Hi,

When I meant both I meant one dev and one 5.3.

The mri_glmfit commands was the next one which was send to a cluster: It consisted in a one group with two covariables design.

mri_glmfit \

* --y cespct.nii.gz \ --fsgd ${fsgd_file}\ --C Int \ --C Age \ --surface fsaverage $hemi \ --glmdir glm_v53 \ --mask $analysisdir/mask.nii.gz \ --nii.gz /net/tsd- evs.tsd.usit.no/p23/data/colossus/psyklab/freesurfer/dev/mri http://evs.tsd.usit.no/p23/data/colossus/psyklab/freesurfer/dev/mri _glmfit \ --y cespct.nii.gz \ --fsgd ${fsgd_file}\ --C ${C1} \ --C ${C2} \ --surface fsaverage $hemi \ --glmdir glm_dev \ --mask $analysisdir/mask.nii.gz \ --nii.gz *

And the output logfile is the following (including the cmdline):

*SETTING UP COLOSSUS ENVIRONMENTStarting job 108235 ("MC_GROUP") on c2-32 at on. 07. okt. 21:45:35 +0200 2015LOADING MATLAB MODULE/cluster/software/VERSIONS/matlab-R2014b/bin/matlabLOADING R FROM PSYKLAB/tsd/p23/data/colossus/psyklab/R/R-3.1.2.devel/bin/RSOURCING FREESURFERSOURCING FSLgdfReadHeader: reading /tsd/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/lists/fsgd/AgeN_sex.fsgdINFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.Continuous Variable Means (all subjects)0 Age -0.172747 20.02381 Sex 5.96046e-09 0.489898Class Means of each Continuous Variable1 Main -0.1727 0.0000 INFO: gd2mtx_method is dodsReading source surface /tsd/p23/data/colossus/psyklab/freesurfer/current/subjects/fsaverage/surf/lh.whiteNumber of vertices 163842Number of faces 327680Total area 65416.648438AvgVtxArea 0.399267AvgVtxDist 0.721953StdVtxDist 0.195470$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $cwd /net/tsd-evs.tsd.usit.no/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/All_GLM/all_subjects/STUDY.sm8.lh/recoll-v-fam http://tsd-evs.tsd.usit.no/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/All_GLM/all_subjects/STUDY.sm8.lh/recoll-v-famcmdline mri_glmfit --y cespct.nii.gz --fsgd /tsd/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/lists/fsgd/AgeN_sex.fsgd --C /tsd/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/lists/fsgd/AgeN_sex_con/Int.mtx --C /tsd/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/lists/fsgd/AgeN_sex_con/Age.mtx --surface fsaverage lh --glmdir glm_53 --mask /tsd/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/All_GLM/all_subjects/STUDY.sm8.lh/mask.nii.gz --nii.gz sysname Linuxhostname compute-2-32.localmachine x86_64user p23-didacvpFixVertexAreaFlag = 1UseMaskWithSmoothing 1OneSampleGroupMean 0y /net/tsd-evs.tsd.usit.no/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/All_GLM/all_subjects/STUDY.sm8.lh/recoll-v-fam/cespct.nii.gz http://tsd-evs.tsd.usit.no/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/All_GLM/all_subjects/STUDY.sm8.lh/recoll-v-fam/cespct.nii.gzlogyflag 0usedti 0FSGD /tsd/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/lists/fsgd/AgeN_sex.fsgdmask /tsd/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/All_GLM/all_subjects/STUDY.sm8.lh/mask.nii.gzmaskinv 0glmdir glm_53IllCondOK 0ReScaleX 1DoFFx 0Creating output directory glm_53Loading y from /net/tsd-evs.tsd.usit.no/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/All_GLM/all_subjects/STUDY.sm8.lh/recoll-v-fam/cespct.nii.gz http://tsd-evs.tsd.usit.no/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/All_GLM/all_subjects/STUDY.sm8.lh/recoll-v-fam/cespct.nii.gzINFO: gd2mtx_method is dodsSaving design matrix to glm_53/Xg.datNormalized matrix condition is 1.19608Matrix condition is 1684.09Pruning voxels by thr: 0.000000Found 147820 voxels in maskSaving mask to glm_53/mask.nii.gzReshaping mriglm->mask...search space = 73503.207889DOF = 137Starting fit and testFit completed in 0.0522 minutesComputing spatial AR1 on surfaceResidual: ar1mn=0.995427, ar1std=0.005476, gstd=5.977767, fwhm=14.076566Writing results Int maxvox sig=13.2217 F=70.0367 at index 137153 0 0 seed=1444611802 Age maxvox sig=3.18022 F=12.1485 at index 66347 0 0 seed=1444611802mri_glmfit donegdfRead(): reading /tsd/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/lists/fsgd/AgeN_sex.fsgdINFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.Continuous Variable Means (all subjects)0 Age -0.172747 20.02381 Sex 5.96046e-09 0.489898Class Means of each Continuous Variable1 Main -0.1727 0.0000 INFO: gd2mtx_method is dodsReading source surface /tsd/p23/data/colossus/psyklab/freesurfer/current/subjects/fsaverage/surf/lh.whiteNumber of vertices 163842Number of faces 327680Total area 65416.984375AvgVtxArea 0.399269AvgVtxDist 0.721953StdVtxDist 0.195470$Id: mri_glmfit.c,v 1.241 2015/08/12 21:03:09 greve Exp $cwd /net/tsd-evs.tsd.usit.no/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/All_GLM/all_subjects/STUDY.sm8.lh/recoll-v-fam http://tsd-evs.tsd.usit.no/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/All_GLM/all_subjects/STUDY.sm8.lh/recoll-v-famcmdline /net/tsd-evs.tsd.usit.no/p23/data/colossus/psyklab/freesurfer/dev/mri_glmfit http://tsd-evs.tsd.usit.no/p23/data/colossus/psyklab/freesurfer/dev/mri_glmfit --y cespct.nii.gz --fsgd /tsd/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/lists/fsgd/AgeN_sex.fsgd --C /tsd/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/lists/fsgd/AgeN_sex_con/Int.mtx --C /tsd/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/lists/fsgd/AgeN_sex_con/Age.mtx --surface fsaverage lh --glmdir glm_dev --mask /tsd/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/All_GLM/all_subjects/STUDY.sm8.lh/mask.nii.gz --nii.gz sysname Linuxhostname compute-2-32.localmachine x86_64user p23-didacvpFixVertexAreaFlag = 1UseMaskWithSmoothing 1OneSampleGroupMean 0y /net/tsd-evs.tsd.usit.no/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/All_GLM/all_subjects/STUDY.sm8.lh/recoll-v-fam/cespct.nii.gz http://tsd-evs.tsd.usit.no/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/All_GLM/all_subjects/STUDY.sm8.lh/recoll-v-fam/cespct.nii.gzlogyflag 0usedti 0FSGD /tsd/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/lists/fsgd/AgeN_sex.fsgdmask /tsd/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/All_GLM/all_subjects/STUDY.sm8.lh/mask.nii.gzmaskinv 0glmdir glm_devIllCondOK 0ReScaleX 1DoFFx 0Creating output directory glm_devLoading y from /net/tsd-evs.tsd.usit.no/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/All_GLM/all_subjects/STUDY.sm8.lh/recoll-v-fam/cespct.nii.gz http://tsd-evs.tsd.usit.no/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/All_GLM/all_subjects/STUDY.sm8.lh/recoll-v-fam/cespct.nii.gz ... done reading.INFO: gd2mtx_method is dodsSaving design matrix to glm_dev/Xg.datComputing normalized matrixNormalized matrix condition is 1.19608Matrix condition is 1684.09Pruning voxels by thr: 1.175494e-38Found 147820 voxels in maskSaving mask to glm_dev/mask.nii.gzReshaping mriglm->mask...search space = 73502.831427DOF = 137Starting fit and testFit completed in 0.194133 minutesComputing spatial AR1 on surfaceResidual: ar1mn=0.995427, ar1std=0.005476, gstd=5.977751, fwhm=14.076528Writing results Int maxvox sig=13.6436 F=70.0366 at index 137153 0 0 seed=1445192785 Age maxvox sig=3.60222 F=12.1485 at index 66347 0 0 seed=1445192785mri_glmfit donegdfReadHeader: reading /tsd/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/lists/fsgd/AgeN_sex.fsgdINFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.Continuous Variable Means (all subjects)0 Age -0.172747 20.02381 Sex 5.96046e-09 0.489898Class Means of each Continuous Variable1 Main -0.1727 0.0000 INFO: gd2mtx_method is dodsReading source surface /tsd/p23/data/colossus/psyklab/freesurfer/current/subjects/fsaverage/surf/rh.whiteNumber of vertices 163842Number of faces 327680Total area 65020.765625AvgVtxArea 0.396850AvgVtxDist 0.717994StdVtxDist 0.193566*

2015-10-07 20:59 GMT+02:00 Douglas Greve greve@nmr.mgh.harvard.edu:

when you say "both versions" what do you mean? Just two different calls to the dev version of mri_glmfit? Or one call to the 5.3 and one call to the dev? What are your command lines? What is the terminal output?

On 10/7/15 10:54 AM, Dídac Vidal wrote:

Hi Freesurfers!

I am using development version of mri_glmfit (as I want to take advantadge of --frame-mask option).

As control analysis I performed an identical (simple) analysis both in mri_glmfit and its dev version. Suprisingly, while F.nii.gz were identical for the given contrast sig.nii.gz map differed betweem both versions. If possible (and If I am not doing anything wrong), I'd like to know the reason why they differ and also which one I should stick with.

Thank you in advance

-- Dídac Vidal Piñeiro

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