The problem persist.
Stefano
----Messaggio originale---- Da: Douglas N Greve greve@nmr.mgh.harvard.edu Data: 19-feb-2016 0.25 A: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] FS-FAST using MRS voxel or .label as seed
I think it may be our fcseed-config command line fcseed-config -segid 1 -seg $SUBJECTS_DIR/Subj/mri/MRS_MASK.mgz -fsd rest -mean -cfg MRS_MASK.config –overwrite
It should be -seg MRS_MASK.mgz
They way you have it, fcseed will use the segmentation for Subj for all subjects, which is why it works for one and not for others
On 02/18/2016 06:10 PM, stdp82@virgilio.it wrote:
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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
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dispose of the e-mail.
Make sure that the MRS_MASK.mgz itself has some voxels with value=1, and make sure that there are enough of them to fit into at least one functional voxel.
Make sure that the registration is accurate.
When you run run fcseed-sess, add -debug, capture the output, and send it to me.
On 02/18/2016 06:43 PM, stdp82@virgilio.it wrote:
The problem persist.
Stefano
----Messaggio originale---- Da: Douglas N Greve greve@nmr.mgh.harvard.edu Data: 19-feb-2016 0.25 A: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] FS-FAST using MRS voxel or .label as seed
I think it may be our fcseed-config command line fcseed-config -segid 1 -seg $SUBJECTS_DIR/Subj/mri/MRS_MASK.mgz -fsd rest -mean -cfg MRS_MASK.config –overwrite
It should be -seg MRS_MASK.mgz
They way you have it, fcseed will use the segmentation for Subj for all subjects, which is why it works for one and not for others
On 02/18/2016 06:10 PM, stdp82@virgilio.it wrote:
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
stdp82＠virgilio.it