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 full
path, just
the> path 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.
edu/mailman/listinfo/freesurfer
>>>> >>>> The information in this e-mail is intended only for
the
person to
>>> whom it is >>>> addressed. If you believe this e-mail was sent to you
in
error
and>>> the e-mail >>>> contains patient information, please contact the
Partners
>> Compliance >>> HelpLine at >>>> http://www.partners.org/complianceline . If the e-
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sender>>> and properly >>>> dispose of the e-mail. >>>> >>>> >>> _______________________________________________ >>> 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
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
-- 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