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 -fsd
rest -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
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 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
thatIshould 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
intothe> 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)
inFSL,>> 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
andthe e-mail> contains patient information, please contact the Partners
ComplianceHelpLine at> http://www.partners.org/complianceline . If the e-mail
was sent
toyou in error> but does not contain patient information, please contact
the
senderand properly> dispose of the e-mail. > > _______________________________________________ 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
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
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.
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-mail
was sent
to> you in error >> but does not contain patient information, please contact
the
sender> and properly >> dispose of the e-mail. >> >> > _______________________________________________ > 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
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@nmr.mgh.harvard.edu
-
Douglas N Greve -
stdp82＠virgilio.it