External Email - Use Caution        

Dear Douglas

please find the terminal output and the log files attached.
when I run this command in FS 6.0.0, no error occurred

thanks in advance

cheers
Jürgen



Am 27.06.2021 um 16:49 schrieb Douglas N. Greve <dgreve@mgh.harvard.edu>:

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.haenggi@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 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
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% 





_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________
Freesurfer mailing list
Freesurfer@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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.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.
Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.