Hi.  I have been working with on a similar problem.  Take a look at this code which we use to convert the hippocampal subfield images into nifti space.  I think the only thing you’re missing is the “orientLAS” command which will should fix the orientation between freesurfer and FSL space.

 

Best,

 

Mark

 

____________________
Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461

Ph: 718-430-4011

FAX: 718-430-3399

Email: [log in to unmask]

 

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From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Daniela Valério
Sent: Tuesday, May 8, 2018 5:41 PM
To: [log in to unmask]
Subject: [FSL] Convert ROIs from FreeSurfer to FSL

 

Dear Experts, 

 

I have some ROIs in FreeSurfer and I want to convert them to FSL  (where I am doing my analysis). I want to convert the aparc+aseg.mgz file (I renamed by subject_aparcAseg.mgz) into different ROIS. These are the commands that I applied: 

 

mri_convert $output_dir/${subject}_aparcAseg.mgz $output_dir/${subject}_aparcAseg.nii.gz

 

applywarp -i ${output_dir}/${subject}_aparcAseg.nii.gz -o ${output_dir}/${subject}_aparcAseg_mni.nii.gz -r ${brain_standard} --interp=trilinear -w ${output_dir}/${subject}_highres2standard_warp.nii.gz

 

 

However, my registration is not okay (I have in attachment the print screen). After the registration, I used this command to extract the specific ROIs that I want (e.g., hippocampus):

 

fslmaths $output_dir/${subject}_aparcAseg_mni.nii.gz -uthr 17 -thr 17 $output_dir/${subject}_LeftHippocampus.nii.gz

 

 

My hippocampus ROI is deviated from the hippocampus anatomical place. For sure the problem is my "applywarp" command. Do you experts have any idea why I'm having these difficulties?

 

 

Thanks in advance for any help, 

 

Best Regards, 

 

 

Daniela Valéri