Hi list,

I'm having problem to use FS-FAST fMRI connectivity using as seed a mask of a MRS voxel or .label obtained by drawing it from surface. In order to resolve my concern, I'm reporting step by step the command lines which I have used. The mask, f.nii.gz, orig.nii.gz and aparc+aseg.nii.gz showed a good overlap.

These are the features of each one: 

fslinfo orig.nii.gz

data_type      UINT8

dim1           256

dim2           256

dim3           256

dim4           1

datatype       2

pixdim1        1.000000

pixdim2        1.000000

pixdim3        1.000000

pixdim4        0.010747

cal_max        0.0000

cal_min        0.0000

file_type      NIFTI-1+

fslinfo aparc+aseg.nii.gz

data_type      INT32

dim1           256

dim2           256

dim3           256

dim4           1

datatype       8

pixdim1        1.000000

pixdim2        1.000000

pixdim3        1.000000

pixdim4        0.010747

cal_max        0.0000

cal_min        0.0000

file_type      NIFTI-1+

fslinfo MRS_MASK.nii.gz

data_type      FLOAT32

dim1           256

dim2           256

dim3           256

dim4           1

datatype       16

pixdim1        1.000000

pixdim2        1.000000

pixdim3        1.000000

pixdim4        0.000000

cal_max        0.0000

cal_min        0.0000

file_type      NIFTI-1+

I’m using MNI2mm for subcortical analysis.

mri_convert $SUBJECTS_DIR/Subj/MRS_Voxel_FS_space.nii.gz $SUBJECTS_DIR/Subj/mri/MRS_MASK.mgz 

fcseed-config -segid 1 -seg $SUBJECTS_DIR/Subj/mri/MRS_MASK.mgz -fsd rest -mean -cfg MRS_MASK.config –overwrite 

fcseed-sess -s Subj -cfg MRS_MASK.config -overwrite

mkanalysis-sess -analysis fc.MRS_MASK.surf.lh -surface fsaverage lh -fwhm 8 -notask -taskreg MRS_MASK 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.1 -per-run -overwrite 

mkanalysis-sess -analysis fc.MRS_MASK.surf.rh -surface fsaverage rh -fwhm 8 -notask -taskreg MRS_MASK 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.1 -per-run -overwrite

mkanalysis-sess -analysis fc.MRS_MASK.mni305 -mni305 -fwhm 8 -notask -taskreg MRS_MASK 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.1 -per-run -overwrite

 selxavg3-sess -sf sessid -a fc.MRS_MASK.surf.rh

selxavg3-sess -sf sessid -a fc.MRS_MASK.surf.lh

selxavg3-sess -sf sessid -a fc.MRS_MASK.mni305

isxconcat-sess -sf sessid -analysis fc.MRS_MASK.surf.rh -contrast MRS_MASK -o my-group

isxconcat-sess -sf sessid -analysis fc.MRS_MASK.surf.lh -contrast MRS_MASK -o my-group

isxconcat-sess -sf sessid -analysis fc.MRS_MASK.mni305 -contrast MRS_MASK -o my-group

When I run fcseed-sess -s Subj -cfg MRS_MASK.config -overwrite, it seem to be functioning for the first subj, but the next subj2 show this error

Loading /Applications/freesurfer/subjects/fMRI/subj2/rest/001/fmcpr.nii.gz

Voxel Volume is 64.5752 mm^3

Generating list of segmentation ids

Found   1 segmentations

Computing statistics for each segmentation

  0     1                                          0       0.000

MRIalloc(0, 1, 1): bad parm

Reporting on   0 segmentations

Computing spatial average of each frame

Writing to //Applications/freesurfer/subjects/fMRI/subj2/rest/001/tmp.fcseed-sess.28328/avgwf.mgh

Segmentation fault