Hi,
I ran probtrackx2 with surfaces using the GUI (FSL 5.0, FDT - FMRIB's diffusion toolbox 3.0). In order to display the results in fslview I projected the probtrackx2 output (fdt_paths.nii) onto the same subject's brain.nii.gz image. I did this because when trying to initially load the MNI152_T1_2mm_brain.nii.gz, I received an error. I assumed that it made more sense to overlay onto brain.nii.gz than MNI152_T1_2mm_brain.nii.gz, since I used the former as the 'seed/surface reference image' when running probtackx2.
Although I'm able to view the fdt_paths.nii output in fslview using brain.nii.gz, the images are being displayed in an unusual manner. The orientations seems correct, e.g., left is still left and superior is still superior, etc., however, the orthogonal view is displaying the coronal section upside down and the midsagittal section in a vertical orientation. All the freesurfer label files used for the seed/surface mask (L_cACC.gii), waypoint mask (L_SFG.gii) and exclusion mask (R_hemi_exclusionmask.gii) are in GIFTI format and the brain.nii.gz was the conformed freesurfer structural image (brain.mgz) that was converted to NIFTI using mri_convert.
I'm wondering why fslview is displaying the images in this manner and if I shouldn't have used the brain.nii.gz as the 'seed/surface reference image' when running probtrackx2 with surfaces. Or is it that fslview displays GIFTI differently, than NIFTI? Any help is greatly appreciated :)
I have attached a screenshot of the display to illustrate the problem and below is my probtrackx2 log:
/usr/share/fsl/5.0/bin/probtrackx2 -x /data/emma/migraine_DTI/006/raw/preprocess/dtifit_bkup/LcACC.gii -l --modeuler --onewaycondition -c 0.2 -S 2000 --steplength=0.5 -P 50 --fibthresh=0.01 --distthresh=0.0 --sampvox=0.0 --
xfm=/data/emma/migraine_DTI/006/raw/preprocess/dtifit_bkup/freesurfer2fa_warp.nii.gz --invxfm=/data/emma/migraine_DTI/006/raw/preprocess/dtifit_bkup/fa2freesurfer_warp.nii.gz --meshspace=freesurfer --
seedref=/data/emma/migraine_DTI/006/raw/preprocess/dtifit_bkup/brain.nii.gz --avoid=/data/emma/migraine_DTI/006/raw/preprocess/dtifit_bkup/R_hemi_exclusionmask.gii --forcedir --opd -s
/data/emma/migraine_DTI/006/raw/preprocess.bedpostX/merged -m /data/emma/migraine_DTI/006/raw/preprocess.bedpostX/nodif_brain_mask --dir=/data/emma/migraine_DTI/006_L_ACC --waypoints=/data/emma/migraine_DTI/006_L_ACC/waypoints.txt --
waycond=AND
---------------------------------------------
Thanks.
Emma
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