Re: [Freesurfer] Time course thalamic subregions

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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 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:

    > > 

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    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


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