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 |& teedoug.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 -
fsdrest -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 00.000
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 MRSvoxel
features. MRS voxel mask is in subj directory where I have run reconall -
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
thatI> 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.
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_______________________________________________ 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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