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Thanks, Valentina. The thalamic nuclei were included in the FreeSurfer lookup table in the development version, so I doubt they’d be included in the FreeSurfer HSV. Is it possible to add them manually? Also: why don’t you use Freeview to visualize your niftis? Cheers, /E
-- 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
From: Valentina Mancini Valentina.Mancini@unige.ch Date: Wednesday, 27 March 2019 at 10:08 To: "Iglesias Gonzalez, Eugenio" e.iglesias@ucl.ac.uk, Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Conversion of thalamic nuclei labels
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 > > >