Dear Flavia,

then, it's maybe not working with your segmentations that are not derived with SPM. You could give the SPM12 segmentation a trial that can deal very well with other image modalities. However, you have to use customized TPMs of infant data.

I will send you an upload link where you can upload one example file and I can see what's going wrong.

Best,

Christian

On Sun, 26 Feb 2017 16:46:03 +0100, Flavia Arduini <[log in to unmask]> wrote:

>Dear Christian,
>I thank you first of all for having responded.
>I tried to follow your advice but you see this error:
>
>Print 'Graphics' figure to:
>  /home/matlab/Scrivania/PROVA_CAT12/CAROFILO/report/catreport_c1*.pdf
>Failed  'CAT12: Segmentation'
>Error using error
>Formatted arguments cannot be non-scalar numeric matrices.
>In file "/home/matlab/Scrivania/spm12/spm12/toolbox/cat12/cat_main.m"
>(v1086), function "cat_main" at line 346.
>In file "/home/matlab/Scrivania/spm12/spm12/toolbox/cat12/cat_run_job.m"
>(v1087), function "cat_run_job" at line 628.
>In file
>"/home/matlab/Scrivania/spm12/spm12/toolbox/cat12/cat_run_newcatch.m"
>(???), function "cat_run_newcatch" at line 13.
>In file "/home/matlab/Scrivania/spm12/spm12/toolbox/cat12/cat_run.m"
>(v1083), function "run_job" at line 265.
>In file "/home/matlab/Scrivania/spm12/spm12/toolbox/cat12/cat_run.m"
>(v1083), function "cat_run" at line 155.
>
>The following modules did not run:
>Failed: CAT12: Segmentation
>
>It 'a different error than it had appeared to me trying to put the T2 weighted
>image, in fact, in that case rightly told me that the image contrast was
>low.
>I do not know if I can solve this problem of size.
>Thank you
>
>2017-02-24 10:36 GMT+01:00 Christian Gaser <[log in to unmask]>:
>
>> Dear Flavia,
>>
>> this will be quite challenging because I am not sure whether the quality
>> of the T2-weighted images and their segmentations will be sufficient to
>> extract cortical surfaces and thickness. Anyway, you could try the
>> following:
>> 1. Name your segmentations with c1* for GM, c2* for WM and c3* for CSF
>> (the names are that from the SPM12 segmentation approach)
>> 2. Call CAT12 in expert mode with cat12('expert')
>> 3. Call in batch mode: SPM->Tools->CAT12->CAT12 SPM Segmentation
>> 4. Select the c1* image(s)
>> 5. Set "Surface and thickness estimation" to "Yes"
>>
>> However, I am not sure this will work, because I have only prepared and
>> tried that for SPM12 segmentations.
>>
>> Best,
>>
>> Christian
>>
>> On Thu, 23 Feb 2017 13:19:11 +0100, Flavia Arduini <
>> [log in to unmask]> wrote:
>>
>> >Hi,
>> >I segmented with Mantis MRI T2-weighted of infants. Now I have to estimate
>> >the cortical thickness and I would do it with CAT12 that instead use MRI
>> >T1-weighted. There is a script extrapolated from segmentation of CAT 12
>> >relating only to the cortical thickness?
>> >I thank you in advance and I hope that there is someone that can help me.
>> >Regards
>> >
>> >Flavia Arduini
>> >
>>
>>
>>
>