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Subject:

Re: CAT12: Questions about the results generated by CAT12

From:

Christian Gaser <[log in to unmask]>

Reply-To:

Christian Gaser <[log in to unmask]>

Date:

Wed, 2 Jan 2019 10:13:22 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (85 lines)

Dear Feng,

switch off writing the 3D cortical thickness maps (which is experimental).

Best,

Christian



Dear Christian,
 
I have tried the first solution that add the line to my batch (attached batch_new): matlabbatch{1}.spm.tools.cat.estwrite.extopts.expertgui    = 1; However, it still did not work: can not generate the mri_atlas folder, csf files and so on.
 
So, I turned to try the second solution: I made a customized cat_default file (attached cat_defaults_feng) and then type:
/THL7/home/qinwen/software/matlab_toolbox/spm12/toolbox/cat12/cat_batch_cat.sh /THL7/home/qinwen/data/liu_test/T1Img_example/010001/co20151102_181340QUMINGYUE.nii -d /THL7/home/qinwen/data/liu_test/tianhe_code/cat_defaults_CHIMGEN.m -m /THL7/home/qinwen/software/matlab/bin/matlab
 
This could generate all the volume files and mri_atlas files. However, there is something wrong after displaying thickness (attached catlog_co20151102_181340QUMINGYUE.txt and catreport_co20151102_181340QUMINGYUE.pdf):
Display thickness: /THL7/home/qinwen/data/liu_test/T1Img_example/010001/surf/lh.thickness.co20151102_181340QUMINGYUE
Display thickness: /THL7/home/qinwen/data/liu_test/T1Img_example/010001/surf/rh.thickness.co20151102_181340QUMINGYUE
 
------------------------------------------------------------------------
CAT Preprocessing error for co20151102_181340QUMINGYUE:
------------------------------------------------------------------------
Too many input arguments.
------------------------------------------------------------------------
  456 - cat_io_writenii
 1863 - cat_main
  721 - cat_run_job1070
   16 - cat_run_newcatch
  398 - run_job
  161 - cat_run
   29 - cfg_run_cm
 1688 - local_runcj
  959 - cfg_util
  469 - fill_run_job
  247 - spm_jobman
   94 - cat_batch_cat
 
Could you give me some suggestions?
 
Best,
Feng
 
发件人:Christian Gaser <[log in to unmask]>
发送时间:2018-12-19 16:37
主题:Re: [SPM] CAT12: Questions about the results generated by CAT12
收件人:"SPM"<[log in to unmask]>
抄送:
 
Dear Feng, 
 
this is indeed somewhat weird. It looks like the expert mode was not recognized by the Linux server system. You can try to add the following line to your batch to force the expert mode: 
matlabbatch{1}.spm.tools.cat.estwrite..extopts.expertgui    = 1; 
 
It might also work if you create a customized cat_default file with your own settings and you call CAT12 from the shell using 
cat_batch_cat.sh your_nifti_files -d your_cat_defaults_file.m -m your_matlab_command 
 
This will automatically distribute your files to the available processors. Please check the help function of cat_batch_cat.sh. 
 
Best, 
 
Christian 
 
On Tue, 18 Dec 2018 17:00:04 +0800, chenhf_uestc <[log in to unmask]> wrote: 
 
>Dear CAT experts: 
> 
>  
> 
>I came across a problem when I use CAT12 expert mode (my version is CAT12.5 (r1364)). Actually, in my case, I would like to program a batch >code (attached) of the CAT12 expert mode, and tested this code (run the batch) in Personal Computer (Windows), virtual box (Linux) and our >server (Linux). The generated results were the same between Personal Computer (Windows) and virtual box (Linux). However, the results by >using server (Linux) was different from above-mentioned two ways. For example, the results generated by server did not have the folder >“mri_atlas” and in the mri folder, there were only about 10 images (the other two generated about 30 images). 
> 
>  
> 
>In addition, if I click the “Run” button on CAT12 expert mode GUI, the results are the same among these three ways (Personal Computer (Windows), virtual box (Linux) and our server (Linux)). Because in the future, we would like to run the batch on our server (Linux). So I am >wondering where is the problem and how could I deal with it? 
> 
>The report files were also attached. 
> 
>  
> 
>Any help would be greatly appreciated! 
> 
>Best, 
> 
>Feng 

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