External Email - Use Caution 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 <[email protected]> > 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 <[email protected]>: > > > 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:* [email protected] < > > [email protected]> *On Behalf Of *REEM ABU BAKR > > BAHATHIQ > > *Sent:* Thursday, February 24, 2022 11:28 AM > > *To:* Freesurfer support list <[email protected]> > > *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 <[email protected]>: > > > > 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:* [email protected] < > > [email protected]> *On Behalf Of *REEM ABU BAKR > > BAHATHIQ > > *Sent:* Thursday, February 24, 2022 7:37 AM > > *To:* Freesurfer support list <[email protected]> > > *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, > > > > _______________________________________________ > > Freesurfer mailing list > > [email protected] > > *MailScanner has detected a possible fraud attempt from > > "secure-web.cisco.com" claiming to be* > > https://secure-web.cisco.com/1CiNr9-ZbORfNwKb1W0N4O_aKMrL58JWVGaLfZmzYohXT5ZVrZSbDj0ak0dItYdzOvdcEvmUeVGQX4bfUQ0u4U_qPdgDQ4Rkjt7MvPKhcY02iHNBl8mt1WLYlYvZAdnOEvBKpUfm5EXQIUcu4NgG4wxcWv-LgXQqrGvNpIS0cZmLE-eE4YEPWoI3LdRAoi-vHAdGiT6D476TKu3RtRMTa_qfFIWUsXmvXJbyApPMsDFSXa_ojCwkelS7Od6t8YWZH6ygXUA5TeuXcuYKnDr3etpduiD6Tx-QohgXLmxvLBSJGyyumIFE9aRr6Vvb-Oq4YPiJq95KxxZf_sObXh-OuIg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > <https://secure-web.cisco.com/1Nhqb_f9HCF_LDzs7mzo8KHO6tP_hOJ_kYWyHgY-7Y-hBhnv1q-tSFjqkdsvtL6uOVeithziUno3bDr3SWwXV0CneXrPaChtC5G24GCuCfeLhCxl0yf24Hr_lzN21IY34PHJMFjGPGijxBlXX3Dem0QtRMo2-XjMu16CnhhNEZTIUzlOyfHmOUkDjyicH1GoqUG1NPwhROefuYCZsNv9XtAbkexx7yxEuk409LmiPwasjYpkbSmiFkDrc70CJPFWJXxV5oDxhjAX_dpX4ofL2QDHHXGjJFI8PRL2fBaGQb8alfhTJ-h7Xi6QQkd_sKzT83EJBAIZJffsnmDZyzGV_Hw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> > > > > _______________________________________________ > > Freesurfer mailing list > > [email protected] > > https://secure-web.cisco.com/1CiNr9-ZbORfNwKb1W0N4O_aKMrL58JWVGaLfZmzYohXT5ZVrZSbDj0ak0dItYdzOvdcEvmUeVGQX4bfUQ0u4U_qPdgDQ4Rkjt7MvPKhcY02iHNBl8mt1WLYlYvZAdnOEvBKpUfm5EXQIUcu4NgG4wxcWv-LgXQqrGvNpIS0cZmLE-eE4YEPWoI3LdRAoi-vHAdGiT6D476TKu3RtRMTa_qfFIWUsXmvXJbyApPMsDFSXa_ojCwkelS7Od6t8YWZH6ygXUA5TeuXcuYKnDr3etpduiD6Tx-QohgXLmxvLBSJGyyumIFE9aRr6Vvb-Oq4YPiJq95KxxZf_sObXh-OuIg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > _______________________________________________ > Freesurfer mailing list > [email protected] > https://secure-web.cisco.com/1_sOxWq-OQDWEOxPcEKBn9q1GB5rQ4sZ4mSunp7W97gJbQHV1J427XdOHj3pwSc5bPSEEAEYy9UAONr1a-hfplg4gCCVv6JHUi0Ag7nxkPuCDRbP4z0Sm9TO_mNznSkw6GZijewdyK18UF1Djd2Fr5mAG_Yu8wbUVF8L5t_3UoMGDreepbHziWXmk8SIcwiyg6aznWRuz0dSqw8dxxYdMIAK4FVI2TUo2u3s_kd_s-HE8VuWHrCSDEUDy6yQ6B3dtA0KSxXyBEmcEVACM3q0NRAXOU5VNz626MImuxGhCfMxvkUv7exIJn3k6rqGhweSA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General Brigham > Compliance HelpLine at > https://secure-web.cisco.com/1xqflSoiP80jlR25KFtboT6lNStxvdTyLiMcgJ3cqhpAxLcVDFcgdSMGE76l3uFlmkwPtexoPAcbfbU7nIONE8jJgVeemF1qCAXoOo3a2bDINqxBy7Ac-7-QRNvBm-ncpdJ9wmeCY9LLFebjSjdmBq3mrNT1qn7UDTl7Ktxlo9_g4-Z1V9U0G7HBJ6ivnqwOBba-XZbEdAKrPQju48rNj587SZkXy9-GXKVNCaiU3jv8OIRRdS7-KyYBMlpEc3M9IEJIf78Lwyq1MVUMlf0P3FTlt56MHpGy0Wgdzu0fOqekj-qruC1HQ6eCQChaB_han/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > > <https://secure-web.cisco.com/1xqflSoiP80jlR25KFtboT6lNStxvdTyLiMcgJ3cqhpAxLcVDFcgdSMGE76l3uFlmkwPtexoPAcbfbU7nIONE8jJgVeemF1qCAXoOo3a2bDINqxBy7Ac-7-QRNvBm-ncpdJ9wmeCY9LLFebjSjdmBq3mrNT1qn7UDTl7Ktxlo9_g4-Z1V9U0G7HBJ6ivnqwOBba-XZbEdAKrPQju48rNj587SZkXy9-GXKVNCaiU3jv8OIRRdS7-KyYBMlpEc3M9IEJIf78Lwyq1MVUMlf0P3FTlt56MHpGy0Wgdzu0fOqekj-qruC1HQ6eCQChaB_han/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . > Please note that this e-mail is not secure (encrypted). If you do not wish > to continue communication over unencrypted e-mail, please notify the sender > of this message immediately. Continuing to send or respond to e-mail after > receiving this message means you understand and accept this risk and wish to > continue to communicate over unencrypted e-mail. -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
