Dear Marko and Stef,

 

Thank you both so much for your help and suggestions.

 

Marko - I will send you a separate link to the TPMs etc. It would be great if there was a new version floating around already that sorts this out. I did just check the latest available and it precedes December 5^th so it doesn’t look like it’s up publicly yet.

 

Steff -  that’s v interesting. Though moving forward rather than backwards in version number will (hopefully!) be the most likely eventual solution, I wouldn’t mind fiddling around with the old one anyway ☺ I’ve had a look and can’t see an archived version for 12.3 anywhere. Any chance you still have a copy somewhere you could send/link me to?

 

Super thanks again to both of you and fingers crossed one of these versions sorts this out!

 

Arjun

 

------------------------------------------------------------

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

 

 

Dear Arjun, dear Marko,

 

To add to this: I came across the same issue when segmenting data of an older population. Interestingly, I have only encountered this error message when using CAT12.5, but not in version 12.3, although I have used the same TPM, participant data, and parameters in both versions.

 

Do you have any thoughts on this?

 

Best regards,

Stef

 

 

___________

Stef Meliss

Doctoral Researcher

Motivation Science Lab

School of Psychology and Clinical Language Sciences

University of Reading

RG6 6AL (Sat Nav: RG6 7BE)

 

[log in to unmask]

+44 (0) 118 378 7937

 

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