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.chhttp://secure-web.cisco.com/1GJFlNOIRufFrF9EI_m9Z0M8ynVxVdXSTvLuBbjjKrTZTIreSGIj10aXOTSZZ0k3Mz7CPsLHLfO8-ZDDrzXknHtuEmmGsrEIwVMxFYq6nLcYjNXGyPLh-NffYLR2Pl3uPv-mmclbsnFGyJcGF6NJSBfUIP5JwMrhkba5bXopX7DgpHyp7Cl_dWy6iA3fsYFQVqdPAJ04inRiEy6PFK3tY5npd4DY456oSRmy6AlhvUk-EMBaX_qmp4ECKKciiYniqdKnjsmgQ4avf1qOgYcxx8g/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.chhttp://secure-web.cisco.com/1GJFlNOIRufFrF9EI_m9Z0M8ynVxVdXSTvLuBbjjKrTZTIreSGIj10aXOTSZZ0k3Mz7CPsLHLfO8-ZDDrzXknHtuEmmGsrEIwVMxFYq6nLcYjNXGyPLh-NffYLR2Pl3uPv-mmclbsnFGyJcGF6NJSBfUIP5JwMrhkba5bXopX7DgpHyp7Cl_dWy6iA3fsYFQVqdPAJ04inRiEy6PFK3tY5npd4DY456oSRmy6AlhvUk-EMBaX_qmp4ECKKciiYniqdKnjsmgQ4avf1qOgYcxx8g/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%