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 >
doug.log
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_______________________________________________ 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.
