Freesurfer

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17 participants
30099 discussions

What is the best method to calculate cohenD or any other map of effective size with lme?
by Knut J Bjuland 09 Aug '14

09 Aug '14

Dear FreeSurfer expert I have calculated the residuals as y-x*beta as described in (Bernal-Rusiel et al., 2012). What is the best method to calculate cohenD or any other map of effective size with lme? Can I calculate cohenD as R=y-desingmatrix*Bhat cohenD=gamma./(sqrt(sum(r.^2)/df2-1)) Reference Bernal-Rusiel, J.L., et al., 2012. Statistical analysis of longitudinal neuroimage data with Linear Mixed Effects models. Neuroimage. 66C, 249-260. Best regards Knut Jørgen

1 0

Cortical Thickness Correction Factor
by David Tate 08 Aug '14

08 Aug '14

We are working on a study that includes data from multiple scanners and initial indication suggest that there may be small differences in cortical thickness measures that are scanner related (human and other phantom data were acquired at both sites). Is it possible to include a correction factor adjusting for the scanner differences when using glmfit or qdec? Thanks, David David F. Tate, Ph.D. Research Neuropsychologist Defense and Veterans Brain Injury Center Contractor, General Dynamics Information Technology Brooke Army Medical Center MCHE MDU (DVBIC) 3551 Roger Brooke Drive JSBA Ft. Sam Houston, TX 78234-4504 Office (210) 916-8090

4 4

Update to Tracula longitudinal?
by Chung, Yoonho 08 Aug '14

08 Aug '14

Dear Freesurfer Experts We decided to reprocess our T1 and DTI data with the latest stream v.5.3 – we would like to give TRACULA longitudinal stream a try. Before we go ahead and reprocess our recons and DTI data with FS v 5.3 we were wondering if you plan to release a new version of the TRACULA DTI longitudinal stream anytime soon. I think I saw somewhere in the email chain that this is likely to happen soon with additional features and bug fixes. If so, I think it would be worth a wait. Thank you! Yoon

1 0

recon-all change for lgi affects NuCorrect
by Kathy L. Pearson 08 Aug '14

08 Aug '14

When I follow the advice to prevent lgi problems with MATLAB 2013 using this update to 5.3 recon-all: For Version 5.3 change the line 6148 in recon-all from if ( ! $found_tpNid ) then to if ( ! $found_tpNid && ! $DoAddTp ) then 11 new subjects that I tested running from scratch fail in NuCorrect. When reverting to the original recon-all, the same subjects all ran to completion without error. Any suggestions on this? I am running on Redhat Linux 6.3 with MATLAB 2013a. Thanks, Kathy Pearson

1 0

Tool which will return the labels associated with a RAS vector ?
by Krieger, Donald N. 08 Aug '14

08 Aug '14

Hi, I am almost there and now need to produce what you might call an atlas for an individual. I have a large set of current source locations extracted from MEG recordings for each volunteer. They are in the individual's RAS MRI coordinates so I can easily convert them to tkr or another of the coordinate systems used by freesurfer. I then need to find or create a tool to which I can hand that vector and get back the labels which have been assigned to it. Can you see a way to do it with existing freesurfer tools, even if it's awkward? Thanks, Don

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mpr2mni305 failed error
by Francesco Deleo 08 Aug '14

08 Aug '14

I all! I am a new freesurfer user. I have a problem when I perform the recon-all -all, in about 15% of MRI scans, all made with the same scanning protocol (T1 MPRAGE in a SIEMENS Avanto 1,5 T). I can't recognize any difference between those scans which work correctly and those not. I have never found the same error on 3T MRI scans. I've already tried to add these flags to the recon-all -all command: -use-mritotal -talairach -use-mritotal -notalairach but I've always received an error message Thank you very much ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Darwin pro-di-villani.besta.local 13.3.0 Darwin Kernel Version 13.3.0: Tue Jun 3 21:27:35 PDT 2014; root:xnu-2422.110.17~1/RELEASE_X86_64 x86_64 Thanks very much for your attention Francesco Milan, Italy --------------------------------------------------------------------- FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Kernel info: Darwin 13.3.0 x86_64 --------------------------------------------------------------------- LAST LINES IN TALAIRACH_AVI.LOG parameters 9.0270 134.9373 110.8627 -84.3566 -7.5458 -11.3475 eta,q 0.95791 3.72402 0.0485 0.0470 0.0477 0.0513 0.0470 0.0452 0.0475 0.0471 0.0478 0.0513 0.0457 0.0435 0.0472 0.0472 0.0476 0.0428 0.0434 0.0415 0.0471 0.0471 0.0476 0.0435 0.0430 0.0415 0.0470 0.0478 0.0457 0.0525 0.0415 0.0430 0.0473 0.0511 0.0430 0.0548 0.0442 0.0453 0.0486 0.0426 0.0406 0.0672 0.0431 0.0503 niter,ni,del,rscale 7 3 12.0000 1.2000 imgrege: no voxels in register ERROR: 'imgreg_4dfp /Applications/freesurfer/average/711-2C_as_mni_average_305 /Applications/freesurfer/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! status=254 ERROR: mpr2mni305 execution aborted

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Compatibility Tracula v.5.3 and recon v.5.2 longitudinal
by Chung, Yoonho 08 Aug '14

08 Aug '14

1 1

Re: [Freesurfer] GLM error in QDEC - SOLUTION
by McLaughlin, Katie 07 Aug '14

07 Aug '14

Solution to the issue with QDEC being unable to find subjects in the subjects directory with the following fix: sudo mv /bin/sh /bin/sh.orig sudo ln -s /bin/bash /bin/sh Thanks, Kate ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of McLaughlin, Katie [Katie.McLaughlin(a)childrens.harvard.edu] Sent: Friday, August 01, 2014 5:45 PM To: Freesurfer support list Subject: Re: [Freesurfer] GLM error in QDEC Hi Doug, Same error when data table created in Linux There are a number of messages about this same issue in the Archive (e.g.): https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/03347… https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2008-October/008618.h… https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-February/036226… In the second message string, there is some information about bash vs sh in ubuntu potentially generating this error. However, I'm working on a cluster used by a number of others and can't use the fix described by another FS user. I'm wondering if you've resolved this using another strategy previously? Thanks, Kate Error Output: Reading /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/tktools/tkUtils.tcl Using /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/lib/tcl/fsgdfPlot.tcl Loading data table /neuro/labs/sheridanlab/projects/SAS/FreeSurfer/FS_5.3/qdec/qdec.table.maltreatment.dat... Number of columns: 8 fsid column: 1 Number of factors: 7 Number of subjects: 42 Data table /neuro/labs/sheridanlab/projects/SAS/FreeSurfer/FS_5.3/qdec/qdec.table.maltreatment.dat loaded. Verifying subject data.sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1009' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1014' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1032' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1034' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1041' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1043' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1047' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1058' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1077' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1094' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1096' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1097' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1099' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1100' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1114' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1119' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1123' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1125' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1126' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1128' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1134' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1137' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1139' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1142' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1143' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1153' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1154' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1157' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1158' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1163' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1165' in SUBJECTS_DIR Too many subjects not found! Input table: /neuro/labs/sheridanlab/projects/SAS/FreeSurfer/FS_5.3/qdec/qdec.table.maltreatment.dat Subj#, SubjID, Data... 1 1009 c 0.763636 m 0.000000 1.500000 -3.547619 348130.000000 2 1014 c 0.098336 m 0.000000 -11.500000 -10.547619 149370.000000 3 1032 c 2.507636 m 0.000000 2.500000 0.452381 -960.000000 4 1034 c 0.101136 m 0.000000 -15.500000 -11.547619 190570.000000 5 1041 m -2.516264 m 1.000000 17.500000 12.452381 -26620.000000 6 1043 m -1.453964 m 0.000000 7.500000 12.452381 205250.000000 7 1047 c -0.933764 m 0.000000 -10.500000 -0.547619 -73620.000000 8 1058 m 1.171636 f 0.000000 14.500000 7.452381 -42730.000000 9 1077 c 0.281836 f 0.000000 -16.500000 -12.547619 -40610.000000 10 1094 m 0.142136 f 0.000000 3.500000 -1.547619 -158930.000000 11 1096 c -1.711364 f 0.000000 -6.500000 -6.547619 31690.000000 12 1097 c -0.323264 f 0.000000 6.500000 0.452381 -218300.000000 13 1099 c 2.488536 m 0.000000 -14.500000 -8.547619 279160.000000 14 1100 m 1.404336 f 0.000000 9.500000 -0.547619 -77570.000000 15 1114 m -0.312264 f 0.000000 -10.500000 -12.547619 141560.000000 16 1119 m -1.374564 m 0.000000 -7.500000 18.452381 110660.000000 17 1123 m 0.988136 m 0.000000 33.500000 16.452381 -27400.000000 18 1125 c 0.287236 f 0.000000 -7.500000 -8.547619 -67320.000000 19 1126 c -1.820864 m 0.000000 -14.500000 -12.547619 348770.000000 20 1128 c -1.338964 f 0.000000 -0.500000 -6.547619 -101590.000000 21 1134 c -2.086464 f 0.000000 -4.500000 -5.547619 -42360.000000 22 1137 m 1.324936 m 0.000000 12.500000 23.452381 -108080.000000 23 1139 m 0.875936 f 0.000000 -4.500000 0.452381 -199980.000000 24 1142 m -0.851664 f 0.000000 10.500000 2.452381 -386850.000000 25 1143 m -2.820164 f 0.000000 11.500000 -13.547619 -109600.000000 26 1153 m -2.458764 f 0.000000 13.500000 10.452381 369170.000000 27 1154 m -1.234964 f 0.000000 -8.500000 -2.547619 -261410.000000 28 1157 c 1.034736 f 1.000000 -10.500000 -6.547619 -67330.000000 29 1158 m 1.163436 f 0.000000 11.500000 11.452381 -71900.000000 30 1163 m 1.371436 m 0.000000 15.500000 7.452381 239550.000000 31 1165 m -0.517664 m 1.000000 -11.500000 -2.547619 16810.000000 32 1166 m -2.302764 m 1.000000 -7.500000 1.452381 220140.000000 33 1167 m 0.292736 f 1.000000 12.500000 11.452381 -117810.000000 34 1171 c 1.385136 f 0.000000 6.500000 -7.547619 59040.000000 35 1173 c 1.075736 f 0.000000 -7.500000 2.452381 -86380.000000 36 1175 c 1.765736 f 0.000000 -1.500000 -6.547619 -31300.000000 37 1176 c 1.732836 m 0.000000 -11.500000 -3.547619 108560.000000 38 1177 m 0.717136 f 0.000000 -5.500000 10.452381 -53070.000000 39 1178 m -0.241164 f 0.000000 33.500000 15.452381 -110020.000000 40 1179 c 0.944336 f 0.000000 -7.500000 0.452381 15300.000000 41 1180 c 0.760936 f 0.000000 -18.500000 -13.547619 -97800.000000 42 1181 c -0.380764 f 0.000000 -9.500000 -7.547619 -60610.000000 1 maltreatment discrete 2 1 c 2 m 2 age_demean continuous 0 3 sex discrete 2 1 m 2 f 4 hs_less continuous 0 5 internal_demean continuous 0 6 external_demean continuous 0 7 ICV_demean continuous 0 Continuous Factors: Mean: StdDev: ------------------- ----- ------- age_demean -0.000 1.410 hs_less 0.119 0.328 internal_demean 0.000 12.769 external_demean 0.000 9.759 ICV_demean 4609.048 168177.248 Number of subjects: 42 Number of factors: 7 (2 discrete, 5 continuous) Number of classes: 4 Number of regressors: 24 ============================================================ Data table loading completed successfully. SUBJECTS_DIR is '/net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/SAS/FreeSurfer/FS_5.3' ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve(a)nmr.mgh.harvard.edu] Sent: Friday, August 01, 2014 5:31 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] GLM error in QDEC How did you create your qdec table? It looks like it might have been created on a windows machine. If so, try creating it in linux. doug On 08/01/2014 04:53 PM, McLaughlin, Katie wrote: > Hi Doug, > > The issue seems to be that qdec can't find the subjects in the SUBJECTS_DIR (see output below) when loading the data table. > > The subjects are all in the directory, however, with permissions set to 777 on all. I've found a number of previous posts with the same error, but no solution. > > Thanks, > Kate > > > Output from loading data table: > Loading data table /neuro/labs/sheridanlab/projects/SAS/FreeSurfer/FS_5.3/qdec/qdec.table.maltreatment.dat... > QdecDataTable::Load: will attempt to open as Mac text file... > Number of columns: 8 > fsid column: 1 > Number of factors: 7 > Number of subjects: 42 > > Data table /neuro/labs/sheridanlab/projects/SAS/FreeSurfer/FS_5.3/qdec/qdec.table.maltreatment.dat loaded. > Verifying subject data.sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1009' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1014' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1032' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1034' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1041' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1043' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1047' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1058' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1077' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1094' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1096' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1097' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1099' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1100' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1114' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1119' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1123' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1125' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1126' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1128' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1134' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1137' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1139' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1142' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1143' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1153' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1154' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1157' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1158' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1163' in SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1165' in SUBJECTS_DIR > Too many subjects not found! > Input table: /neuro/labs/sheridanlab/projects/SAS/FreeSurfer/FS_5.3/qdec/qdec.table.maltreatment.dat > > > ________________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve(a)nmr.mgh.harvard.edu] > Sent: Friday, August 01, 2014 4:09 PM > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] GLM error in QDEC > > So, did it generate the error when you loaded the table or when you hit > analyze? List the steps and buttons that produce this error. > doug > > On 07/31/2014 05:20 PM, McLaughlin, Katie wrote: >> Hi Doug, >> >> I'm using 5.3. >> >> This error was generated when I had more variables in the model, so I used the option within qdec to remove variables from the data table to see if that had any effect (i.e., deleted everything except one categorical variable). Still got the error you see below. >> >> Thanks, >> Kate >> >> ________________________________________ >> From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve(a)nmr.mgh.harvard.edu] >> Sent: Thursday, July 31, 2014 5:14 PM >> To: freesurfer(a)nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] GLM error in QDEC >> >> What version of FS are you using? When I load that file in 5.3 qdec, it >> creates several discrete classes, see below >> doug >> >> >> 40 1179 c 17.514000 0.944336 f 12.000000 14.000000 0.000000 >> -7.500000 0.452381 1565300.000000 15300.000000 >> 41 1180 c 17.330600 0.760936 f 1.000000 0.000000 0.000000 -18.500000 >> -13.547619 1452200.000000 -97800.000000 >> 42 1181 c 16.188900 -0.380764 f 10.000000 6.000000 0.000000 >> -9.500000 -7.547619 1489390.000000 -60610.000000 >> 1 maltreatment discrete 2 >> 1 c >> 2 m >> 2 age continuous 0 >> 3 age_demean continuous 0 >> 4 sex discrete 2 >> 1 m >> 2 f >> 5 internalizing continuous 0 >> 6 externalizing continuous 0 >> 7 hs_less continuous 0 >> 8 internal_demean continuous 0 >> 9 external_demean continuous 0 >> 10 ICV continuous 0 >> 11 ICV_demean continuous 0 >> Continuous Factors: Mean: StdDev: >> ------------------- ----- ------- >> age 16.570 1.410 >> age_demean -0.000 1.410 >> internalizing 19.500 12.769 >> externalizing 13.548 9.759 >> hs_less 0.119 0.328 >> internal_demean 0.000 12.769 >> external_demean 0.000 9.759 >> ICV 1554609.048 168177.248 >> ICV_demean 4609.048 168177.248 >> >> Number of subjects: 42 >> Number of factors: 11 (2 discrete, 9 continuous) >> Number of classes: 4 >> Number of regressors: 40 >> >> >> >> >> On 07/31/2014 02:27 PM, McLaughlin, Katie wrote: >>> Hi Doug et al, >>> >>> I'm trying to run an analysis in QDEC and continue to get an error >>> that says that the QDEC GLM design creates 0 factors. >>> >>> I'm attaching my data table here as well as the output of QDEC. I've >>> tried deleting all variables in my data file other than one and >>> testing just that comparison, but no luck. >>> >>> Any thoughts are much appreciated. >>> >>> Thanks, >>> Kate >>> >>> SUBJECTS_DIR is >>> '/net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/SAS/FreeSurfer/FS_5.3' >>> Input table: >>> /neuro/labs/sheridanlab/projects/SAS/FreeSurfer/FS_5.3/qdec/qdec.table.maltreatment.dat >>> Subj#, SubjID, Data... >>> 1 1009 c >>> 2 1014 c >>> 3 1032 c >>> 4 1034 c >>> 5 1041 m >>> 6 1043 m >>> 7 1047 c >>> 8 1058 m >>> 9 1077 c >>> 10 1094 m >>> 11 1096 c >>> 12 1097 c >>> 13 1099 c >>> 14 1100 m >>> 15 1114 m >>> 16 1119 m >>> 17 1123 m >>> 18 1125 c >>> 19 1126 c >>> 20 1128 c >>> 21 1134 c >>> 22 1137 m >>> 23 1139 m >>> 24 1142 m >>> 25 1143 m >>> 26 1153 m >>> 27 1154 m >>> 28 1157 c >>> 29 1158 m >>> 30 1163 m >>> 31 1165 m >>> 32 1166 m >>> 33 1167 m >>> 34 1171 c >>> 35 1173 c >>> 36 1175 c >>> 37 1176 c >>> 38 1177 m >>> 39 1178 m >>> 40 1179 c >>> 41 1180 c >>> 42 1181 c >>> 1 maltreatment discrete 2 >>> 1 c >>> 2 m >>> Continuous Factors: Mean: StdDev: >>> ------------------- ----- ------- >>> >>> Number of subjects: 42 >>> Number of factors: 1 (1 discrete, 0 continuous) >>> Number of classes: 2 >>> Number of regressors: 2 >>> ============================================================ >>> ERROR: QdecGlmDesign::Create: zero factors! >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> -- >> 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/ >> >> _______________________________________________ >> 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. >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > -- > 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/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- 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/ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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QdecGlmDesign::Create: zero factors!
by McLaughlin, Katie 07 Aug '14

07 Aug '14

Hi Doug et al, After solving one issue with QDEC we have run into another. I previously posted an error related to QDEC being unable to find subjects in the subjects directory. That problem was solved by updating the /bin/sh location for ubuntu (will post the solution that worked for us to the archive). The data table now loads fine, it finds all the discrete and continuous factors. However, I am still getting the following error about the GLM Design creating zero factors. See below. I can't find any info about this error in the archive. Any thoughts are much appreciated! Data table attached. Thanks, Kate Loading data table /neuro/labs/sheridanlab/projects/SAS/FreeSurfer/FS_5.3/qdec/qdec.table.maltreatment.dat... Number of columns: 8 fsid column: 1 Number of factors: 7 Number of subjects: 42 Data table /neuro/labs/sheridanlab/projects/SAS/FreeSurfer/FS_5.3/qdec/qdec.table.maltreatment.dat loaded. Verifying subject data..........................................Subject verification complete. Input table: /neuro/labs/sheridanlab/projects/SAS/FreeSurfer/FS_5.3/qdec/qdec.table.maltreatment.dat Subj#, SubjID, Data... 1 1009 0.000000 0.763636 0.000000 0.000000 1.500000 -3.547619 348130.000000 2 1014 0.000000 0.098336 0.000000 0.000000 -11.500000 -10.547619 149370.000000 3 1032 0.000000 2.507636 0.000000 0.000000 2.500000 0.452381 -960.000000 4 1034 0.000000 0.101136 0.000000 0.000000 -15.500000 -11.547619 190570.000000 5 1041 1.000000 -2.516264 0.000000 1.000000 17.500000 12.452381 -26620.000000 6 1043 1.000000 -1.453964 0.000000 0.000000 7.500000 12.452381 205250.000000 7 1047 0.000000 -0.933764 0.000000 0.000000 -10.500000 -0.547619 -73620.000000 8 1058 1.000000 1.171636 1.000000 0.000000 14.500000 7.452381 -42730.000000 9 1077 0.000000 0.281836 1.000000 0.000000 -16.500000 -12.547619 -40610.000000 10 1094 1.000000 0.142136 1.000000 0.000000 3.500000 -1.547619 -158930.000000 11 1096 0.000000 -1.711364 1.000000 0.000000 -6.500000 -6.547619 31690.000000 12 1097 0.000000 -0.323264 1.000000 0.000000 6.500000 0.452381 -218300.000000 13 1099 0.000000 2.488536 0.000000 0.000000 -14.500000 -8.547619 279160.000000 14 1100 1.000000 1.404336 1.000000 0.000000 9.500000 -0.547619 -77570.000000 15 1114 1.000000 -0.312264 1.000000 0.000000 -10.500000 -12.547619 141560.000000 16 1119 1.000000 -1.374564 0.000000 0.000000 -7.500000 18.452381 110660.000000 17 1123 1.000000 0.988136 0.000000 0.000000 33.500000 16.452381 -27400.000000 18 1125 0.000000 0.287236 1.000000 0.000000 -7.500000 -8.547619 -67320.000000 19 1126 0.000000 -1.820864 0.000000 0.000000 -14.500000 -12.547619 348770.000000 20 1128 0.000000 -1.338964 1.000000 0.000000 -0.500000 -6.547619 -101590.000000 21 1134 0.000000 -2.086464 1.000000 0.000000 -4.500000 -5.547619 -42360.000000 22 1137 1.000000 1.324936 0.000000 0.000000 12.500000 23.452381 -108080.000000 23 1139 1.000000 0.875936 1.000000 0.000000 -4.500000 0.452381 -199980.000000 24 1142 1.000000 -0.851664 1.000000 0.000000 10.500000 2.452381 -386850.000000 25 1143 1.000000 -2.820164 1.000000 0.000000 11.500000 -13.547619 -109600.000000 26 1153 1.000000 -2.458764 1.000000 0.000000 13.500000 10.452381 369170.000000 27 1154 1.000000 -1.234964 1.000000 0.000000 -8.500000 -2.547619 -261410.000000 28 1157 0.000000 1.034736 1.000000 1.000000 -10.500000 -6.547619 -67330.000000 29 1158 1.000000 1.163436 1.000000 0.000000 11.500000 11.452381 -71900.000000 30 1163 1.000000 1.371436 0.000000 0.000000 15.500000 7.452381 239550.000000 31 1165 1.000000 -0.517664 0.000000 1.000000 -11.500000 -2.547619 16810.000000 32 1166 1.000000 -2.302764 0.000000 1.000000 -7.500000 1.452381 220140.000000 33 1167 1.000000 0.292736 1.000000 1.000000 12.500000 11.452381 -117810.000000 34 1171 0.000000 1.385136 1.000000 0.000000 6.500000 -7.547619 59040.000000 35 1173 0.000000 1.075736 1.000000 0.000000 -7.500000 2.452381 -86380.000000 36 1175 0.000000 1.765736 1.000000 0.000000 -1.500000 -6.547619 -31300.000000 37 1176 0.000000 1.732836 0.000000 0.000000 -11.500000 -3.547619 108560.000000 38 1177 1.000000 0.717136 1.000000 0.000000 -5.500000 10.452381 -53070.000000 39 1178 1.000000 -0.241164 1.000000 0.000000 33.500000 15.452381 -110020.000000 40 1179 0.000000 0.944336 1.000000 0.000000 -7.500000 0.452381 15300.000000 41 1180 0.000000 0.760936 1.000000 0.000000 -18.500000 -13.547619 -97800.000000 42 1181 0.000000 -0.380764 1.000000 0.000000 -9.500000 -7.547619 -60610.000000 1 maltreatment continuous 0 2 age_demean continuous 0 3 sex continuous 0 4 hs_less continuous 0 5 internal_demean continuous 0 6 external_demean continuous 0 7 ICV_demean continuous 0 Continuous Factors: Mean: StdDev: ------------------- ----- ------- maltreatment 0.500 0.506 age_demean -0.000 1.410 sex 0.619 0.492 hs_less 0.119 0.328 internal_demean 0.000 12.769 external_demean 0.000 9.759 ICV_demean 4609.048 168177.248 Number of subjects: 42 Number of factors: 7 (0 discrete, 7 continuous) Number of classes: 1 Number of regressors: 8 ============================================================ Data table loading completed successfully. SUBJECTS_DIR is '/net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/SAS/FreeSurfer/FS_5.3' ERROR: QdecGlmDesign::Create: zero factors!

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Post-doctoral position in cognitive neurophysiology/epilepsy
by Pierre Mégevand 07 Aug '14

07 Aug '14

The Laboratory for Multimodal Human Brain Mapping, at New York’s Feinstein Institute for Medical Research, has an immediate opening for a postdoctoral fellow with interests in epilepsy, cognitive neuroscience, and functional connectivity. The lab uses human intracranial EEG, direct electrical stimulation of the brain, and functional MRI to study: (1) neural mechanisms of cognitive abilities such as attention, visual processing, and language; (2) extent and dynamics of macroscale functional networks in the human brain; (3) how to improve the identification of functional and pathological brain regions in individuals suffering from epilepsy. The fellow will be involved in all aspects of experimental design, data collection and analysis, and publication of research. In addition, they will have extensive opportunities for work with colleagues in collaborating groups, including researchers at Columbia University, Albert Einstein College of Medicine, Child Mind Institute, and Nathan Kline Institute (all in New York), and the Weizmann Institute of Science in Israel. Candidates should have a background in at least one of the major techniques used in the lab: neurophysiology (EEG/MEG), neuroimaging (structural and functional MRI), or brain stimulation (direct electrical stimulation, TMS, tDCS/ACS). Additional experience in another of these techniques would be a plus. Strong programming skills (especially in the MATLAB environment) are required. Candidates with Ph.D. and/or M.D. degrees are welcome to apply. For more information about the lab, please visit: http://www.feinsteininstitute.org/faculty/ashesh-mehta-md-phd/ Interested candidates should submit CV and brief statement of interest to Dr. Ashesh Mehta at amehta(a)nshs.edu.

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