External Email - Use Caution converting the time series data into the conformed space
mri_vol2vol --reg /Applications/freesurfer/subjects/fMRI_ADNI/subj/rest/001/register.dof6.lta --mov /Applications/freesurfer/subjects/fMRI_ADNI/subj/rest/001/fmcpr.nii.gz --fstarg --o subj/rest/001/fmpr.conformed.mgz mri_segstats --seg $SUBJECTS_DIR/subj/mri/ThalamicNuclei.v10.T1.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i subj/rest/001/fmpr.conformed.mgz --avgwf /Users/Stefano/Desktop/FS_FAST_ADNI_Results/Thalami_nuclei/Time_Series/subj.MNI --id 8103 --id 8104 --id 8105 --id 8106 --id 8108 --id 8109 --id 8110 --id 8111 --id 8112 --id 8113 --id 8115 --id 8116 --id 8117 --id 8118 --id 8119 --id 8120 --id 8121 --id 8122 --id 8123 --id 8125 --id 8126 --id 8127 --id 8128 --id 8129 --id 8130 --id 8133 ERROR: dimension mismatch between input volume and seg input 256 256 256 seg 169 105 118 > Il 12 aprile 2019 alle 20.42 "Greve, Douglas N.,Ph.D." > <dgr...@mgh.harvard.edu> ha scritto: > > 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 1:46 PM, std...@virgilio.it mailto:std...@virgilio.it wrote: > > > > > > External Email - Use Caution > > > > Thanks!! > > > > 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> mailto: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 > > > 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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