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 wrote:

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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 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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