Did it create the output folder and some output files? I noticed that
there is a "error: No such file or directory" error ....
On 2/14/2022 8:46 PM, 정현우 wrote:
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Hi Dr. Greve,
Thank you for your reply. I attached the fsgd file, mtx file and the
Xg.dat file below.
Hyunwoo Jeong
2022년 2월 15일 (화) 오전 1:21, Douglas N. Greve
<dgr...@mgh.harvard.edu>님이 작성:
can you send your fsgd file and the Xg.dat file?
On 2/14/2022 1:21 AM, 정현우 wrote:
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Hello FreeSurfer Developers,
I'm attempting to compare cortical surface area among three
groups while controlling for estimated total intracranial volume
(eTIV), as described on the Surface Based Group Analysis tutorial
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I ran the following command:
mri_glmfit --y three_group_comparison.area.lh.10.mgh --fsgd
three_group_comparison.area.fsgd dods --C
three_group_comparison.area.mtx --surf fsaverage lh --cortex
--glmdir three_group_comparison.area.lh.glmdir --eres-save
Then I got the following error:
gdfRead(): reading three_group_comparison.area.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 eTIV 1.53351e+06 139455
Class Size and Means of each Continuous Variable
1 0 42 1566070.5417
2 1 34 1515147.1360
3 2 15 1483959.5000
INFO: gd2mtx_method is dods
Reading source surface
/media/sjkim/hd2/subject_data/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces 327680
Total area 65417.000000
AvgVtxArea 0.399269
AvgVtxDist 0.721953
StdVtxDist 0.195472
7.2.0
cwd /media/sjkim/hd2/subject_data/glm
cmdline mri_glmfit --y three_group_comparison.area.lh.10.mgh
--fsgd three_group_comparison.area.fsgd dods --C
three_group_comparison.area.mtx --surf fsaverage lh --cortex
--glmdir three_group_comparison.area.lh.glmdir --eres-save
sysname Linux
hostname sjkim-System-Product-Name
machine x86_64
user sjkim
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y
/media/sjkim/hd2/subject_data/glm/three_group_comparison.area.lh.10.mgh
logyflag 0
usedti 0
FSGD three_group_comparison.area.fsgd
labelmask
/media/sjkim/hd2/subject_data/fsaverage/label/lh.cortex.label
maskinv 0
glmdir three_group_comparison.area.lh.glmdir
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory three_group_comparison.area.lh.glmdir
Loading y from
/media/sjkim/hd2/subject_data/glm/three_group_comparison.area.lh.10.mgh
... done reading.
INFO: gd2mtx_method is dods
Saving design matrix to three_group_comparison.area.lh.glmdir/Xg.dat
Computing normalized matrix
Normalized matrix condition is 833.575
Matrix condition is 1e+08
Found 149955 points in label.
Pruning voxels by thr: 1.175494e-38
Found 149953 voxels in mask
Saving mask to three_group_comparison.area.lh.glmdir/mask.mgh
Reshaping mriglm->mask...
search space = 74612.059149
DOF = 85
Starting fit and test
Fit completed in 0.0373833 minutes
Computing spatial AR1 on surface
Residual: ar1mn=0.997826, ar1std=0.000886, gstd=8.674183,
fwhm=20.426140
Writing results
three_group_comparison.area
maxvox sig=3.0263 F=7.57212 at index 107440 0 0
seed=1645215319
error: No such file or directory
error: MatrixMultiplyD(): m2 is null
break
/home/rd521/space_freesurfer/build/docker_ubuntu18/trunk/rd521-7.2.0/utils/matrix.cpp:596
I used FreeSurfer version 7.2.0 and Ubuntu 20.04.
I've searched the mail archives and similar errors have been
reported in qdec, but I could not find any specific solution for
this problem. Do you have any suggestions to solve this problem?
Thank you in advance,
Hyunwoo Jeong
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