I have resolve the previous error (there was a typo in the fsdg file) but re-running I obtain this error:

Normalized matrix condition is 1

Matrix condition is 1

mghRead(/Applications/freesurfer/subjects/rh.GROUP.thickness.10B.mgh, -1): could not open file

fsgd file is:

GroupDescriptorFile 1 
Title All
Class Main
Input 032_XX Main
Input 047_XX Main
Input 049_XX Main
Input 060_XX Main

and I have two contrast (intercept 1 0; slope 0 1)

command line that runs:

mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --surface fsaverage rh --glmdir Thickness.wls --nii.gz --fsgd g1v1_thickness.fsgd --C intercept.mtx --C slope.mtx --pvr $SUBJECTS_DIR/rh.GROUP1.thickness.10B.mgh

Il 5 febbraio 2018 alle 19.36 stdp82@virgilio.it ha scritto:

 

I obtain this error: 

mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --surface fsaverage rh --glmdir Thickness.wls --nii.gz --fsgd g1v1_thickness.fsgd --C intercept.mtx --C slope.mtx --pvr $SUBJECTS_DIR/rh.MCI.thickness.10B.mgh

Reading source surface /Applications/freesurfer/subjects/fsaverage/surf/rh.white

gdfRead(): reading g1v1_thickness.fsgd

ERROR: fio_FileHasCarriageReturn(): cannot open g1v1_thickness.fsgd

Il 5 febbraio 2018 alle 18.26 Douglas Greve <greve@nmr.mgh.harvard.edu> ha scritto:

On 2/4/18 10:06 AM, stdp82@virgilio.it wrote:

I have run:

1)

mris_preproc --fsgd GROUP1.fsgd --target fsaverage --hemi rh --meas thickness --out rh.GROUP1.thickness.00.mgh
mri_surf2surf --hemi rh --s fsaverage --sval rh.GROUP1.thickness.00.mgh --fwhm 10 --cortex --tval rh.GROUP1.thickness.10B.mgh

looks good

2)

mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --surface fsaverage rh --glmdir Age.wls --nii.gz --fsgd g1v1_Age.fsgd --C intercept.mtx --C slope.mtx --pvr rh.GROUP1.thickness.10B.mgh

The command line is correct?

Yes, though I'm not sure about the effect of using --wls and --pvr. I guess it will be ok, I just have not used it.

My concern is on the fsgd file.

I have 

GroupDescriptorFile 1
Title All
Class Main
Variables thickness
Input ADNI0XX_GROUP1 Main ????
Input ADNI0XY_GROUP1 Main ????
Input ADNI0YX.GROUP1 Main ????
...

What I should add after Main if I would like to assess the vertex by vertex correlation between FC (between seed and target vertex) and thickness (in the target vertex)?

Don't represent the PVR in the FSGD file. You only need to include items in the contrast matrix. Eg, for intercept use [1 0] and for slope use [0 1] eventhough you only have a single class.

Should I add the path where is contained rh.thickness.mgh of each subject?

No

Please give me an help because I did not find these information using --help or mail list.

Thanks

Stefano

Il 3 febbraio 2018 alle 19.55 Douglas Greve <greve@nmr.mgh.harvard.edu> ha scritto:

Yes, use the --pvr option to mri_glmfit (per-voxel regressor). Search through the mail archives for an example on how to use it

On 2/3/18 12:10 PM, stdp82@virgilio.it wrote:

Hi list,

Is there a way to obtain a map that report the "vertex by vertex" correlation between the FC (obtained by FS-FAST) and cortical thickness?

Thanks

Stefano

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