External Email - Use Caution
This seems to have something to do with the image read/write tools in FS's
Python tools not being able to handle ushort pixel types. One way around
this would be to convert the input image into e.g., floats before calling
samseg, but for a real fix in the code I'm looking at Andrew... (?)
On Wednesday, March 9, 2022, <daedalu...@aol.com> wrote:
> Thank you Koen,
>
> Your suggestion allowed run_samseg to run for a few minutes, but...
>
>
> daedalus@DESKTOP-TILLA3B:/usr/local/freesurfer/7-dev/subjects$ run_samseg
> --input o_ADNI_002_S_4654__MRI-m072.nii --output T1-only
> ##----------------------------------------------
> Samsegment Options
> ##----------------------------------------------
> output directory: T1-only
> input images: o_ADNI_002_S_4654__MRI-m072.nii
> modelSpecifications: {'FreeSurferLabels': [0, 165, 258, ...
>
> ........ process ran for an additional few minutes and then crashed with
> the following statements (Any Thoughts?) ..........
>
>
> maximalDeformation=0.0750 minLogLikelihood=-0.8762
> maximalDeformation=0.0000 minLogLikelihood=-0.8762
> appliedScaling: 1.0021
> INFO: This is an unsigined short.
> Traceback (most recent call last):
> File "/usr/local/freesurfer/7-dev/python/scripts/run_samseg", line 179,
> in <module>
> reg_only=args.reg_only
> File
> "/usr/local/freesurfer/7-dev/python/packages/freesurfer/samseg/Samseg.py",
> line 252, in segment
> initTransform=initTransform
> File
> "/usr/local/freesurfer/7-dev/python/packages/freesurfer/samseg/Samseg.py",
> line 271, in register
> initTransform=initTransform
> File
> "/usr/local/freesurfer/7-dev/python/packages/freesurfer/samseg/Affine.py",
> line 72, in registerAtlas
> self.saveResults( savePath, worldToWorldTransformMatrix,
> imageToImageTransformMatrix )
> File
> "/usr/local/freesurfer/7-dev/python/packages/freesurfer/samseg/Affine.py",
> line 473, in saveResults
> inputImage = fs.Volume.read(self.imageFileName)
> File "/usr/local/freesurfer/7-dev/python/packages/freesurfer/ndarray.py",
> line 103, in read
> result = bindings.vol.read(filename)
> ValueError: unknown MRI data type ID: 10
> daedalus@DESKTOP-TILLA3B:/usr/local/freesurfer/7-dev/subjects$
>
>
> The image that I am trying to test with this process is a standard
> T1-weighted image from ADNI, and Freesurfer had been able to run the basic
> segmentation (-recon-all, took about four hours and ran to completion
> without errors), so I'm not sure why Samseg can't identify the "MRI data
> type".
>
> Thanks in advance for any insights you might be able to share.
>
> -Randy
>
>
>
> -----Original Message-----
> From: Koen Van Leemput <leem...@gmail.com>
> To: daedalu...@aol.com <daedalu...@aol.com>; Freesurfer support list <
> freesurfer@nmr.mgh.harvard.edu>
> Sent: Tue, Mar 8, 2022 11:18 pm
> Subject: Re: [Freesurfer] run_samseg output folder permissions error
>
> It looks like you have an extra slash in front of the output file name, so
> you're trying to write in the root directory...
>
> On Tuesday, March 8, 2022, <daedalu...@aol.com> wrote:
>
> External Email - Use Caution
> Dear experts,
>
> Having installed Freesurfer on WSL2, I was able to get the basic FS
> segmentation to run without error. However, when I tried to run_samseg on
> a single T1 image, I received the following error message (permissions
> denied creating the "output folder")
>
> Is there anything in the trace (below) that provides a clue?
>
> daedalus@DESKTOP-TILLA3B:/usr/ local/freesurfer/7-dev/ subjects$
> run_samseg --input o_ADNI_002_S_4654__MRI-m072. nii --output /T1-only
> -samsegOutput/
> Traceback (most recent call last):
> File "/usr/local/freesurfer/7-dev/ python/scripts/run_samseg", line 67,
> in <module>
> os.makedirs(args. outputDirectory, exist_ok=True)
> File "/usr/local/freesurfer/7-dev/ python/lib/python3.6/os.py", line
> 220, in makedirs
> mkdir(name, mode)
> PermissionError: [Errno 13] Permission denied: '/T1-only-samsegOutput/'
>
>
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