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Hi Marko,
Thank you for the quick reply. I don't think I was sufficiently clear in my original message. The t1 used in the segment is one volume, not 192 images. In other words, just the one T1 file is specified in the "volume" section of the segment module, so I don't think that is the issue. Thanks again!
Cory
> On Jun 10, 2015, at 2:10 AM, Marko Wilke <[log in to unmask]> wrote:
>
> Hi Cory,
>
> just a hunch, but could it be that the 192 images in the place of the T1 are the problem? I assume these represent single slices from the acquisition but they should be in one volume with 192 slices, not provided separately. Try converting them to one volume using the DICOM import function and see if that helps.
>
> Cheers,
> Marko
>
> Cory Inman wrote:
>> Hi all,
>>
>> I'm looking for a solution to an error (below) I came across recently when trying to run the preproc_fmri.m batch job. I've localized the error to the spm_preproc8.m file in the toolbox/Seg folder, but I'm not sure how to address the error that comes up. For some background, I'm just trying out the new batch preprocessing on some data I recently acquired. I've fed in 4 sessions of multiband EPI images into the realign and unwarp module and a standard mprage_T1.img (192 images) into the volume section of the Segment module. All other information for subsequent steps have been left as their dependents (the defaults). Is there something I'm missing here? I've seen several previous comments referring to issues with the fudge factor (the ff variable in spm_preproc8 below), but I'm not sure if those same issues are relevant here. I'd just like to get my data to run through this new batch preprocessing. Please let me know if any other information would be helpful. Thank you in adva
> nce for your time and help!
>>
>> Cory Inman
>> Postdoctoral Fellow
>> Emory University
>>
>> Failed 'Segment'
>> Error using *
>> Inner matrix dimensions must agree.
>> In file "/spm12/toolbox/Seg/spm_preproc8.m" (v4148), function "spm_preproc8" at line 115.
>> In file "/spm12/toolbox/Seg/spm_preproc_run.m" (v4334), function "run_job" at line 102.
>> In file "/spm12/toolbox/Seg/spm_preproc_run.m" (v4334), function "spm_preproc_run" at line 30.
>> In file "/spm12/config/spm_cfg_preproc8.m" (v6148), function "spm_local_preproc_run" at line 417.
>>
>> This seems to be an issue with the calculation of the param variable (see Initialise Deformation below). Specifically the *, but I'm not sure how to address this issue.
>>
>> % Initialise Deformation
>> %-----------------------------------------------------------------------
>> param = [2 sk.*vx ff*obj.reg*[1 1e-4 0]];
>> lam = [0 0 0 0 0 0.01 1e-4];
>> scal = sk;
>> d = [size(x0) length(z0)];
>> if isfield(obj,'Twarp'),
>> Twarp = obj.Twarp;
>> llr = -0.5*sum(sum(sum(sum(Twarp.*optimNn('vel2mom',Twarp,param,scal)))));
>> else
>> Twarp = zeros([d,3],'single');
>> llr = 0;
>> end
>
> --
> ____________________________________________________
> PD Dr. med. Marko Wilke
> Facharzt für Kinder- und Jugendmedizin
> Leiter, Experimentelle Pädiatrische Neurobildgebung
> Universitäts-Kinderklinik
> Abt. III (Neuropädiatrie)
>
> Marko Wilke, MD, PhD
> Pediatrician
> Head, Experimental Pediatric Neuroimaging
> University Children's Hospital
> Dept. III (Pediatric Neurology)
>
> 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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