External Email - Use Caution
The link to msg 74015 did not work for me in the freesurfer mail list archive, so I don’t know how that relates to what you are inquiring about. But the freesurfer Intel Mac binaries generally run (automatically) using the built-in Rosetta emulation environment provided with M1/M2 silicon Macs. Not clear to me what you are trying to do that would prevent you from running the Intel binaries. -R.
On Jun 14, 2023, at 18:20, Sorby-Adams, Annabel <ASORBY-ADAMS@mgh.harvard.edu> wrote: External Email - Use Caution Dear Freesurfers, A workaround was previously posted for Apple M1/2 processors to download and run the 7.3.2 release of Freesurfer (here MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1VXXHlA3ejXWeaDSw3Gia-hr1Np9HVFX36eSBXmpFEuiQkQ..., I require some tools currently available in the development version. Is there a possible workaround for Apple M1/2 chips and Freesurfer dev compatibility? Cheers!Annabel Annabel Sorby-Adams, PhDPostdoctoral Research Fellow Department of NeurologyMassachusetts General HospitalLunder 6 55 Fruit Street, Boston MAMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1zk-Uu_2eHEfe2i1XJ6tALsAaD_hTmuiBHqh9svQoJR0vXs... Medical SchoolMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1GvMNQk6ewGYBxnB-olGLBbtOxrT1j5h8GqgpfAxz9PKqfM...; +1 617 251 6465Pager ID 23944_______________________________________________Freesurfer mailing listFreesurfer@nmr..mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Thank you so much,
I previously used the workaround to uninstall and reinstall tensorflow that was posted on the forum on 12th December 2022 for 7.3.2. This workaround worked for the development version also this evening, but several tools are failing, namely SynthSR. When running mri_synthsr, I get the following errors:
mri_synthsr Traceback (most recent call last): File "/Applications/freesurfer/dev/python/scripts/mri_synthsr", line 10, in <module> import surfa as sf File "/Applications/freesurfer/dev/python/lib/python3.8/site-packages/surfa/__init__.py", line 19, in <module> from .image import Volume File "/Applications/freesurfer/dev/python/lib/python3.8/site-packages/surfa/image/__init__.py", line 1, in <module> from .framed import FramedImage File "/Applications/freesurfer/dev/python/lib/python3.8/site-packages/surfa/image/framed.py", line 24, in <module> from surfa.image.interp import interpolate File "surfa/image/interp.pyx", line 1, in init surfa.image.interp ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 96 from C header, got 80 from PyObject
I am not sure if this is due to un/re installation of tensorflow, or if anyone has any suggestions/if I should follow up with Eugenio directly.
Cheers! Annabel
Annabel Sorby-Adams, PhD Postdoctoral Research Fellow
Department of Neurology Massachusetts General Hospital Lunder 6 55 Fruit Street, Boston MA https://secure-web.cisco.com/1ZjJsFA9JxVSsH_upKeiQuWbHljmr8BGznO-9dgmSaPqbgF...
Harvard Medical School https://secure-web.cisco.com/1Hi7GEkZLErpEc2ZXlYuWWfJBXX77-piLbYN2TxnEZv8MBh...
E asorby-adams@mgh.harvard.edu T +1 617 251 6465 Pager ID 23944
From: fsbuild fsbuild@contbay.com Date: Wednesday, 14 June 2023 at 19:08 To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Development Version Apple M1/2 Chip Compatability
External Email - Use Caution
The link to msg 74015 did not work for me in the freesurfer mail list archive, so I don’t know how that relates to what you are inquiring about. But the freesurfer Intel Mac binaries generally run (automatically) using the built-in Rosetta emulation environment provided with M1/M2 silicon Macs. Not clear to me what you are trying to do that would prevent you from running the Intel binaries.
-R.
On Jun 14, 2023, at 18:20, Sorby-Adams, Annabel ASORBY-ADAMS@mgh.harvard.edu wrote:
External Email - Use Caution
Dear Freesurfers,
A workaround was previously posted for Apple M1/2 processors to download and run the 7.3.2 release of Freesurfer (here MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1FMTHsb9zsgCup_lUOA9MD8NSyi1e-LwQKFFBVv7u_Er8Ns...https://secure-web.cisco.com/1rhZOY7nbxViNYlSuKEbROlDwv_vRR7DM96i7_vRQr7LlSqcmvFEhYXdZFpoeBc1TBMDEWPtqEjNCaoPN_8AQ0bNmsRynwn5Qt36T-Ls5prE1SRRHh74NiEUDTtc6OcX_6EWl0Pirxe4PzN54uspOccH_uUCS7eIfMiLlzU01T_9Ik7HjhS1V9P7JHKjXsUwRT9MBfs_HVm4fX1wki2nXaN8B4CBp4Tc_huXePHJJM88Z8Ae7CXewWJcA1lF61j4N0LIo1ivC6yBtgXFJy1RHhA/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg74015.htmlº.
Unfortunately, I require some tools currently available in the development version. Is there a possible workaround for Apple M1/2 chips and Freesurfer dev compatibility?
Cheers! Annabel
Annabel Sorby-Adams, PhD Postdoctoral Research Fellow
Department of Neurology Massachusetts General Hospital Lunder 6 55 Fruit Street, Boston MA MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1ZjJsFA9JxVSsH_upKeiQuWbHljmr8BGznO-9dgmSaPqbgF...https://secure-web.cisco.com/1B91TQil3Y4INxdY8w5C3v5N-ew8l8og0Oc08GLlsPmXa-_dJV1AogVAlO7a2g6mZWloYAxgQVd-L03gUlAZjGfi9GzGNLh6tkAUo9p1W1EpKslEgLRg4OBMS4bwIUPAfOcfA6SvPbMwA3evmkWF6ZbQw2FD45hy2J3ESaWdHhl0aiqPJQvYpJGKAgt4XhpTVxVRXRU2H-w8l8w2nnOLxj9fz6AmZ8jMsWM65C0nB9DQcbNnpDXdnOWZZu8tMZYVtDcwZ1l22wm6E1oPqXvxU-Q/https%3A%2F%2Fwww.massgeneral.org%2F
Harvard Medical School MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1Hi7GEkZLErpEc2ZXlYuWWfJBXX77-piLbYN2TxnEZv8MBh...https://secure-web.cisco.com/1yUJ5q0N36h2EgNqS9cfyhhlYpEJQJPWX8i6IfcDEPAcNsqW2dUnmyEc7BAb04h5A1je_oGh7_DXFrUEbPW1K3PSStKwFi1gfBBVYlS85ycd8GZK_YutzTrdsjAIE9Z53X-_SSVqJodbeTB68S2f1c5jiLSCS3754Wn6-2SYMr4y8Iwn5ERkVHIa8Nwb6B5JsWUvO5nmJKol-Up4WPXRHoJpuKMVC1cZa2OHkokXvZdyQFla1chOdWBZGpHPoUoYF7gR8uM9ylb1s54ryiZW3EQ/https%3A%2F%2Fhms.harvard.edu%2F
E asorby-adams@mgh.harvard.edumailto:asorby-adams@mgh.harvard.edu T +1 617 251 6465 Pager ID 23944 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1vRw5nbre3KsVZ2eUt4Gt2GtQ5lxy4t8actBQig2wyavgk3...https://secure-web.cisco.com/1SozzvABBOsF6tajLEd-S6XwPuOw1XN7AvuOW5YzjuCI3SWEH_011xLBtY1XU4UB8HwnpDfiTmgWOgvwSu9hWn4WfCjd76bZW1tuNUuiXm7Xulr_9VCdWsAUNEgrKui9f1KNdefiBVW1Ih_9NHwILcXBRWVHrDxiezgWDKJZTVV6K2MZrUgeQjkaklEuwixFwXWiqLpgVmtgRxu-d2lWHO_gZo3vSNvTG9STU5PiTXiYFXFgQFa8YuAEVt_HD5Tm-j60_uZ_F8NJIUXGklxjABjmmKQzhkPACp3NTTh5jllNxBLeoXplhE5pW07lIzoSP/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
External Email - Use Caution
Can you share what version of numpy you are using?
Best, Avnish ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Sorby-Adams, Annabel ASORBY-ADAMS@mgh.harvard.edu Sent: Wednesday, June 14, 2023 8:09 PM To: fsbuild fsbuild@contbay.com; freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] SynthSR Freesurfer Development Version Apple M1/2 Chip Compatability
External Email - Use Caution
Thank you so much,
I previously used the workaround to uninstall and reinstall tensorflow that was posted on the forum on 12th December 2022 for 7.3.2. This workaround worked for the development version also this evening, but several tools are failing, namely SynthSR. When running mri_synthsr, I get the following errors:
mri_synthsr
Traceback (most recent call last):
File "/Applications/freesurfer/dev/python/scripts/mri_synthsr", line 10, in <module>
import surfa as sf
File "/Applications/freesurfer/dev/python/lib/python3.8/site-packages/surfa/__init__.py", line 19, in <module>
from .image import Volume
File "/Applications/freesurfer/dev/python/lib/python3.8/site-packages/surfa/image/__init__.py", line 1, in <module>
from .framed import FramedImage
File "/Applications/freesurfer/dev/python/lib/python3.8/site-packages/surfa/image/framed.py", line 24, in <module>
from surfa.image.interp import interpolate
File "surfa/image/interp.pyx", line 1, in init surfa.image.interp
ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 96 from C header, got 80 from PyObject
I am not sure if this is due to un/re installation of tensorflow, or if anyone has any suggestions/if I should follow up with Eugenio directly.
Cheers!
Annabel
Annabel Sorby-Adams, PhD
Postdoctoral Research Fellow
Department of Neurology
Massachusetts General Hospital
Lunder 6 55 Fruit Street, Boston MA
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1-LwjaeFp_0VMWpySuHJ67i5hcxu4k5hzFCe1wt5fktmN3w...https://secure-web.cisco.com/1ZjJsFA9JxVSsH_upKeiQuWbHljmr8BGznO-9dgmSaPqbgFqClu7D_OBuc1NHuQZwGhz0ncYGiVJ0ilzmZuZDXpjyH5L44udW5U3BsqEo87ooduMQdT43p7aJOpWWWOfkfNKkFZ3sSfDvvJjTcGunIldoIdRnxuGZ5xp38N8GEM-hURRR-aUcB5QBd4raGA_ry7Vr110R2QKQ2nAoybM6AF6EKb808bLvsqq8K9pcruU6Yu6MoByzgz7sdFeLj8Ka5yUrHj-m6S-r709B3Qxsvg/https%3A%2F%2Fwww.massgeneral.org%2F
Harvard Medical School
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1nRWT8FPRkdNIsJhADpmXaEamnxe_-IDKV4lhVTr_TjQxo1...https://secure-web.cisco.com/1Hi7GEkZLErpEc2ZXlYuWWfJBXX77-piLbYN2TxnEZv8MBhRq4VoppmukMRHKnWh4gvtt2ZY8BjUTuiuCEOg3j9ECHnabf9tzXjBKpio1I1uzbUR3OPIudCnjO_pPKZHSfV0RTqWR4cBJ6bnQaqsF-Vge-x-YWGhoR4kJnvscXOY6PhPElc42GMc2j0OypJwHHRsGPRdpxihCmN8bUd-oUQquwTNza_SZBwS1wIp4D9P0yAFUg8xQvpjTe5_py2uDKxlYu4ZUCmOKKwGsVd2JXw/https%3A%2F%2Fhms.harvard.edu%2F
E asorby-adams@mgh.harvard.edu
T +1 617 251 6465
Pager ID 23944
From: fsbuild fsbuild@contbay.com Date: Wednesday, 14 June 2023 at 19:08 To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Development Version Apple M1/2 Chip Compatability
External Email - Use Caution
The link to msg 74015 did not work for me in the freesurfer mail list archive, so I don’t know how that relates to what you are inquiring about. But the freesurfer Intel Mac binaries generally run (automatically) using the built-in Rosetta emulation environment provided with M1/M2 silicon Macs. Not clear to me what you are trying to do that would prevent you from running the Intel binaries.
-R.
On Jun 14, 2023, at 18:20, Sorby-Adams, Annabel ASORBY-ADAMS@mgh.harvard.edu wrote:
External Email - Use Caution
Dear Freesurfers,
A workaround was previously posted for Apple M1/2 processors to download and run the 7.3.2 release of Freesurfer (here MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/16HUpmh6xc3x1sLBUTVwcShO-lRkvrqqwkqF2l8QKwgJnu5...https://secure-web.cisco.com/1rhZOY7nbxViNYlSuKEbROlDwv_vRR7DM96i7_vRQr7LlSqcmvFEhYXdZFpoeBc1TBMDEWPtqEjNCaoPN_8AQ0bNmsRynwn5Qt36T-Ls5prE1SRRHh74NiEUDTtc6OcX_6EWl0Pirxe4PzN54uspOccH_uUCS7eIfMiLlzU01T_9Ik7HjhS1V9P7JHKjXsUwRT9MBfs_HVm4fX1wki2nXaN8B4CBp4Tc_huXePHJJM88Z8Ae7CXewWJcA1lF61j4N0LIo1ivC6yBtgXFJy1RHhA/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg74015.htmlº.
Unfortunately, I require some tools currently available in the development version. Is there a possible workaround for Apple M1/2 chips and Freesurfer dev compatibility?
Cheers!
Annabel
Annabel Sorby-Adams, PhD
Postdoctoral Research Fellow
Department of Neurology
Massachusetts General Hospital
Lunder 6 55 Fruit Street, Boston MA
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1-LwjaeFp_0VMWpySuHJ67i5hcxu4k5hzFCe1wt5fktmN3w...https://secure-web.cisco.com/1B91TQil3Y4INxdY8w5C3v5N-ew8l8og0Oc08GLlsPmXa-_dJV1AogVAlO7a2g6mZWloYAxgQVd-L03gUlAZjGfi9GzGNLh6tkAUo9p1W1EpKslEgLRg4OBMS4bwIUPAfOcfA6SvPbMwA3evmkWF6ZbQw2FD45hy2J3ESaWdHhl0aiqPJQvYpJGKAgt4XhpTVxVRXRU2H-w8l8w2nnOLxj9fz6AmZ8jMsWM65C0nB9DQcbNnpDXdnOWZZu8tMZYVtDcwZ1l22wm6E1oPqXvxU-Q/https%3A%2F%2Fwww.massgeneral.org%2F
Harvard Medical School
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1nRWT8FPRkdNIsJhADpmXaEamnxe_-IDKV4lhVTr_TjQxo1...https://secure-web.cisco.com/1yUJ5q0N36h2EgNqS9cfyhhlYpEJQJPWX8i6IfcDEPAcNsqW2dUnmyEc7BAb04h5A1je_oGh7_DXFrUEbPW1K3PSStKwFi1gfBBVYlS85ycd8GZK_YutzTrdsjAIE9Z53X-_SSVqJodbeTB68S2f1c5jiLSCS3754Wn6-2SYMr4y8Iwn5ERkVHIa8Nwb6B5JsWUvO5nmJKol-Up4WPXRHoJpuKMVC1cZa2OHkokXvZdyQFla1chOdWBZGpHPoUoYF7gR8uM9ylb1s54ryiZW3EQ/https%3A%2F%2Fhms.harvard.edu%2F
E asorby-adams@mgh.harvard.edumailto:asorby-adams@mgh.harvard.edu
T +1 617 251 6465
Pager ID 23944
_______________________________________________ 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/1JgyB7bLEcHFCcQQEkwo_O84Tcxv-FFkZwSju54o_LLWGMd...https://secure-web.cisco.com/1SozzvABBOsF6tajLEd-S6XwPuOw1XN7AvuOW5YzjuCI3SWEH_011xLBtY1XU4UB8HwnpDfiTmgWOgvwSu9hWn4WfCjd76bZW1tuNUuiXm7Xulr_9VCdWsAUNEgrKui9f1KNdefiBVW1Ih_9NHwILcXBRWVHrDxiezgWDKJZTVV6K2MZrUgeQjkaklEuwixFwXWiqLpgVmtgRxu-d2lWHO_gZo3vSNvTG9STU5PiTXiYFXFgQFa8YuAEVt_HD5Tm-j60_uZ_F8NJIUXGklxjABjmmKQzhkPACp3NTTh5jllNxBLeoXplhE5pW07lIzoSP/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
freesurfer@nmr.mgh.harvard.edu
-
fsbuild -
Kumar, Avnish -
Sorby-Adams, Annabel