Thanks. But the MRS_mask should be in Tal, MNI or native? Now I'm using a masks that overlaps orig.nii.gz. Second, if I would like to create a sphere and use it as seed, there is a specific command line?
Stefano
----Messaggio originale---- Da: greve@nmr.mgh.harvard.edu Data: 9-nov-2015 23.24 A: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: error MRS voxel as seed in
FS-FAST
So that mask has 22926 non-zero voxels? The only other thing I can
think
of is that the registration is off. Have you checked that?
On 11/06/2015 07:16 AM, stdp82@virgilio.it wrote:
I hope that this information are fine
fslinfo $SUBJECTS_DIR/Control22/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+
fslstats $SUBJECTS_DIR/Control22/MRS_MASK.nii.gz -V 22926 22926.000000
Thanks,
Stefano
----Messaggio originale---- Da: greve@nmr.mgh.harvard.edu Data: 5-nov-2015 23.43 A: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: error MRS voxel as seed in FS-
FAST
How many non-zero voxels are in MRS_MASK.mgz? Is MRS_MASK.mgz
256^3,
1mm3 ?
On 11/05/2015 04:47 PM, stdp82@virgilio.it wrote:
Please see the file attached. Thanks
Stefanofile
----Messaggio originale---- Da: greve@nmr.mgh.harvard.edu Data: 5-nov-2015 15.43 A: <freesurfer@nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: error MRS voxel as seed in FS-
FAST
sorry, should have been fcseed-sess -debug -s Control22_FS -cfg MRS_MASK.config |&
tee
doug.log
On 11/4/15 6:05 PM, stdp82@virgilio.it wrote:Hi Dough, in summary: I have the MRS_MASK.mgz within $SUBJECTS_DIR/Control22/mri thus, I have copy this file in fMRI directory(fMRI/Control22_FS) the
MRS_MASK.mgz and run: fcseed-config -segid 1 -seg Control22_FS/MRS_MASK.mgz -fsdrest -mean -
cfg MRS_MASK.config fcseed-sess -s Control22_FS -cfg MRS_MASK.config ...Writing to/Applications/freesurfer/subjects/fMRI/Control22_FS/rest/001/tmp. fcseed-
sess.12305/avgwf.mgh Segmentation fault Therefore, according with your suggestion, I have now run: fcseed-sess -debug -s -cfg MRS_MASK.config | & tee doug.log ERROR: cound not find session -cfg The doug.log is attached. Thanks, Stefano----Messaggio originale---- Da:greve@nmr.mgh.harvard.edu Data: 4-nov-2015 16.58 A:<freesurfer@nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] error MRS voxel as seed in FS-FAST First, when running fcseed-config, don't give it the fullpath, just
thepath relative to subject/mri (in this case only MRS_MASK.
mgz)
However, I don't think that is the problem. Please run fcseed-sess -debug -s -cfg MRS_MASK.config |& tee doug.log and send me doug.log On 11/04/2015 04:14 AM,stdp82@virgilio.it wrote:> Hi list, this error is still occurring: > > mri_convert $SUBJECTS_DIR/subj/mri/MRS_MASK.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 > fcseed-sess -s -cfg MRS_MASK.config > > During > > fcseed-sess -s subj -cfg MRS_MASK.config > > 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/sub/rest/001/tmp.
> fcseed-sess.97908/avgwf.mgh > Segmentation fault > > I have read your previous message and you can check the
MRS
voxel
> features. > MRS voxel mask is in subj directory where I have run
recon
all -
all.> data_type FLOAT32 > dim1 256 > dim2 256 > dim3 256 > dim4 1 > datatype 16 > pixdim1 1.000000 > pixdim2 1.000000 > pixdim3 1.000000 > pixdim4 0.010747 > cal_max 0.0000 > cal_min 0.0000 > file_type NIFTI-1+ > > > The features are same of other subject that runs fine. > data_type FLOAT32 > dim1 256 > dim2 256 > dim3 256 > dim4 1 > datatype 16 > pixdim1 1.000000 > pixdim2 1.000000 > pixdim3 1.000000 > pixdim4 0.010747 > cal_max 0.0000 > cal_min 0.0000 > file_type NIFTI-1+ > > Thank you very much. > > > Stefano > > >> ----Messaggio originale---- >> Da:stdp82@virgilio.it >> Data: 16-ott-2015 23.15 >> A:freesurfer@nmr.mgh.harvard.edu >> Ogg: [Freesurfer] R: Re: R: import FS-FAST results in
FSL
>> >> I'd like to open with FSLview the sig.nii.gz which is
produced by
>> selxavg3-sess. >> If I use mri_surf2vol, which is the template to added in
--
template?>> It should be in Tailairach space? Where can I find the
template
that> I >> should added? >> Thanks, >> >> Stefano >> >> subj/rest/fc.seed.surf.lh/L_seed/sig.nii.gz >> data_type FLOAT32 >> dim1 27307 >> dim2 1 >> dim3 6 >> dim4 1 >> datatype 16 >> pixdim1 1.000000 >> pixdim2 1.000000 >> pixdim3 1.000000 >> pixdim4 1100.000000 >> cal_max 49.1815 >> cal_min -12.3855 >> file_type NIFTI-1+ >> >> >> >> >> >> >> >> Thanks, >> >> Stefano >> >> >>> ----Messaggio originale---- >>> Da:greve@nmr.mgh.harvard.edu >>> Data: 29-set-2015 22.09 >>> A:freesurfer@nmr.mgh.harvard.edu >>> Ogg: Re: [Freesurfer] R: import FS-FAST results in FSL >>> >>> Do you mean surface-based analysis? You'd have to put
them
back
> into >> the >>> volume using mri_surf2vol, write them out as nifti and
then run
>> fslview >>> on them >>> >>> On 09/29/2015 11:17 AM,stdp82@virgilio.it wrote: >>>> Hi list, >>>> >>>> I would like to import FS-FAST results
(conjunction
maps)
in>> FSL, >>>> opening them by fslview. >>>> Could you provide me any suggestion? >>>> >>>> Thank you very much >>>> Best regards, >>>> >>>> >>>> Stefano >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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.
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and>> the e-mail >>> contains patient information, please contact the
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>
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.
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-- 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/
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-- 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.
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stdp82＠virgilio.it