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." DGREVE@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, stdp82@virgilio.it mailto:stdp82@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." <DGREVE@mgh.harvard.edu> mailto:DGREVE@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, stdp82@virgilio.it mailto:stdp82@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 > >>
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