----Messaggio originale----
Da: stdp82@virgilio.it
Data: 12-feb-2016 0.23
A: "Freesurfer support list"<freesurfer@nmr.mgh.harvard.edu>
Ogg: [Freesurfer] R: Re: To use a ROI.label as seed in FS-FAST

I have used:

mri_label2vol --label RIGHT_ROI.label --temp subj/rest/001/f.nii --reg subj/rest/001/register.dof6.dat --fillthresh .5 --o RIGHT_ROI.nii.gz

When I open with freeview the f.nii.gz and the RIGHT_ROI they are fine overlapped.

But, after FS-FAST the sig.ii.gz seem to be wrong, probably bad reoriented, especially I have noted this on subcortical connectivity (MNI2mm).

Thanks

Stefano

----Messaggio originale----
Da: Douglas Greve <greve@nmr.mgh.harvard.edu>
Data: 11-feb-2016 4.48
A: <freesurfer@nmr.mgh.harvard.edu>
Ogg: Re: [Freesurfer] To use a ROI.label as seed in FS-FAST

 I may have gotten the exact form of the flag wrong. When it says an option is not known, you should try running the command with --help to see if something similar is there. In this way,  you might be able to figure it out for yourself rather than have to wait a day or so for us to respond.
doug

On 2/10/16 4:20 PM, stdp82@virgilio.it wrote:

If I use:

mri_label2vol --label ramgseed_rhsurf.label --temp $SUBJECTS_DIR/subj/mri/orig.mgz --identity --subject fsaverage --hemi rh --o RIGHT_ROI.nii.gz --fill-ribbon

ERROR: Option --fill-ribbon unknown

----Messaggio originale----
Da: stdp82@virgilio.it
Data: 8-feb-2016 20.35
A: "Freesurfer support list"<freesurfer@nmr.mgh.harvard.edu>
Ogg: [Freesurfer] R: Re: To use a ROI.label as seed in FS-FAST

Thanks.

I have down a right ad left ROI on the surface.

Next, I have run:

mri_label2vol --label ramgseed_rhsurf.label --temp $SUBJECTS_DIR/fsaverage/mri/orig.mgz --identity --subject fsaverage --hemi rh --o RIGHT_ROI.nii.gz

mri_label2vol --label ramgseed_lhsurf.label --temp $SUBJECTS_DIR/fsaverage/mri/orig.mgz --identity --subject fsaverage --hemi rh --o LEFT_ROI.nii.gz

mri_convert RIGHT_ROI.nii.gz RIGHT_ROI.mgz

mri_convert LEFT_ROI.nii.gz LEFT_ROI.mgz

fcseed-config -segid 1 -seg RIGHT_ROI.mgz -fsd rest -mean -cfg RIGHT_ROI.config

fcseed-config -segid 1 -seg LEFT_ROI.mgz -fsd rest -mean -cfg LEFT_ROI.config

fcseed-sess -s subj1_FS -cfg RIGHT_ROI.config

fcseed-sess -s subj1_FS -cfg LEFT_ROI.config

but during fcseed-sess this error occurs:

$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $

cwd 

cmdline mri_segstats --i /Applications/freesurfer/subjects/fMRI/subj1/rest/001/fmcpr.nii.gz --seg /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/mask.nii.gz --id 1 --sum /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/junk.sum --avgwfvol /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/avgwf.mgh 

sysname  Darwin

hostname iMac-di-Stefano.local

machine  x86_64

user     Stefano

UseRobust  0

Loading /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/mask.nii.gz

Loading /Applications/freesurfer/subjects/fMRI/subj1/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/subj1/rest/001/tmp.fcseed-sess.55700/avgwf.mgh

Segmentation fault 

----Messaggio originale----
Da: Douglas Greve <greve@nmr.mgh.harvard.edu>
Data: 8-feb-2016 4.38
A: <freesurfer@nmr.mgh.harvard.edu>
Ogg: Re: [Freesurfer] To use a ROI.label as seed in FS-FAST

Use mri_label2vol to convert the label into a volume in the anatomical space and store it in $SUBJECTS_DIR/subject/mri. Make sure to use --fill-ribbon if the label is surface-based. When running fcseed-config, specify the volume with the -seg option and use -segid 1

On 2/7/16 3:16 PM, stdp82@virgilio.it wrote:

Hi list,

I would like to use as seed in FS-FAST a ROI.label which I have drawn on a cluster in tksurfer.

How can I do it?

Should I use mri_label2vol?

Thanks.

Stefano

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