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 using 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).
Stefano
----Messaggio originale----
Da: Douglas Greve <gr...@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, std...@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: std...@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 <gr...@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, std...@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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