 2013, at 2:32 PM, Bruce Fischl wrote: go back and look at the dicoms I guess. Can you post these questions to the list so that others can answer? thanks Bruce On Tue, 10 Dec 2013, Chan, Noel Yan-Ki,Ph.D. wrote: How do I check if they are echoes of a multi-echo mprage? They should have... I mean all other subjects are fine (all others generated RMS automatically) besides these 2 subjects, I don't know if that's something wrong at the time with the data collection. On Dec 10, 2013, at 2:03 PM, Bruce Fischl wrote: you can use mri_average -sqr ... I believe, as long as these really are the echoes of a multi-echo mprage. Are you sure you didn't just point recon-all at the wrong series? It should have generated one automatically On Tue, 10 Dec 2013, Chan, Noel Yan-Ki,Ph.D. wrote: Hi Bruce, Only these two subjects didn't create the RMS automatically, I don't know why. How can I generate the RMS? Thanks, Noel On Dec 10, 2013, at 1:52 PM, Bruce Fischl wrote: Hi Noel what were the acquisitions? If they were multi-echo mprage than you will either have to generate the RMS or find the series that is the RMS (since it should have been generated automatically) cheers Bruce On Tue, 10 Dec 2013, Chan, Noel Yan-Ki,Ph.D. wrote: Hi, I'm trying to do recon-all for a file, and it gave me this multiple frame error message: #@# MotionCor Mon Nov 25 13:11:40 EST 2013 Found 1 runs /autofs/cluster/lazar/projects/Noel/SUBJECTS_DIR/BHI_BJU-345_pre_lazar/mri/ orig/001.mgz Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /autofs/cluster/lazar/projects/Noel/SUBJECTS_DIR/BHI_BJU-345_pre_lazar/mri/ orig/001.mgz has 4 frames If this is a multi-frame MEMPRAGE image, use mri_concat --rms to combine echo frames. Linux compute-0-73 2.6.32-358.23.2.el6.x86_64 #1 SMP Wed Oct 16 18:37:12 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s BHI_BJU-345_pre_lazar exited with ERRORS at Mon Nov 25 13:11:47 EST 2013 For more details, see thelogfile/autofs/cluster/lazar/projects/Noel/SUBJECTS_DIR/BHI_BJU-345_pre_laz ar/ scri pts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting May I ask what should I do to solve this problem? There are actually two files which give me the same error message: BHI_BJU-345_pre_lazar (pbsjob_30) and BHI_JJA-329_pre_lazar (pbsjob_33) Thanks, Noel --- Noel Yanki Chan, PhD Department of Psychiatry Neuroscience Laboratory of Sara Lazar, PhD Harvard Medical School Massachusetts General Hospital Building 120, 2nd avenue, Suite 103 Charlestown, MA 02129 Tel: 617-643-5078 (lab) 607-229-7096 (cell)

2 1

optseq enforcing consecutive trials
by Chris McNorgan 10 Dec '13

10 Dec '13

Hi all, I posed a question back in November but got no replies, so I'll try to restate it briefly: Is there a means of enforcing at least one set of consecutive trials for a condition in an optseq schedule (or even consecutive trials with an intervening NULL event)? I am trying to produce a schedule for a 1-back task, and consecutive events for a given condition will only appear by chance. Getting at least one set of consecutive trials for each of 8 conditions has proven exceedingly difficult. Thanks, Chris

2 1

Re: [Freesurfer] qdec analysis with 2 covariates
by Douglas N Greve 10 Dec '13

10 Dec '13

hmmm, it should be there. What version of FS are you using? On 12/10/2013 12:57 PM, Jon Wieser wrote: > i was getting the values for the command terminal, when I press the "find clusters and GOTo Max" button on the qdec GUI. > there is no file named cache.th20.abs.y.dat or something similar. i did a "find" command to list all the *abs*.dat files in the directory > > qdec/MTA_ADHD_MJ/lh-Diff-MJnonuser-MJuser-Intercept-thickness/mc-z.abs.th13.pdf.dat > qdec/MTA_ADHD_MJ/lh-X-ADHD-MJ_group-Intercept-thickness/mc-z.abs.th20.pdf.dat > qdec/Untitled/lh-Avg-thickness-Age-Cor/mc-z.abs.th13.pdf.dat > qdec/Untitled/lh-Avg-thickness-Gender-Cor/mc-z.abs.th13.pdf.dat > qdec/Untitled/lh-Diff-ADHD-nonADHD-Intercept-thickness/mc-z.abs.th13.pdf.dat > qdec/Untitled/lh-Diff-MJnonuser-MJuser-Intercept-thickness/mc-z.abs.th13.pdf.dat > qdec/Untitled/lh-X-ADHD-MJ_group-Intercept-thickness/mc-z.abs.th13.pdf.dat > > > > > these files contain: > > # CSD PDF/CDF > # simtype null-z > # anattype surface fsaverage lh > # FixGroupSubjectArea 1 > # merged 0 > # contrast NA > # seed 1271277527 > # thresh 1.300000 > # threshsign 0.000000 > # searchspace 74612.965197 > # nullfwhm 15.000000 > # varfwhm -1.000000 > # nrepetitions 10000 > # NOTE: nreps and nrepetitions are both valid for volume data. > # NOTE: nreps is invalid (-1) for surface data to assure. > # NOTE: backwards INcompatibility. > # $Id: volcluster.c,v 1.50.2.1 2011/03/28 15:32:36 greve Exp $ > # nreps -1 > # FixSurfClusterArea 1 > # $Id: surfcluster.c,v 1.26.2.2 2011/11/10 16:01:11 greve Exp $ > # nbins 100 > # BinNo MaxClustBin MaxClustPDF MaxClustCDF GRFCDF MaxSigBin MaxSigPDF MaxSigCDF > 0 204.826004 0.000500 0.999500 0.998289 2.456050 0.000500 0.999500 > 1 220.348267 0.001800 0.997700 0.996805 2.811329 0.008100 0.991400 > 2 235.870529 0.004300 0.993400 0.994388 3.166609 0.022200 0.969200 > 3 251.392792 0.007100 0.986300 0.990673 3.521888 0.030300 0.938900 > 4 266.915039 0.015600 0.970700 0.985251 3.877167 0.028900 0.910000 > 5 282.437317 0.017500 0.953200 0.977702 4.232447 0.022600 0.887400 > 6 297.959595 0.021400 0.931800 0.967628 4.587726 0.015200 0.872200 > 7 313.481842 0.033600 0.898200 0.954689 4.943005 0.012300 0.859900 > 8 329.004089 0.036100 0.862100 0.938634 5.298285 0.009800 0.850100 > 9 344.526367 0.038000 0.824100 0.919325 5.653563 0.007300 0.842800 > 10 360.048645 0.042500 0.781600 0.896747 6.008843 0.009200 0.833600 > 11 375.570892 0.050000 0.731600 0.871009 6.364122 0.006900 0.826700 > 12 391.093140 0.043400 0.688200 0.842332 6.719401 0.007100 0.819600 > 13 406.615417 0.047300 0.640900 0.811034 7.074681 0.005500 0.814100 > 14 422.137695 0.050700 0.590200 0.777508 7.429960 0.005500 0.808600 > 15 437.659943 0.047400 0.542800 0.742195 7.785239 0.005200 0.803400 > 16 453.182190 0.044100 0.498700 0.705560 8.140518 0.004900 0.798500 > 17 468.704468 0.042700 0.456000 0.668070 8.495798 0.005100 0.793400 > 18 484.226746 0.040600 0.415400 0.630176 8.851077 0.006100 0.787300 > 19 499.748962 0.034900 0.380500 0.592300 9.206356 0.004800 0.782500 > 20 515.271240 0.032200 0.348300 0.554820 9.561636 0.003600 0.778900 > 21 530.793518 0.031400 0.316900 0.518067 9.916915 0.003400 0.775500 > 22 546.315796 0.032400 0.284500 0.482320 10.272194 0.004000 0.771500 > 23 561.838013 0.023800 0.260700 0.447809 10.627474 0.004800 0.766700 > 24 577.360291 0.026100 0.234600 0.414711 10.982753 0.004500 0.762200 > 25 592.882568 0.022700 0.211900 0.383160 11.338033 0.003300 0.758900 > 26 608.404846 0.017500 0.194400 0.353244 11.693312 0.003100 0.755800 > 27 623.927063 0.018200 0.176200 0.325018 12.048591 0.003700 0.752100 > 28 639.449341 0.017400 0.158800 0.298504 12.403871 0.003800 0.748300 > 29 654.971619 0.014900 0.143900 0.273697 12.759150 0.004400 0.743900 > 30 670.493896 0.014200 0.129700 0.250569 13.114429 0.003700 0.740200 > 31 686.016113 0.014300 0.115400 0.229078 13.469708 0.002800 0.737400 > 32 701.538391 0.013100 0.102300 0.209165 13.824987 0.003800 0.733600 > 33 717.060669 0.011700 0.090600 0.190763 14.180266 0.003700 0.729900 > 34 732.582947 0.008500 0.082100 0.173798 14.535546 0.002900 0.727000 > 35 748.105164 0.008400 0.073700 0.158191 14.890825 0.003200 0.723800 > 36 763.627441 0.006800 0.066900 0.143861 15.246104 0.003300 0.720500 > 37 779.149719 0.007100 0.059800 0.130727 15.601384 0.004600 0.715900 > 38 794.671936 0.007200 0.052600 0.118707 15.956663 0.000000 0.715900 > 39 810.194214 0.005400 0.047200 0.107723 16.311943 0.000000 0.715900 > 40 825.716492 0.005400 0.041800 0.097698 16.667221 0.000000 0.715900 > 41 841.238770 0.004800 0.037000 0.088559 17.022501 0.000000 0.715900 > 42 856.761047 0.004600 0.032400 0.080237 17.377781 0.000000 0.715900 > 43 872.283264 0.003200 0.029200 0.072665 17.733059 0.000000 0.715900 > 44 887.805542 0.003400 0.025800 0.065783 18.088339 0.000000 0.715900 > 45 903.327820 0.002200 0.023600 0.059531 18.443619 0.000000 0.715900 > 46 918.850037 0.002600 0.021000 0.053855 18.798897 0.000000 0.715900 > 47 934.372314 0.002200 0.018800 0.048707 19.154179 0.000000 0.715900 > 48 949.894592 0.001900 0.016900 0.044040 19.509457 0.000000 0.715900 > 49 965.416870 0.002200 0.014700 0.039810 19.864735 0.000000 0.715900 > 50 980.939148 0.000700 0.014000 0.035979 20.220016 0.000000 0.715900 > 51 996.461365 0.002100 0.011900 0.032510 20.575294 0.000000 0.715900 > 52 1011.983643 0.000800 0.011100 0.029371 20.930573 0.000000 0.715900 > 53 1027.505981 0.000800 0.010300 0.026530 21.285854 0.000000 0.715900 > 54 1043.028198 0.001000 0.009300 0.023961 21.641132 0.000000 0.715900 > 55 1058.550415 0.001000 0.008300 0.021638 21.996410 0.000000 0.715900 > 56 1074.072754 0.000900 0.007400 0.019538 22.351692 0.000000 0.715900 > 57 1089.594971 0.000900 0.006500 0.017640 22.706970 0.000000 0.715900 > 58 1105.117310 0.000800 0.005700 0.015925 23.062248 0.000000 0.715900 > 59 1120.639526 0.000100 0.005600 0.014375 23.417530 0.000000 0.715900 > 60 1136.161743 0.000300 0.005300 0.012975 23.772808 0.000000 0.715900 > 61 1151.684082 0.000800 0.004500 0.011711 24.128086 0.000000 0.715900 > 62 1167.206299 0.000400 0.004100 0.010569 24.483368 0.000000 0.715900 > 63 1182.728516 0.000200 0.003900 0.009538 24.838646 0.000000 0.715900 > 64 1198.250854 0.000200 0.003700 0.008607 25.193924 0.000000 0.715900 > 65 1213.773071 0.000300 0.003400 0.007767 25.549206 0.000000 0.715900 > 66 1229.295410 0.000400 0.003000 0.007008 25.904484 0.000000 0.715900 > 67 1244.817627 0.000400 0.002600 0.006323 26.259762 0.000000 0.715900 > 68 1260.339966 0.000300 0.002300 0.005705 26.615044 0.000000 0.715900 > 69 1275.862183 0.000400 0.001900 0.005147 26.970322 0.000000 0.715900 > 70 1291.384399 0.000100 0.001800 0.004644 27.325600 0.000000 0.715900 > 71 1306.906738 0.000000 0.001800 0.004190 27.680882 0.000000 0.715900 > 72 1322.428955 0.000400 0.001400 0.003780 28.036160 0.000000 0.715900 > 73 1337.951172 0.000100 0.001300 0.003410 28.391438 0.000000 0.715900 > 74 1353.473511 0.000100 0.001200 0.003076 28.746719 0.000000 0.715900 > 75 1368.995728 0.000100 0.001100 0.002775 29.101997 0.000000 0.715900 > 76 1384.517944 0.000100 0.001000 0.002503 29.457275 0.000000 0.715900 > 77 1400.040283 0.000300 0.000700 0.002258 29.812557 0.000000 0.715900 > 78 1415.562500 0.000100 0.000600 0.002037 30.167835 0.000000 0.715900 > 79 1431.084839 0.000000 0.000600 0.001838 30.523113 0.000000 0.715900 > 80 1446.607056 0.000100 0.000500 0.001658 30.878395 0.000000 0.715900 > 81 1462.129272 0.000200 0.000300 0.001495 31.233673 0.000000 0.715900 > 82 1477.651611 0.000000 0.000300 0.001349 31.588951 0.000000 0.715900 > 83 1493.173828 0.000200 0.000100 0.001217 31.944233 0.000000 0.715900 > 84 1508.696167 0.000000 0.000100 0.001098 32.299511 0.000000 0.715900 > 85 1524.218384 0.000000 0.000100 0.000990 32.654789 0.000000 0.715900 > 86 1539.740601 0.000000 0.000100 0.000893 33.010071 0.000000 0.715900 > 87 1555.262939 0.000000 0.000100 0.000805 33.365349 0.000000 0.715900 > 88 1570.785156 0.000000 0.000100 0.000727 33.720627 0.000000 0.715900 > 89 1586.307373 0.000000 0.000100 0.000655 34.075909 0.000000 0.715900 > 90 1601.829712 0.000000 0.000100 0.000591 34.431187 0.000000 0.715900 > 91 1617.351929 0.000000 0.000100 0.000533 34.786469 0.000000 0.715900 > 92 1632.874146 0.000000 0.000100 0.000481 35.141747 0.000000 0.715900 > 93 1648.396484 0.000000 0.000100 0.000434 35.497025 0.000000 0.715900 > 94 1663.918701 0.000000 0.000100 0.000391 35.852306 0.000000 0.715900 > 95 1679.441040 0.000000 0.000100 0.000353 36.207584 0.000000 0.715900 > 96 1694.963257 0.000000 0.000100 0.000318 36.562862 0.000000 0.715900 > 97 1710.485474 0.000000 0.000100 0.000287 36.918144 0.000000 0.715900 > 98 1726.007812 0.000000 0.000100 0.000259 37.273422 0.000000 0.715900 > 99 1741.530029 0.000100 -0.000000 0.000234 37.628700 0.715900 0.000000 > > ----- Original Message ----- > From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> > To: "Jon Wieser" <wieser(a)uwm.edu> > Cc: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu> > Sent: Monday, December 9, 2013 5:02:41 PM > Subject: Re: [Freesurfer] qdec analysis with 2 covariates > > which file did you look in? It should have a name like > cache.th20.abs.y.ocn.dat > > On 12/09/2013 05:09 PM, Jon Wieser wrote: >> I found data for the average thickness all subjects for each cluster, but I haven't found the individual subject's thickness for each cluster. can you direct me to that data? >> Jon >> ----- Original Message ----- >> From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >> To: "Jon Wieser" <wieser(a)uwm.edu> >> Cc: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu> >> Sent: Monday, December 9, 2013 2:15:39 PM >> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >> >> It is in one of the output files. Look for the .dat file in >> mri_glmfit-sim --help >> >> On 12/09/2013 03:01 PM, Jon Wieser wrote: >>> thanks doug, >>> >>> We've run a 2x2 analysis for thickness in Qdec and want the get the average thickness value for each cluster, for each subject. >>> How can i get a table of thickness data , for feach subject in the analysis >>> Jon >>> >>> ----- Original Message ----- >>> From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>> To: freesurfer(a)nmr.mgh.harvard.edu >>> Sent: Monday, December 9, 2013 1:48:15 PM >>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>> >>> >>> Hi Jon, QDEC does not currently allow more than one covariates of >>> interest. You will have to use the command-line stream (ie, >>> mris_preproc, mri_surf2surf, mri_glmfit, mri_glmfit-sim) >>> >>> doug >>> >>> >>> On 12/05/2013 02:57 PM, Jon Wieser wrote: >>>> HI freesurfer experts >>>> >>>> I want to do an analysis in qdec with 2 groups(ADHD, and Marijuana usage) and 2 covariates(age and gender) to study the effect of these factors on cortical thickness. I can only select a covariate in the qdec gui. is there a way to select both covariates in the qdec GUI? >>>> Thanks >>>> Jon >>>> -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

1 0

multiple frames error message for recon-all
by Chan, Noel Yan-Ki,Ph.D. 10 Dec '13

10 Dec '13

Hi, I'm trying to do recon-all for a file, and it gave me this multiple frame error message: #@# MotionCor Mon Nov 25 13:11:40 EST 2013 Found 1 runs /autofs/cluster/lazar/projects/Noel/SUBJECTS_DIR/BHI_BJU-345_pre_lazar/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /autofs/cluster/lazar/projects/Noel/SUBJECTS_DIR/BHI_BJU-345_pre_lazar/mri/orig/001.mgz has 4 frames If this is a multi-frame MEMPRAGE image, use mri_concat --rms to combine echo frames. Linux compute-0-73 2.6.32-358.23.2.el6.x86_64 #1 SMP Wed Oct 16 18:37:12 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s BHI_BJU-345_pre_lazar exited with ERRORS at Mon Nov 25 13:11:47 EST 2013 For more details, see the log file /autofs/cluster/lazar/projects/Noel/SUBJECTS_DIR/BHI_BJU-345_pre_lazar/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting May I ask what should I do to solve this problem? There are actually two files which give me the same error message: BHI_BJU-345_pre_lazar (pbsjob_30) and BHI_JJA-329_pre_lazar (pbsjob_33) Thanks, Noel --- Noel Yanki Chan, PhD Department of Psychiatry Neuroscience Laboratory of Sara Lazar, PhD Harvard Medical School Massachusetts General Hospital Building 120, 2nd avenue, Suite 103 Charlestown, MA 02129 Tel: 617-643-5078 (lab) 607-229-7096 (cell)

2 1

Cortical thickness values of significant clusters
by Sinead Kelly 10 Dec '13

10 Dec '13

Dear Freesurfer users, I have just ran mri-glmfit on cortical thickness data and corrected for multiple comparisons using Monte Carlo Simulation. I have significant clusters (cwp < .05), however, when I analyse the average thickness measures from the xxx.y.ocn.dat file in SPSS, there are no significant differences between my groups. I'm not sure if I am using the correct approach to extract thickness values for the significant clusters. Thank you for your help, Sinead -- Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8

3 3

after PialEdit_tktools
by Rujing Zha 10 Dec '13

10 Dec '13

Dear all, I run "recon-all -autorecon-pial -s subjects" after editing the pial by PialEdit_tktools. However I only find "-autorecon2-pial" option in recon-all manual. So I donot know whether I should run the "recon-all -s subjects -autorecon3" to complete all the 31 stages? Thanks. All the best. 2013-12-10 Rujing Zha School of Life Science University of Science and Technology of China E-mail: zharj(a)mail.ustc.edu.cn charujing(a)gmail.com charujing123(a)163.com

3 6

Occipital cortex segmentation
by Megha K. 10 Dec '13

10 Dec '13

Dear Sir/Madam, I am using freesurfer for 3T MRI analysis of visual cortical thickness in elderly patients with ophthalmic disease. We are having a bit of trouble with the accuracy of cortical segmentation in the visual cortex (namely the pericalcarine region) as the cortex is quite thin in our patients (compared to controls). You can see in the attached image that whilst there is smooth cortical segmentation in the peri-calcarine region, the cortex is not visible to the naked eye. If you have any ideas on improving accuracy, I would be very grateful. Thanks Megha

3 2

viewing the atlas?
by Gregg, Brian E. 09 Dec '13

09 Dec '13

Hello, I'm looking for a way to view the Desikan-Killiany atlas. I'd like to open the file $FREESURFER_HOME/average/?h.curvature.buckner40.filled.desikan_killiany.gcs in Freeview (or Tkmedit, or similar) and be able to see the segmentations and segmentation names, as well as pan through all of the slices. I've searched the archives and the wiki, but I haven't found anything. Can anyone point me in the right direction please? Thanks, Brian

2 1

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Freesurfer December 2013