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Dear freesurfer experts
I got an error that I don't understand when running mri_glmfit on
cortical volume in the right hemisphere. I only have one group and one
covariate of interest (+ age and ICV).
ERROR: dimension mismatch between y and X. y has 102 inputs, X has 105 rows.
I attached the log, fsgd and mtx files. I included 105 subjects and I
don't get any errors when running the same command for surface area or
cortical thickness. I can run my analysis for cortical volume in the
left hemisphere, but not in the right hemisphere. The error message
sounds like there is data missing for 3 subjects, but as far as I can
see, that is not the case.
Thanks a lot for you help,
Meike
x $ mri_glmfit --y rh.resilience_extra.volume.10.mgh --fsgd
resilience_WMC2_extra.fsgd --C resilience.mtx --surf fsaverage rh --cortex
--glmdir rh.resilience_WMC2_extra.volume.10.glmdir
gdfRead(): reading resilience_WMC2_extra.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 resilience 5.89838e-10 0.995227
1 ICV -3.20198e-09 0.995227
2 Age -4.87836e-10 0.995227
Class Means of each Continuous Variable
1 1 0.0000 -0.0000 -0.0000
INFO: gd2mtx_method is dods
Reading source surface
/data/Psychiatrie/Meike_Hettwer/CTFreesurfer/WMC2_new_n4/fsaverage/surf/rh.white
Number of vertices 163842
Number of faces 327680
Total area 65020.839844
AvgVtxArea 0.396851
AvgVtxDist 0.717994
StdVtxDist 0.193566
$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $
cwd /data/Psychiatrie/Meike_Hettwer/CTFreesurfer/WMC2_new_n4
cmdline mri_glmfit.bin --y rh.resilience_extra.volume.10.mgh --fsgd
resilience_WMC2_extra.fsgd --C resilience.mtx --surf fsaverage rh --cortex
--glmdir rh.resilience_WMC2_extra.volume.10.glmdir
sysname Linux
hostname beo-05
machine x86_64
user mhettwer
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y
/data/Psychiatrie/Meike_Hettwer/CTFreesurfer/WMC2_new_n4/rh.resilience_extra.volume.10.mgh
logyflag 0
usedti 0
FSGD resilience_WMC2_extra.fsgd
labelmask
/data/Psychiatrie/Meike_Hettwer/CTFreesurfer/WMC2_new_n4/fsaverage/label/rh.cortex.label
maskinv 0
glmdir rh.resilience_WMC2_extra.volume.10.glmdir
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory rh.resilience_WMC2_extra.volume.10.glmdir
Loading y from
/data/Psychiatrie/Meike_Hettwer/CTFreesurfer/WMC2_new_n4/rh.resilience_extra.volume.10.mgh
... done reading.
INFO: gd2mtx_method is dods
Saving design matrix to rh.resilience_WMC2_extra.volume.10.glmdir/Xg.dat
Computing normalized matrix
Normalized matrix condition is 1.21685
Matrix condition is 1.21685
Found 149926 points in label.
Pruning voxels by thr: 1.175494e-38
Found 148496 voxels in mask
Saving mask to rh.resilience_WMC2_extra.volume.10.glmdir/mask.mgh
Reshaping mriglm->mask...
search space = 73652.696318
ERROR: dimension mismatch between y and X.
y has 102 inputs, X has 105 rows.
GroupDescriptorFile 1
Title PRS_Resilience
Class 1
Variables resilience ICV Age
Input AHCV569656773_n4_new 1 0.214475017 1.123836081
-0.012343647
Input AQYL698766354_n4_cp 1 -0.305553767 -0.169229625
-0.094330049
Input AYNU469696773_n4_cp 1 -0.814803224 -0.527589517
1.540746284
Input AZWC558757673_n4_cp 1 -0.574549034 0.110340896
-0.104214934
Input CDJQ786727374_n4_cp 1 -1.295276001 -0.121493023
-1.024090737
Input CHYZ756726874_n4_cp 1 -1.151161028 0.05896391
-0.134451054
Input CNYT776972662_n4_cp 1 0.283888942 1.115265896
1.462248665
Input CXPW262758891_n4_cp 1 -0.999725489 0.94990239
0.907532156
Input CZQH786657554_n4_cp 1 -0.021018143 0.215710096
-0.037346592
Input DQMC896637794_n4_cp 1 0.151328335 0.075885608
-0.06118661
Input DWCQ768368772_n4_cp 1 -1.672750997 1.07263755
0.067898364
Input DYLC826827094_n4_cp 1 1.204373848 0.40193051
1.200589934
Input DYPC658856264_n4_cp 1 0.710046941 -0.604637988
-0.557756734
Input DZPY656896364_n4_cp 1 -1.25762412 -0.606839953
-1.116543489
Input EGRV896726594_n4_cp 1 -0.119147508 -0.547182955
-0.350755605
Input EJGV987707364_n4_cp 1 -0.425322682 -1.131480748
-0.618810437
Input EJLV757886434_n4_cp 1 -1.007898284 0.479259536
-0.38331758
Input EQKU788592662_n4_cp 1 1.270626665 3.32491354
-0.840348162
Input EZAU289796873_n4_cp 1 -0.285096572 0.369238612
0.243500445
Input FJNY797766834_n4_cp 1 0.072270438 -1.885683795
0.597030463
Input FUJV857836364_n4_cp 1 -0.06910242 0.078881868
-1.01246146
Input FVCE685822782_n4_cp 1 1.29394646 -0.160247292
-1.145035217
Input GUDE675880772_n4_cp 1 -0.747853129 0.155127091
-0.298423859
Input GUJE762468872_n4_cp 1 -0.268003574 -0.138218313
0.287691697
Input GUPA882596672_n4_cp 1 2.021487555 -0.373653693
-0.386224899
Input GWDH788323782_n4_cp 1 0.9169366 1.149378748
0.246989228
Input HEYR886727394_n4_cp 1 -0.878587654 -0.232537718
0.383633232
Input HPQD958606844_n4_cp 1 2.069209521 -1.265051998
-1.086307369
Input HYJF798340782_n4_cp 1 -0.279308708 0.091741672
-0.104214934
Input HZRN738628544_n4_cp 1 -0.392701002 0.124374255
-0.200737933
Input JATV880839721_n4_cp 1 1.639938836 0.502912517
-0.286213118
Input JREM395766763_n4_cp 1 -0.001246832 -1.633940706
-0.344359502
Input JRML738737673_n4_cp 1 1.371662495 0.014206042
-1.212485023
Input JTPL756766894_n4_cp 1 -0.254851279 -0.417275188
0.212682861
Input KCHV761269872_n4_cp 1 -0.000863158 1.072262035
2.82403699
Input KUHM077727831_n4_cp 1 1.369626204 3.047312264
0.241756054
Input KXUY389886721_n4_cp 1 -0.091312495 0.307453791
-0.2623731
Input KXYM874658711_n4_cp 1 0.187976738 -0.871043061
-0.410646381
Input LARF856726494_n4_cp 1 1.07678619 -1.556346636
-0.055371971
Input LFTG757786884_n4_cp 1 -1.524328167 -0.774109058
-1.136894723
Input LHTE862658791_n4_cp 1 -0.020652129 -0.421434837
0.31385757
Input LYKG679298772_n4_cp 1 0.623774437 -0.00813735
-0.257721389
Input LZKF883292862_n4_cp 1 -1.540691701 0.108161176
-0.296098003
Input MCKL757716834_n4_cp 1 -0.146972837 0.354907047
2.396661064
Input MCZQ886627594_n4_cp 1 0.97489984 0.133800569
0.865085296
Input MFNR295796863_n4_cp 1 -0.154565706 -0.654345451
-0.28505019
Input MJEL583796663_n4_cp 1 -0.35855716 0.565100077
-0.1867828
Input MXHP785667773_n4_cp 1 0.9130597 0.304890138
-0.908379432
Input NMEF773973662_n4_cp 1 -0.515639855 1.742116131
-0.4135537
Input NMKU685893762_n4_cp 1 0.757169043 -1.034108723
-0.718822219
Input NQKY679585772_n4_cp 1 0.796404041 -0.627486942
0.012659299
Input NXDY776931672_n4_cp 1 0.9636474 0.852461376
-0.334474617
Input NXRC384658821_n4_cp 1 -0.71590879 -0.912429726
-0.537405499
Input PCGW757786234_n4_cp 1 0.01001102 -0.413293987
-0.139102765
Input PERU788768304_n4_cp 1 -1.158236635 2.004061748
0.227800921
Input PFEQ756886394_n4_cp 1 0.612635647 -0.579173789
-0.228066733
Input PNYK756756854_n4_cp 1 0.416965386 -0.38569538
-1.140383506
Input PWTJ280658801_n4_cp 1 -0.453248842 -0.18164693
-0.241440402
Input QHXZ688697544_n4_cp 1 0.280801606 1.401362539
-1.058397104
Input QTME466727891_n4_cp 1 -0.908110034 -1.988317649
-0.044324158
Input QTNA779757651_n4_cp 1 -0.309062091 0.673639613
-0.978736557
Input QYKX988707344_n4_cp 1 0.141612584 -0.659666663
-0.986295587
Input RHDZ353787873_n4_cp 1 -0.714034285 0.141916218
-1.568340896
Input RHPJ853767673_n4_cp 1 -0.795777899 0.932862895
-1.077585411
Input RJAL478657781_n4_cp 1 0.597224319 0.072603728
-0.15189497
Input RKPD374788711_n4_cp 1 -1.552460833 1.193801647
0.926138999
Input RLEW382657741_n4_cp 1 0.039326609 -1.616380576
-1.265979697
Input RPCU886627594_n4_cp 1 -0.725901401 -0.498628158
0.991844414
Input TPKX883787673_n4_cp 1 0.744971803 -1.100067197
0.490041115
Input TRDZ677787364_n4_cp 1 -1.021507455 0.441467989
3.145005032
Input TRHN765229872_n4_cp 1 1.092584895 -0.714619655
0.685994431
Input TXUF778360772_n4_cp 1 0.549347117 0.313000155
-0.437975181
Input UFTC862758791_n4_cp 1 -0.620110805 -0.132714393
0.278388276
Input UVKJ647677934_n4_cp 1 0.640306594 0.571713468
-0.221089167
Input UZAQ212896873_n4_cp 1 -0.495078979 0.005513699
2.115232563
Input VHKD298796863_n4_cp 1 -1.044029995 -1.156149549
-0.017576821
Input VJNY758716424_n4_cp 1 -0.399902792 -1.512644523
0.052780304
Input VKRA857806374_n4_cp 1 0.025936761 -0.216129045
-0.09607444
Input VTAL657756854_n4_cp 1 -0.241978692 -1.7769201
1.079063991
Input VYXF727688994_n4_cp 1 0.913568417 2.799542237
-0.993273154
Input WAHE896726394_n4_cp 1 -0.617517945 -1.07135912
0.659828558
Input WANR758766854_n4_cp 1 -1.637567219 -0.930355815
-0.084445164
Input WATQ927608964_n4_cp 1 0.816931876 -0.493643494
-1.099099573
Input WAXK898746834_n4_cp 1 0.590031644 1.079353725
2.105929141
Input WAZN896726594_n4_cp 1 -1.050624514 -1.225068875
3.06301863
Input WCKG756716254_n4_cp 1 1.691511498 0.027018129
0.868574079
Input XMRA873588672_n4_cp 1 3.021395518 0.669969869
1.213963603
Input XMUK868647924_n4_cp 1 -1.694396812 0.90078578
-1.0729337
Input XQDV866726994_n4_cp 1 -0.551226105 1.494158757
0.912765331
Input XWPR897746364_n4_cp_new 1 1.251229059 -0.362751192
0.190005771
Input YALJ895796763_n4_cp_new 1 -0.312210951 -0.496603684
-1.126428374
Input YNQA807809474_n4_cp 1 -0.404881153 1.323993714
-0.717077827
Input YVEZ685897772_n4_cp 1 -0.659716375 -0.686882309
-0.089678338
Input ZDLA787786884_n4_cp 1 -1.774948388 1.527570185
-0.146080331
Input ZDRX886627554_n4_cp 1 2.79958929 -0.515171482
-0.704285622
Input AGHJ896736894_n4_cp 1 0.680390118 -0.879698724
3.011849812
Input DXRE677687584_n4_cp 1 -0.780844241 -0.965078825
0.071968611
Input HFWU778321782_n4_cp 1 -0.542861046 0.272308446
-1.617183859
Input QUMH225696883_n4_cp 1 -0.352973238 1.076906618
-1.119450808
Input TNJX757786834_n4_cp 1 -1.0851432 -1.556719108
-0.556012342
Input UEML668697934_n4_cp 1 0.72178702 0.442231054
0.698786636
Input UNYR782592662_n4_cp 1 -2.149077133 -0.87414366
1.386076901
Input VHUL858746124_n4_cp 1 1.085959898 -0.02305668
-1.038627333
Input XDVN857826324_n4_cp 1 0.877626976 0.193832087
-0.828137422
Input ZQGT756766894_n4_cp 1 1.459221603 0.22449913
0.081853496
0 1 0 0
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