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I have a python module that extracts everything I considered useful from a full recon-all output folder for machine learning. I actually used it for predicting ASD.
Have a look here: https://secure-web.cisco.com/1y2aCFTmfPbByJKeWu1_Uh_jIlFUNKJ_d_VL40iCrt_69BxnK5knYslqw8wEDtvoum1ShsMi0Nc8X86liS3KqKE0ITcEdCFbLApCbgGQhtmmCBrYAzrJ2Z59CURoPhchVH8XeQK9JA81XV67C-k2nZxRnCKWj-N4sQRfpBBYELnWiJ2x3GWPB3rb5_oMLBidpzhXQRZ_zsOziCt5VN9Jz47k0rb1q8OI85DFzl-LDwHemXEUh0zys5uA-3NQAzL89jV2lQPjWIuaz_Av7j4Zng_U3B6mB0tBfsQ9AgQWKmye3eBo3PS-OZaqzGKfBJhpu/https%3A%2F%2Fdfsp-spirit.github.io%2Fbrainload%2Fv0.3.5%2Fbrainload.html%23module-brainload.braindescriptors
Best,
Tim
> On 03/10/2022 4:06 PM REEM ABU BAKR BAHATHIQ <rbahathiq0001@stu.kau.edu.sa> wrote:
>
>
> External Email - Use Caution
>
> great ..
>
> I want the sizes of the sub-cortical regions, will I depend here on the
> output of the mri folder, for example the image wmparc .mgz, or do I need
> another image or other data?
>
> Is there a reference that can help me extract image features for deep
> learning?
>
> Thanks in advance
>
> في الخميس، 24 فبراير 2022 في 7:35 م تمت كتابة ما يلي بواسطة Fischl,
> Bruce <BFISCHL@mgh.harvard.edu>:
>
> > I see. Well, you will probably want some combination of cortical thickness
> > maps and subcortical volumes at the least, although of course other
> > information might be important as well (connectivity, myelin content,
> > etc…). These things have different shapes (in the python sense) so you’ll
> > have to sort out a network architecture that lets you combine them
> >
> >
> >
> > Cheers
> >
> > Bruce
> >
> >
> >
> > *From:* freesurfer-bounces@nmr.mgh.harvard.edu <
> > freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *REEM ABU BAKR
> > BAHATHIQ
> > *Sent:* Thursday, February 24, 2022 11:28 AM
> > *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> > *Subject:* Re: [Freesurfer] recon-all outpputs for deep learning
> >
> >
> >
> > * External Email - Use Caution *
> >
> > Sorry for not making it clear
> >
> > you are right.
> >
> > Yes, I want to diagnose autism spectrum disorder from brain images using
> > structural measurements such as the gray matter volumes of regions or at
> > the voxel level.
> > Then, since deep learning is a black box that simply cannot know what it
> > has learned, there is a so-called "unit of attention" that can point to the
> > most important areas involved in the decision-making of the deep learning
> > model.
> >
> >
> >
> > في الخميس، 24 فبراير 2022 في 6:19 م تمت كتابة ما يلي بواسطة Fischl,
> > Bruce <BFISCHL@mgh.harvard.edu>:
> >
> > Sorry, can you explain a bit more about what you want to do. What does
> > “demonstrate morphological variation” mean? Just quantify variability? Are
> > there any variables that you are correlating it with (e.g. disease status,
> > cognitive measure, etc…)? I don’t understand what you are trying to do
> >
> > Cheers
> >
> > Bruce
> >
> >
> >
> > *From:* freesurfer-bounces@nmr.mgh.harvard.edu <
> > freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *REEM ABU BAKR
> > BAHATHIQ
> > *Sent:* Thursday, February 24, 2022 7:37 AM
> > *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> > *Subject:* [Freesurfer] recon-all outpputs for deep learning
> >
> >
> >
> > * External Email - Use Caution *
> >
> > Hello Freesurfer experts
> >
> > I want to apply deep learning to structural brain images processed by
> > Recon-all. My goal is to demonstrate the morphological variation(e.g., gray
> > matter volumes or cortical thickness) of brain regions in structural
> > magnetic resonance imaging using convolutional neural networks (CNN). Then
> > interpret those models on the basis of the region of interest.
> >
> >
> >
> > But I'm still distracted by the model input . I searched before but still
> > couldn't decide which Recon-all output I should use to perform the task. I
> > think I'll use the folder(mri) but I'm not sure which file.
> >
> >
> >
> > can any one guide me .
> >
> >
> >
> > Thanks,
> >
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--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
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