I'm sorry but I do not understand my error. Stefano
>----Messaggio originale---- >Da: Douglas N Greve <gr...@nmr.mgh.harvard.edu> >Data: 19-feb-2016 18.05 >A: <freesurfer@nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] R: Re: R: FS-FAST using MRS voxel or .label as seed > >Yes, that is expected given your command line. > >On 02/18/2016 06:52 PM, std...@virgilio.it wrote: >> By running >> mri_cor2label --i $SUBJECTS_DIR/mri/MRS_MASK.nii.gz --id 1 --l MRS.label >> >> and opening the MRS.label by tksurfer fsaverage rh inflate -aparc -overlay MRS. >> label >> the inflate is empty. >> >> >> Stefano >> >> >> >>> ----Messaggio originale---- >>> Da: Douglas N Greve <gr...@nmr.mgh.harvard.edu> >>> Data: 19-feb-2016 0.34 >>> A: <freesurfer@nmr.mgh.harvard.edu> >>> Ogg: Re: [Freesurfer] R: FS-FAST using MRS voxel or .label as seed >>> >>> That is an incorrect usage of mri_cor2label. MRS_MASK.nii.gz is a >>> volume, not a surface overlay. By using --surf, you are indicating that >>> it is a surface overlay >>> >>> On 02/18/2016 06:30 PM, std...@virgilio.it wrote: >>>> Furthermore, if I use mir_cor2label in order to show the location of >>>> MRS voxel (in native space) this error occurs: >>>> >>>> mri_cor2label --c $SUBJECTS_DIR/subj/MRS_MASK.nii.gz --id 1 --l >>>> MRS.label --surf fsaverage lh >>>> $Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $ >>>> Loading mri >>>> /Applications/freesurfer/subjects/subject_dir/subj/MRS_MASK.nii.gz >>>> Loading >>>> /Applications/freesurfer/subjects/subject_dir/fsaverage/surf/lh.white >>>> ERROR: dim mismatch between surface (163842) and input (16777216) >>>> >>>> ----Messaggio originale---- >>>> Da: std...@virgilio.it >>>> Data: 19-feb-2016 0.10 >>>> A: <freesurfer@nmr.mgh.harvard.edu> >>>> Ogg: [Freesurfer] FS-FAST using MRS voxel or .label as seed >>>> >>>> Hi list, >>>> >>>> I'm having problem to use FS-FAST fMRI connectivity using as seed >>>> a mask of a MRS voxel or .label obtained by drawing it from >>>> surface. In order to resolve my concern, I'm reporting step by >>>> step the command lines which I have used. The mask, f.nii.gz, >>>> orig.nii.gz and aparc+aseg.nii.gz showed a good overlap. >>>> >>>> These are the features of each one: >>>> >>>> fslinfo orig.nii.gz >>>> >>>> data_type UINT8 >>>> >>>> dim1 256 >>>> >>>> dim2 256 >>>> >>>> dim3 256 >>>> >>>> dim4 1 >>>> >>>> datatype 2 >>>> >>>> pixdim1 1.000000 >>>> >>>> pixdim2 1.000000 >>>> >>>> pixdim3 1.000000 >>>> >>>> pixdim4 0.010747 >>>> >>>> cal_max 0.0000 >>>> >>>> cal_min 0.0000 >>>> >>>> file_type NIFTI-1+ >>>> >>>> fslinfo aparc+aseg.nii.gz >>>> >>>> data_type INT32 >>>> >>>> dim1 256 >>>> >>>> dim2 256 >>>> >>>> dim3 256 >>>> >>>> dim4 1 >>>> >>>> datatype 8 >>>> >>>> pixdim1 1.000000 >>>> >>>> pixdim2 1.000000 >>>> >>>> pixdim3 1.000000 >>>> >>>> pixdim4 0.010747 >>>> >>>> cal_max 0.0000 >>>> >>>> cal_min 0.0000 >>>> >>>> file_type NIFTI-1+ >>>> >>>> fslinfo 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+ >>>> >>>> I’m using MNI2mm for subcortical analysis. >>>> >>>> mri_convert $SUBJECTS_DIR/Subj/MRS_Voxel_FS_space.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 –overwrite >>>> >>>> fcseed-sess -s Subj -cfg MRS_MASK.config -overwrite >>>> >>>> mkanalysis-sess -analysis fc.MRS_MASK.surf.lh -surface fsaverage >>>> lh -fwhm 8 -notask -taskreg MRS_MASK 1 -nuisreg vcsf.dat 5 >>>> -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.1 >>>> -per-run -overwrite >>>> >>>> mkanalysis-sess -analysis fc.MRS_MASK.surf.rh -surface fsaverage >>>> rh -fwhm 8 -notask -taskreg MRS_MASK 1 -nuisreg vcsf.dat 5 >>>> -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.1 >>>> -per-run -overwrite >>>> >>>> mkanalysis-sess -analysis fc.MRS_MASK.mni305 -mni305 -fwhm 8 >>>> -notask -taskreg MRS_MASK 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 >>>> -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.1 -per-run -overwrite >>>> >>>> selxavg3-sess -sf sessid -a fc.MRS_MASK.surf.rh >>>> >>>> selxavg3-sess -sf sessid -a fc.MRS_MASK.surf.lh >>>> >>>> selxavg3-sess -sf sessid -a fc.MRS_MASK.mni305 >>>> >>>> isxconcat-sess -sf sessid -analysis fc.MRS_MASK.surf.rh -contrast >>>> MRS_MASK -o my-group >>>> >>>> isxconcat-sess -sf sessid -analysis fc.MRS_MASK.surf.lh -contrast >>>> MRS_MASK -o my-group >>>> >>>> isxconcat-sess -sf sessid -analysis fc.MRS_MASK.mni305 -contrast >>>> MRS_MASK -o my-group >>>> >>>> When I run fcseed-sess -s Subj -cfg MRS_MASK.config -overwrite, >>>> it seem to be functioning for the first subj, but the next subj2 >>>> show this error >>>> >>>> Loading >>>> /Applications/freesurfer/subjects/fMRI/subj2/rest/001/fmcpr.nii.gz >>>> >>>> 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/subj2/rest/001/tmp.fcseed- sess. >> 28328/avgwf.mgh >>>> Segmentation fault >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 >> >> > >-- >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
