The problem is that your design matrix is badly scaled. The eTIV values
are much larger than the group membership (value=1). Try subtracting the
mean of the eTIV and dividing by the stddev to normalize it.
On 2/25/2022 8:07 PM, 정현우 wrote:
External Email - Use Caution
Hi Dr. Greve,
Thank you for your response. I uploaded the .mgh, .fsgd, and .mtx
files that I used to run the mri_glmfit command. I can upload
the recon-all outputs of the individual samples as well, if needed.
The files are uploaded in google drive, please access them via the
link below.
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"secure-web.cisco.com" claiming to be*
https://drive.google.com/drive/folders/1QNzMxJdmc7Bo1KGlh9OC9f7DVzZ9ej2k?usp=sharing
<https://secure-web.cisco.com/1dyd7-xjzX4Lq_6TpVFINCBx2OzGb31QOy2b8WE4RlFK-rQW7JTWTbadgXYRKAnzQhyfbYr9ZYTmLKlwKzSSQ4tMlXDsMkhJgQ181lHtFxzXgb_Dry1feAP8aKFqOXA1x-F4FuNAsaU8BolN83rf62nnKC8adsct_OhZVZYRMXe1RciKtM0FCMjooYYAmkUm3qRc7PDz8BtLyoRaBXtfZE5nsVlYanmwZSr2cbx0n4upHQjEdEUkJRoX-4GMRt5qLHTNxfJ1mrN8SJ3vMTeBuBdNo8CCqaFKBm3Lb0rAycL-Ir-ihasFHFqKxRhpfCxVCNtXsrjGigkWr7ym9LaK0nw/https%3A%2F%2Fdrive.google.com%2Fdrive%2Ffolders%2F1QNzMxJdmc7Bo1KGlh9OC9f7DVzZ9ej2k%3Fusp%3Dsharing>
Thank you in advance,
Hyunwoo Jeong.
2022년 2월 26일 (토) 오전 8:16, Douglas N. Greve
<dgr...@mgh.harvard.edu>님이 작성:
Can you upload the data to me somewhere? I'd need the input volume
and the fsgd and any contrasts
On 2/21/2022 10:24 PM, 정현우 wrote:
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Hi Dr. Greve,
Thank you for your suggestion. Unfortunately, the same problem
occurred when I ran the command with --no-pcc. Folders and files
with the same names were created. and the following error message
(identical to the previous one) appeared.
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
Do you have any other suggestions? I appreciate your help so far.
Best,
Hyunwoo Jeong
2022년 2월 17일 (목) 오전 10:18, 정현우 <hwj418...@gmail.com>님이
작성:
Hi Dr. Greve,
Thank you for your suggestion. Unfortunately, the same
problem occurred when I ran the command with --no-pcc.
Folders and files with the same names were created. and the
following error message (identical to the previous one) appeared.
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
Do you have any other suggestions? I appreciate your help so far.
Best,
Hyunwoo Jeong
2022년 2월 17일 (목) 오전 1:41, Douglas N. Greve
<dgr...@mgh.harvard.edu>님이 작성:
It looks like it is failing when computing the partial
correlation coef. Try running it with --no-pcc
On 2/16/2022 10:53 AM, 정현우 wrote:
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Hi Dr. Greve,
Yes, it seems like the output folder and some output
files were created.
After running the mri_glmfit,
'three_group_comparison.area.lh.glmdir' folder was
created. In the glmdir folder,
'three_group_comparison.area' folder was created, and
the following files were also created: beta.mgh,
dof.dat, eres.mgh, fwhm.dat, mask.mgh, mri_glmfit.log,
rstd.mgh, rvar.mgh, sar1.mgh, surface, and Xg.dat.
In the 'three_group_comparison.area' folder, the
following files were created: C.dat, F.mgh, gamma.mgh,
maxvox.dat, sig.mgh, and z.mgh.
Do you have any idea what could have been the problem?
Thanks,
Hyunwoo Jeong
2022년 2월 17일 (목) 오전 12:36, Douglas N. Greve
<dgr...@mgh.harvard.edu>님이 작성:
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:
External Email - Use Caution
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 (*MailScanner has detected a possible
fraud attempt from "secure-web.cisco.com"
claiming to be*
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisV6.0
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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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