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robdahn / boney

Bone evaluation toolbox for SPM12
GNU General Public License v3.0
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Does CAT12 pipeline works? #10

Closed iPsych closed 1 month ago

iPsych commented 2 months ago

In boney_preprocessing file case {2,'cat'} % not working

It seems CAT12 integration is still not fully implemented, right? Can I use already processed CAT12 result from outside now? or CAT implementation is not yet developed at all?

iPsych commented 1 month ago

Below is full error log. It seems like SPM or CAT12 version incompatibility. Can you specify exact versions of those software you are using ? I guess that It would be easier to use that specific version instead of debugging code accord to CAT12/SPM12 update. If command approach works, would you let me know the working command using CAT for segmentation?

`` SPM12: v7771 12:58:43 - 26/09/2024

Initialising SPM : ........done

SPM present working directory: /media/user/disk/Boney

SPM12: spm_boney (v0.1) 12:58:55 - 26/09/2024

Boney Toolbox
Version 0.1 alpha

26-Sep-2024 12:59:27 - Running job #1

26-Sep-2024 12:59:27 - Running 'Bone segmentation' 0 of 1 SPM segmentations can be used. 1 of 1 files need preprocessing. Item opts: No field(s) named ngaus warpreg redspmres biasstr accstr Item registration: No field(s) named T1 brainmask cat12atlas darteltpm shootingtpm regstr bb vox Item extopts: No field(s) named segmentation surface admin Item atlases: No field(s) named aal3 mori anatomy3 julichbrain Tian_Subcortex_S4_7T Schaefer2018_100Parcels_17Networks_order Schaefer2018_200Parcels_17Networks_order Schaefer2018_400Parcels_17Networks_order Schaefer2018_600Parcels_17Networks_order Item GM: No field(s) named warped Item WM: No field(s) named warped Item atlas: No field(s) named warped dartel Item bias: No field(s) named native dartel 26-Sep-2024 12:59:28 - Failed 'Bone segmentation' Error using spm_jobman>fill_run_job (line 472) No executable modules, but still unresolved dependencies or incomplete module inputs. In file "/media/ipsych/EVEESS_10TB_15/Boney/spm12/spm_jobman.m" (v7744), function "fill_run_job" at line 472. In file "/media/ipsych/EVEESS_10TB_15/Boney/spm12/spm_jobman.m" (v7744), function "spm_jobman" at line 247. In file "/media/ipsych/EVEESS_10TB_15/Boney/spm12/toolbox/boney/boney_segment_preprocessing.m" (???), function "boney_segment_preprocessing" at line 89. In file "/media/user/disk/Boney/spm12/toolbox/boney/boney_segment.m" (???), function "boney_segment" at line 128.

The following modules did not run: Failed: Bone segmentation ``

robdahn commented 1 month ago

No, it was already working (at least under some conditions) but I hadn't removed the comment ;-)

I did not test CAT so often as it uses nearly the same segmentation as SPM for the head classes with some correction those are mainly to optimise the brain brain classes. Relevant differences, as I was able to see so far, are given in case of children when the SPM registration failed. Moreover, I observed various problems with the head/bone segmentation in CAT that is coming from the focus on brain tissue (what I have to fix some day).

I have just tested some of the settings again to avoid problems with the different expertgui settings in CAT.

PolonaCa commented 1 month ago

We would strongly suggest to use the SPM segmentation for the bones.