Hi Stef,
sorry, I was out of office for a few days. I don't quite see why this
happens - have you tried to call the functions directly as described in
the manual? In either case, the error seems to stem from spm_vol which
is called by spm_check_registration which only wants to show you the
images. There may be an issue with doing this remotely or with
-nodisplay which is why I already put this call to
spm_check_registration into a try, ... end; wrapper in the latest
version of mw_com_gen, which I will send to you in a minute. Try this
one and see what happens.
Cheers
Marko
Stef Meliss schrieb:
> Hello Marko,
>
> Thanks again for your explanations and suggestions.
>
> We tried to use COM to produce an age-specific TPM and T1 image.
> However, running this code
>
> %% TPM and T1
>
> spm('defaults','fmri');
>
> spm_jobman('initcfg');
>
> matlabbatch{1}.spm.tools.com_cfg.predicts = {'/Volumes/DATA
> UOR/HippoKid/Templates
> etc./mw_com_predictors_HPK_unified-segmentation.mat'};
>
> matlabbatch{1}.spm.tools.com_cfg.domean = 1;
>
> matlabbatch{1}.spm.tools.com_cfg.smooth = 2;
>
> matlabbatch{1}.spm.tools.com_cfg.wsmooth = -1;
>
> matlabbatch{1}.spm.tools.com_cfg.mrf = 0;
>
> matlabbatch{1}.spm.tools.com_cfg.SANLM = 0;
>
> matlabbatch{1}.spm.tools.com_cfg.outd = '/Volumes/DATA
> UOR/HippoKid/Templates etc.';
>
> matlabbatch{1}.spm.tools.com_cfg.outf = 2;
>
> spm_jobman('run',matlabbatch);
>
> Resulted in the following error:
>
> Hello stefaniemeliss, welcome to mw_com_gen...
>
> ... checking provided data file
> mw_com_predictors_HPK_unified-segmentation from /Volumes/DATA
> UOR/HippoKid/Templates etc., please wait...
>
> ... thank you for providing data for 158 subjects with 4
> predictors each...
>
> ... processing tissue class 1/6, please wait...
>
> ... processing tissue class 2/6, please wait...
>
> ... processing tissue class 3/6, please wait...
>
> ... processing tissue class 4/6, please wait...
>
> ... processing tissue class 5/6, please wait...
>
> ... processing tissue class 6/6, please wait...
>
> ... processing T1 data, please wait...
>
> ... saving averaged tissue classes to a single prior file, please
> wait...
>
> Failed 'Cerebromatic Toolbox'
>
> Error using spm_vol>spm_vol_hdr (line 80)
>
> File "/Volumes/DATA UOR/HippoKid/Templates
> etc./mw_com_prior_Age_0074.nii" does not exist.
>
> In file "/Users/stefaniemeliss/Dropbox/Matlab/spm12/spm_vol.m" (v5958),
> function "spm_vol_hdr" at line 80.
>
> In file "/Users/stefaniemeliss/Dropbox/Matlab/spm12/spm_vol.m" (v5958),
> function "spm_vol" at line 61.
>
> In file
> "/Users/stefaniemeliss/Dropbox/Matlab/spm12/spm_check_registration.m"
> (v6245), function "spm_check_registration" at line 34.
>
> In file
> "/Users/stefaniemeliss/Dropbox/Matlab/spm12/toolbox/com_toolbox/mw_com_gen.m"
> (???), function "mw_com_gen" at line 1110.
>
> In file
> "/Users/stefaniemeliss/Dropbox/Matlab/spm12/toolbox/com_toolbox/tbx_cfg_com.m"
> (???), function "com_run_tbx" at line 154.
>
> The following modules did not run:
>
> Failed: Cerebromatic Toolbox
>
> Do you have any thoughts on this? That would be very helpful!
>
> Best regards,
>
> Stef
>
> On 18/06/2018, 08:08, "Marko Wilke" <[log in to unmask]>
> wrote:
>
> Hi Stef,
>
> thanks for your mail. Let's see:
>
> > There are three sets of parameters online - derived from different
>
> > strategies for spatial normalisation if I understand it correctly.
>
> Yes.
>
> > Given that our sample is quite homogeneous (age range: 62.04 - 90.48
>
> > months; 53% female, all scanned using a 3T Siemens Trio), which
>
> > mw_com_info.mat should we use?
>
> I would suggest to use the "unified segmentation" dataset which seemed
>
> like the best compromise overall. The "affine only" was used as a
>
> reference point from earlier days.
>
> > Does the choice affect later steps in the pre-processing?
>
> In terms of obtained results, it really should otherwise I would have
>
> wasted a lot of time ;) You could argue that the likely ensuing DARTEL
>
> procedure will effectively supersede the initial choice, but that
> would
>
> be up to you to find out.
>
> > Further, the batch mode of mw_com_gen states, that one
>
> > should make sure that the requested output is available with the
>
> > selected data file. Could you please explain which data file is
>
> > necessary to obtain a certain output?
>
> I was not referring to a file, but to information, as in age, gender,
>
> and field strength for each subject. This remark refers to you
> trying to
>
> enter, e.g., subject age outside of the specified range, which
> would not
>
> work.
>
> > My layman understanding would be
>
> > that it would only possible to get Dartel/Shoot template output
> if the
>
> > mw_com_info.mat saved in the com_parameters_Dartel folder was
> used. Does
>
> > that mean that TPM and T1 can only be generated using either
>
> > com_parameters_affine/mw_com_info.mat or
>
> > com_parameters_unified-segmentation/mw_com_info.mat as initial
> input?
>
> Yes, you will likely want to generate a "standard" TPM (one 6 class
> TPM)
>
> using the "unified segmentation" dataset and then a DARTEL TPM (6
>
> iterations of GM and WM) using the DARTEL dataset described in the
>
> second publication. These should then be entered into your processing
>
> stream at the appropriate places.
>
> > After reading both papers, I was wondering whether it is
> generally more
>
> > recommended to use CAT12 for segmentation and pre-processing when
>
> > dealing with unusual (i.e. 6-year-old children) populations
> compared to
>
> > the implementations in SPM - especially when handling structural
> data. I
>
> > am not sure which preprocessing pipeline is more appropriate in our
>
> > case. I am weighing up two options (after creating both Dartel
> template
>
> > and TPM using COM): Would it be better to use the SPM12 segmentation
>
> > that - to my understanding - relies more on tissue priors given
> the fact
>
> > that we will create an age-appropriate TPM in COM followed by Run
> Dartel
>
> > (existing Templates) using the COM Dartel template? Or would it be
>
> > better to use the CAT12 segmentation specifying sample-specific
> COM TPM
>
> > and template to assist the spatial normalisation?
>
> That, as John likes to state, depends on your definition of
> "better" and
>
> can likely only be answered empirically. You (in my opinion) correctly
>
> describe the problem, but what the answer is is hard to say.
>
> > Would you recommend to
>
> > always run an initial round of SPM segmentation to obtain the
>
> > bias-corrected image and segment the obtained bias-corrected images
>
> > afterwards as described in the referred publications?
>
> No, that was only done in this case as I had data from different
> sources
>
> and wanted to have equal starting estimates for the final processing
>
> round. In a homogeneous sample, I would suggest to rather play with
> the
>
> bias estimate options.
>
> > Thanks for sharing your expertise with us!
>
> For what it's worth ;)
>
> Cheers
>
> Marko
>
> > On 18/05/2018, 16:08, "Marko Wilke"
> <[log in to unmask]>
>
> > wrote:
>
> >
>
> > Hello Stef,
>
> >
>
> > as it seems no-one has answered your query, I will at least
> have a
>
> > stab
>
> >
>
> > at the pediatric aspects of it:
>
> >
>
> > > 4. Last but not least, we would like to create a study
> specific
>
> > sample
>
> >
>
> > > using the Dartel algorithm. How many structural scans are
>
> >
>
> > > recommended to use in order to run this procedure
>
> > successfully? In
>
> >
>
> > > total, we have around 100 structural scans, but some
> images
>
> > are only
>
> >
>
> > > rated as moderately good in terms of their quality. So
> when
>
> > creating
>
> >
>
> > > the template, should we only use the high quality
> images or
>
> > would it
>
> >
>
> > > be better to include all images that will be used in the
>
> > analysis?
>
> >
>
> > > Related to that, if we use a study-specific template,
> will it
>
> > still
>
> >
>
> > > be possible to perform ROI analysis? If so, what steps
> would be
>
> >
>
> > > necessary to do that and does that have any
> implications on the
>
> >
>
> > > pre-processing steps?
>
> >
>
> > One, you should always use all contributing subjects if you
> want to
>
> >
>
> > generate your own template. This has actually been discussed
> once or
>
> >
>
> > twice before on this list (which using the archive search
> function at
>
> >
>
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?S1=spm may have
> revealed ;)
>
> >
>
> > Two, more images are usually better, but if you look at the
>
> > simulations
>
> >
>
> > shown in Figures 5-8 in a recent paper
>
> >
>
> >
> (https://www.frontiersin.org/articles/10.3389/fncom.2017.00005/full) you
>
> >
>
> > will see that the quality of the generated tissue maps
> continues to
>
> >
>
> > increase way after reaching 100 subjects. Hence, in your
> case you may
>
> >
>
> > want to consider looking into alternative methods of
> generating a
>
> >
>
> > template matched to your pediatric population (as a hint,
> also try
>
> >
>
> > https://doi.org/10.1016/j.dib.2017.12.001).
>
> >
>
> > Three, using standard ROIs with a custom template is always
> a tricky
>
> >
>
> > question. The larger and more general the regions are, the less
>
> > relevant
>
> >
>
> > this will be, but an issue it is. There is a number of
> things you can
>
> >
>
> > do: you could manually define your own regions of interest
> on your own
>
> >
>
> > template, you could match the ROI to your template (e.g.,
> the original
>
> >
>
> > GM map forming the basis for the standard ROI to your final
> DARTEL GM
>
> >
>
> > template), you could use larger ROIs and assume that they
> will broadly
>
> >
>
> > match the regions you are interested in, or you could use
> functionally
>
> >
>
> > and/or diffusion-MRI-defined ROIs from your own population.
> Or you
>
> > could
>
> >
>
> > come up with an approach I did not yet mention, of which
> certainly
>
> > there
>
> >
>
> > are many. In other words, it will depend on the very
> question you
>
> > have,
>
> >
>
> > on your data, and your requirements for spatial specificity.
>
> >
>
> > > Thank you for taking the time to consider this request. I
> am looking
>
> >
>
> > > forward to your thoughts on the issues mentioned.
>
> >
>
> > Not sure I have helped but I tried :)
>
> >
>
> > Cheers
>
> >
>
> > Marko
>
> >
>
> > --
>
> >
>
> > ____________________________________________________
>
> >
>
> > Prof. Dr. med. Marko Wilke
>
> >
>
> > Facharzt für Kinder- und Jugendmedizin
>
> >
>
> > Leiter, Experimentelle Pädiatrische Neurobildgebung
>
> >
>
> > Oberarzt der Abteilung Neuropädiatrie
>
> >
>
> > Universitäts-Kinderklinik
>
> >
>
> > Marko Wilke, MD, PhD
>
> >
>
> > Pediatrician
>
> >
>
> > Head, Experimental Pediatric Neuroimaging
>
> >
>
> > Consultant in Pediatric Neurology
>
> >
>
> > University Children's Hospital
>
> >
>
> > 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/
>
>>
>
> > ____________________________________________________
>
> >
>
> --
>
> ____________________________________________________
>
> Prof. Dr. med. Marko Wilke
>
> Facharzt für Kinder- und Jugendmedizin
>
> Leiter, Experimentelle Pädiatrische Neurobildgebung
>
> Oberarzt der Abteilung Neuropädiatrie
>
> Universitäts-Kinderklinik
>
> Marko Wilke, MD, PhD
>
> Pediatrician
>
> Head, Experimental Pediatric Neuroimaging
>
> Consultant in Pediatric Neurology
>
> University Children's Hospital
>
> 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/
>
> ____________________________________________________
>
--
____________________________________________________
Prof. Dr. med. Marko Wilke
Facharzt für Kinder- und Jugendmedizin
Leiter, Experimentelle Pädiatrische Neurobildgebung
Oberarzt der Abteilung Neuropädiatrie
Universitäts-Kinderklinik
Marko Wilke, MD, PhD
Pediatrician
Head, Experimental Pediatric Neuroimaging
Consultant in Pediatric Neurology
University Children's Hospital
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/
____________________________________________________
|