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    _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 ENVIRONMENT
Starting job 108235 ("MC_GROUP") on c2-32 at on. 07. okt. 21:45:35 +0200 2015
LOADING MATLAB MODULE
/cluster/software/VERSIONS/matlab-R2014b/bin/matlab
LOADING R FROM PSYKLAB
/tsd/p23/data/colossus/psyklab/R/R-3.1.2.devel/bin/R
SOURCING FREESURFER
SOURCING FSL
gdfReadHeader: reading /tsd/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/lists/fsgd/AgeN_sex.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 Age -0.172747 20.0238
1 Sex 5.96046e-09 0.489898
Class Means of each Continuous Variable
1 Main -0.1727   0.0000
INFO: gd2mtx_method is dods
Reading source surface /tsd/p23/data/colossus/psyklab/freesurfer/current/subjects/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces    327680
Total area         65416.648438
AvgVtxArea       0.399267
AvgVtxDist       0.721953
StdVtxDist       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
cmdline 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 Linux
hostname compute-2-32.local
machine x86_64
user     p23-didacvp
FixVertexAreaFlag = 1
UseMaskWithSmoothing     1
OneSampleGroupMean 0
y    /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
logyflag 0
usedti 0
FSGD /tsd/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/lists/fsgd/AgeN_sex.fsgd
mask /tsd/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/All_GLM/all_subjects/STUDY.sm8.lh/mask.nii.gz
maskinv 0
glmdir glm_53
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory glm_53
Loading 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
INFO: gd2mtx_method is dods
Saving design matrix to glm_53/Xg.dat
Normalized matrix condition is 1.19608
Matrix condition is 1684.09
Pruning voxels by thr: 0.000000
Found 147820 voxels in mask
Saving mask to glm_53/mask.nii.gz
Reshaping mriglm->mask...
search space = 73503.207889
DOF = 137
Starting fit and test
Fit completed in 0.0522 minutes
Computing spatial AR1 on surface
Residual: ar1mn=0.995427, ar1std=0.005476, gstd=5.977767, fwhm=14.076566
Writing 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=1444611802
mri_glmfit done
gdfRead(): reading /tsd/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/lists/fsgd/AgeN_sex.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 Age -0.172747 20.0238
1 Sex 5.96046e-09 0.489898
Class Means of each Continuous Variable
1 Main -0.1727   0.0000
INFO: gd2mtx_method is dods
Reading source surface /tsd/p23/data/colossus/psyklab/freesurfer/current/subjects/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces    327680
Total area         65416.984375
AvgVtxArea       0.399269
AvgVtxDist       0.721953
StdVtxDist       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
cmdline /net/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 Linux
hostname compute-2-32.local
machine x86_64
user     p23-didacvp
FixVertexAreaFlag = 1
UseMaskWithSmoothing     1
OneSampleGroupMean 0
y    /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
logyflag 0
usedti 0
FSGD /tsd/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/lists/fsgd/AgeN_sex.fsgd
mask /tsd/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/All_GLM/all_subjects/STUDY.sm8.lh/mask.nii.gz
maskinv 0
glmdir glm_dev
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory glm_dev
Loading 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
   ... done reading.
INFO: gd2mtx_method is dods
Saving design matrix to glm_dev/Xg.dat
Computing normalized matrix
Normalized matrix condition is 1.19608
Matrix condition is 1684.09
Pruning voxels by thr: 1.175494e-38
Found 147820 voxels in mask
Saving mask to glm_dev/mask.nii.gz
Reshaping mriglm->mask...
search space = 73502.831427
DOF = 137
Starting fit and test
Fit completed in 0.194133 minutes
Computing spatial AR1 on surface
Residual: ar1mn=0.995427, ar1std=0.005476, gstd=5.977751, fwhm=14.076528
Writing 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=1445192785
mri_glmfit done
gdfReadHeader: reading /tsd/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/lists/fsgd/AgeN_sex.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 Age -0.172747 20.0238
1 Sex 5.96046e-09 0.489898
Class Means of each Continuous Variable
1 Main -0.1727   0.0000
INFO: gd2mtx_method is dods
Reading source surface /tsd/p23/data/colossus/psyklab/freesurfer/current/subjects/fsaverage/surf/rh.white
Number of vertices 163842
Number of faces    327680
Total area         65020.765625
AvgVtxArea       0.396850
AvgVtxDist       0.717994
StdVtxDist       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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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 Partners Compliance HelpLine at
http://www.partners.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.

Dídac Vidal Piñeiro