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.gzLoading /Applications/freesurfer/subjects/subject_dir/fsaverage/surf/lh.whiteERROR: 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
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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
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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freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
stdp82＠virgilio.it