Freesurfer August 2014

freesurfer@nmr.mgh.harvard.edu

146 participants
208 discussions

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

2 4

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

3 6

Compatibility Tracula v.5.3 and recon v.5.2 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 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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PhD-position Research Centre Juelich
by Jacobs H (NP) 07 Aug '14

07 Aug '14

With a staff of 4700, Forschungszentrum Jülich – a member of the Helmholtz Association – is one of the largest interdisciplinary research centres in Europe. Work with us on the grand challenges in the fields of health, energy & environment, and information technology, as well as on the many and varied tasks of research management. The Institute for Neuroscience and Medicine (INM) explores the structure and function of the brain in healthy people and in patients with neurological and psychiatric diseases. It conducts translational research with the aim to establish new procedures for the prevention, diagnosis and treatment of these diseases. The Cognitive Neuroscience Division of the Institute for Neuroscience and Medicine (INM-3, director: Prof. G. R. Fink) cooperates closely with the Department of Neurology at the University Hospital of Cologne in order to investigate fundamental as well as clinical neuroscience questions. For the INM-3 we are currently seeking a Ph.D. Student (f/m) in neuropsychology or neuroscience Your tasks: You will work on scientific projects focused on multi-modal longitudinal network mapping and modulating network breakdown in older individuals and patients with early Alzheimer’s disease (funded by the DFG). This work will be performed within the spatial cognition group and the Memory Clinic Köln-Jülich. Together with Dr. Jacobs and a team of neuropsychologists and medical doctors you will be trained in all research and organization aspects, ranging from data acquisition (neuropsychological assessments, MRI-PET scanning, cognitive and tDCS interventions) data analysis and writing. Your profile: A master’s degree neuropsychology or psychology Experience in neuropsychological assessment Experience with and interest in patients with cognitive deficits and dementia Experience in neuroimaging ((f)MRI) Experience with statistical analysis of data (SPSS), neuroimaging software packages (e.g., SPM, FSL) and programming languages (Matlab, UNIX) Mother tongue: German In-depth knowledge of spoken and written English Good interpersonal skills. Our offer: Challenging and varied work in an interdisciplinary and international team A wide spectrum of individual training opportunities A three year doctorate programme including salary conforming to salary grade 13 of the Collective Agreement for the German Civil Service (TVöD). Forschungszentrum Jülich aims to employ more women in this area and therefore particularly welcomes applications from women. We also welcome applications from disabled persons. Please submit your enquiries and application quoting the reference number D095/2014 to: Dr. Heidi Jacobs, INM-3 Email: h.jacobs(a)fz-juelich.de Phone: (+ 49) 02461-61-3441 See als: www.fz-juelich.de

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extending the pial line in scans with low signal
by Christine Smith 07 Aug '14

07 Aug '14

Hello, I am working with some scans that have poor signal, particularly at the lateral aspects of the cortex (i.e., lateral temporal lobes). The measures of the cortical volumes for each of the lobes of the brain are reduced by 2-4 standard deviations in these healthy subjects compared to scans collected from healthy subjects at a different scanner. The measures of white matter for the lobes appears to be ok. To show you the problem, I have attached two pictures. The first is of the surfaces as they come out of freesurfer (reference.jpg). The second is the same slice if you increase the brightness of the image to highlight that the signal is so low in some cortex (e.g., lateral temporal lobes) that it appears 'black' and absent with the default brightness/contrast settings in tkmedit. This missing cortex is visible at high brightness and low contrast (reference_lowcontrasthighbright.jpg). We have been using several commands that have an effect on the pial line based on an earlier request for help. recon-all -seg-ghi ## -autorecon2 -autorecon3 -s SUBJECT_ID OR recon-all -seg-wlo ## -autorecon2 -autorecon3 -s SUBJECT_ID seg-ghi: maximum for gm at border with wm seg-wlo: minimum for wm at border with gm We found that a ghi value of 60 captures all the grey matter that we were missing (see ghi60.jpg). However, for the superior part of the scans (i.e., above the temporal lobes), it also extends out the white matter such that sulci are missing or too shallow. This means that the grey matter is also very thin. Combining seg-ghi and seg-wlo commands in the same call was not the solution: recon-all -seg-ghi 60 -seg-wlo 60 -autorecon2 -autorecon3 -s SubjectID The resultant image had the same problems with the white matter. I have examples of the scans after seg-ghi 60 alone, seg-wlo 60 alone, and both commands together, if these would be useful. We have experimented with changing the values after each these commands and had had little success identifying how they talk to each other and what the magic combination of values might be, if it exists. If these weren't scans from patients who were very difficult to scan in the first place, I would love to just forget about them. However, these scans are precious to us and may not be able to be reacquired. Thus, I am employing heroic efforts to salvage usable data from them. I am open to a solution that might come from two separate runs of freesurfer: one to get the white matter boundary (as it appears in the reference scan attached) and one to get the pial boundary (as it appears after using seg-ghi 60 alone); if this is a reasonable course of action. Thank you for any support you may provide. Best, Christine -- Christine N. Smith, Ph.D. Department of Psychiatry University of California, San Diego

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Re: [Freesurfer] Need help with mris_convert
by Tara Miskovich 07 Aug '14

07 Aug '14

Thank you for the help Bruce. I really appreciate it! So if we have a custom made label to we need to somehow add it to the FreeSurferColorLUT.txt. mris_convert --label lh.cluster1.label lh.white lh.cluster1.label.gii The above is not working for me. I keep getting no errors or anything, just the usage in the terminal. Thanks again! Tara On Thu, Aug 7, 2014 at 12:51 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > p.s. oh, and lh.white is so that we have a surface. The label is just a > (small) set of points on the surface, and doesn't contain other information > needed to generate a surface (like connectivity) > > On Thu, 7 Aug 2014, Tara Miskovich wrote: > > Hi Doug thank you for the response. I just wasn't sure what was required >> here. Specifically why we need to call on the white matter surface. And >> what >> the second V1 would be for. >> Thank you, >> Tara >> [cleardot.gif] >> >> >> >> On Thu, Aug 7, 2014 at 11:05 AM, Tara Miskovich <miskovi2(a)uwm.edu> wrote: >> Hi all, >> >> I could really use some help with this >> >> I am trying to convert a group cluster to GIFTI (.gii) format. I just >> need some help running mris_convert. >> >> The example for a label to GIFTI is >> >> mris_convert --label lh.V1.label V1 lh.white lh.V1.label.gii >> >> I'm trying to figure out what is required here. I understand I put in >> the label after label and the output at the end, but in this example I >> am not sure what the V1 and lh.white are for. >> >> Thanks, >> Tara >> >> >> >> >> > _______________________________________________ > 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. > >

2 2

Need help with mris_convert
by Tara Miskovich 07 Aug '14

07 Aug '14

Hi all, I could really use some help with this I am trying to convert a group cluster to GIFTI (.gii) format. I just need some help running mris_convert. The example for a label to GIFTI is mris_convert --label lh.V1.label V1 lh.white lh.V1.label.gii I'm trying to figure out what is required here. I understand I put in the label after label and the output at the end, but in this example I am not sure what the V1 and lh.white are for. Thanks, Tara

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Freesurfer August 2014