Dear SPMers, dear Helmut & Christian,
thank you very much for your kind responses and for the information on background masking. For my analyses using the cat12 toolbox I now started to use background masked MP2Rage images. Interestingly, however, using the SPM segmentation without the cat12 toolbox always allowed me to simply put in the raw images without any prior "noise" reduction steps and the segmentation procedure worked out perfectly fine. Is the segmentation algorithm different in cat12 and the "normal" segmentation pipeline?
Additionally, I also ugraded to CAT12 r886 and finally got an error report (See attachments). I also copied the text in the matlab main window (MATLAB_notes). Hope that helps.
Thank you very much for your help.
Elisabeth
----- Original Message -----
From: "Julian Macoveanu" <[log in to unmask]>
To: [log in to unmask]
Sent: Monday, March 7, 2016 11:56:07 AM
Subject: Re: [SPM] cat12 longitudinal tlbx processing
Hi all,
After upgrading to CAT12 r886 the segmentation seem to work, but not
the normalisation. I also get like Imis, only the p1r* and p2r* files
and not the normalised modulated wmp* ones. I do get the wmavg* file.
However, I get some errors during the segmentation of the
pre-intervention file, not sure if it is related or not, the segmented
files look fine:
Final cleanup (gcutstr=0.50):
Level 1 cleanup (ROI estimation)
Exception in thread "AWT-EventQueue-0"
javax.swing.text.StateInvariantError: Can't render line: 186
at javax.swing.text.PlainView.drawLine(Unknown Source)
at com.mathworks.mde.cmdwin.CmdWinSyntaxUI$SyntaxPlainView.drawLine(CmdWinSyntaxUI.java:539)
at javax.swing.text.PlainView.paint(Unknown Source)
Br,
Julian
On Fri, Mar 4, 2016 at 2:26 PM, Imis Dogan <[log in to unmask]> wrote:
> Dear Christian,
>
> I had the same problem using cat12_r864. After installing the latest version cat12_r878 (published March 1st) the segmentation seems to work now.
> However, only p1r* and p2r* files are written, but no mwp[12]r* files, although both normalization and modulation are included in the script.
>
> Thank you very much!
> Best, Imis
...
------------------------------------------------------------------------
CAT12 r886: ./avg_CON_A_BH18_Post_UNI_struc.nii
------------------------------------------------------------------------
APP: Rough bias correction:
Initialize 7s
Estimate background 2s
Initial correction 7s
Refine background 2s
Final correction 6s
Background correction 1s
Final scaling 2s
27s
Coarse affine registration 5s
Affine registration 5s
SPM preprocessing 1: 77s
SPM preprocessing 2: 89s
Global intensity correction:
WARNING: Peaks of SPM segmentation do not fit to average segmentation intensity!
spm[0.39,0.71,1.00] ~= [0.17,0.73,1.00]median 16s
SANLM noise correction (NCstr=0.75):
...
Global intensity correction:
Failed 'CAT12: Segmentation'
Error using cat_main_gintnorm (line 347)
Bad SPM-Segmentation. Check image orientation!
In file "/home/chris/Documents/MATLAB/spm/spm12/toolbox/cat12/cat_main_gintnorm.m" (v882), function "cat_main_gintnorm" at line 347.
In file "/home/chris/Documents/MATLAB/spm/spm12/toolbox/cat12/cat_main.m" (v884), function "cat_main" at line 567.
In file "/home/chris/Documents/MATLAB/spm/spm12/toolbox/cat12/cat_run_job.m" (v886), function "cat_run_job" at line 519.
In file "/home/chris/Documents/MATLAB/spm/spm12/toolbox/cat12/cat_run.m" (v877), function "run_job" at line 208.
In file "/home/chris/Documents/MATLAB/spm/spm12/toolbox/cat12/cat_run.m" (v877), function "cat_run" at line 117.
No executable modules, but still unresolved dependencies or incomplete module inputs.
The following modules did not run:
Failed: CAT12: Segmentation
Skipped: Apply deformations (many images)
Skipped: Move/Delete Files
Failed 'Segment longitudinal data'
Error using MATLABbatch system
Job execution failed. The full log of this run can be found in MATLAB command window, starting with the lines (look for the line showing the exact #job as displayed in this error message)
------------------
Running job #2
------------------
The following modules did not run:
Failed: Segment longitudinal data
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