A Problem Regarding Comman Line in DSI

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maede...@gmail.com

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Sep 15, 2021, 9:40:42 AMSep 15
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Dear frank
I wanna  read a track trk file, filter it by an ROA (r8.nii), and output as another trk file.
the point is that my ROA is not in the space of my dwi and its reference is "spm152.nii".
I run the following code in a bash script but I get the error "cannot parse: dsi_studio".
 

 dsi_studio --action=ana --source=sub-CC310008_dwi.src.gz.gqi.1.25.fib.gz --tract=sub-CC310008_dwi.src.gz.gqi.1.25.fib.gz.trk.gz   --t1t2=spm152.nii  --roa=r8.nii  --output=filtered_track.trk.gz  > A.log.txt

I would be grateful if you could check and  let me know if the code is correct.
Best regards
Maedeh

Frank Yeh

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Sep 15, 2021, 10:23:13 AMSep 15
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Hi Maedeh,

You need to set the PATH to the dsi studio directory
PATH=C:\where_dsi_studio_is\

Also, rename spm152.nii to mni_spm152.nii so DSI Studio will treat it as an MNI space ROI.

Hope this helps,
Frank

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maede...@gmail.com

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Sep 15, 2021, 10:30:13 AMSep 15
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Thank you very much dear Frank
I did what u said and  I face an error again.
The following is what I get in log.txt:

DSI Studio Mar 14 2021, Fang-Cheng Yeh
source=D:/Lesion/LesionTesting/sub-CC310008_dwi.src.gz.gqi.1.25.fib.gz
action=ana
loading D:/Lesion/LesionTesting/sub-CC310008_dwi.src.gz.gqi.1.25.fib.gz...
tract=D:/Lesion/LesionTesting/sub-CC310008_dwi.src.gz.gqi.1.25.fib.gz.trk.gz
loading D:/Lesion/LesionTesting/sub-CC310008_dwi.src.gz.gqi.1.25.fib.gz.trk.gz...
loading D:/Lesion/LesionTesting/sub-CC310008_dwi.src.gz.gqi.1.25.fib.gz.trk.gz
D:/Lesion/LesionTesting/sub-CC310008_dwi.src.gz.gqi.1.25.fib.gz.trk.gz loaded
roa=r8.nii
read region from r8.nii
r8.nii dimension: (207,256,215)
DWI dimension: (96,96,66)
r8.nii has a different dimension from DWI
checking if there is --t1t2 assigned for registration
t1t2=mni_spm152.nii
registeration complete
1.07219e-06 3.13891e-43 -3.03165e-13 3.03165e-13
0 0 -nan -nan
-nan -nan -6.01535e-34 7.27274e-43
T1T2 dimension: (207,256,215)
T1T2 voxel size: 0.737463 0.737463 0.737463 
using t1t2 as the reference to load r8.nii
loading r8.niias an MNI space region
ERROR: please assign region name of an atlas.
Warning: --output is not used. Please check command line syntax.

Frank Yeh

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Sep 15, 2021, 11:11:09 AMSep 15
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Is r8.nii in the subject space or the MNI space?
Is spm152.nii in the subject space or the MNI space?

maedeh khalilian

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Sep 15, 2021, 11:25:44 AMSep 15
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I think they are both in subject space.
Actually spm152.nii is spm normalized version of ICBM152NLin2009.

Frank Yeh

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Sep 15, 2021, 11:33:31 AMSep 15
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I see. Then please don't rename spm152.nii to mni_spm.nii
Also, please update DSI Studio again and see what the output is.
It looks like the registration with spm152.nii failed.
Frank

maedeh khalilian

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Sep 15, 2021, 11:55:40 AMSep 15
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The problem got solved by updating
Thank you very much dear frank.
Best regards

Frank Yeh

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Sep 15, 2021, 12:39:14 PMSep 15
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Glad to know it works.
Frank

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