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: gr...@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, 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 > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
