Hi Steven
Why wouldn’t they be the same size? The qcache files have all been mapped to an
fs average icosahedral space, so they all have the same number of vertices (and
hence the same size)
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Steven Meisler
Sent: Monday, February 6, 2023 3:32 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] qcache morphometry measures are empty
External Email - Use Caution
Hi,
Following up in reporting that it does appear to be an issue with Nibabel and
not FreeSurfer. mri_diff between the metric files reveals that they are not
empty. I have found an alternative for loading the morphological metrics in
python, so consider this issue solved, though I am curious why the files are
all the same sizes.
Best,
Steven
On Feb 6, 2023, at 14:17, Steven Meisler
<smeis...@g.harvard.edu<mailto:smeis...@g.harvard.edu>> wrote:
Hello FreeSurfer developers,
(This issue is described in detail at the following link: MailScanner has
detected a possible fraud attempt from "secure-web.cisco.com" claiming to be
https://neurostars.org/t/freesurfer-qcache-outputs-empty/24677<https://secure-web.cisco.com/1z_dCK4QH-iYz_hvm5u5SeBYQFVo2AjBUeGX7L1n6t9FIatK_rvq8rdAZKVdiPiUw465zj3pUMnNwRbIBnSpaiV2XGNfnfiILhwXgxFa2ifYd75ObFHNn-gRbCJsGri9JJDWWB2TVP_0xd0HiNGfO-Sc7yrm3rAE1YANk05J9t4chYh6jl2Q8SbbqNcb3CASmui_Dh_wmj1uYMZhXnW8tDtZQhyYztmVXeRtjkIxUxwiyliBSmO2hMxjfKz9X8bCPoJIRjrERpXGe_wuK1WHTNBxOWP5wr2-Cfz_5duSwGSIO6BHNpYPnPY2tveDiAdQWBQUN1VNBGiDMmHiRaqskVg/https%3A%2F%2Fneurostars.org%2Ft%2Ffreesurfer-qcache-outputs-empty%2F24677>)
I am preparing a surface-based morphometry analysis. I ran recon-all v7.3.2
with qcache enabled. It completes without error and I do see the output files
in fsaverage space at the various smoothing kernels, as expected. However, the
fsaverage space smooth files appear to be empty, based upon trying to load
their data with the Python package Nibabel. Some other notes:
1) When I load the QCACHE files, there are no errors in loading the file, but
the data array returned is empty, so the files appear to be properly formatted
morphological files.
2) When I load the native space thickness file (e.g. surf/lh.thickness), I get
the expected full output with all data there, so I doubt it is a Nibabel issue.
3) This happens for all subjects, measurement types (e.g. area, volume, etc)
and smoothing kernels.
4) All qcache outputs are the same file size (668.6 kb), which doesn’t seem
like it should be right.
I am planning on running models on the data outside of Freesurfer since I have
to deal with complex tasks such as site harmonization and general additive
modeling, which is why I cannot proceed using the typical mris_preproc method.
Please let me know if I can provide any other helpful information in addressing
this.
Best,
Steven
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