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Dear Experts,

Sorry for my delay and thank you for your help.

Mark you used just the flirt command to register your ROIs into MNI space.
Do you think that the fnirt registration is not necessary?  Because I'm
using both and after to apply fnirt my hippocampus ROI decreased the size
significantly.


Thanks in advance,

Best regards,

Daniela Valério


2018-05-14 0:24 GMT+01:00 Mark Wagshul <[log in to unmask]>:

> 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}_highr
> es2standard_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
>
>
>