ERROR: problem defining fixed image dimension + align: failed executing: ' + cmd about clearmap2

[SaibotMagd]

Did you stitch the Data before you run the alignment? Use:

s = ws.source('raw') 
print(s)
print(s.shape)

[ywang219]

s = ws.source('raw')
print(s)
print(s.shape)

Hi, thank you for the response. It doesn't seem to resolve the issue...

the same error came up:

~/ClearMap2/ClearMap/Alignment/Elastix.py in align(fixed_image, moving_image, affine_parameter_file, bspline_parameter_file, result_directory, processes)
550
551 if res != 0:
--> 552 raise RuntimeError('align: failed executing: ' + cmd);
553
554 return result_directory

RuntimeError: align: failed executing: /home/yidan/ClearMap2/ClearMap/External/elastix/build/bin/elastix -threads 1 -m /home/yidan/test/brain7test/resampled_autofluorescence.tif -f /home/yidan/test/brain7test/resampled.tif -p /home/yidan/ClearMap2/ClearMap/Resources/Alignment/align_affine.txt -out /home/yidan/test/brain7test/elastix_resampled_to_auto

[SaibotMagd]

But this is another problem. Now it seems like he can't find the files. Did you check if every file is in the right folder?
Also try to change the parameter to:

"result_directory" : ws.filename('resampled_to_auto')"

aka delete the "elastix_". I think the last update solved this problem.

[ywang219]

But this is another problem. Now it seems like he can't find the files. Did you check if every file is in the right folder?
Also try to change the parameter to:

"result_directory" : ws.filename('resampled_to_auto')"

aka delete the "elastix_". I think the last update solved this problem.

Thank you for your help! oops my bad. Yes there are 2 problems at once. And I did delete the "elastix_", the same 2 problems still occur.

I checked that files are in the right folder.

---

Running elastix with parameter file 0: "/home/yidan/ClearMap2/ClearMap/Resources/Alignment/align_affine.txt".

Current time: Tue Jul 28 10:39:03 2020.
Reading the elastix parameters from file ...

ERROR: problem defining fixed image dimension.
The parameter file says: 3
The fixed image header says: 2
Note that from elastix 4.6 the parameter file definition "FixedImageDimension" is not needed anymore.
Please remove this entry from your parameter file.
Errors occurred!

RuntimeError Traceback (most recent call last)
in
13 };
14
---> 15 elx.align(**align_channels_parameter);

~/ClearMap2/ClearMap/Alignment/Elastix.py in align(fixed_image, moving_image, affine_parameter_file, bspline_parameter_file, result_directory, processes)
550
551 if res != 0:
--> 552 raise RuntimeError('align: failed executing: ' + cmd);
553
554 return result_directory

RuntimeError: align: failed executing: /home/yidan/elastix/bin/elastix -threads 1 -m /home/yidan/test/brain7test/resampled_autofluorescence.tif -f /home/yidan/test/brain7test/resampled.tif -p /home/yidan/ClearMap2/ClearMap/Resources/Alignment/align_affine.txt -out /home/yidan/test/brain7test/elastix_resampled_to_auto

[SaibotMagd]

Did you check if the raw/cfos file was stitched correctly? What dataset are you using? If you use slices you have to build a stitched stack before:

source = ws.source('raw');
  sink   = ws.filename('stitched')
  io.delete_file(sink)
  io.convert(source, sink, processes=None, verbose=True);

If it's in tiles you have to stitch it using the wobbly stitcher. Be aware of the missing autofluorescence files in the new 2020 Dataset for Cellmap, so this dataset can't work at all.

[umedtb]

Hi,

I have the same issue. If I run "result_directory" : ws.filename('elastix_resampled_to_auto'), I get

ValueError: Cannot find name for type 'elastix_resampled_to_auto'!

If I change to "result_directory" : ws.filename('resampled_to_auto'), I get

RuntimeError: align: failed executing: /home/ClearMap/dataDisk/clearmap_git/ClearMap2/ClearMap/External/elastix/build/bin/elastix -threads 48 -m /home/ClearMap/scratchDisk/ImageSample/200929_Subject99_Saline _12-03-42/resampled_autofluorescence.tif -f /home/ClearMap/scratchDisk/ImageSample/200929_Subject99_Saline _12-03-42/resampled.tif -p /home/ClearMap/dataDisk/clearmap_git/ClearMap2/ClearMap/Resources/Alignment/align_affine.txt -out /home/ClearMap/scratchDisk/ImageSample/200929_Subject99_Saline _12-03-42/elastix_resampled_to_auto

In this case, an empty "elastix_resampled_to_auto" directory also appears in the image folder (along with other files).

Have you solved this issue? What does "-threads 48" in the error message could indicate to?

I have RTX 3090 which according to forums is not compatible with CUDA10 or older. Could this be an issue?

[umedtb]

I think I found the issue. elastix that comes in the external folder does not load properly. Here is the message:

error while loading shared libraries: libANNlib-4.9.so.1

Any ideas how to fix this?

[umedtb]

I have found the solution. The following lines must be added to .bashrc file (located in home folder):

export PATH=/home/.../ClearMap/External/elastix/build/bin:$PATH
export LD_LIBRARY_PATH=/home/.../ClearMap/External/elastix/build/bin:$LD_LIBRARY_PATH

From the web search it looks to be a recurring issue on CentOS.

[ChristophKirst]

This seems solved now that elastix is working. I close it.
We will try to include more documentation for this in the next updates of ClearMap.

[Hesham3esa]

can i please know how did you get over this problem?
RuntimeError: align: failed executing: /home/hesham/ClearMap2/ClearMap/External/elastix/build/bin/elastix -threads 16 -m /media/hesham/Extra/1.1 final/resampled_autofluorescence.tif -f /media/hesham/Extra/1.1 final/resampled.tif -p /home/hesham/ClearMap2/ClearMap/Resources/Alignment/align_affine.txt -out /media/hesham/Extra/1.1 final/elastix_resampled_to_auto

i tried the bashrc stuff and it didnt work