Please also consider that the T1, f.nii and ROI.ii.gz (obtained by label2vol)
are nice overlapped. The brain.mni305.2mm.nii seem to be strange (see the image
attached). In the sig.nii.gz the cluster are bad coregistered and some of those
out are of the brain. Thanks
Stefano
----Messaggio originale----
Da: std...@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 <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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