External Email - Use Caution        

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
 
http://www.jeiglesias.com
 

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
    >
    >
    >