External Email - Use Caution That is what I´m planning to do. Actually since some subjects have more than 2 time-points I was thinking that calculating slopes rather than pair-diff may be a better option.
Can I use long_mris_slopes with --do-spc (etc…) in my mapped PET images to the longitudinal surfaces within each subject? Since qdec long table is required, I am unsure how to provide my surface-mapped PET images instead of default (i.e. thickness). Alternatively, do I need to run my own GLMs within subject to compute slopes of PET signal? Much appreciated! Jesus From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Adam Martersteck Sent: Wednesday, September 21, 2022 2:46 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] [EXTERNAL] Re: Longitudinal PET analysis External Email. Do not click links or open attachments unless you trust the sender and content. Report suspicious emails using Report Phishing button or forward email to ph...@northwell.edu<mailto:ph...@northwell.edu> External Email - Use Caution On other thought: You may want to do Doug's suggestion of calculating the paired-diff in the longitudinal stream's subject-specific unbiased template space of each participant instead of doing it all in fsaverage. Then take the resultant file, the symmetrized percent change, or pc1, etc. from the subject-specific template space to fsaverage for your group statistics. On Wed, Sep 21, 2022 at 12:39 PM Gomar, Jesus <jgo...@northwell.edu<mailto:jgo...@northwell.edu>> wrote: External Email - Use Caution Thank you Doug, I will follow your suggestion. From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] On Behalf Of Douglas N. Greve Sent: Wednesday, September 21, 2022 9:58 AM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [EXTERNAL] Re: [Freesurfer] Longitudinal PET analysis External Email. Do not click links or open attachments unless you trust the sender and content. Report suspicious emails using Report Phishing button or forward email to ph...@northwell.edu<mailto:ph...@northwell.edu> You may be able to use one of the paired diff options in mris_preproc. Run it with --help. I also put some info on it below. QDEC has been deprecated --paired-diff After concatenating all the inputs together, create a new output file by computing paired differences, ie, Input1-Input2, Input3-Input4, etc. There must be an even number of inputs. The inputs are "pruned" before taking the difference, meaning that values for all inputs are set to 0 if any individual is 0. --paired-diff-norm Same as --paired-diff, but normalizes by average of time points, ie, (Input1-Input2)/((Input1+Input2)/2). --paired-diff-norm1 Same as --paired-diff, but normalizes by time point 1, ie, (Input1-Input2)/Input1. --paired-diff-norm2 Same as --paired-diff, but normalizes by time point 2, ie, (Input1-Input2)/Input2. On 9/20/2022 3:31 PM, Gomar, Jesus wrote: External Email - Use Caution Hello Freesurfer developers, I am interested in analyzing PET data following a longitudinal design. I have co-registered each PET image to the closest MRI in time processed through the longitudinal stream. I have sampled each co-registered PET image time-point onto fsaverage surface via the individual's subject surface (mri_vol2surf). From this point: 1. Is it possible to obtain spc (symmetrized percent change) using long_mris_slopes for each subject? 2. Is there a way to input the sampled surfaces into a qdec file for long_mris_slopes command? 1) FreeSurfer version: freesurfer-linux-centos6_x86_64-7.2.0. 2) Platform: Ubuntu 18,04.6 LTS 3) uname -a: Linux ubuntu 5.4.0-122-generic-Ubuntu UTC 2022 x86_64 x86_64 x86_64 GNU/Linux Thank you! Jesus The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1g7a4VHou5mIFBJdm_b4Sfpw37gRoUnVTTbcSjRVgelD6H4ySRSYAjjsDMaSsTp3jL8E7PUH1i9g-Zup0C8pdibnbfrr6cfm9i4OFvNEm3sn4zCqfFF4Yna3vXaOcqRk_PIS0uTk_46atqXOhRsBmeqd9ejHTjMUDDXoQBbc2nnzelpfODHNayFKYEeWFt1R-N9J5FUk55IXKiBzd6Z8NYvDAeKByFIEHH2Zl4L76ldfewStmyA5CXMRqVkLw9oxqmmK2R-m-E3L4EsxWx_1rP-fMB7PtrksnZJdfXgfc1Nuu6OVDiKU_Aya4i9DxJVgzCsknM76KfeBTz3Ibvk8G-g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<https://secure-web.cisco.com/1uGP3hYN_tD72oTOpV6w3aIje0O-s3pehp5O8gK_pPqbCa6FUsiC6aIJ4njY1mx6QJ2gTItxXtn5-5bXEVjY05n6E2nK21heEEZupTXxhf4w5hkqv6pX4ir2L7_tYiRlQktQZWGanZh1gZ7qXeeC2DAmGMHVkR1SFuTNzKQer5mAmePAi3GRS2tGkqISTxz6tECex1oxg34PsHgq_2CQZ1_jalgnI6hnp6HjQp7Fb6A-Ih9-tejqVttqKtfdN9u-CzMCEFTecGbxlghZZPoVZANVF5w1nKHvNkUDkR7nbT6piBamAJs-QlujNW_1pOZQUjamnNIhSY1VAN8nuXatKSw/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F11so9U0SwtG-cBzsNjclpJh_cfKDFsdBpIJMrrCh_9epBQwJrikfuS7PKaXgK4UeQpHwhgMD835hV3Khocv8_x0BsWX6eOuWWyPmKL_BGYYQYi3VY8E6Oc8MamgDZ2gMxK4RRNgOQxt7tLih9L-pkfv80oyDOLp_8BuswCrSfRZ0JiHJKoCOl8VNdpMlFjt0uYZs9MeXBjUNJVWh6-e8zd7ndEf9ltl7rYKc3VYIcraCzBXZtnSF27GV6XsWeVdTd0BBeW-WV_qrwluC8-NpQmSVynYZL6_wT-yx8_z6onecvtgUUQBQTKWc6dasi-3YH%2Fhttps*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fmail.nmr.mgh.harvard.edu*2Fmailman*2Flistinfo*2Ffreesurfer__*3B*21*21BWcElQ*21zpXQ3PuxLW9tVGEUbn6rORuqvIvCVR7yKbVoNInK7f64Mdnrn_h72CrZ4V0uYbNb4-3ss-bucRG3K810hSZNWr87XA*24__;JSUlJSUlJSUlJSUlJSUl!!BWcElQ!0b0p9v8O3dIacMpYGjU01dO2YzeFPIqkHkHTqormtsq83wuiJYHGlD6vHAyX35U4Ihtt2qcRJqfJttTIJxNq$> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1g7a4VHou5mIFBJdm_b4Sfpw37gRoUnVTTbcSjRVgelD6H4ySRSYAjjsDMaSsTp3jL8E7PUH1i9g-Zup0C8pdibnbfrr6cfm9i4OFvNEm3sn4zCqfFF4Yna3vXaOcqRk_PIS0uTk_46atqXOhRsBmeqd9ejHTjMUDDXoQBbc2nnzelpfODHNayFKYEeWFt1R-N9J5FUk55IXKiBzd6Z8NYvDAeKByFIEHH2Zl4L76ldfewStmyA5CXMRqVkLw9oxqmmK2R-m-E3L4EsxWx_1rP-fMB7PtrksnZJdfXgfc1Nuu6OVDiKU_Aya4i9DxJVgzCsknM76KfeBTz3Ibvk8G-g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<https://secure-web.cisco.com/1vIBLLp5bifJtFoUfyQB-n0xdMn1uRQWPUcn0xUWK3Kaa32baMnda5C89M6RshtxxF4uSqiHw75v78WfxRLB5fGU5A_MAoI4-AaFUXy6txXVLNovzkVfK151Ngsbqzxj9XzsEZmyq6XpLehcEw4kA4fznVDvheT15-J-XedtSC7LfZtMlKzspgM_xz_exwGttiKbqJyqZFNLbEsxxrdqQXGRgjDUm6ZAT1ydYbY28yKy9uNVziumRbVqLLHElfTt0tNHp-mU8iTWOh58UEKNnnGYjldbAeyOMhIwymrr_MwM0uXkuU1c1JElF4KcZ0OO6QE8bPPkPXlJA1y7VnKK-LA/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F18mFZH1oeMoQGQyv89urVEcv_Z1_0L5eJyGw4RAV6aSoAWPPT9IF-kVbC_czhm4bnYlg4sNQ2v6eGTwm1ADVZYFcoqLXB2ktO3JewOXmh29z4hakyg5ux5OOrFCCYwo3xpXVctEIDkmyaiPhUBTGdU-maKl91MdXOyFi6Q2-SDIEbXDVADj0gUfIcisuHi8GfyOSLeg0zDrXQOlXqueJDSUKZSVK9OJecZhENVF55dzIeXDj42ZxKVwCEDKUi_y_yUYnE9Ipbp8eIOses-SHKPezcYfQh_4NMhxkhHophATxtKVZbEooQP-rEvYsMcmN0%2Fhttps*3A*2F*2Fmail.nmr.mgh.harvard.edu*2Fmailman*2Flistinfo*2Ffreesurfer__;JSUlJSUl!!BWcElQ!0b0p9v8O3dIacMpYGjU01dO2YzeFPIqkHkHTqormtsq83wuiJYHGlD6vHAyX35U4Ihtt2qcRJqfJtr1zynz7$> 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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1oENVPp00W5iqm6tJoFVrgZXGkKT7kuo9iM25sjKtEkodJNAGV-4FJ7x4YivK2-pnHL249jGR-LXJXjGWlQZRyDi4qEeyQ18clDQJDKb3oViT3NeZBCElhpvBImfRLL28wzyZPH2jARnqAZ4qS8YYe6sj41x_sqcbw_WiRYoMsnS4JmAwyWox6uqtrKzwW43_BX2q9NPZt3PxWxq-0t0EuDB52DvzbAJV1uwbHNn-bC6NZHaP4dTX-Cz3QVUdrWtcJ0ouaH0BJLwdKjJ6XkPMIrnIK8a7_13eZ_2BgDPA5wxntL4Z-vnCX37Cgp3tqUTGOSxlV-yAT8iwQN7NutYHhg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline<https://secure-web.cisco.com/1YozBpj1ZKpBCvtALYgteqqCzU6XFQmPoXhxu9bKOJoexBaZOmmT9ST911_GGTq3pHIJlYpqgDD_aTPaVpIKfEOYGs2Jv4eQfveCwx1NZSfJy4KU15raM4T3NjjBpjgox4PKmQC3Aeixg1OYe4FNU1rI7WqpjVzWEXA7L42sgbjCXGsY0j15uhQw8aaHiTvQyt8YC2Yqzc1xv-Ds2lUJliRtKElB6FP7BrDSleCOHsmiDrnjoesAQcsp4bd9ss4LkTO2J_n-tIFVzeeM7uQANu-BHUE2sM8LKWNUynXBSQ6TT1Bdf1sSKY5T_X4PZ56Onwaxxwbx2sydTGYR2-yncmg/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1e6kLNCsHfTaO3peysgsOUAVp_O_8t2rkScDFL9BT78Qdr7SLiK0DyNqb5yrMhgDi1qkiYMPrHTA0slhFzCi34tu5nqtEVTAIzRg52rA-O77I0lYzww_I7X6YZHHS3LFA_9F1_YLg8AgpNiWAoyG0ulRNZ_CQkTgPCCFYXZ5GnVH_c8O4tUkOwDRkpwbQRj_z1YxgCDEeNefSdfNsyeA4XndYzJJEI19_H8ehpZg39HEu4OwdG2HwN5MfUp4nk43YZ9C-JPlnhWNOpUFMB8lypxuw7sJ4GHzr2MTuagtEdYFmBMjevEo2_hCQDeQCe1oZ%2Fhttps*3A*2F*2Fwww.massgeneralbrigham.org*2Fcomplianceline__;JSUlJQ!!BWcElQ!0b0p9v8O3dIacMpYGjU01dO2YzeFPIqkHkHTqormtsq83wuiJYHGlD6vHAyX35U4Ihtt2qcRJqfJtl03Ndwr$> <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1oENVPp00W5iqm6tJoFVrgZXGkKT7kuo9iM25sjKtEkodJNAGV-4FJ7x4YivK2-pnHL249jGR-LXJXjGWlQZRyDi4qEeyQ18clDQJDKb3oViT3NeZBCElhpvBImfRLL28wzyZPH2jARnqAZ4qS8YYe6sj41x_sqcbw_WiRYoMsnS4JmAwyWox6uqtrKzwW43_BX2q9NPZt3PxWxq-0t0EuDB52DvzbAJV1uwbHNn-bC6NZHaP4dTX-Cz3QVUdrWtcJ0ouaH0BJLwdKjJ6XkPMIrnIK8a7_13eZ_2BgDPA5wxntL4Z-vnCX37Cgp3tqUTGOSxlV-yAT8iwQN7NutYHhg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline<https://secure-web.cisco.com/1YozBpj1ZKpBCvtALYgteqqCzU6XFQmPoXhxu9bKOJoexBaZOmmT9ST911_GGTq3pHIJlYpqgDD_aTPaVpIKfEOYGs2Jv4eQfveCwx1NZSfJy4KU15raM4T3NjjBpjgox4PKmQC3Aeixg1OYe4FNU1rI7WqpjVzWEXA7L42sgbjCXGsY0j15uhQw8aaHiTvQyt8YC2Yqzc1xv-Ds2lUJliRtKElB6FP7BrDSleCOHsmiDrnjoesAQcsp4bd9ss4LkTO2J_n-tIFVzeeM7uQANu-BHUE2sM8LKWNUynXBSQ6TT1Bdf1sSKY5T_X4PZ56Onwaxxwbx2sydTGYR2-yncmg/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1e6kLNCsHfTaO3peysgsOUAVp_O_8t2rkScDFL9BT78Qdr7SLiK0DyNqb5yrMhgDi1qkiYMPrHTA0slhFzCi34tu5nqtEVTAIzRg52rA-O77I0lYzww_I7X6YZHHS3LFA_9F1_YLg8AgpNiWAoyG0ulRNZ_CQkTgPCCFYXZ5GnVH_c8O4tUkOwDRkpwbQRj_z1YxgCDEeNefSdfNsyeA4XndYzJJEI19_H8ehpZg39HEu4OwdG2HwN5MfUp4nk43YZ9C-JPlnhWNOpUFMB8lypxuw7sJ4GHzr2MTuagtEdYFmBMjevEo2_hCQDeQCe1oZ%2Fhttps*3A*2F*2Fwww.massgeneralbrigham.org*2Fcomplianceline__;JSUlJQ!!BWcElQ!0b0p9v8O3dIacMpYGjU01dO2YzeFPIqkHkHTqormtsq83wuiJYHGlD6vHAyX35U4Ihtt2qcRJqfJtl03Ndwr$>> .
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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.
