Hello Arjun,
sorry to hear that you are having issues with the COM toolbox.
I have had feedback from some people that the generated TPMs are not
working well, but that was usually due to people assessing their own
small population using the "Estimate regression parameters" without
changing the estimation parameters (which are designed for a huge
sample). This does not seem to be the case here.
Also, if you checked the TPM for overall appearance, and they work when
fed to spm12, they seem to generally work alright (which is a relief to
me ;) If you want, you can send me the file off-list and I can look at them.
My best guess would be that, as indicated in the error message, the
affine registration is the issue. Not surprisingly, children's brains
are different (the whole point of COM), so too stringently using the
affine parameters from an adult population may bring about trouble. I
have had a similar failure a while ago, and the solution as usual came
from Christian with a new, more robust version of the affine estimation
part of CAT12. I have not seen this error since updating (on December
5th; I am not sure these changes are already available in the public
version).
Also, w.r.t. your bonus question, COM will also generate SHOOT templates
for you if you so desire. They are actually quite similar to DARTEL ones
but contain an extra 1-sum(1:n) tissue class volume. If you are
paranoid, you could generate both DARTEL and SHOOT templates using COM
(using the same parameters, of course) and supply both to CAT12.
Hope this helps
Marko
Sethi, Arjun schrieb:
> Dear SPMers,
>
> I’ve been bashing my head against this one for a while now, and thought
> I’d ask the hive mind.
>
> I’m analysing data from a study of kids (mean age around 8.6 years
> [range: 5-11]) with CAT12 and making TPMs and dartel templates with COM.
> The problem is I keep on getting an ‘Empty segmentation error’ (see
> underneath the main body of this email, or attached error file; Versions
> are: Matlab r2017a, SPM 7487, com 1.1, CAT12.5 r1364). This only occurs
> when I’m using the TPMs created using COM. The segmentation actually
> works fine with the standard SPM TPMs in CAT12, and the custom COM TPMs
> seem to produce a reasonable segmentation when using the standard SPM
> segment module. In short, it seems like there is nothing fatally wrong
> with either component alone (CAT12, COM TPMs), but they do not seem to
> want to play nice together.
>
> Here are a few troubleshooting steps that I have run so far:
>
> Within CAT12:
>
> 1. I have ensured the origin is appropriately close to the AC on the
> T1w (moving) image and checked that this lines up well with the TPMs
> 2. I have fiddled with pretty much every available GUI option to no
> avail (Affine Regularisation method, Strength of inhomogeneity
> correction, Affine preprocessing, skull stripping method)
> 3. In addition to the above points re: the specificity of this problem
> to CAT12 and the COM TPMs, I thought I’d also mention that the
> custom DARTEL templates from COM also work fine in CAT12 segmentation.
> 4. The study is longitudinal in nature, but this error occurs
> regardless of whether I use the regular or longitudinal segmentation
> options. I’m doing most of my troubleshooting with the
> cross-sectional segment to keep things simple.
>
> Within COM (using unified segmentation regression parameters):
>
> 1. I’ve tried with a variety of age sets as input to make sure there
> was no unexpected behaviour associated with a specific combination.
> Beyond that all our data are from male subjects collected at 3T, so
> these are the only changes to regression parameters I have tried)
> 2. I’ve tried using the affine only regression parameters, but still no
> dice.
> 3. I noticed that the final COM TPM is visually quite different (more
> ‘detail’ within the brain, which appears as greyscale rather than
> just zeros) from the default SPM TPMs, and surmised this is because
> of how the COM TPMs are calculated (which ensures that TPM values
> sum to one, and adds the remainder to the last tissue class). When I
> change this so that the remainder isn’t added (and the final TPM is
> more visually similar to the SPM default), there was still no change.
>
> If anyone has any input it would be hugely appreciated as I’m a little
> stumped at this point. It’s looking more and more to me like there is
> nothing wrong with the segmentation or affine registration (as SPM does
> this just fine, it would seem), but some kind of write error or
> orientation issue that isn’t immediately obvious or observable (wrt the
> latter, I’ve also checked the header info of the SPM and COM TPMs and
> there were no differences that stuck out to me). I’ve noticed there have
> been a few empty segmentation errors reported about this on the board
> but I haven’t seen any resolution applicable here.
>
> Best wishes,
>
> Arjun
>
> PS I also have a bonus (☺), hopefully much simpler question: - I just
> wanted to confirm that when the DARTEL registration option is selected,
> that the shooting template within the GUI is not used. I notice that the
> DARTEL does run some ‘fast shooting’ and just wanted to clarify this
> does not rely on the shooting template input.
>
> ------------------------------------------------------------
>
> Arjun Sethi, PhD
>
> Postdoctoral Research Associate
>
> Forensic & Neurodevelopmental Sciences
>
> Institute of Psychiatry, Psychology & Neuroscience
>
> King’s College London
>
> 16 De Crespigny Park
>
> London SE5 8AF
>
> Tel: +44(0)207 848 5267
>
> ------------------------------------------------------------------------
>
> 15-Jan-2019 12:12:27 - Running job #10
>
> ------------------------------------------------------------------------
>
> 15-Jan-2019 12:12:27 - Running 'CAT12: Segmentation'
>
> Warning: Dartel template was changed: Please be aware that ROI analysis
>
> and other template-specific options cannot be used and ROI
>
> output has been deselected.
>
> > In cat_run>update_job (line 331)
>
> In cat_run (line 159)
>
> In cfg_run_cm (line 29)
>
> In cfg_util>local_runcj (line 1717)
>
> In cfg_util (line 972)
>
> In cfg_ui>MenuFileRun_Callback (line 710)
>
> In gui_mainfcn (line 95)
>
> In cfg_ui (line 53)
>
> ------------------------------------------------------------------------
>
> CAT12.5 r1364: 1/1: ./04_T1/ABC002A/anat9/ABC002A_4903_run1_T1w.nii
>
> ------------------------------------------------------------------------
>
> SANLM denoising (medium): 16s
>
> Internal resampling (1.20x1.05x1.05mm > 1.00x1.05x1.05mm): 2s
>
> APP: Rough bias correction:
>
> Initialize 5s
>
> Estimate background 32s
>
> Initial correction 15s
>
> Refine background 32s
>
> Final correction 12s
>
> Background correction 0s
>
> Final scaling 1s
>
> 99s
>
> Coarse affine registration 11s
>
> Affine registration 20s
>
> SPM preprocessing 1 (estimate 1): 32s
>
> SPM preprocessing 1 (estimate 2): 119s
>
> SPM preprocessing 1 (estimate skull-stripped): 104s
>
> SPM preprocessing 1 (estimate skull-stripped): 105s
>
> SPM preprocessing 2 (write):
>
> Write Segmentation 18s
>
> Update Segmentation
>
> ------------------------------------------------------------------------
>
> CAT Preprocessing error for ABC002A_4903_run1_T1w:
>
> ------------------------------------------------------------------------
>
> Empty Segmentation:
>
> Possibly the affine registration failed. Pleace check image orientation.
>
> Tissue class: BG CSF GM WM
> HDH HDL
>
> Rel. to image volume: 33.70 0.00 0.00 0.00
> 37.86 28.43
>
> Rel. to brain volume: Inf NaN NaN NaN
> Inf Inf
>
> Tissue intensity: 0.47 748.77 1522.66 2296.56
> 1986.58 1138.68
>
> ------------------------------------------------------------------------
>
> 216 - cat_main
>
> 721 - cat_run_job1070
>
> 16 - cat_run_newcatch
>
> 398 - run_job
>
> 161 - cat_run
>
> 29 - cfg_run_cm
>
> 1717 - local_runcj
>
> 972 - cfg_util
>
> 710 - MenuFileRun_Callback
>
> 95 - gui_mainfcn
>
> 53 - cfg_ui
>
> ------------------------------------------------------------------------
>
> Warning:cat_io_report:CATgui: Incomplete report creation in
> cat_io_report because of incomplete CAT parameters.
>
> Print 'Graphics' figure to:
>
> /data/project/abc/03_Sorted/04_T1/ABC002A/anat9/report/catreport_ABC002A_4903_run1_T1w.pdf
>
> 15-Jan-2019 12:21:51 - Failed 'CAT12: Segmentation'
>
> Error using cat_main (line 216)
>
> Empty Segmentation:
>
> Possibly the affine registration failed. Pleace check image orientation.
>
> Tissue class: BG CSF GM WM
> HDH HDL
>
> Rel. to image volume: 33.70 0.00 0.00 0.00
> 37.86 28.43
>
> Rel. to brain volume: Inf NaN NaN NaN
> Inf Inf
>
> Tissue intensity: 0.47 748.77 1522.66 2296.56
> 1986.58 1138.68
>
> In file "/data/project/abc/MatlabPath/spm12/toolbox/cat12/cat_main.m"
> (v1361), function "cat_main" at line 216.
>
> In file
> "/data/project/abc/MatlabPath/spm12/toolbox/cat12/cat_run_job1070.m"
> (v1348), function "cat_run_job1070" at line 721.
>
> In file
> "/data/project/abc/MatlabPath/spm12/toolbox/cat12/cat_run_newcatch.m"
> (???), function "cat_run_newcatch" at line 16.
>
> In file "/data/project/abc/MatlabPath/spm12/toolbox/cat12/cat_run.m"
> (v1332), function "run_job" at line 398.
>
> In file "/data/project/abc/MatlabPath/spm12/toolbox/cat12/cat_run.m"
> (v1332), function "cat_run" at line 161.
>
> The following modules did not run:
>
> Failed: CAT12: Segmentation
>
--
____________________________________________________
Prof. Dr. med. Marko Wilke
Facharzt für Kinder- und Jugendmedizin
Leiter, Experimentelle Pädiatrische Neurobildgebung
Oberarzt der Abteilung Neuropädiatrie
Universitäts-Kinderklinik
Marko Wilke, MD, PhD
Pediatrician
Head, Experimental Pediatric Neuroimaging
Consultant in Pediatric Neurology
University Children's Hospital
Hoppe-Seyler-Str. 1
D - 72076 Tübingen, Germany
Tel. +49 7071 29-83416
Fax +49 7071 29-5473
[log in to unmask]
http://www.medizin.uni-tuebingen.de/kinder/epn/
____________________________________________________
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