Re: [dsi-studio] Cannot align ROI file with DWI

[Frank Yeh]

Sorry about the problem, and hope I can help provide some insights

 

The final analysis results in 2942 tracts.

saving to data.src.gz.dti.fib.gz.tt.gz

connectivity=AAL2,FreeSurferDKT

connectivity_type=end

connectivity_value=count,mean_length

loading AAL2

searching AAL2 from the atlas pool...

ERROR: fail to open AAL2 failed. There is no such an atlas installed in the DSI Studio.

ERROR: file or atlas does not exist:AAL2

DSI Studio is looking for aal2.nii.gz under the /atlas/icbm152 directory but did not find it.

Additionally, if I define the whole path to the atlas it says that I need to insert the MRI T1:

command - 

path=D:\Users\Jesus CabreraAlvarez\Desktop\dsi_studio_win

for /f "delims=" %%x in ('dir *.fib.gz /b /d /s') do (

call dsi_studio.exe --action=trk --source="%%x" --min_length=15 --max_length=180 --seed_count=5000 --connectivity="D:\Users\Jesus CabreraAlvarez\Desktop\dsi_studio_win\atlas\ICBM152\AAL2.nii.gz" --connectivity_value=count,mean_length --connectivity_type=end --connectivity_threshold=0.0001 > "%%x.log.txt"

DSI Studio thought AAL2 is a native space ROI, but the image dimension is different from the DWI.

Here, AAL2 is the MNI space ROI, and you can signal DSI Studio this by renaming the file as AAL2_mni.nii.gz

This way, DSI Studio will treat it as MNI ROI and apply spatial normalization.

Hope this helps.

Frank