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Using mri_segstats, is the input subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz? Or should I use the .odd like fmcpr.odd.sm6.mni305.1mm.nii.gz or fmcpr.odd.sm6.mni305.2mm.nii.gz? > Il 12 aprile 2019 alle 16.59 "Greve, Douglas N.,Ph.D." > <dgr...@mgh.harvard.edu> ha scritto: > > You'll need to either convert the time series data into the conformed > space or the segmentation into the functional space. The first is probably > better (it will create a huge file but you can delete it when you are done). > Use mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o > fmpr.conformed.mgz > Then use the conformed thalamic nuclei volume when running mri_segstats > > On 4/12/2019 7:39 AM, std...@virgilio.it mailto:std...@virgilio.it wrote: > > > > > > External Email - Use Caution > > > > Hi list, > > I would like to extract fMRI time series from the thalamic > > subregions that I obtained by the recent tool implemented in FS. > > > > I have run > > mri_segstats --seg subj/mri/ThalamicNuclei.v10.T1.mgz --ctab > > $FREESURFER_HOME/FreeSurferColorLUT.txt --i > > subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz --avgwf > > Time_Seriesfolder/ADNI011_HC.MNI --id 8120 --id 8121 --id 8122 --id 8123 > > --id 8220 --id 8221 --id 8222 --id 8223 > > > > The command produces this error: > > ERROR: dimension mismatch between input volume and seg > > input 76 76 93 > > seg 169 105 118 > > > > Please, I have other questions for you. > > > > 1) At starting, I have used the command line reported below: > > > > preproc-sess -sf sessid -fwhm 6 -surface fsaverage lhrh -mni305 > > -fsd rest -per-run -sliceorder odd > > > > The -mni305-1mm could be more useful? > > My raw-data are: > > data_type UINT16 > > dim1 64 > > dim2 64 > > dim3 48 > > dim4 140 > > datatype 512 > > pixdim1 3.312500 > > pixdim2 3.312500 > > pixdim3 3.312500 > > pixdim4 3.000000 > > cal_max 0.0000 > > cal_min 0.0000 > > file_type NIFTI-1+ > > > > 2) In the mri_segstats the input is > > subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz. > > Do you agree? Conversely, should I use the .odd like > > fmcpr.odd.sm6.mni305.1mm.nii.gz or fmcpr.odd.sm6.mni305.2mm.nii.gz? > > > > 3) If I interested to obtained the time course from a unique region > > expressing the merging of some thalamic regions (i.e. 8121plus 8122 plus > > 8123), which is the options that should I added? > > > > Thanks, > > > > Stefano > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu mailto: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 >
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