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First of all, I would like to thank you all for your help.

#Eugenio: yes probably there is a way to manually import the thalamic lookup table in FSLeyes. However, I don't have to use the thalamic segmentation in FSL, but in SPM and it would be much better if I could find a way to visualize the subnuclei in SPM.

#Juan: are you suggesting to convert the nifti files that I obtained from the mgz into cifti space or to directly convert from mgz to cifti space? Do you know if then it is possible to import the cifti files in SPM and to use them as ROIs?

Da: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> per conto di Sanchez, Juan (NYSPI) <Juan.Sanchez@nyspi.columbia.edu>
Inviato: mercoledì 27 marzo 2019 15:17:41
A: Iglesias Gonzalez, Eugenio; Freesurfer support list
Oggetto: Re: [Freesurfer] Conversion of thalamic nuclei labels

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wb_command -volume-label-import LR_amyhipthal.nii.gz $templatedir/SUBCORT_LR.txt LR_amyhipthal_labeled.nii.gz

this is with the amy and hip but can be done with just the thalamus

you just need to edit the label file

From: Sanchez, Juan (NYSPI)
Sent: Wednesday, March 27, 2019 10:15:18 AM
To: Iglesias Gonzalez, Eugenio; Freesurfer support list
Subject: Re: [Freesurfer] Conversion of thalamic nuclei labels

We have run the thalamic and amyhip segmentation scripts on HCP data and were convert the segmented native nuclei into cifti space including the subcortial nifti

set thal = ${subjid}_ThalamicNuclei.v10.T1

mri_convert -rt nearest -rl $projdir/$subjid/T1w/T1w_acpc_dc_restore.nii.gz {$thal}.mgz {$thal}.nii.gz

applywarp --rel --interp=nn -i {$thal}.nii.gz -r $projdir/$subjid/MNINonLinear/T1w_restore.nii.gz -w $projdir/$subjid/MNINonLinear/xfms/acpc_dc2standard -o {$thal}_native.nii.gz

applywarp --interp=nn -i {$thal}_native.nii.gz -r $projdir/$subjid/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz -o {$thal}_Atlas_2mm.nii.gz

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Valentina Mancini <Valentina.Mancini@unige.ch>
Sent: Wednesday, March 27, 2019 10:08:36 AM
To: Iglesias Gonzalez, Eugenio; Freesurfer support list
Subject: Re: [Freesurfer] Conversion of thalamic nuclei labels

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Hi Eugenio,

Yes, when I move the cursor I can see different pixel values corresponding to the different areas of the thalamus.

In FSLeyes you can select different lookup tables, and there is one called "Freeseurfer HSV", but it doesn't work anyway.

However, I used FSLeyes only because it was the default programm to open nifti files, but it was the same in SPM ad Conn.

Can you please suggest me any other way to open the nifti file with its lookup table?

As I was planning to use it in SPM, the ideal would be to manage to visualize the different subnuclei in SPM/Conn.

Best,

Valentina

Da: Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.uk>
Inviato: mercoledì 27 marzo 2019 14:55:00
A: Freesurfer support list
Cc: Valentina Mancini
Oggetto: Re: [Freesurfer] Conversion of thalamic nuclei labels

Hi Valentina,
I've never used FSLeyes but I suspect you'd need a lookup table to visualize the nuclei properly. Do you see different pixel values when you move your cursor over the different areas of the thalamus in FSLeyes?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias

ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London

Research staff
Martinos Center for Biomedical Imaging
Massachusetts General Hospital

Research Affiliate
Computer Science and Artificial Intelligence Laboratory (CSAIL)
Massachusetts Institute of Technology

Lecturer on Radiology
Harvard Medical School

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On 27/03/2019, 09:53, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:

    and your full command line for conversion?
    On Wed, 27 Mar 2019, Iglesias
    Gonzalez, Eugenio wrote:

    >
    >         External Email - Use Caution
    >
    > Dear Valentina
    > Resolution should not be affected by MRI_convert. Can you please send us an example/screen capture?
    > Cheers
    > Eugenio
    >
    > Sent from mobile, please excuse brevity and typos
    >
    > ____________________________________________________________________________________________________
    > From: Valentina Mancini <Valentina.Mancini@unige.ch>
    > Sent: Wednesday, March 27, 2019 5:56:34 AM
    > To: freesurfer@nmr.mgh.harvard.edu
    > Cc: Iglesias Gonzalez, Eugenio
    > Subject: Conversion of thalamic nuclei labels
    >
    > Dear all,
    >
    >
    > I ran the thalamic segmentation implemented in FreeSurfer and, according to visual inspection, I got
    > nice results with a good delineation of all the nuclei.
    >
    > Then, I wanted to use the label of the thalamic nuclei to select an ROI in the MGN and the MD to
    > perform functional connectivity with cortical regions in SPM.
    >
    > Therefore, I converted the outputs of the segmentation
    > (ThalamicNuclei.v10.T1.mgz and ThalamicNuclei.v10.FSvoxelSpace.mgz) into nifti files by using the
    > command "mri_convert .mgz .nii".
    >
    > However, the resulting labels of the thalamus have a different resolution and I cannot visualize
    > anymore the different thalamic subnuclei but only the entire thalamus.
    >
    >
    >
    > Do you have any suggestion to convert thalamic labels into nifti without losing the different
    > subnuclei?
    >
    > Do you think that the thalamic segmentation is accurate enough to be used to perform functional
    > connectivity?
    >
    >
    >
    > Thank you and best regards,
    >
    >
    >
    > Valentina Mancini
    >
    >
    >