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In addition,

a) to convert the time series data into the conformed space and viceversa, I have run the command line listed below:

Il 26 agosto 2019 alle 20.02 stdp82@virgilio.it ha scritto:

Thanks. By specifying f-in-anat.nii as output the mri_vol2vol command runs fine.

How can I convert into the functional space the ThalamicNuclei.v10.T1.mgz? Of note, to convert the orig.mgz I have already added to the line --inv.

Il 26 agosto 2019 alle 15.35 "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu> ha scritto:

Is that all it prints out? BTW, you can just specify f-in-anat.nii as the output of mri_vol2vol, you never have to go into mgh format

On 8/23/2019 5:20 PM, stdp82@virgilio.it wrote:

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Hi,

I have used:

mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o f-in-anat.mgh
mri_binarize --i mri/ThalamicNuclei.v10.T1.mgz --min 8112 --max 8114 --o merged_ROIs.nii.gz
mri_segstats --seg merged_ROIs.nii.gz --id 1 --i f-in-anat.mgh --avgwf time_course

The error occurs when the followed command is running:
mri_convert.bin f-in-anat.mgh f-in-anat.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from f-in-anat.mgh...
/usr/local/freesurfer/bin/mri_convert: line 3: 29749 Killed 

Thanks

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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