The name is a long story but it is not a FLAIR acquisition it is a T1. I used Lesion Sgementation Toolbox in SPM to fill the lesions. Now I have this T1 filled and that is all I am using. 

On 11 Jun 2020, at 16:03, Niels Bergsland <[log in to unmask]> wrote:

While there may still be some other issue, you cannot run SIENA using different acquisition types (i.e. FLAIR and T1 in your case).

On Thu, Jun 11, 2020 at 3:32 PM Renew Andrade <[log in to unmask]> wrote:
I have these errors . I think the orientation is still a problem after fslreorient2std and robustfov.


siena IMG_505091_1mm_filled_lga_0.2_rmIMG_505091_FLAIR_1mm.nii.gz  T1.nii.gz
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
Image Exception : #63 :: No image files match: A_halfwayto_B_brain_seg
Image Exception : #22 :: Failed to read volume A_halfwayto_B_brain_seg
Error : No image files match: A_halfwayto_B_brain_seg
libc++abi.dylib: terminating with uncaught exception of type armawrap::AWException: Failed to read volume A_halfwayto_B_brain_seg
Error : No image files match: A_halfwayto_B_brain_seg
/usr/local/fsl/bin/siena: line 288: 75112 Abort trap: 6           ${FSLDIR}/bin/siena_diff ${A} ${B} -c $corr $sdo $sdopts >> report.siena
Image Exception : #63 :: No image files match: A_halfwayto_B_brain_seg
Image Exception : #22 :: Failed to read volume A_halfwayto_B_brain_seg
Error : No image files match: A_halfwayto_B_brain_seg
libc++abi.dylib: terminating with uncaught exception of type armawrap::AWException: Failed to read volume A_halfwayto_B_brain_seg
Error : No image files match: A_halfwayto_B_brain_seg
/usr/local/fsl/bin/siena: line 289: 75718 Abort trap: 6           ${FSLDIR}/bin/overlay 1 0 -c ${A}_halfwayto_${B} -a ${A}_halfwayto_${B}_brain_seg 1.1 3 ${A}_halfwayto_${B}_brain_seg_grot
Image Exception : #63 :: No image files match: A_halfwayto_B_brain_seg_grot
Image Exception : #22 :: Failed to read volume A_halfwayto_B_brain_seg_grot
Error : No image files match: A_halfwayto_B_brain_seg_grot
Error in slicer input, exiting...
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
Image Exception : #63 :: No image files match: A_to_B_flow
libc++abi.dylib: terminating with uncaught exception of type armawrap::AWException: No image files match: A_to_B_flow
/usr/local/fsl/bin/siena: line 299: 75753 Abort trap: 6           ${FSLDIR}/bin/fslmaths ${A}_to_${B}_flow -mul -1 ${A}_to_${B}_flowneg
Image Exception : #63 :: No image files match: A_to_B_flow
Image Exception : #22 :: Failed to read volume A_to_B_flow
Error : No image files match: A_to_B_flow
libc++abi.dylib: terminating with uncaught exception of type armawrap::AWException: Failed to read volume A_to_B_flow
Error : No image files match: A_to_B_flow
/usr/local/fsl/bin/siena: line 300: 75754 Abort trap: 6           ${FSLDIR}/bin/overlay 0 0 ${A}_halfwayto_${B} -a ${A}_to_${B}_flow 0.01 1 ${A}_to_${B}_flowneg 0.01 1 ${A}_halfwayto_${B}_render
Image Exception : #63 :: No image files match: A_halfwayto_B_render
Image Exception : #22 :: Failed to read volume A_halfwayto_B_render
Error : No image files match: A_halfwayto_B_render
Error in slicer input, exiting...

 Cannot open grA_halfwayto_Ba.png for reading
rm: grA_halfwayto_B?.???: No such file or directory

Finished. The SIENA report can be viewed by pointing your web browser at:
file:/Users/andraderenew/Downloads/IMG_505091_1mm_filled_lga_0.2_rmIMG_505091_FLAIR_1mm_to_T1_siena/report.html
Estimated percentage brain volume change (PBVC) = 
2.0



On 11 Jun 2020, at 12:30, paul mccarthy <[log in to unmask]> wrote:

Hi Andrade,

I would recommend running fslreorient2std (and robustfov, if necessary) on your images before starting SIENA, to see if that fixes the problem.

Paul

On Thu, 11 Jun 2020 at 11:13, Renew Andrade <[log in to unmask]> wrote:
Dear FSL experts:

All I have is that dc: stack empty. I am running siena on 2 images but it seem to me that when I see the report after bet  processing images have different orientations. Could that be teh problem?

Best,
Andrade.
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Buffalo Neuroimaging Analysis Center / University at Buffalo
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