Can you send the mri_glmfit.log file from your mri_glmfit run?
Can you run mri_glmfit-sim with --debug as the first option and capture
and send the output?
On 6/23/2021 4:42 AM, juergen.haen...@upd.unibe.ch wrote:
External Email - Use Caution
Dear FS experts
I have run stats using mri_glmfit (FS 7.1.1 on Mac) with the following
command
mri_glmfit --y IPS_2groups_n135_lh_thickness.10.mgh --fsgd
IPS_fsgd_2groups.txt --glmdir IPS_2groups_n135_Thickness_LH.glmdir
--surf fsaverage lh --C IPS_2groups.mat --cortex
and everything worked fine. When trying to run simulations with
mri_glmfit-sim with the following command
mri_glmfit-sim --glmdir IPS_2groups_n135_Thickness_LH.glmdir --sim
mc-z 500 1.302 lh_mc-z.abs_500p1.3 --sim-sign abs --overwrite
--cwpvalthresh 0.25
the following error occurred
Loading y from
/Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135/--perm-force
error: mri_read(): couldn't determine type of file
/Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135/--perm-force
... done reading.
ERROR: loading y
/Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135/--perm-force
The entire output is shown below.
I do not understand why after the —y option in the command reported by
FS in the terminal, i.e.
mri_glmfit --C
IPS_2groups_n135_Thickness_LH.glmdir/tmp.mri_glmfit-sim-96372/IPS_2groups.mtx
--sim mc-z 500 1.302
IPS_2groups_n135_Thickness_LH.glmdir/csd/lh_mc-z.abs_500p1.3.j001
--sim-sign abs --fwhm 14.598750 --fsgd
IPS_2groups_n135_Thickness_LH.glmdir/y.fsgd dods --mask
IPS_2groups_n135_Thickness_LH.glmdir/mask.mgh --y --perm-force --surf
fsaverage lh white
the input file (IPS_2groups_n135_lh_thickness.10.mgh) is missed and
hence the following option —perm-force is interpreted as input file.
How can I fix this problem?
Thanks in advance for any advise
Regards
Jürgen
---------------------------------------------------
entire output:
[upddkp224:average_IPS_FS7_Linux/stats/glm_group_n135] jurgenhanggi%
mri_glmfit-sim --glmdir IPS_2groups_n135_Thickness_LH.glmdir --sim
mc-z 500 1.302 lh_mc-z.abs_500p1.3 --sim-sign abs --overwrite
--cwpvalthresh 0.25
cmdline mri_glmfit --y IPS_2groups_n135_lh_thickness.10.mgh --fsgd
IPS_fsgd_2groups.txt --glmdir IPS_2groups_n135_Thickness_LH.glmdir
--surf fsaverage lh --C IPS_2groups.mat --cortex
SURFACE: fsaverage lh
log file is
IPS_2groups_n135_Thickness_LH.glmdir/lh_mc-z.abs_500p1.3.mri_glmfit-sim.log
cd
/Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135
/Applications/freesurfer/bin/mri_glmfit-sim
--glmdir IPS_2groups_n135_Thickness_LH.glmdir --sim mc-z 500 1.302
lh_mc-z.abs_500p1.3 --sim-sign abs --overwrite --cwpvalthresh 0.25
FreeSurferEnv.csh 7.1.1
Wed Jun 23 10:19:19 CEST 2021
Darwin upddkp224.unibe.ch
<http://secure-web.cisco.com/1kqev2VghLiWSg5kIlxOKq_VbJZc9JK-pk9pBXL8_xh9udahFBCv8EvuJ9GuriYfcowB1DAoh5MAMRkYqUO02V_5nmE4VP10JT85LV5FW_dqPd3gGa14VqqkgWLHu9xxCHFT7s8bFskBPK-8PML54WB77N_8bUtYd1r3Qh3VZu7eaRw1teNI4YSlpPAPOHZOvFY8TRdxlfSUjQd7VN9nd_7zJRz4srPlQzrTlohVaHWsmlRNB9lVm4YVYKBaKL7JtQp2863TnS1zUJjRGu3rV-A/http%3A%2F%2Fupddkp224.unibe.ch>
19.6.0 Darwin Kernel Version 19.6.0: Thu May 6 00:48:39 PDT 2021;
root:xnu-6153.141.33~1/RELEASE_X86_64 x86_64
jurgenhanggi
setenv SUBJECTS_DIR /Applications/freesurfer/subjects
FREESURFER_HOME /Applications/freesurfer
Original mri_glmfit command line:
cmdline mri_glmfit --y IPS_2groups_n135_lh_thickness.10.mgh --fsgd
IPS_fsgd_2groups.txt --glmdir IPS_2groups_n135_Thickness_LH.glmdir
--surf fsaverage lh --C IPS_2groups.mat --cortex
DoSim = 1
UseCache = 0
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 14.598750
nSimPerJob = 500
1/1 Wed Jun 23 10:19:19 CEST 2021
mri_glmfit --C
IPS_2groups_n135_Thickness_LH.glmdir/tmp.mri_glmfit-sim-96372/IPS_2groups.mtx
--sim mc-z 500 1.302
IPS_2groups_n135_Thickness_LH.glmdir/csd/lh_mc-z.abs_500p1.3.j001
--sim-sign abs --fwhm 14.598750 --fsgd
IPS_2groups_n135_Thickness_LH.glmdir/y.fsgd dods --mask
IPS_2groups_n135_Thickness_LH.glmdir/mask.mgh --y --perm-force --surf
fsaverage lh white
INFO: ignoring tag Creator
INFO: ignoring tag SUBJECTS_DIR
INFO: ignoring tag SynthSeed
simbase IPS_2groups_n135_Thickness_LH.glmdir/csd/lh_mc-z.abs_500p1.3.j001
FWHM = 14.598750
gdfRead(): reading IPS_2groups_n135_Thickness_LH.glmdir/y.fsgd
WARNING: carriage returns have been detected in file
IPS_2groups_n135_Thickness_LH.glmdir/y.fsgd
Was it created on a Windows computer?
This may cause an error in reading the FSGD file.
If so, try running:
cat IPS_2groups_n135_Thickness_LH.glmdir/y.fsgd | sed 's/\r/\n/g'
> new.IPS_2groups_n135_Thickness_LH.glmdir/y.fsgd
Then use new.IPS_2groups_n135_Thickness_LH.glmdir/y.fsgd
INFO: gd2mtx_method is dods
Reading source surface
/Applications/freesurfer/subjects/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
Surface smoothing by fwhm=14.598750, niters=157.000000
7.1.1
cwd
/Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135
cmdline mri_glmfit --C
IPS_2groups_n135_Thickness_LH.glmdir/tmp.mri_glmfit-sim-96372/IPS_2groups.mtx
--sim mc-z 500 1.302
IPS_2groups_n135_Thickness_LH.glmdir/csd/lh_mc-z.abs_500p1.3.j001
--sim-sign abs --fwhm 14.598750 --fsgd
IPS_2groups_n135_Thickness_LH.glmdir/y.fsgd dods --mask
IPS_2groups_n135_Thickness_LH.glmdir/mask.mgh --y --perm-force --surf
fsaverage lh white
sysname Darwin
hostname upddkp224.unibe.ch
<http://secure-web.cisco.com/1kqev2VghLiWSg5kIlxOKq_VbJZc9JK-pk9pBXL8_xh9udahFBCv8EvuJ9GuriYfcowB1DAoh5MAMRkYqUO02V_5nmE4VP10JT85LV5FW_dqPd3gGa14VqqkgWLHu9xxCHFT7s8bFskBPK-8PML54WB77N_8bUtYd1r3Qh3VZu7eaRw1teNI4YSlpPAPOHZOvFY8TRdxlfSUjQd7VN9nd_7zJRz4srPlQzrTlohVaHWsmlRNB9lVm4YVYKBaKL7JtQp2863TnS1zUJjRGu3rV-A/http%3A%2F%2Fupddkp224.unibe.ch>
machine x86_64
user jurgenhanggi
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
fwhm 14.598750
niters 157.000000
OneSampleGroupMean 0
y
/Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135/--perm-force
logyflag 0
usedti 0
FSGD IPS_2groups_n135_Thickness_LH.glmdir/y.fsgd
mask IPS_2groups_n135_Thickness_LH.glmdir/mask.mgh
maskinv 0
glmdir (null)
IllCondOK 0
ReScaleX 1
DoFFx 0
Loading y from
/Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135/--perm-force
error: mri_read(): couldn't determine type of file
/Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135/--perm-force
... done reading.
ERROR: loading y
/Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135/--perm-force
[upddkp224:average_IPS_FS7_Linux/stats/glm_group_n135] jurgenhanggi%
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