Re: [Freesurfer] R: FS-FAST using MRS voxel or .label as seed

That is an incorrect usage of mri_cor2label. MRS_MASK.nii.gz is a volume, not a surface overlay. By using --surf, you are indicating that it is a surface overlay

On 02/18/2016 06:30 PM, stdp82@virgilio.it wrote:

Furthermore, if I use mir_cor2label in order to show the location of MRS voxel (in native space) this error occurs:

mri_cor2label --c $SUBJECTS_DIR/subj/MRS_MASK.nii.gz --id 1 --l MRS.label --surf fsaverage lh $Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $ Loading mri /Applications/freesurfer/subjects/subject_dir/subj/MRS_MASK.nii.gz Loading /Applications/freesurfer/subjects/subject_dir/fsaverage/surf/lh.white ERROR: dim mismatch between surface (163842) and input (16777216)

----Messaggio originale----
Da: stdp82@virgilio.it
Data: 19-feb-2016 0.10
A: <freesurfer@nmr.mgh.harvard.edu>
Ogg: [Freesurfer] FS-FAST using MRS voxel or .label as seed

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

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