Hi All, as some of you have figured out, we have a beta version of FS 8.0.0. Please give it a spin and let us know if you have any problems or concerns.
The release notes are here https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes which I have copied below. One bug that we have already found is that you must set environment variable FS_ALLOW_DEEP to 1, eg, export FS_ALLOW_DEEP=1 (for bash) or setenv FS_ALLOW_DEEP 1 (for csh/tcsh)
thanks doug
*
Now uses SynthSeg https://surfer.nmr.mgh.harvard.edu/fswiki/SynthSeg, SynthStrip https://synthstrip.io, and SynthMorph https://synthmorph.io (deep learning algorithms). These make recon-all more robust and much faster. Technically, SynthMorph https://synthmorph.io is not needed for recon-all to run, but the nonlinear registration can be used in multimodal analysis to map to the MNI152.
* There is now DL automatic segmentation of regions that often cause errors in pial surface placement. These include the major sinuses (sagittal and transverse) as well as a spot between frontal and temporal lobes where the middle cerebral artery (MCA) and dura cause bright areas. * Several fixes in entorhinal cortex. First, the WM in EC is segmented using DL. The WM is often only 0.5mm thick and very hard to see; this often resulted in severe white surface areas in this location requiring manual editing to fix. The new surface now represents gyrus ambiens much better. Second, The white surface is extended to the front of amygdala. Third, the binary cortex of label now covers entorhinal cortex and parts of the temporal pole better allowing the pial surface to extend out to its true edge. * Some bugs where found in and around inferior frontal cortex causes the white surface to extend too far into basal ganglia. This has been fixed. This is above and beyond the issue reported in 7.3.2 below. * All the bug fixes described below are now turned on by default. * These changes will work with longitudinal with the caveat that the volumetric segmentation will not be fully longitudinal. The segmentation will be applied to the time point in the base space, but it will not (and cannot) be initialized with the base segmentation. Initial tests indicated that the change in power was minimal and mixed. * recon-all will now run in about 2h vs 8h on a single CPU. It will, however, required about 24GB of memory to run. *
The use of SynthStrip https://synthstrip.io should make recon-all much more robust as the old skull stripping method often included extra cerebral tissue.
* With synthseg, we are now supplying a segmentation-based total intracrainial volume (sTIV) along with the registration-based estimated TIV (eTIV) * We have applied v8 to several studies (aging, AD crossectional, AD longitudinnal, schizophrenia). There were no major changes in the ability to detect effects, and there was no interaction between effect and version. But let us know how it performs on your studies.
External Email - Use Caution
Awesome, Will this version be able to process over older versions of FreeSurfer?
On Thu, Nov 7, 2024 at 11:54 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Hi All, as some of you have figured out, we have a beta version of FS 8.0.0. Please give it a spin and let us know if you have any problems or concerns.
The release notes are here https://secure-web.cisco.com/1nfzJIH7mosYphab5nKXdF6Pe6cRILHpFbuENvvf0xNybGX... which I have copied below. One bug that we have already found is that you must set environment variable FS_ALLOW_DEEP to 1, eg, export FS_ALLOW_DEEP=1 (for bash) or setenv FS_ALLOW_DEEP 1 (for csh/tcsh)
thanks doug
Now uses SynthSeg https://secure-web.cisco.com/1KBsMN2BPKXgFi2gdkFpM55EcglFvUieMSC91xEli7Gih0z7b614Aab1GJgskTCYke2PuFnswV1hgD8u4nKYa8qMZ56B8A8PyQ1PWichRRzI-OEimPC821sAeiu-pzo0Pi66Y3tKOQEmBj3zsy3LPEca2e35qnmjk8bQlUMIK420Yl0Wyp-2Zun1yWx-KcSQ6HeWNeT06W8plWjAv65wqzY3Jlo3jB_ee1aglB1FAOFqy5Ue5RU63BdmWOeX36flyPoiFNj6XyHrYmLsoqNf9bNHQrtUgysUnQtNo0E0CCsb6HLinq_gY7ix7_FqSVBMQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSynthSeg, SynthStrip https://secure-web.cisco.com/1VXLmpw2yihWcZU0vul0tnP_5VpqF82JyCCwIVae31F_LCDzCk2x448Vt7fow8QIvtbXMZ0KHWP-fAgLeSiV9LIg_azUp_nU-10_YJYDCO42xs5WTgpbTq3O8Y_-dKGgalVqigH2xrUmVtw_oUcXxxLEt1gKz61xWqwwFan2pn5t9igJpdDLkSAJCZfxusDF95EYrUeaCBVIJfqe8q3mnfC3ujb5Ul8nz79yOJaOAMJbm4zkKysaeyMzaiNnYsVkGsraKHAz20mNCwC65TDzZ2ZJp4yWkJKEKXS2JEklcjidLF9AZZJll4UvKzjL9wfVw/https%3A%2F%2Fsynthstrip.io, and SynthMorph https://secure-web.cisco.com/1gV8mZhIt5XFZ04MEHNjyef68jYwr64lzOgyCeaG_kXAM5rQmht_BVbkfa7EIgfGgCmVQuMNSxCd9Hmssboq7tP1ZkCjBTjgCE3QgKJYVmV5qs-XLzi0L2U_7DhKUfdYcD1BEg2UDOwUq9yl33C1sGtlHC1bx_bE_d3s_dJpG55I-BaJWCIgRnBQETLH9e3Rflmr8pl4mCUpETAZSuHKKV3FXyqeOYL_aPhXo18yP-BEvaK-O8Dasd4cyY8xWmnBC3xj2n5-VQrwa4z_jeqeBCs_yJmYFJXAo10ruHtKEnCMQKY8VUamhlr39tJil6EXB/https%3A%2F%2Fsynthmorph.io (deep learning algorithms). These make recon-all more robust and much faster. Technically, SynthMorph https://secure-web.cisco.com/1gV8mZhIt5XFZ04MEHNjyef68jYwr64lzOgyCeaG_kXAM5rQmht_BVbkfa7EIgfGgCmVQuMNSxCd9Hmssboq7tP1ZkCjBTjgCE3QgKJYVmV5qs-XLzi0L2U_7DhKUfdYcD1BEg2UDOwUq9yl33C1sGtlHC1bx_bE_d3s_dJpG55I-BaJWCIgRnBQETLH9e3Rflmr8pl4mCUpETAZSuHKKV3FXyqeOYL_aPhXo18yP-BEvaK-O8Dasd4cyY8xWmnBC3xj2n5-VQrwa4z_jeqeBCs_yJmYFJXAo10ruHtKEnCMQKY8VUamhlr39tJil6EXB/https%3A%2F%2Fsynthmorph.io is not needed for recon-all to run, but the nonlinear registration can be used in multimodal analysis to map to the MNI152.
- There is now DL automatic segmentation of regions that often cause
errors in pial surface placement. These include the major sinuses (sagittal and transverse) as well as a spot between frontal and temporal lobes where the middle cerebral artery (MCA) and dura cause bright areas.
- Several fixes in entorhinal cortex. First, the WM in EC is segmented
using DL. The WM is often only 0.5mm thick and very hard to see; this often resulted in severe white surface areas in this location requiring manual editing to fix. The new surface now represents gyrus ambiens much better. Second, The white surface is extended to the front of amygdala. Third, the binary cortex of label now covers entorhinal cortex and parts of the temporal pole better allowing the pial surface to extend out to its true edge.
- Some bugs where found in and around inferior frontal cortex causes
the white surface to extend too far into basal ganglia. This has been fixed. This is above and beyond the issue reported in 7.3.2 below.
- All the bug fixes described below are now turned on by default.
- These changes will work with longitudinal with the caveat that the
volumetric segmentation will not be fully longitudinal. The segmentation will be applied to the time point in the base space, but it will not (and cannot) be initialized with the base segmentation. Initial tests indicated that the change in power was minimal and mixed.
- recon-all will now run in about 2h vs 8h on a single CPU. It will,
however, required about 24GB of memory to run.
The use of SynthStrip https://secure-web.cisco.com/1VXLmpw2yihWcZU0vul0tnP_5VpqF82JyCCwIVae31F_LCDzCk2x448Vt7fow8QIvtbXMZ0KHWP-fAgLeSiV9LIg_azUp_nU-10_YJYDCO42xs5WTgpbTq3O8Y_-dKGgalVqigH2xrUmVtw_oUcXxxLEt1gKz61xWqwwFan2pn5t9igJpdDLkSAJCZfxusDF95EYrUeaCBVIJfqe8q3mnfC3ujb5Ul8nz79yOJaOAMJbm4zkKysaeyMzaiNnYsVkGsraKHAz20mNCwC65TDzZ2ZJp4yWkJKEKXS2JEklcjidLF9AZZJll4UvKzjL9wfVw/https%3A%2F%2Fsynthstrip.io should make recon-all much more robust as the old skull stripping method often included extra cerebral tissue.
- With synthseg, we are now supplying a segmentation-based total
intracrainial volume (sTIV) along with the registration-based estimated TIV (eTIV)
- We have applied v8 to several studies (aging, AD crossectional, AD
longitudinnal, schizophrenia). There were no major changes in the ability to detect effects, and there was no interaction between effect and version. But let us know how it performs on your studies.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1b-cPuJWzQBzLy0_-M8aROcibuzq_sUgLFR5Yb6e_hQKozj... 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/1ok6iOBH7po92Ia3L7aAkmzT9tBthRzz5CN1XiXL70dCSdU... < https://secure-web.cisco.com/1ok6iOBH7po92Ia3L7aAkmzT9tBthRzz5CN1XiXL70dCSdU... .
External Email - Use Caution
Hi,
Thanks a lot.
I am particularly excited to the Synth* tools. I am trying SynthMorph from docker. I see that it does not use GPU (nvtop). I tried adding —gpus=0 but still see that inference runs on CPU (htop).
Are there any experiences in registering DTI to T1 to correct for distortions, instead of topup? I do not have AP-PA images.
Thanks
Martin
On Thu, 7 Nov 2024 at 20:38, Aaron Tanenbaum aaron.b.tanenbaum@gmail.com wrote:
External Email - Use CautionAwesome, Will this version be able to process over older versions of FreeSurfer?
On Thu, Nov 7, 2024 at 11:54 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Hi All, as some of you have figured out, we have a beta version of FS 8.0.0. Please give it a spin and let us know if you have any problems or concerns.
The release notes are here *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1td4oeYsAgCA5bcKPgu170qZGi75PbfL_6VqfOpm3iMYYaE... https://secure-web.cisco.com/1nfzJIH7mosYphab5nKXdF6Pe6cRILHpFbuENvvf0xNybGXN5dFVNHJpGgR0en61nEygdqxr_r1Wc2lzTP8tMxj2Mm5Kd12legZwYkmuUNI6W1pV128FFEKR50sXw0SWoAhimRb0wA4zNSb8vHOLda-h3SFtiXHW3UijR_Q2VNWxXg9Mf_u2QEuTxw6FSxJfmShpM3jaSD_K-mKrVmEKpykxD0152nXBL4MJ2LBp6Rio8mv0TzalahFHdHUqcEqnNmqL-1p1v1D3WuBFgM7CaT1LKZ5UQdNaQRKtd65tOkK2y1wIdk-WpFqLJknkohHGN/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes which I have copied below. One bug that we have already found is that you must set environment variable FS_ALLOW_DEEP to 1, eg, export FS_ALLOW_DEEP=1 (for bash) or setenv FS_ALLOW_DEEP 1 (for csh/tcsh)
thanks doug
Now uses SynthSeg https://secure-web.cisco.com/1KBsMN2BPKXgFi2gdkFpM55EcglFvUieMSC91xEli7Gih0z7b614Aab1GJgskTCYke2PuFnswV1hgD8u4nKYa8qMZ56B8A8PyQ1PWichRRzI-OEimPC821sAeiu-pzo0Pi66Y3tKOQEmBj3zsy3LPEca2e35qnmjk8bQlUMIK420Yl0Wyp-2Zun1yWx-KcSQ6HeWNeT06W8plWjAv65wqzY3Jlo3jB_ee1aglB1FAOFqy5Ue5RU63BdmWOeX36flyPoiFNj6XyHrYmLsoqNf9bNHQrtUgysUnQtNo0E0CCsb6HLinq_gY7ix7_FqSVBMQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSynthSeg, SynthStrip https://secure-web.cisco.com/1VXLmpw2yihWcZU0vul0tnP_5VpqF82JyCCwIVae31F_LCDzCk2x448Vt7fow8QIvtbXMZ0KHWP-fAgLeSiV9LIg_azUp_nU-10_YJYDCO42xs5WTgpbTq3O8Y_-dKGgalVqigH2xrUmVtw_oUcXxxLEt1gKz61xWqwwFan2pn5t9igJpdDLkSAJCZfxusDF95EYrUeaCBVIJfqe8q3mnfC3ujb5Ul8nz79yOJaOAMJbm4zkKysaeyMzaiNnYsVkGsraKHAz20mNCwC65TDzZ2ZJp4yWkJKEKXS2JEklcjidLF9AZZJll4UvKzjL9wfVw/https%3A%2F%2Fsynthstrip.io, and SynthMorph https://secure-web.cisco.com/1gV8mZhIt5XFZ04MEHNjyef68jYwr64lzOgyCeaG_kXAM5rQmht_BVbkfa7EIgfGgCmVQuMNSxCd9Hmssboq7tP1ZkCjBTjgCE3QgKJYVmV5qs-XLzi0L2U_7DhKUfdYcD1BEg2UDOwUq9yl33C1sGtlHC1bx_bE_d3s_dJpG55I-BaJWCIgRnBQETLH9e3Rflmr8pl4mCUpETAZSuHKKV3FXyqeOYL_aPhXo18yP-BEvaK-O8Dasd4cyY8xWmnBC3xj2n5-VQrwa4z_jeqeBCs_yJmYFJXAo10ruHtKEnCMQKY8VUamhlr39tJil6EXB/https%3A%2F%2Fsynthmorph.io (deep learning algorithms). These make recon-all more robust and much faster. Technically, SynthMorph https://secure-web.cisco.com/1gV8mZhIt5XFZ04MEHNjyef68jYwr64lzOgyCeaG_kXAM5rQmht_BVbkfa7EIgfGgCmVQuMNSxCd9Hmssboq7tP1ZkCjBTjgCE3QgKJYVmV5qs-XLzi0L2U_7DhKUfdYcD1BEg2UDOwUq9yl33C1sGtlHC1bx_bE_d3s_dJpG55I-BaJWCIgRnBQETLH9e3Rflmr8pl4mCUpETAZSuHKKV3FXyqeOYL_aPhXo18yP-BEvaK-O8Dasd4cyY8xWmnBC3xj2n5-VQrwa4z_jeqeBCs_yJmYFJXAo10ruHtKEnCMQKY8VUamhlr39tJil6EXB/https%3A%2F%2Fsynthmorph.io is not needed for recon-all to run, but the nonlinear registration can be used in multimodal analysis to map to the MNI152.
- There is now DL automatic segmentation of regions that often cause
errors in pial surface placement. These include the major sinuses (sagittal and transverse) as well as a spot between frontal and temporal lobes where the middle cerebral artery (MCA) and dura cause bright areas.
- Several fixes in entorhinal cortex. First, the WM in EC is
segmented using DL. The WM is often only 0.5mm thick and very hard to see; this often resulted in severe white surface areas in this location requiring manual editing to fix. The new surface now represents gyrus ambiens much better. Second, The white surface is extended to the front of amygdala. Third, the binary cortex of label now covers entorhinal cortex and parts of the temporal pole better allowing the pial surface to extend out to its true edge.
- Some bugs where found in and around inferior frontal cortex causes
the white surface to extend too far into basal ganglia. This has been fixed. This is above and beyond the issue reported in 7.3.2 below.
- All the bug fixes described below are now turned on by default.
- These changes will work with longitudinal with the caveat that the
volumetric segmentation will not be fully longitudinal. The segmentation will be applied to the time point in the base space, but it will not (and cannot) be initialized with the base segmentation. Initial tests indicated that the change in power was minimal and mixed.
- recon-all will now run in about 2h vs 8h on a single CPU. It will,
however, required about 24GB of memory to run.
The use of SynthStrip https://secure-web.cisco.com/1VXLmpw2yihWcZU0vul0tnP_5VpqF82JyCCwIVae31F_LCDzCk2x448Vt7fow8QIvtbXMZ0KHWP-fAgLeSiV9LIg_azUp_nU-10_YJYDCO42xs5WTgpbTq3O8Y_-dKGgalVqigH2xrUmVtw_oUcXxxLEt1gKz61xWqwwFan2pn5t9igJpdDLkSAJCZfxusDF95EYrUeaCBVIJfqe8q3mnfC3ujb5Ul8nz79yOJaOAMJbm4zkKysaeyMzaiNnYsVkGsraKHAz20mNCwC65TDzZ2ZJp4yWkJKEKXS2JEklcjidLF9AZZJll4UvKzjL9wfVw/https%3A%2F%2Fsynthstrip.io should make recon-all much more robust as the old skull stripping method often included extra cerebral tissue.
- With synthseg, we are now supplying a segmentation-based total
intracrainial volume (sTIV) along with the registration-based estimated TIV (eTIV)
- We have applied v8 to several studies (aging, AD crossectional, AD
longitudinnal, schizophrenia). There were no major changes in the ability to detect effects, and there was no interaction between effect and version. But let us know how it performs on your studies.
Freesurfer mailing list 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/1l1QKcpJRCligd46zdzMJTUM10NR4JAgod2JeccuUJFBGuD... https://secure-web.cisco.com/1b-cPuJWzQBzLy0_-M8aROcibuzq_sUgLFR5Yb6e_hQKozjmE8B5STLMyZau0HLaBHVV4DMkawFTOxb7I_n7YG5CHXME6vnOLzeoNfsRSy0WjvCS_7sBSnH6j9uoqgf-ciQKbBFcXYp76dnbQpP6qcq9canmI5nCYx_3Avp4OG5s65PvcuNoHYnp8vzrDuTEV78cdvD712MAKtOzc8xDnCKn1fQcF8Or0c-_LGPrhcZz3NJdDx-5uWhnoIplcNeo9dWAlVnrAHj8temxnWbTP4lDBAT428ldCflGSLB1bAOccs6Xg3Z0zVztaGXuZYaPF/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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1uvq3eTR4oFIZMX12hVTi8YAnfH2law_wswuxAIdl5Ah9sg... https://secure-web.cisco.com/1ok6iOBH7po92Ia3L7aAkmzT9tBthRzz5CN1XiXL70dCSdUo-vfcLXAIHzpZqd1D5Xn-5GrRtv5PnqH_ufaIlOrJTWZQbshrp03b0meKeHzNXxPrpDntcxVCIVoN3zUtSK8H87Fq8KkDQQB9-H0_QuXrjNLin_V5QcIOILgqZemDBAxu-PZ-QTAAwyJo93PJop2ciJ7c3GnLBqhftQdHrzAhkj3aO8m3M1SrSvn4Wk6VjKOezUslLa8DHyp2jIycofkmM4CkhalVedCIucpI99kOK4heexBTDZ-dnl0UE6TAg11dLNasZ3Q3-ygwdMBed/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1uvq3eTR4oFIZMX12hVTi8YAnfH2law_wswuxAIdl5Ah9sg... https://secure-web.cisco.com/1ok6iOBH7po92Ia3L7aAkmzT9tBthRzz5CN1XiXL70dCSdUo-vfcLXAIHzpZqd1D5Xn-5GrRtv5PnqH_ufaIlOrJTWZQbshrp03b0meKeHzNXxPrpDntcxVCIVoN3zUtSK8H87Fq8KkDQQB9-H0_QuXrjNLin_V5QcIOILgqZemDBAxu-PZ-QTAAwyJo93PJop2ciJ7c3GnLBqhftQdHrzAhkj3aO8m3M1SrSvn4Wk6VjKOezUslLa8DHyp2jIycofkmM4CkhalVedCIucpI99kOK4heexBTDZ-dnl0UE6TAg11dLNasZ3Q3-ygwdMBed/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1l1QKcpJRCligd46zdzMJTUM10NR4JAgod2JeccuUJFBGuD... 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/1uvq3eTR4oFIZMX12hVTi8YAnfH2law_wswuxAIdl5Ah9sg... < https://secure-web.cisco.com/1uvq3eTR4oFIZMX12hVTi8YAnfH2law_wswuxAIdl5Ah9sg... .
Hi Martin,
In addition to the --gpu=all or 0 flag for Docker, you'll need to include the -g flag for SynthMorph to enable the GPU. You can choose the device by setting CUDA_VISIBLE_DEVICES; SynthMorph will default to 0. Affine registration should require at least 16 GB of device memory, and the deformable model needs 24 GB.
While there may be some speed-up, keep in mind that there are several resampling steps that SynthMorph delegates to surfa, and these will still use the CPU. I'm not aware of anyone having tested it for distortion correction.
Best wishes, Malte
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Martin Kavec martin.kavec@gmail.com Sent: Friday, November 8, 2024 06:12 To: Freesurfer support list Subject: Re: [Freesurfer] FS version 8-beta
External Email - Use Caution
Hi,
Thanks a lot.
I am particularly excited to the Synth* tools. I am trying SynthMorph from docker. I see that it does not use GPU (nvtop). I tried adding —gpus=0 but still see that inference runs on CPU (htop).
Are there any experiences in registering DTI to T1 to correct for distortions, instead of topup? I do not have AP-PA images.
Thanks
Martin
On Thu, 7 Nov 2024 at 20:38, Aaron Tanenbaum <aaron.b.tanenbaum@gmail.commailto:aaron.b.tanenbaum@gmail.com> wrote:
External Email - Use Caution
Awesome, Will this version be able to process over older versions of FreeSurfer?
On Thu, Nov 7, 2024 at 11:54 AM Douglas N. Greve <dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu> wrote: Hi All, as some of you have figured out, we have a beta version of FS 8.0.0. Please give it a spin and let us know if you have any problems or concerns.
The release notes are here MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNoteshttps://secure-web.cisco.com/1nfzJIH7mosYphab5nKXdF6Pe6cRILHpFbuENvvf0xNybGXN5dFVNHJpGgR0en61nEygdqxr_r1Wc2lzTP8tMxj2Mm5Kd12legZwYkmuUNI6W1pV128FFEKR50sXw0SWoAhimRb0wA4zNSb8vHOLda-h3SFtiXHW3UijR_Q2VNWxXg9Mf_u2QEuTxw6FSxJfmShpM3jaSD_K-mKrVmEKpykxD0152nXBL4MJ2LBp6Rio8mv0TzalahFHdHUqcEqnNmqL-1p1v1D3WuBFgM7CaT1LKZ5UQdNaQRKtd65tOkK2y1wIdk-WpFqLJknkohHGN/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes which I have copied below. One bug that we have already found is that you must set environment variable FS_ALLOW_DEEP to 1, eg, export FS_ALLOW_DEEP=1 (for bash) or setenv FS_ALLOW_DEEP 1 (for csh/tcsh)
thanks doug
* Now uses SynthSeghttps://secure-web.cisco.com/1KBsMN2BPKXgFi2gdkFpM55EcglFvUieMSC91xEli7Gih0z7b614Aab1GJgskTCYke2PuFnswV1hgD8u4nKYa8qMZ56B8A8PyQ1PWichRRzI-OEimPC821sAeiu-pzo0Pi66Y3tKOQEmBj3zsy3LPEca2e35qnmjk8bQlUMIK420Yl0Wyp-2Zun1yWx-KcSQ6HeWNeT06W8plWjAv65wqzY3Jlo3jB_ee1aglB1FAOFqy5Ue5RU63BdmWOeX36flyPoiFNj6XyHrYmLsoqNf9bNHQrtUgysUnQtNo0E0CCsb6HLinq_gY7ix7_FqSVBMQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSynthSeg, SynthStriphttps://secure-web.cisco.com/1VXLmpw2yihWcZU0vul0tnP_5VpqF82JyCCwIVae31F_LCDzCk2x448Vt7fow8QIvtbXMZ0KHWP-fAgLeSiV9LIg_azUp_nU-10_YJYDCO42xs5WTgpbTq3O8Y_-dKGgalVqigH2xrUmVtw_oUcXxxLEt1gKz61xWqwwFan2pn5t9igJpdDLkSAJCZfxusDF95EYrUeaCBVIJfqe8q3mnfC3ujb5Ul8nz79yOJaOAMJbm4zkKysaeyMzaiNnYsVkGsraKHAz20mNCwC65TDzZ2ZJp4yWkJKEKXS2JEklcjidLF9AZZJll4UvKzjL9wfVw/https%3A%2F%2Fsynthstrip.io, and SynthMorphhttps://secure-web.cisco.com/1gV8mZhIt5XFZ04MEHNjyef68jYwr64lzOgyCeaG_kXAM5rQmht_BVbkfa7EIgfGgCmVQuMNSxCd9Hmssboq7tP1ZkCjBTjgCE3QgKJYVmV5qs-XLzi0L2U_7DhKUfdYcD1BEg2UDOwUq9yl33C1sGtlHC1bx_bE_d3s_dJpG55I-BaJWCIgRnBQETLH9e3Rflmr8pl4mCUpETAZSuHKKV3FXyqeOYL_aPhXo18yP-BEvaK-O8Dasd4cyY8xWmnBC3xj2n5-VQrwa4z_jeqeBCs_yJmYFJXAo10ruHtKEnCMQKY8VUamhlr39tJil6EXB/https%3A%2F%2Fsynthmorph.io (deep learning algorithms). These make recon-all more robust and much faster. Technically, SynthMorphhttps://secure-web.cisco.com/1gV8mZhIt5XFZ04MEHNjyef68jYwr64lzOgyCeaG_kXAM5rQmht_BVbkfa7EIgfGgCmVQuMNSxCd9Hmssboq7tP1ZkCjBTjgCE3QgKJYVmV5qs-XLzi0L2U_7DhKUfdYcD1BEg2UDOwUq9yl33C1sGtlHC1bx_bE_d3s_dJpG55I-BaJWCIgRnBQETLH9e3Rflmr8pl4mCUpETAZSuHKKV3FXyqeOYL_aPhXo18yP-BEvaK-O8Dasd4cyY8xWmnBC3xj2n5-VQrwa4z_jeqeBCs_yJmYFJXAo10ruHtKEnCMQKY8VUamhlr39tJil6EXB/https%3A%2F%2Fsynthmorph.io is not needed for recon-all to run, but the nonlinear registration can be used in multimodal analysis to map to the MNI152.
* There is now DL automatic segmentation of regions that often cause errors in pial surface placement. These include the major sinuses (sagittal and transverse) as well as a spot between frontal and temporal lobes where the middle cerebral artery (MCA) and dura cause bright areas. * Several fixes in entorhinal cortex. First, the WM in EC is segmented using DL. The WM is often only 0.5mm thick and very hard to see; this often resulted in severe white surface areas in this location requiring manual editing to fix. The new surface now represents gyrus ambiens much better. Second, The white surface is extended to the front of amygdala. Third, the binary cortex of label now covers entorhinal cortex and parts of the temporal pole better allowing the pial surface to extend out to its true edge. * Some bugs where found in and around inferior frontal cortex causes the white surface to extend too far into basal ganglia. This has been fixed. This is above and beyond the issue reported in 7.3.2 below. * All the bug fixes described below are now turned on by default. * These changes will work with longitudinal with the caveat that the volumetric segmentation will not be fully longitudinal. The segmentation will be applied to the time point in the base space, but it will not (and cannot) be initialized with the base segmentation. Initial tests indicated that the change in power was minimal and mixed. * recon-all will now run in about 2h vs 8h on a single CPU. It will, however, required about 24GB of memory to run. * The use of SynthStriphttps://secure-web.cisco.com/1VXLmpw2yihWcZU0vul0tnP_5VpqF82JyCCwIVae31F_LCDzCk2x448Vt7fow8QIvtbXMZ0KHWP-fAgLeSiV9LIg_azUp_nU-10_YJYDCO42xs5WTgpbTq3O8Y_-dKGgalVqigH2xrUmVtw_oUcXxxLEt1gKz61xWqwwFan2pn5t9igJpdDLkSAJCZfxusDF95EYrUeaCBVIJfqe8q3mnfC3ujb5Ul8nz79yOJaOAMJbm4zkKysaeyMzaiNnYsVkGsraKHAz20mNCwC65TDzZ2ZJp4yWkJKEKXS2JEklcjidLF9AZZJll4UvKzjL9wfVw/https%3A%2F%2Fsynthstrip.io should make recon-all much more robust as the old skull stripping method often included extra cerebral tissue.
* With synthseg, we are now supplying a segmentation-based total intracrainial volume (sTIV) along with the registration-based estimated TIV (eTIV) * We have applied v8 to several studies (aging, AD crossectional, AD longitudinnal, schizophrenia). There were no major changes in the ability to detect effects, and there was no interaction between effect and version. But let us know how it performs on your studies.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1b-cPuJWzQBzLy0_-M8aROcibuzq_sUgLFR5Yb6e_hQKozjmE8B5STLMyZau0HLaBHVV4DMkawFTOxb7I_n7YG5CHXME6vnOLzeoNfsRSy0WjvCS_7sBSnH6j9uoqgf-ciQKbBFcXYp76dnbQpP6qcq9canmI5nCYx_3Avp4OG5s65PvcuNoHYnp8vzrDuTEV78cdvD712MAKtOzc8xDnCKn1fQcF8Or0c-_LGPrhcZz3NJdDx-5uWhnoIplcNeo9dWAlVnrAHj8temxnWbTP4lDBAT428ldCflGSLB1bAOccs6Xg3Z0zVztaGXuZYaPF/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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1ok6iOBH7po92Ia3L7aAkmzT9tBthRzz5CN1XiXL70dCSdUo-vfcLXAIHzpZqd1D5Xn-5GrRtv5PnqH_ufaIlOrJTWZQbshrp03b0meKeHzNXxPrpDntcxVCIVoN3zUtSK8H87Fq8KkDQQB9-H0_QuXrjNLin_V5QcIOILgqZemDBAxu-PZ-QTAAwyJo93PJop2ciJ7c3GnLBqhftQdHrzAhkj3aO8m3M1SrSvn4Wk6VjKOezUslLa8DHyp2jIycofkmM4CkhalVedCIucpI99kOK4heexBTDZ-dnl0UE6TAg11dLNasZ3Q3-ygwdMBed/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1ok6iOBH7po92Ia3L7aAkmzT9tBthRzz5CN1XiXL70dCSdUo-vfcLXAIHzpZqd1D5Xn-5GrRtv5PnqH_ufaIlOrJTWZQbshrp03b0meKeHzNXxPrpDntcxVCIVoN3zUtSK8H87Fq8KkDQQB9-H0_QuXrjNLin_V5QcIOILgqZemDBAxu-PZ-QTAAwyJo93PJop2ciJ7c3GnLBqhftQdHrzAhkj3aO8m3M1SrSvn4Wk6VjKOezUslLa8DHyp2jIycofkmM4CkhalVedCIucpI99kOK4heexBTDZ-dnl0UE6TAg11dLNasZ3Q3-ygwdMBed/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1l1QKcpJRCligd46zdzMJTUM10NR4JAgod2JeccuUJFBGuDhzlB4csrbn_TNghE-nqNvO_gnOCOef4odQHCC5vpQTVex9yi_XuKoGWAAsFaalq0iE0d_4SONmJENcCrJEOWD8YppGrH5OKuFg8qQxceLaz-7nnji3UzVqVlHUcHOrPo67R3ok3w-9d9EQO1pSeRvzuwcis_ZxC__ZIM7uf4Vn1zsHFlikH1s7g6RuCynpfICiNCnczfLHf0mJfl0O5rYRjganY1sONTQt-TThMFkOTzHtkB_WbxvKcAiUajg5PMrS5_S_HxAP7MtxZx2s/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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1uvq3eTR4oFIZMX12hVTi8YAnfH2law_wswuxAIdl5Ah9sgdgIqrb5mBCyN-NMe4A3cm7c2wbCNWTJDqPesa-zsHYSAgNaJgH5eAiUDlkod0C9P5iVRGWL3aaVtq-3_Goz5Z2r19Usc96uCkV6Olo5sFYiGhzJ3bDhfYWOFcJHhiri6hhYY3cTiD_t_ja_m1rl-XsMbnW_FyytJ8wI-D8c01OszNg-M23A6oL5dkJEb9lcK1CUlCisxSr_Qi3xXOYbG4_tggxJYioq_9vaboubbOGHKbFSYXzB9froXft4nXf04gzyEWacOAgWwMc1Px3/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1uvq3eTR4oFIZMX12hVTi8YAnfH2law_wswuxAIdl5Ah9sgdgIqrb5mBCyN-NMe4A3cm7c2wbCNWTJDqPesa-zsHYSAgNaJgH5eAiUDlkod0C9P5iVRGWL3aaVtq-3_Goz5Z2r19Usc96uCkV6Olo5sFYiGhzJ3bDhfYWOFcJHhiri6hhYY3cTiD_t_ja_m1rl-XsMbnW_FyytJ8wI-D8c01OszNg-M23A6oL5dkJEb9lcK1CUlCisxSr_Qi3xXOYbG4_tggxJYioq_9vaboubbOGHKbFSYXzB9froXft4nXf04gzyEWacOAgWwMc1Px3/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .
External Email - Use Caution
Hi Malte,
indeed the -g helped to execute on GPU, but it exhausted my resources. Have only 23GB on GPU :(
Thanks and best wishes,
Martin
On Fri, Nov 8, 2024 at 1:34 PM Hoffmann, Malte,PhD MHOFFMANN@mgh.harvard.edu wrote:
Hi Martin,
In addition to the --gpu=all or 0 flag for Docker, you'll need to include the -g flag for SynthMorph to enable the GPU. You can choose the device by setting CUDA_VISIBLE_DEVICES; SynthMorph will default to 0. Affine registration should require at least 16 GB of device memory, and the deformable model needs 24 GB.
While there may be some speed-up, keep in mind that there are several resampling steps that SynthMorph delegates to surfa, and these will still use the CPU. I'm not aware of anyone having tested it for distortion correction.
Best wishes, Malte
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Martin Kavec martin.kavec@gmail.com Sent: Friday, November 8, 2024 06:12 To: Freesurfer support list Subject: Re: [Freesurfer] FS version 8-beta
External Email - Use CautionHi,
Thanks a lot.
I am particularly excited to the Synth* tools. I am trying SynthMorph from docker. I see that it does not use GPU (nvtop). I tried adding —gpus=0 but still see that inference runs on CPU (htop).
Are there any experiences in registering DTI to T1 to correct for distortions, instead of topup? I do not have AP-PA images.
Thanks
Martin
On Thu, 7 Nov 2024 at 20:38, Aaron Tanenbaum <aaron.b.tanenbaum@gmail.commailto:aaron.b.tanenbaum@gmail.com> wrote:
External Email - Use CautionAwesome, Will this version be able to process over older versions of FreeSurfer?
On Thu, Nov 7, 2024 at 11:54 AM Douglas N. Greve <dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu> wrote: Hi All, as some of you have figured out, we have a beta version of FS 8.0.0. Please give it a spin and let us know if you have any problems or concerns.
The release notes are here MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1BBKyUZRdUGQqzszGycfm_vbOAlUW4K5jdYUP5acKnED1Dh...https://secure-web.cisco.com/1nfzJIH7mosYphab5nKXdF6Pe6cRILHpFbuENvvf0xNybGXN5dFVNHJpGgR0en61nEygdqxr_r1Wc2lzTP8tMxj2Mm5Kd12legZwYkmuUNI6W1pV128FFEKR50sXw0SWoAhimRb0wA4zNSb8vHOLda-h3SFtiXHW3UijR_Q2VNWxXg9Mf_u2QEuTxw6FSxJfmShpM3jaSD_K-mKrVmEKpykxD0152nXBL4MJ2LBp6Rio8mv0TzalahFHdHUqcEqnNmqL-1p1v1D3WuBFgM7CaT1LKZ5UQdNaQRKtd65tOkK2y1wIdk-WpFqLJknkohHGN/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes which I have copied below. One bug that we have already found is that you must set environment variable FS_ALLOW_DEEP to 1, eg, export FS_ALLOW_DEEP=1 (for bash) or setenv FS_ALLOW_DEEP 1 (for csh/tcsh)
thanks doug
Now uses SynthSeghttps://secure-web.cisco.com/1KBsMN2BPKXgFi2gdkFpM55EcglFvUieMSC91xEli7Gih0z7b614Aab1GJgskTCYke2PuFnswV1hgD8u4nKYa8qMZ56B8A8PyQ1PWichRRzI-OEimPC821sAeiu-pzo0Pi66Y3tKOQEmBj3zsy3LPEca2e35qnmjk8bQlUMIK420Yl0Wyp-2Zun1yWx-KcSQ6HeWNeT06W8plWjAv65wqzY3Jlo3jB_ee1aglB1FAOFqy5Ue5RU63BdmWOeX36flyPoiFNj6XyHrYmLsoqNf9bNHQrtUgysUnQtNo0E0CCsb6HLinq_gY7ix7_FqSVBMQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSynthSeg, SynthStriphttps://secure-web.cisco.com/1VXLmpw2yihWcZU0vul0tnP_5VpqF82JyCCwIVae31F_LCDzCk2x448Vt7fow8QIvtbXMZ0KHWP-fAgLeSiV9LIg_azUp_nU-10_YJYDCO42xs5WTgpbTq3O8Y_-dKGgalVqigH2xrUmVtw_oUcXxxLEt1gKz61xWqwwFan2pn5t9igJpdDLkSAJCZfxusDF95EYrUeaCBVIJfqe8q3mnfC3ujb5Ul8nz79yOJaOAMJbm4zkKysaeyMzaiNnYsVkGsraKHAz20mNCwC65TDzZ2ZJp4yWkJKEKXS2JEklcjidLF9AZZJll4UvKzjL9wfVw/https%3A%2F%2Fsynthstrip.io, and SynthMorphhttps://secure-web.cisco.com/1gV8mZhIt5XFZ04MEHNjyef68jYwr64lzOgyCeaG_kXAM5rQmht_BVbkfa7EIgfGgCmVQuMNSxCd9Hmssboq7tP1ZkCjBTjgCE3QgKJYVmV5qs-XLzi0L2U_7DhKUfdYcD1BEg2UDOwUq9yl33C1sGtlHC1bx_bE_d3s_dJpG55I-BaJWCIgRnBQETLH9e3Rflmr8pl4mCUpETAZSuHKKV3FXyqeOYL_aPhXo18yP-BEvaK-O8Dasd4cyY8xWmnBC3xj2n5-VQrwa4z_jeqeBCs_yJmYFJXAo10ruHtKEnCMQKY8VUamhlr39tJil6EXB/https%3A%2F%2Fsynthmorph.io (deep learning algorithms). These make recon-all more robust and much faster. Technically, SynthMorphhttps://secure-web.cisco.com/1gV8mZhIt5XFZ04MEHNjyef68jYwr64lzOgyCeaG_kXAM5rQmht_BVbkfa7EIgfGgCmVQuMNSxCd9Hmssboq7tP1ZkCjBTjgCE3QgKJYVmV5qs-XLzi0L2U_7DhKUfdYcD1BEg2UDOwUq9yl33C1sGtlHC1bx_bE_d3s_dJpG55I-BaJWCIgRnBQETLH9e3Rflmr8pl4mCUpETAZSuHKKV3FXyqeOYL_aPhXo18yP-BEvaK-O8Dasd4cyY8xWmnBC3xj2n5-VQrwa4z_jeqeBCs_yJmYFJXAo10ruHtKEnCMQKY8VUamhlr39tJil6EXB/https%3A%2F%2Fsynthmorph.io is not needed for recon-all to run, but the nonlinear registration can be used in multimodal analysis to map to the MNI152.
There is now DL automatic segmentation of regions that often cause errors in pial surface placement. These include the major sinuses (sagittal and transverse) as well as a spot between frontal and temporal lobes where the middle cerebral artery (MCA) and dura cause bright areas.
Several fixes in entorhinal cortex. First, the WM in EC is segmented using DL. The WM is often only 0.5mm thick and very hard to see; this often resulted in severe white surface areas in this location requiring manual editing to fix. The new surface now represents gyrus ambiens much better. Second, The white surface is extended to the front of amygdala. Third, the binary cortex of label now covers entorhinal cortex and parts of the temporal pole better allowing the pial surface to extend out to its true edge.
Some bugs where found in and around inferior frontal cortex causes the white surface to extend too far into basal ganglia. This has been fixed. This is above and beyond the issue reported in 7.3.2 below.
All the bug fixes described below are now turned on by default.
These changes will work with longitudinal with the caveat that the volumetric segmentation will not be fully longitudinal. The segmentation will be applied to the time point in the base space, but it will not (and cannot) be initialized with the base segmentation. Initial tests indicated that the change in power was minimal and mixed.
recon-all will now run in about 2h vs 8h on a single CPU. It will, however, required about 24GB of memory to run.
The use of SynthStriphttps://secure-web.cisco.com/1VXLmpw2yihWcZU0vul0tnP_5VpqF82JyCCwIVae31F_LCDzCk2x448Vt7fow8QIvtbXMZ0KHWP-fAgLeSiV9LIg_azUp_nU-10_YJYDCO42xs5WTgpbTq3O8Y_-dKGgalVqigH2xrUmVtw_oUcXxxLEt1gKz61xWqwwFan2pn5t9igJpdDLkSAJCZfxusDF95EYrUeaCBVIJfqe8q3mnfC3ujb5Ul8nz79yOJaOAMJbm4zkKysaeyMzaiNnYsVkGsraKHAz20mNCwC65TDzZ2ZJp4yWkJKEKXS2JEklcjidLF9AZZJll4UvKzjL9wfVw/https%3A%2F%2Fsynthstrip.io should make recon-all much more robust as the old skull stripping method often included extra cerebral tissue.
With synthseg, we are now supplying a segmentation-based total intracrainial volume (sTIV) along with the registration-based estimated TIV (eTIV)
We have applied v8 to several studies (aging, AD crossectional, AD longitudinnal, schizophrenia). There were no major changes in the ability to detect effects, and there was no interaction between effect and version. But let us know how it performs on your studies.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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/1cifVw0ixxCcv0YRm6u-kBeXI6ZORquywQVarJ9-yt6dRkx...https://secure-web.cisco.com/1b-cPuJWzQBzLy0_-M8aROcibuzq_sUgLFR5Yb6e_hQKozjmE8B5STLMyZau0HLaBHVV4DMkawFTOxb7I_n7YG5CHXME6vnOLzeoNfsRSy0WjvCS_7sBSnH6j9uoqgf-ciQKbBFcXYp76dnbQpP6qcq9canmI5nCYx_3Avp4OG5s65PvcuNoHYnp8vzrDuTEV78cdvD712MAKtOzc8xDnCKn1fQcF8Or0c-_LGPrhcZz3NJdDx-5uWhnoIplcNeo9dWAlVnrAHj8temxnWbTP4lDBAT428ldCflGSLB1bAOccs6Xg3Z0zVztaGXuZYaPF/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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1dVzKSI1N4qoOdWiQxYBJbp1C4Es36kfAWGquCDTlH-6Frz...https://secure-web.cisco.com/1ok6iOBH7po92Ia3L7aAkmzT9tBthRzz5CN1XiXL70dCSdUo-vfcLXAIHzpZqd1D5Xn-5GrRtv5PnqH_ufaIlOrJTWZQbshrp03b0meKeHzNXxPrpDntcxVCIVoN3zUtSK8H87Fq8KkDQQB9-H0_QuXrjNLin_V5QcIOILgqZemDBAxu-PZ-QTAAwyJo93PJop2ciJ7c3GnLBqhftQdHrzAhkj3aO8m3M1SrSvn4Wk6VjKOezUslLa8DHyp2jIycofkmM4CkhalVedCIucpI99kOK4heexBTDZ-dnl0UE6TAg11dLNasZ3Q3-ygwdMBed/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1dVzKSI1N4qoOdWiQxYBJbp1C4Es36kfAWGquCDTlH-6Frz...<https://secure-web.cisco.com/1ok6iOBH7po92Ia3L7aAkmzT9tBthRzz5CN1XiXL70dCSdU...
igham.org%2Fcomplianceline>> .
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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/1cifVw0ixxCcv0YRm6u-kBeXI6ZORquywQVarJ9-yt6dRkx...https://secure-web.cisco.com/1l1QKcpJRCligd46zdzMJTUM10NR4JAgod2JeccuUJFBGuDhzlB4csrbn_TNghE-nqNvO_gnOCOef4odQHCC5vpQTVex9yi_XuKoGWAAsFaalq0iE0d_4SONmJENcCrJEOWD8YppGrH5OKuFg8qQxceLaz-7nnji3UzVqVlHUcHOrPo67R3ok3w-9d9EQO1pSeRvzuwcis_ZxC__ZIM7uf4Vn1zsHFlikH1s7g6RuCynpfICiNCnczfLHf0mJfl0O5rYRjganY1sONTQt-TThMFkOTzHtkB_WbxvKcAiUajg5PMrS5_S_HxAP7MtxZx2s/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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1dVzKSI1N4qoOdWiQxYBJbp1C4Es36kfAWGquCDTlH-6Frz...https://secure-web.cisco.com/1uvq3eTR4oFIZMX12hVTi8YAnfH2law_wswuxAIdl5Ah9sgdgIqrb5mBCyN-NMe4A3cm7c2wbCNWTJDqPesa-zsHYSAgNaJgH5eAiUDlkod0C9P5iVRGWL3aaVtq-3_Goz5Z2r19Usc96uCkV6Olo5sFYiGhzJ3bDhfYWOFcJHhiri6hhYY3cTiD_t_ja_m1rl-XsMbnW_FyytJ8wI-D8c01OszNg-M23A6oL5dkJEb9lcK1CUlCisxSr_Qi3xXOYbG4_tggxJYioq_9vaboubbOGHKbFSYXzB9froXft4nXf04gzyEWacOAgWwMc1Px3/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1dVzKSI1N4qoOdWiQxYBJbp1C4Es36kfAWGquCDTlH-6Frz...<https://secure-web.cisco.com/1uvq3eTR4oFIZMX12hVTi8YAnfH2law_wswuxAIdl5Ah9sg...
igham.org%2Fcomplianceline>> .
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1cifVw0ixxCcv0YRm6u-kBeXI6ZORquywQVarJ9-yt6dRkx... 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/1dVzKSI1N4qoOdWiQxYBJbp1C4Es36kfAWGquCDTlH-6Frz... https://secure-web.cisco.com/1dVzKSI1N4qoOdWiQxYBJbp1C4Es36kfAWGquCDTlH-6Frz33Y1TwjIda-_amT73_aA0I5yWJ1gjBCCVszj93X9iCO0PmmRreTJOlJLEZAWDWsuo-YOugB2AG_Zx0L8oa0uvihRCXy7Q1mkIpO-sScRjnVjznOuXUIPR-UvmnxsQcWSQEvQDpCM9bGkEiGvcWDehgfOH1vNk7sDzNIvTqX_cYsEK0dIzgXUS4z8d9kRSprLZX9hGC264x-xpgHknruCz8tNJdZqKjqeVIhhYDw5S0GBzJRTaOUx9UTgWugX6PuHwBBBCUeo7clpNXiapv/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline .
I think this should work, though it might exit early due to the bug that I just posted. But a fixed version should be able to do this.
On 11/7/2024 2:37 PM, Aaron Tanenbaum wrote:
External Email - Use Caution
Awesome, Will this version be able to process over older versions of FreeSurfer?
On Thu, Nov 7, 2024 at 11:54 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Hi All, as some of you have figured out, we have a beta version of FS 8.0.0. Please give it a spin and let us know if you have any problems or concerns. The release notes are here *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes <https://secure-web.cisco.com/1nfzJIH7mosYphab5nKXdF6Pe6cRILHpFbuENvvf0xNybGXN5dFVNHJpGgR0en61nEygdqxr_r1Wc2lzTP8tMxj2Mm5Kd12legZwYkmuUNI6W1pV128FFEKR50sXw0SWoAhimRb0wA4zNSb8vHOLda-h3SFtiXHW3UijR_Q2VNWxXg9Mf_u2QEuTxw6FSxJfmShpM3jaSD_K-mKrVmEKpykxD0152nXBL4MJ2LBp6Rio8mv0TzalahFHdHUqcEqnNmqL-1p1v1D3WuBFgM7CaT1LKZ5UQdNaQRKtd65tOkK2y1wIdk-WpFqLJknkohHGN/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes> which I have copied below. One bug that we have already found is that you must set environment variable FS_ALLOW_DEEP to 1, eg, export FS_ALLOW_DEEP=1 (for bash) or setenv FS_ALLOW_DEEP 1 (for csh/tcsh) thanks doug * Now uses SynthSeg <https://secure-web.cisco.com/1KBsMN2BPKXgFi2gdkFpM55EcglFvUieMSC91xEli7Gih0z7b614Aab1GJgskTCYke2PuFnswV1hgD8u4nKYa8qMZ56B8A8PyQ1PWichRRzI-OEimPC821sAeiu-pzo0Pi66Y3tKOQEmBj3zsy3LPEca2e35qnmjk8bQlUMIK420Yl0Wyp-2Zun1yWx-KcSQ6HeWNeT06W8plWjAv65wqzY3Jlo3jB_ee1aglB1FAOFqy5Ue5RU63BdmWOeX36flyPoiFNj6XyHrYmLsoqNf9bNHQrtUgysUnQtNo0E0CCsb6HLinq_gY7ix7_FqSVBMQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSynthSeg>, SynthStrip <https://secure-web.cisco.com/1VXLmpw2yihWcZU0vul0tnP_5VpqF82JyCCwIVae31F_LCDzCk2x448Vt7fow8QIvtbXMZ0KHWP-fAgLeSiV9LIg_azUp_nU-10_YJYDCO42xs5WTgpbTq3O8Y_-dKGgalVqigH2xrUmVtw_oUcXxxLEt1gKz61xWqwwFan2pn5t9igJpdDLkSAJCZfxusDF95EYrUeaCBVIJfqe8q3mnfC3ujb5Ul8nz79yOJaOAMJbm4zkKysaeyMzaiNnYsVkGsraKHAz20mNCwC65TDzZ2ZJp4yWkJKEKXS2JEklcjidLF9AZZJll4UvKzjL9wfVw/https%3A%2F%2Fsynthstrip.io>, and SynthMorph <https://secure-web.cisco.com/1gV8mZhIt5XFZ04MEHNjyef68jYwr64lzOgyCeaG_kXAM5rQmht_BVbkfa7EIgfGgCmVQuMNSxCd9Hmssboq7tP1ZkCjBTjgCE3QgKJYVmV5qs-XLzi0L2U_7DhKUfdYcD1BEg2UDOwUq9yl33C1sGtlHC1bx_bE_d3s_dJpG55I-BaJWCIgRnBQETLH9e3Rflmr8pl4mCUpETAZSuHKKV3FXyqeOYL_aPhXo18yP-BEvaK-O8Dasd4cyY8xWmnBC3xj2n5-VQrwa4z_jeqeBCs_yJmYFJXAo10ruHtKEnCMQKY8VUamhlr39tJil6EXB/https%3A%2F%2Fsynthmorph.io> (deep learning algorithms). These make recon-all more robust and much faster. Technically, SynthMorph <https://secure-web.cisco.com/1gV8mZhIt5XFZ04MEHNjyef68jYwr64lzOgyCeaG_kXAM5rQmht_BVbkfa7EIgfGgCmVQuMNSxCd9Hmssboq7tP1ZkCjBTjgCE3QgKJYVmV5qs-XLzi0L2U_7DhKUfdYcD1BEg2UDOwUq9yl33C1sGtlHC1bx_bE_d3s_dJpG55I-BaJWCIgRnBQETLH9e3Rflmr8pl4mCUpETAZSuHKKV3FXyqeOYL_aPhXo18yP-BEvaK-O8Dasd4cyY8xWmnBC3xj2n5-VQrwa4z_jeqeBCs_yJmYFJXAo10ruHtKEnCMQKY8VUamhlr39tJil6EXB/https%3A%2F%2Fsynthmorph.io> is not needed for recon-all to run, but the nonlinear registration can be used in multimodal analysis to map to the MNI152. * There is now DL automatic segmentation of regions that often cause errors in pial surface placement. These include the major sinuses (sagittal and transverse) as well as a spot between frontal and temporal lobes where the middle cerebral artery (MCA) and dura cause bright areas. * Several fixes in entorhinal cortex. First, the WM in EC is segmented using DL. The WM is often only 0.5mm thick and very hard to see; this often resulted in severe white surface areas in this location requiring manual editing to fix. The new surface now represents gyrus ambiens much better. Second, The white surface is extended to the front of amygdala. Third, the binary cortex of label now covers entorhinal cortex and parts of the temporal pole better allowing the pial surface to extend out to its true edge. * Some bugs where found in and around inferior frontal cortex causes the white surface to extend too far into basal ganglia. This has been fixed. This is above and beyond the issue reported in 7.3.2 below. * All the bug fixes described below are now turned on by default. * These changes will work with longitudinal with the caveat that the volumetric segmentation will not be fully longitudinal. The segmentation will be applied to the time point in the base space, but it will not (and cannot) be initialized with the base segmentation. Initial tests indicated that the change in power was minimal and mixed. * recon-all will now run in about 2h vs 8h on a single CPU. It will, however, required about 24GB of memory to run. * The use of SynthStrip <https://secure-web.cisco.com/1VXLmpw2yihWcZU0vul0tnP_5VpqF82JyCCwIVae31F_LCDzCk2x448Vt7fow8QIvtbXMZ0KHWP-fAgLeSiV9LIg_azUp_nU-10_YJYDCO42xs5WTgpbTq3O8Y_-dKGgalVqigH2xrUmVtw_oUcXxxLEt1gKz61xWqwwFan2pn5t9igJpdDLkSAJCZfxusDF95EYrUeaCBVIJfqe8q3mnfC3ujb5Ul8nz79yOJaOAMJbm4zkKysaeyMzaiNnYsVkGsraKHAz20mNCwC65TDzZ2ZJp4yWkJKEKXS2JEklcjidLF9AZZJll4UvKzjL9wfVw/https%3A%2F%2Fsynthstrip.io> should make recon-all much more robust as the old skull stripping method often included extra cerebral tissue. * With synthseg, we are now supplying a segmentation-based total intracrainial volume (sTIV) along with the registration-based estimated TIV (eTIV) * We have applied v8 to several studies (aging, AD crossectional, AD longitudinnal, schizophrenia). There were no major changes in the ability to detect effects, and there was no interaction between effect and version. But let us know how it performs on your studies. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1b-cPuJWzQBzLy0_-M8aROcibuzq_sUgLFR5Yb6e_hQKozjmE8B5STLMyZau0HLaBHVV4DMkawFTOxb7I_n7YG5CHXME6vnOLzeoNfsRSy0WjvCS_7sBSnH6j9uoqgf-ciQKbBFcXYp76dnbQpP6qcq9canmI5nCYx_3Avp4OG5s65PvcuNoHYnp8vzrDuTEV78cdvD712MAKtOzc8xDnCKn1fQcF8Or0c-_LGPrhcZz3NJdDx-5uWhnoIplcNeo9dWAlVnrAHj8temxnWbTP4lDBAT428ldCflGSLB1bAOccs6Xg3Z0zVztaGXuZYaPF/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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://www.massgeneralbrigham.org/complianceline <https://secure-web.cisco.com/1ok6iOBH7po92Ia3L7aAkmzT9tBthRzz5CN1XiXL70dCSdUo-vfcLXAIHzpZqd1D5Xn-5GrRtv5PnqH_ufaIlOrJTWZQbshrp03b0meKeHzNXxPrpDntcxVCIVoN3zUtSK8H87Fq8KkDQQB9-H0_QuXrjNLin_V5QcIOILgqZemDBAxu-PZ-QTAAwyJo93PJop2ciJ7c3GnLBqhftQdHrzAhkj3aO8m3M1SrSvn4Wk6VjKOezUslLa8DHyp2jIycofkmM4CkhalVedCIucpI99kOK4heexBTDZ-dnl0UE6TAg11dLNasZ3Q3-ygwdMBed/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> <*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://www.massgeneralbrigham.org/complianceline <https://secure-web.cisco.com/1ok6iOBH7po92Ia3L7aAkmzT9tBthRzz5CN1XiXL70dCSdUo-vfcLXAIHzpZqd1D5Xn-5GrRtv5PnqH_ufaIlOrJTWZQbshrp03b0meKeHzNXxPrpDntcxVCIVoN3zUtSK8H87Fq8KkDQQB9-H0_QuXrjNLin_V5QcIOILgqZemDBAxu-PZ-QTAAwyJo93PJop2ciJ7c3GnLBqhftQdHrzAhkj3aO8m3M1SrSvn4Wk6VjKOezUslLa8DHyp2jIycofkmM4CkhalVedCIucpI99kOK4heexBTDZ-dnl0UE6TAg11dLNasZ3Q3-ygwdMBed/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>> .
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi,
I am giving a try to FS 8-beta, but I am not seeing such a speed up as in the release notes: 2 hours and 24 GB of memory. In my case a case runs on average in 4.5 - 5 hours. Also I do not see such a high demands for memory, which could be related to speed.
Besides t1 I also have t2 as input. Could this have an influence? I have 24-core CPU, 96 GB RAM, 24 GB GPU running on Ubuntu 24.
recon-all -all -s sub_fs -i ./sub/mri/orig/001.nii.gz -T2 ./sub/mri/orig/T2raw.nii.gz
Thanks,
Martin
On Thu, Nov 7, 2024 at 6:54 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Hi All, as some of you have figured out, we have a beta version of FS 8.0.0. Please give it a spin and let us know if you have any problems or concerns.
The release notes are here https://secure-web.cisco.com/1WZjdr8LjQY4Je-aSRZUkzxn05p-5a_0hVrm6R-DwjleJe2... which I have copied below. One bug that we have already found is that you must set environment variable FS_ALLOW_DEEP to 1, eg, export FS_ALLOW_DEEP=1 (for bash) or setenv FS_ALLOW_DEEP 1 (for csh/tcsh)
thanks doug
Now uses SynthSeg, SynthStrip, and SynthMorph (deep learning algorithms). These make recon-all more robust and much faster. Technically, SynthMorph is not needed for recon-all to run, but the nonlinear registration can be used in multimodal analysis to map to the MNI152.
There is now DL automatic segmentation of regions that often cause errors in pial surface placement. These include the major sinuses (sagittal and transverse) as well as a spot between frontal and temporal lobes where the middle cerebral artery (MCA) and dura cause bright areas. Several fixes in entorhinal cortex. First, the WM in EC is segmented using DL. The WM is often only 0.5mm thick and very hard to see; this often resulted in severe white surface areas in this location requiring manual editing to fix. The new surface now represents gyrus ambiens much better. Second, The white surface is extended to the front of amygdala. Third, the binary cortex of label now covers entorhinal cortex and parts of the temporal pole better allowing the pial surface to extend out to its true edge. Some bugs where found in and around inferior frontal cortex causes the white surface to extend too far into basal ganglia. This has been fixed. This is above and beyond the issue reported in 7.3.2 below. All the bug fixes described below are now turned on by default. These changes will work with longitudinal with the caveat that the volumetric segmentation will not be fully longitudinal. The segmentation will be applied to the time point in the base space, but it will not (and cannot) be initialized with the base segmentation. Initial tests indicated that the change in power was minimal and mixed. recon-all will now run in about 2h vs 8h on a single CPU. It will, however, required about 24GB of memory to run.
The use of SynthStrip should make recon-all much more robust as the old skull stripping method often included extra cerebral tissue.
With synthseg, we are now supplying a segmentation-based total intracrainial volume (sTIV) along with the registration-based estimated TIV (eTIV) We have applied v8 to several studies (aging, AD crossectional, AD longitudinnal, schizophrenia). There were no major changes in the ability to detect effects, and there was no interaction between effect and version. But let us know how it performs on your studies.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1ng-lb9IRCeQMllO5GufVHweINjiZZcKqOzjzTLPh3F1U37... 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/1s2iiA3z1C-5dNAky6meVm6sROlx1q9-MmwD0_F-UM1jc9Z... https://secure-web.cisco.com/1s2iiA3z1C-5dNAky6meVm6sROlx1q9-MmwD0_F-UM1jc9ZsFJkCoaK-ypoV27laWA8-QXySl1rs6Ix8g1lWftpt34Qi_1jyrnx0aF-nAwE1-dMJPhDA71fGn_uS-Pr1qp7N9CPcGp04o6qjnkPpDeRrZRPd9zXQgI7fhEJxwuOOsGIjg0bkwGO0cH9JsBlNZTVvK8ddA4bFRpYCvYzmz5CGr-Sn8c6bxHwt7h2oyQL35LKlh2FROn5kHnl-xe1c6VeswzZRQYtBi4qorpJDOrWHjMagobwL8KThaAEO4YAIPq8n2fcAt3_kasI5FXjDI/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline .
Not sure. Does it have access to as much memory as it wants? Can you send the log file?
On 11/25/2024 1:29 PM, Martin Kavec wrote:
External Email - Use CautionHi,
I am giving a try to FS 8-beta, but I am not seeing such a speed up as in the release notes: 2 hours and 24 GB of memory. In my case a case runs on average in 4.5 - 5 hours. Also I do not see such a high demands for memory, which could be related to speed.
Besides t1 I also have t2 as input. Could this have an influence? I have 24-core CPU, 96 GB RAM, 24 GB GPU running on Ubuntu 24.
recon-all -all -s sub_fs -i ./sub/mri/orig/001.nii.gz -T2 ./sub/mri/orig/T2raw.nii.gz
Thanks,
Martin
On Thu, Nov 7, 2024 at 6:54 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Hi All, as some of you have figured out, we have a beta version of FS 8.0.0. Please give it a spin and let us know if you have any problems or concerns.
The release notes are here https://secure-web.cisco.com/1WZjdr8LjQY4Je-aSRZUkzxn05p-5a_0hVrm6R-DwjleJe2... which I have copied below. One bug that we have already found is that you must set environment variable FS_ALLOW_DEEP to 1, eg, export FS_ALLOW_DEEP=1 (for bash) or setenv FS_ALLOW_DEEP 1 (for csh/tcsh)
thanks doug
Now uses SynthSeg, SynthStrip, and SynthMorph (deep learning algorithms). These make recon-all more robust and much faster. Technically, SynthMorph is not needed for recon-all to run, but the nonlinear registration can be used in multimodal analysis to map to the MNI152.
There is now DL automatic segmentation of regions that often cause errors in pial surface placement. These include the major sinuses (sagittal and transverse) as well as a spot between frontal and temporal lobes where the middle cerebral artery (MCA) and dura cause bright areas. Several fixes in entorhinal cortex. First, the WM in EC is segmented using DL. The WM is often only 0.5mm thick and very hard to see; this often resulted in severe white surface areas in this location requiring manual editing to fix. The new surface now represents gyrus ambiens much better. Second, The white surface is extended to the front of amygdala. Third, the binary cortex of label now covers entorhinal cortex and parts of the temporal pole better allowing the pial surface to extend out to its true edge. Some bugs where found in and around inferior frontal cortex causes the white surface to extend too far into basal ganglia. This has been fixed. This is above and beyond the issue reported in 7.3.2 below. All the bug fixes described below are now turned on by default. These changes will work with longitudinal with the caveat that the volumetric segmentation will not be fully longitudinal. The segmentation will be applied to the time point in the base space, but it will not (and cannot) be initialized with the base segmentation. Initial tests indicated that the change in power was minimal and mixed. recon-all will now run in about 2h vs 8h on a single CPU. It will, however, required about 24GB of memory to run.
The use of SynthStrip should make recon-all much more robust as the old skull stripping method often included extra cerebral tissue.
With synthseg, we are now supplying a segmentation-based total intracrainial volume (sTIV) along with the registration-based estimated TIV (eTIV) We have applied v8 to several studies (aging, AD crossectional, AD longitudinnal, schizophrenia). There were no major changes in the ability to detect effects, and there was no interaction between effect and version. But let us know how it performs on your studies.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1ng-lb9IRCeQMllO5GufVHweINjiZZcKqOzjzTLPh3F1U37... 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/1s2iiA3z1C-5dNAky6meVm6sROlx1q9-MmwD0_F-UM1jc9Z... https://secure-web.cisco.com/1s2iiA3z1C-5dNAky6meVm6sROlx1q9-MmwD0_F-UM1jc9ZsFJkCoaK-ypoV27laWA8-QXySl1rs6Ix8g1lWftpt34Qi_1jyrnx0aF-nAwE1-dMJPhDA71fGn_uS-Pr1qp7N9CPcGp04o6qjnkPpDeRrZRPd9zXQgI7fhEJxwuOOsGIjg0bkwGO0cH9JsBlNZTVvK8ddA4bFRpYCvYzmz5CGr-Sn8c6bxHwt7h2oyQL35LKlh2FROn5kHnl-xe1c6VeswzZRQYtBi4qorpJDOrWHjMagobwL8KThaAEO4YAIPq8n2fcAt3_kasI5FXjDI/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline .
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Aaron Tanenbaum -
Douglas N. Greve -
Hoffmann, Malte,PhD -
Martin Kavec