How many non-zero voxels are in MRS_MASK.mgz? Is MRS_MASK.mgz 256^3, 1mm3 ?
On 11/05/2015 04:47 PM, std...@virgilio.it wrote: > Please see the file attached. > Thanks > > Stefanofile > > ----Messaggio originale---- > Da: gr...@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, std...@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:gr...@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,std...@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:std...@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:gr...@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,std...@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 >>>>>> gr...@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 >>> gr...@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 gr...@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
