External Email - Use Caution
Hello FreeSurfer Developers,
I am attempting to run the recon-all pipeline on one subject using the following code:
recon-all -all -i t1.nii -s p03_1
Although, I get the following error in the command line:
mris_calc -o rh.area.mid rh.area add rh.area.pial error: No such file or directory error: read_signa(/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/I.001): could not open file error: No such file or directory error: mris_calc: could not establish read access to 'rh.area'.
Tue Aug 1 15:58:13 EDT 2023 ERROR: vertexvol mris_calc -o rh.area.mid rh.area add rh.area.pial Darwin C02F10PVPN5W.local 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:56 PDT 2023; root:xnu-8796.141.3~6/RELEASE_X86_64 x86_64
recon-all -s p03_8 exited with ERRORS at Tue Aug 1 15:58:13 EDT 2023
To report a problem, see http://secure-web.cisco.com/1dFtz9tfZWpoyZVj7mXFMLhzADOYxytPQ-lAzdm9SS0VD1FT...
The recon-all.error file contains:
------------------------------ SUBJECT p03_8 DATE Tue Aug 1 15:58:13 EDT 2023 USER taylorariko HOST C02F10PVPN5W.local PROCESSOR x86_64 OS Darwin Darwin C02F10PVPN5W.local 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:56 PDT 2023; root:xnu-8796.141.3~6/RELEASE_X86_64 x86_64 7.2.0 (freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b) /Applications/freesurfer/7.2.0/bin/recon-all PWD /Volumes/Beta/Carmen/t1/p03_8/p03_8/mri CMD vertexvol --s p03_8 --rh --th3
I have made sure that I have read, write, and execute access to the folder /path/to/subject/surf and the file rh.area. I can successfully run the command to make rh.area (mris_place_surface --area-map ../surf/rh.white ../surf/rh.area), but the error persists in using rh.area. I have disk space and can run other commands such as this fake one (mris_calc -o rh.area.Test rh.area.pial add rh.area.pial), but not if it contains rh.area. I have tried to rerun the command from root and get the same error message.
I found 2 similar threads of the mail-archive, though I didn’t find any remedies:
1. https://secure-web.cisco.com/1s_8L81vMyC0-KdGicsKrUniSkh4Egg5_LxXz-_YnmsgL0G... 2. https://secure-web.cisco.com/1MW6Y468pIeNLaB3ruN22mzrkJIjqalKQmsNncuNqyZW9S9...
Does anyone have any thoughts on how to trouble-shoot this? I have included my recon-all.log in the case it is of any use.
1. Freesurfer version: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b 2. Platform: macOS Sonoma 14.3.1 3. uname -a: Darwin C02F10PVPN5W.local 23.3.0 Darwin Kernel Version 23.3.0: Wed Dec 20 21:28:58 PST 2023; root:xnu-10002.81.5~7/RELEASE_X86_64 x86_64 4. recon-all.log: see attached
Thanks in advance!
Taylor Ariko
Hi Taylor,
I don't understand how you could get that error. It seems to me that read_signa() is for reading .signa files.
Can you try 'mris_calc -o rh.area.mid rh.area add rh.area.pial' directly? Pass full path to your rh.area and rh.area.pial.
What does 'mri_info rh.area' report?
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Ariko, Taylor Sent: Tuesday, March 5, 2024 2:35 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] recon-all hard error: mris_calc could not establish read access to rh.area
External Email - Use Caution Hello FreeSurfer Developers,
I am attempting to run the recon-all pipeline on one subject using the following code:
recon-all -all -i t1.nii -s p03_1
Although, I get the following error in the command line:
mris_calc -o rh.area.mid rh.area add rh.area.pial error: No such file or directory error: read_signa(/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/I.001): could not open file error: No such file or directory error: mris_calc: could not establish read access to 'rh.area'.
Tue Aug 1 15:58:13 EDT 2023 ERROR: vertexvol mris_calc -o rh.area.mid rh.area add rh.area.pial Darwin C02F10PVPN5W.local 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:56 PDT 2023; root:xnu-8796.141.3~6/RELEASE_X86_64 x86_64
recon-all -s p03_8 exited with ERRORS at Tue Aug 1 15:58:13 EDT 2023
To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttp://secure-web.cisco.com/1dFtz9tfZWpoyZVj7mXFMLhzADOYxytPQ-lAzdm9SS0VD1FTbz45enl8IaOWz6IRp_KLvd-O07tGlRWlew0e-tEz_uiSd7h7vjXFLqsJ43sz_QtFlRODTxSyXDZGJH-L2KeK1nXuICROZ0fCFy4KhTJxJ3haAuYRWOZcUa5BBA0fS4iGoh92xzUyORn8wvcaGQ3GMrAFxd-bI-V_SZY3tfGjNWqrLPpayxctYehni827EcLH8K0REtJUxl1SPpG6Pe3Emtor75zz-0Hm9qjm0-uKKTYgh6I5B9-s-Y0K05FI459LrA6nQEDmQc7Af7uhtsjN1f1kK5Ejciw7kqOfhnQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting
The recon-all.error file contains:
------------------------------ SUBJECT p03_8 DATE Tue Aug 1 15:58:13 EDT 2023 USER taylorariko HOST C02F10PVPN5W.local PROCESSOR x86_64 OS Darwin Darwin C02F10PVPN5W.local 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:56 PDT 2023; root:xnu-8796.141.3~6/RELEASE_X86_64 x86_64 7.2.0 (freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b) /Applications/freesurfer/7.2.0/bin/recon-all PWD /Volumes/Beta/Carmen/t1/p03_8/p03_8/mri CMD vertexvol --s p03_8 --rh --th3
I have made sure that I have read, write, and execute access to the folder /path/to/subject/surf and the file rh.area. I can successfully run the command to make rh.area (mris_place_surface --area-map ../surf/rh.white ../surf/rh.area), but the error persists in using rh.area. I have disk space and can run other commands such as this fake one (mris_calc -o rh.area.Test rh.area.pial add rh.area.pial), but not if it contains rh.area. I have tried to rerun the command from root and get the same error message.
I found 2 similar threads of the mail-archive, though I didn't find any remedies:
1. MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg44230.htmlhttps://secure-web.cisco.com/1s_8L81vMyC0-KdGicsKrUniSkh4Egg5_LxXz-_YnmsgL0Gm5kE9GJdy_R08c77fGYQTPDdQWTXx7zHH94KsUkxY5QpVUmicO4epJQCmrRk9qMFABnrFnqeMNWHf8BMzYZT9-_q55fpDjwdwtbSup33zXWmZ7_Qaxd-4Z5VhTLIcQnzdH1PATkHpAO-TTMDS2pwJXoqBJWfCdjq5iu6ZD_6K0lrHqWnH3JudltTqMg3oGYhVXWbXscFSmN__-ZRnNfVJ8CDc90XN86oLWU105NH4AaObyV0lLfIM82_MyoJeAcNXkfuOpxqrOcWWH_mbDB5W0KbiD_DVkA4CTMYOqPQ/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg44230.html 2. MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51444.htmlhttps://secure-web.cisco.com/1MW6Y468pIeNLaB3ruN22mzrkJIjqalKQmsNncuNqyZW9S97Lqt_NIPp9ILpSPWI1wipv6Yr0BpbNmGPSoS-nDLaWTSHWRvXjPBhx6OWaUG3ykAth8rcrPy56gCpMo8EJHuhvxzkr3J5a8gg_8hfpQn3rWeGwxvT0rbc0ADxMrz98-mzO1bI4_zT80IcHOH6lIka2UdyAuC6gQplfb_eWpXafHuJDUR-JbSxIKSJcWIraGWK6JhoVQfgB3PNWSVgFkCVarUhylVDULGGQwPvt8XCNNPOC-bX_PoKwRMM7irjngRXBU0TPYBqY3QjiI4O9FrPJMQEQNW3NadmyXb4uhQ/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg51444.html
Does anyone have any thoughts on how to trouble-shoot this? I have included my recon-all.log in the case it is of any use.
1. Freesurfer version: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b 2. Platform: macOS Sonoma 14.3.1 3. uname -a: Darwin C02F10PVPN5W.local 23.3.0 Darwin Kernel Version 23.3.0: Wed Dec 20 21:28:58 PST 2023; root:xnu-10002.81.5~7/RELEASE_X86_64 x86_64 4. recon-all.log: see attached
Thanks in advance!
Taylor Ariko
External Email - Use Caution
Hello Yujing,
Thank you for your quick response!
When I run:
mris_calc -o rh.area.mid /path/to/subject/surf/rh.area add /path/to/subject/surf/rh.area.pial
I get the following error:
error: No such file or directory error: read_signa(/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/I.001): could not open file error: No such file or directory error: mris_calc: could not establish read access to '/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/rh.area'.
But when I run:
mri_info rh.area
I get the following output:
Volume information for rh.area type: unknown dimensions: 831 x 10015 x 25953 voxel sizes: -0.000000, -0.000000, nan type: SHORT (4) fov: 1016.473 dof: 1 xstart: 0.0, xend: 990983162970892849632569550308376576.0 ystart: -0.0, yend: 3079152361728581627851833344.0 zstart: -0.0, zend: -3815443229699337177012458129513775104.0 TR: 0.00 msec, TE: -0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -18770011487391973376.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = nan : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -0.0000 Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: 0.0000 -0.0000 nan nan -0.0000 -0.0000 nan nan -0.0000 0.0000 nan nan 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant nan
ras to voxel transform: error: mat = NULL!
It appears that this is where the issue is coming from. Any ideas on why this is occurring? The brain is normal and has good rh.white and rh.pial surfaces.
Many thanks, Taylor
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Huang, Yujing YHUANG43@mgh.harvard.edu Date: Tuesday, March 5, 2024 at 4:25 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [EXTERNAL] Re: [Freesurfer] recon-all hard error: mris_calc could not establish read access to rh.area CAUTION: This email originated from outside the organization. DO NOT CLICK ON LINKS or OPEN ATTACHMENTS unless you know and trust the sender. Hi Taylor,
I don’t understand how you could get that error. It seems to me that read_signa() is for reading .signa files.
Can you try ‘mris_calc -o rh.area.mid rh.area add rh.area.pial’ directly? Pass full path to your rh.area and rh.area.pial.
What does ‘mri_info rh.area’ report?
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Ariko, Taylor Sent: Tuesday, March 5, 2024 2:35 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] recon-all hard error: mris_calc could not establish read access to rh.area
External Email - Use Caution Hello FreeSurfer Developers,
I am attempting to run the recon-all pipeline on one subject using the following code:
recon-all -all -i t1.nii -s p03_1
Although, I get the following error in the command line:
mris_calc -o rh.area.mid rh.area add rh.area.pial error: No such file or directory error: read_signa(/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/I.001): could not open file error: No such file or directory error: mris_calc: could not establish read access to 'rh.area'.
Tue Aug 1 15:58:13 EDT 2023 ERROR: vertexvol mris_calc -o rh.area.mid rh.area add rh.area.pial Darwin C02F10PVPN5W.local 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:56 PDT 2023; root:xnu-8796.141.3~6/RELEASE_X86_64 x86_64
recon-all -s p03_8 exited with ERRORS at Tue Aug 1 15:58:13 EDT 2023
To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1YEiKrKcbgSdrDxUh7Jnp3JDZTJ2pl3aYMzWocJZCv7iRtCy...https://secure-web.cisco.com/1CaodTHEqFJANum5lQmPIsKlyhTH58_SFJAGKZ6TTZNhYT-fbfTLA9poANerCrvu536F8AYoZacVgaOD-ftvfPlqDF6QmL0Kb_P0tJ-4KhhHXgPW0vCPbd3l28KVQWjxJ04Kb9TwsvBV_Xy1P7M_ubxDUBSiWWSRpTp184jmSqlaIvz3hu9TLqfJomN--WblU1askcRJnzmRlQp34CUUGIIMUyAyC21dP6TqobB9jxRi8G8bQeP3mLqAxxeCpCnFo7Cq4g8v6HZhxoqyNcsl2PLWQjvRWYWwgb-ZzPqU5FfUVfQBfIKAEOLzoA9GPcXpD0VYfTHOGD7lIskaFG-3Rgg/https%3A%2F%2Furldefense.com%2Fv3%2F__http%3A%2Fsecure-web.cisco.com%2F1dFtz9tfZWpoyZVj7mXFMLhzADOYxytPQ-lAzdm9SS0VD1FTbz45enl8IaOWz6IRp_KLvd-O07tGlRWlew0e-tEz_uiSd7h7vjXFLqsJ43sz_QtFlRODTxSyXDZGJH-L2KeK1nXuICROZ0fCFy4KhTJxJ3haAuYRWOZcUa5BBA0fS4iGoh92xzUyORn8wvcaGQ3GMrAFxd-bI-V_SZY3tfGjNWqrLPpayxctYehni827EcLH8K0REtJUxl1SPpG6Pe3Emtor75zz-0Hm9qjm0-uKKTYgh6I5B9-s-Y0K05FI459LrA6nQEDmQc7Af7uhtsjN1f1kK5Ejciw7kqOfhnQ%2Fhttp*3A*2F*2Fsurfer.nmr.mgh.harvard.edu*2Ffswiki*2FBugReporting__;JSUlJSU!!KVu0SnhVq1hAFvslES2Y!IF_PyIoN46gdEwAovSOrLvwK3TfosortPgW4RoFCW1D0uGc53eu3quu-JN8Jgna7cnZtnrrNAAZ4Th2md4U5n7NY7g_I$
The recon-all.error file contains:
------------------------------ SUBJECT p03_8 DATE Tue Aug 1 15:58:13 EDT 2023 USER taylorariko HOST C02F10PVPN5W.local PROCESSOR x86_64 OS Darwin Darwin C02F10PVPN5W.local 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:56 PDT 2023; root:xnu-8796.141.3~6/RELEASE_X86_64 x86_64 7.2.0 (freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b) /Applications/freesurfer/7.2.0/bin/recon-all PWD /Volumes/Beta/Carmen/t1/p03_8/p03_8/mri CMD vertexvol --s p03_8 --rh --th3
I have made sure that I have read, write, and execute access to the folder /path/to/subject/surf and the file rh.area. I can successfully run the command to make rh.area (mris_place_surface --area-map ../surf/rh.white ../surf/rh.area), but the error persists in using rh.area. I have disk space and can run other commands such as this fake one (mris_calc -o rh.area.Test rh.area.pial add rh.area.pial), but not if it contains rh.area. I have tried to rerun the command from root and get the same error message.
I found 2 similar threads of the mail-archive, though I didn’t find any remedies:
1. MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/10965F_-vx89OvlFIrwsrqGlp69cVaZlvnVopyNAJMex2tK...https://secure-web.cisco.com/1HRAbYBdu1aYd6rb_hmfIZeCTevnrqTggTE81Yqe-w-rpg3N6eyCNTsrX1MZZhTxgkjWpbNCqB185OmPcmNoVb8M1S9U3LI1kCf7qQY6-2pd93ytq7_oxfhbc2Iouztc_ZCpGTwEMNpO0gvkF9vgeLcyn2mOo16nwdd4v7NMoXPHrZTQlBGjLu4yOQ6yXsLOCE9utsiCcoKCsgWePCEdU27r49bq0zraxYuQRHbFZK-f1xBGiLZUEffbZ2e292BA5aMH0IzrQYOKOx3GE_zYCKWaT51kVatf-cr-mCXNfQZms2XzORInWHKognXd51wxxDKoPDiRn7jJv-P52x75FVg/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1s_8L81vMyC0-KdGicsKrUniSkh4Egg5_LxXz-_YnmsgL0Gm5kE9GJdy_R08c77fGYQTPDdQWTXx7zHH94KsUkxY5QpVUmicO4epJQCmrRk9qMFABnrFnqeMNWHf8BMzYZT9-_q55fpDjwdwtbSup33zXWmZ7_Qaxd-4Z5VhTLIcQnzdH1PATkHpAO-TTMDS2pwJXoqBJWfCdjq5iu6ZD_6K0lrHqWnH3JudltTqMg3oGYhVXWbXscFSmN__-ZRnNfVJ8CDc90XN86oLWU105NH4AaObyV0lLfIM82_MyoJeAcNXkfuOpxqrOcWWH_mbDB5W0KbiD_DVkA4CTMYOqPQ%2Fhttps*3A*2F*2Fwww.mail-archive.com*2Ffreesurfer*40nmr.mgh.harvard.edu*2Fmsg44230.html__;JSUlJSUl!!KVu0SnhVq1hAFvslES2Y!IF_PyIoN46gdEwAovSOrLvwK3TfosortPgW4RoFCW1D0uGc53eu3quu-JN8Jgna7cnZtnrrNAAZ4Th2md4U5n7lbwM4K$ 2. MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/14-F4-Lvl2DdoySNTqqzSIpRsRtnJOgs1o_kqgvqA1Wt16d...https://secure-web.cisco.com/1wtd7OWyV-jikcNrXYwCtgg4FYC03UamZhSkD7jlbXHetManaZQRizDTrEx0OObiVQBJk9_BijZ5X77JUQx9SnaysdjdNuZsVjoC9VUlk0c-tLHpWCguaQGc7JxwvZkUnOun-K2AXPAb2yr8jEmojlv9_l5LrGW-2xsCy9FdKR0GNEJAI81QEj2KWa8dWBEzgzwhob-NT5tqOuuQ9f-BImwolFyEhZUEHg5qwq18oCeC4J3Ac-I6HLFi104OLkrMRpurL2d4qBKeHfdfsgH-1oqlXY26E54T-271T-yMPdGAlM6YwDVjS61vBfWKcEIWbFTtFzyTjeGl0flIDhmiMfQ/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1MW6Y468pIeNLaB3ruN22mzrkJIjqalKQmsNncuNqyZW9S97Lqt_NIPp9ILpSPWI1wipv6Yr0BpbNmGPSoS-nDLaWTSHWRvXjPBhx6OWaUG3ykAth8rcrPy56gCpMo8EJHuhvxzkr3J5a8gg_8hfpQn3rWeGwxvT0rbc0ADxMrz98-mzO1bI4_zT80IcHOH6lIka2UdyAuC6gQplfb_eWpXafHuJDUR-JbSxIKSJcWIraGWK6JhoVQfgB3PNWSVgFkCVarUhylVDULGGQwPvt8XCNNPOC-bX_PoKwRMM7irjngRXBU0TPYBqY3QjiI4O9FrPJMQEQNW3NadmyXb4uhQ%2Fhttps*3A*2F*2Fwww.mail-archive.com*2Ffreesurfer*40nmr.mgh.harvard.edu*2Fmsg51444.html__;JSUlJSUl!!KVu0SnhVq1hAFvslES2Y!IF_PyIoN46gdEwAovSOrLvwK3TfosortPgW4RoFCW1D0uGc53eu3quu-JN8Jgna7cnZtnrrNAAZ4Th2md4U5n5i6wwN6$
Does anyone have any thoughts on how to trouble-shoot this? I have included my recon-all.log in the case it is of any use.
1. Freesurfer version: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b 2. Platform: macOS Sonoma 14.3.1 3. uname -a: Darwin C02F10PVPN5W.local 23.3.0 Darwin Kernel Version 23.3.0: Wed Dec 20 21:28:58 PST 2023; root:xnu-10002.81.5~7/RELEASE_X86_64 x86_64 4. recon-all.log: see attached
Thanks in advance!
Taylor Ariko
It doesn’t look like rh.area is recognized correctly. ‘mri_info rh.area’ should show it is a ‘curv’ file with nvertices x 1 x 1 dimensions.
I’m not sure where exactly the area values are calculated. What happen if you re-run this step? mris_place_surface --area-map ../surf/rh.white ../surf/rh.area
Can you share the ?h.white and ?h.area?
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Ariko, Taylor Sent: Tuesday, March 5, 2024 7:24 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could not establish read access to rh.area
External Email - Use Caution Hello Yujing,
Thank you for your quick response!
When I run:
mris_calc -o rh.area.mid /path/to/subject/surf/rh.area add /path/to/subject/surf/rh.area.pial
I get the following error:
error: No such file or directory error: read_signa(/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/I.001): could not open file error: No such file or directory error: mris_calc: could not establish read access to '/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/rh.area'.
But when I run:
mri_info rh.area
I get the following output:
Volume information for rh.area type: unknown dimensions: 831 x 10015 x 25953 voxel sizes: -0.000000, -0.000000, nan type: SHORT (4) fov: 1016.473 dof: 1 xstart: 0.0, xend: 990983162970892849632569550308376576.0 ystart: -0.0, yend: 3079152361728581627851833344.0 zstart: -0.0, zend: -3815443229699337177012458129513775104.0 TR: 0.00 msec, TE: -0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -18770011487391973376.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = nan : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -0.0000 Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: 0.0000 -0.0000 nan nan -0.0000 -0.0000 nan nan -0.0000 0.0000 nan nan 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant nan
ras to voxel transform: error: mat = NULL!
It appears that this is where the issue is coming from. Any ideas on why this is occurring? The brain is normal and has good rh.white and rh.pial surfaces.
Many thanks, Taylor
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Date: Tuesday, March 5, 2024 at 4:25 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [EXTERNAL] Re: [Freesurfer] recon-all hard error: mris_calc could not establish read access to rh.area CAUTION: This email originated from outside the organization. DO NOT CLICK ON LINKS or OPEN ATTACHMENTS unless you know and trust the sender. Hi Taylor,
I don’t understand how you could get that error. It seems to me that read_signa() is for reading .signa files.
Can you try ‘mris_calc -o rh.area.mid rh.area add rh.area.pial’ directly? Pass full path to your rh.area and rh.area.pial.
What does ‘mri_info rh.area’ report?
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Ariko, Taylor Sent: Tuesday, March 5, 2024 2:35 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] recon-all hard error: mris_calc could not establish read access to rh.area
External Email - Use Caution Hello FreeSurfer Developers,
I am attempting to run the recon-all pipeline on one subject using the following code:
recon-all -all -i t1.nii -s p03_1
Although, I get the following error in the command line:
mris_calc -o rh.area.mid rh.area add rh.area.pial error: No such file or directory error: read_signa(/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/I.001): could not open file error: No such file or directory error: mris_calc: could not establish read access to 'rh.area'.
Tue Aug 1 15:58:13 EDT 2023 ERROR: vertexvol mris_calc -o rh.area.mid rh.area add rh.area.pial Darwin C02F10PVPN5W.local 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:56 PDT 2023; root:xnu-8796.141.3~6/RELEASE_X86_64 x86_64
recon-all -s p03_8 exited with ERRORS at Tue Aug 1 15:58:13 EDT 2023
To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttps://secure-web.cisco.com/1jPGfvEBFLG40bsU54UXs7wMCIp3C8zH7DpuFNxTMYcjl-sVJRX-_aLyLuGndGPWZVt9BS5c6qE7Ec_SFuNMDiQEsLM13mSxNH8JZdOiEsFCBb7otWnSANHdoam-CFMvwHH2hW6fpR1lNkOLCrAjWoOuEjE4RFiC_LZHPOCyvhfx01Lu2p1JcialLX_-bHtZq55Upe0GiY_sfOInNMp__KAE98N6nJAVI8k7ino9WC1uOZ6u-fUoCz7gesDsnzK2Za9jdm-HBAp2v_3YQz8mWlhQaTCBkKivWJgFqVjadKzcj7OeVU3QeptI7IaQhTMRXgjxd69R77-389ZRcdil8dw/https%3A%2F%2Furldefense.com%2Fv3%2F__http%3A%2Fsecure-web.cisco.com%2F1dFtz9tfZWpoyZVj7mXFMLhzADOYxytPQ-lAzdm9SS0VD1FTbz45enl8IaOWz6IRp_KLvd-O07tGlRWlew0e-tEz_uiSd7h7vjXFLqsJ43sz_QtFlRODTxSyXDZGJH-L2KeK1nXuICROZ0fCFy4KhTJxJ3haAuYRWOZcUa5BBA0fS4iGoh92xzUyORn8wvcaGQ3GMrAFxd-bI-V_SZY3tfGjNWqrLPpayxctYehni827EcLH8K0REtJUxl1SPpG6Pe3Emtor75zz-0Hm9qjm0-uKKTYgh6I5B9-s-Y0K05FI459LrA6nQEDmQc7Af7uhtsjN1f1kK5Ejciw7kqOfhnQ%2Fhttp%2A3A%2A2F%2A2Fsurfer.nmr.mgh.harvard.edu%2A2Ffswiki%2A2FBugReporting__%3BJSUlJSU%21%21KVu0SnhVq1hAFvslES2Y%21IF_PyIoN46gdEwAovSOrLvwK3TfosortPgW4RoFCW1D0uGc53eu3quu-JN8Jgna7cnZtnrrNAAZ4Th2md4U5n7NY7g_I%24
The recon-all.error file contains:
------------------------------ SUBJECT p03_8 DATE Tue Aug 1 15:58:13 EDT 2023 USER taylorariko HOST C02F10PVPN5W.local PROCESSOR x86_64 OS Darwin Darwin C02F10PVPN5W.local 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:56 PDT 2023; root:xnu-8796.141.3~6/RELEASE_X86_64 x86_64 7.2.0 (freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b) /Applications/freesurfer/7.2.0/bin/recon-all PWD /Volumes/Beta/Carmen/t1/p03_8/p03_8/mri CMD vertexvol --s p03_8 --rh --th3
I have made sure that I have read, write, and execute access to the folder /path/to/subject/surf and the file rh.area. I can successfully run the command to make rh.area (mris_place_surface --area-map ../surf/rh.white ../surf/rh.area), but the error persists in using rh.area. I have disk space and can run other commands such as this fake one (mris_calc -o rh.area.Test rh.area.pial add rh.area.pial), but not if it contains rh.area. I have tried to rerun the command from root and get the same error message.
I found 2 similar threads of the mail-archive, though I didn’t find any remedies:
1. MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg44230.htmlhttps://secure-web.cisco.com/1E6jIKLSpw7NluXRn2D-isCeIzODPsiH3Jo9Vn7j1NkSzEdgQFqIT-yFUk40J8xiqLyQ4x_Y-RZaw5Qaxs1jNi3GT0PDsMI3-1lAhOZwAqLQokIDS8eGVG8WkKccEyR3UQkKVKZvtyTme9bufG_TtMM4ThQ9jnFYOyRa6v9ATrUQ8bi0wuLfAL5SfQN2moagVYcvVEuAQuavwcQOnM37pGTqBD_tsEUghyFNAGMCw7s6w-Jyz88PXMchP4wUb7Snok2Y7uzRLa3e8MJ1S1brOJYa7Bd27riu_krNV26r6R74z7XICgwmILuLsVi6wfEV3xrALAbkeZhVCdteqBhGRug/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1s_8L81vMyC0-KdGicsKrUniSkh4Egg5_LxXz-_YnmsgL0Gm5kE9GJdy_R08c77fGYQTPDdQWTXx7zHH94KsUkxY5QpVUmicO4epJQCmrRk9qMFABnrFnqeMNWHf8BMzYZT9-_q55fpDjwdwtbSup33zXWmZ7_Qaxd-4Z5VhTLIcQnzdH1PATkHpAO-TTMDS2pwJXoqBJWfCdjq5iu6ZD_6K0lrHqWnH3JudltTqMg3oGYhVXWbXscFSmN__-ZRnNfVJ8CDc90XN86oLWU105NH4AaObyV0lLfIM82_MyoJeAcNXkfuOpxqrOcWWH_mbDB5W0KbiD_DVkA4CTMYOqPQ%2Fhttps%2A3A%2A2F%2A2Fwww.mail-archive.com%2A2Ffreesurfer%2A40nmr.mgh.harvard.edu%2A2Fmsg44230.html__%3BJSUlJSUl%21%21KVu0SnhVq1hAFvslES2Y%21IF_PyIoN46gdEwAovSOrLvwK3TfosortPgW4RoFCW1D0uGc53eu3quu-JN8Jgna7cnZtnrrNAAZ4Th2md4U5n7lbwM4K%24 2. MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51444.htmlhttps://secure-web.cisco.com/1hv_iWDGNbq3Dw5TXCTGVNYP7K-1AejQF4PsF7SwERE6z4zX6BWyPDvAfpegjx9pMz4kxqOemvJDo9Ykz041NnNwKpfe_sK4VTXDeNE_H_JFGiZ7vkBbiTuk5LWP3CMYt8pvtVaPCUvQuzfCnmz3tvZ1kr_7728ysSbcT0NX6Ms6PcI5yE2JzbhBi5dhWRytXVe6Dn1fJX4CeTHqPFBXccDefHmalE2xRO8WbyOAGEbG7iODT8IEHjguLHAGQtgfpNzXEmwH32gIx6nomosNn7YIcKFYD63x8Q0Pvm6anhUoRE6fHjO3NSt74t9FrDoUoXO7AC2Olk0KYSNF6jP7axA/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1MW6Y468pIeNLaB3ruN22mzrkJIjqalKQmsNncuNqyZW9S97Lqt_NIPp9ILpSPWI1wipv6Yr0BpbNmGPSoS-nDLaWTSHWRvXjPBhx6OWaUG3ykAth8rcrPy56gCpMo8EJHuhvxzkr3J5a8gg_8hfpQn3rWeGwxvT0rbc0ADxMrz98-mzO1bI4_zT80IcHOH6lIka2UdyAuC6gQplfb_eWpXafHuJDUR-JbSxIKSJcWIraGWK6JhoVQfgB3PNWSVgFkCVarUhylVDULGGQwPvt8XCNNPOC-bX_PoKwRMM7irjngRXBU0TPYBqY3QjiI4O9FrPJMQEQNW3NadmyXb4uhQ%2Fhttps%2A3A%2A2F%2A2Fwww.mail-archive.com%2A2Ffreesurfer%2A40nmr.mgh.harvard.edu%2A2Fmsg51444.html__%3BJSUlJSUl%21%21KVu0SnhVq1hAFvslES2Y%21IF_PyIoN46gdEwAovSOrLvwK3TfosortPgW4RoFCW1D0uGc53eu3quu-JN8Jgna7cnZtnrrNAAZ4Th2md4U5n5i6wwN6%24
Does anyone have any thoughts on how to trouble-shoot this? I have included my recon-all.log in the case it is of any use.
1. Freesurfer version: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b 2. Platform: macOS Sonoma 14.3.1 3. uname -a: Darwin C02F10PVPN5W.local 23.3.0 Darwin Kernel Version 23.3.0: Wed Dec 20 21:28:58 PST 2023; root:xnu-10002.81.5~7/RELEASE_X86_64 x86_64 4. recon-all.log: see attached
Thanks in advance!
Taylor Ariko
External Email - Use Caution
Hello Yujing,
If I rerun this command:
mris_place_surface --area-map ../surf/rh.white ../surf/rh.area
It says it is writing curvature file in the command line output:
writing curvature file ../surf/rh.area
Though the problem persists (mri_info says same thing as before). I have attached rh.white and rh.area for your review.
Many thanks, Taylor
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Huang, Yujing YHUANG43@mgh.harvard.edu Date: Wednesday, March 6, 2024 at 8:37 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could not establish read access to rh.area It doesn’t look like rh.area is recognized correctly. ‘mri_info rh.area’ should show it is a ‘curv’ file with nvertices x 1 x 1 dimensions.
I’m not sure where exactly the area values are calculated. What happen if you re-run this step? mris_place_surface --area-map ../surf/rh.white ../surf/rh.area
Can you share the ?h.white and ?h.area?
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Ariko, Taylor Sent: Tuesday, March 5, 2024 7:24 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could not establish read access to rh.area
External Email - Use Caution Hello Yujing,
Thank you for your quick response!
When I run:
mris_calc -o rh.area.mid /path/to/subject/surf/rh.area add /path/to/subject/surf/rh.area.pial
I get the following error:
error: No such file or directory error: read_signa(/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/I.001): could not open file error: No such file or directory error: mris_calc: could not establish read access to '/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/rh.area'.
But when I run:
mri_info rh.area
I get the following output:
Volume information for rh.area type: unknown dimensions: 831 x 10015 x 25953 voxel sizes: -0.000000, -0.000000, nan type: SHORT (4) fov: 1016.473 dof: 1 xstart: 0.0, xend: 990983162970892849632569550308376576.0 ystart: -0.0, yend: 3079152361728581627851833344.0 zstart: -0.0, zend: -3815443229699337177012458129513775104.0 TR: 0.00 msec, TE: -0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -18770011487391973376.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = nan : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -0.0000 Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: 0.0000 -0.0000 nan nan -0.0000 -0.0000 nan nan -0.0000 0.0000 nan nan 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant nan
ras to voxel transform: error: mat = NULL!
It appears that this is where the issue is coming from. Any ideas on why this is occurring? The brain is normal and has good rh.white and rh.pial surfaces.
Many thanks, Taylor
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Date: Tuesday, March 5, 2024 at 4:25 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [EXTERNAL] Re: [Freesurfer] recon-all hard error: mris_calc could not establish read access to rh.area CAUTION: This email originated from outside the organization. DO NOT CLICK ON LINKS or OPEN ATTACHMENTS unless you know and trust the sender. Hi Taylor,
I don’t understand how you could get that error. It seems to me that read_signa() is for reading .signa files.
Can you try ‘mris_calc -o rh.area.mid rh.area add rh.area.pial’ directly? Pass full path to your rh.area and rh.area.pial.
What does ‘mri_info rh.area’ report?
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Ariko, Taylor Sent: Tuesday, March 5, 2024 2:35 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] recon-all hard error: mris_calc could not establish read access to rh.area
External Email - Use Caution Hello FreeSurfer Developers,
I am attempting to run the recon-all pipeline on one subject using the following code:
recon-all -all -i t1.nii -s p03_1
Although, I get the following error in the command line:
mris_calc -o rh.area.mid rh.area add rh.area.pial error: No such file or directory error: read_signa(/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/I.001): could not open file error: No such file or directory error: mris_calc: could not establish read access to 'rh.area'.
Tue Aug 1 15:58:13 EDT 2023 ERROR: vertexvol mris_calc -o rh.area.mid rh.area add rh.area.pial Darwin C02F10PVPN5W.local 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:56 PDT 2023; root:xnu-8796.141.3~6/RELEASE_X86_64 x86_64
recon-all -s p03_8 exited with ERRORS at Tue Aug 1 15:58:13 EDT 2023
To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1h3GHH13wrz5bDxajhsROZ9d9PxBciu2dRUBOQ_mc5B-c8pI...https://secure-web.cisco.com/1QkLZSqXem5PLlxJSRRqUFWP18ja5JB58XPG1SdgXDGE_8BeeLiY_xWEKBPUmuZv1f3Be7u-_c_hF887AGPOyDRPzZIzBIVhCpgAXKA1DJCXDLWVGHIB1viBNCGdDdW7It-z7WKIlMxviq6iN_kh0h-TuYxoE9OlzfcHOdfds9cWatp5paEqLSKdDg9X3OR6PkSqWAysG6A6FgCoQi69sHvf648VFrnuWHeqqM2xCcIUhm9vYVrljZ52YZ4kDQvpPXjjjM9IjibKuIUTuAe9GuIYv8nbYwccw6ff31FqhxIHADQ8qYr9j-ygSiplcfczmogyC_Xjc6AuYDMHn64RR1w/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1jPGfvEBFLG40bsU54UXs7wMCIp3C8zH7DpuFNxTMYcjl-sVJRX-_aLyLuGndGPWZVt9BS5c6qE7Ec_SFuNMDiQEsLM13mSxNH8JZdOiEsFCBb7otWnSANHdoam-CFMvwHH2hW6fpR1lNkOLCrAjWoOuEjE4RFiC_LZHPOCyvhfx01Lu2p1JcialLX_-bHtZq55Upe0GiY_sfOInNMp__KAE98N6nJAVI8k7ino9WC1uOZ6u-fUoCz7gesDsnzK2Za9jdm-HBAp2v_3YQz8mWlhQaTCBkKivWJgFqVjadKzcj7OeVU3QeptI7IaQhTMRXgjxd69R77-389ZRcdil8dw%2Fhttps*3A*2F*2Furldefense.com*2Fv3*2F__http*3A*2Fsecure-web.cisco.com*2F1dFtz9tfZWpoyZVj7mXFMLhzADOYxytPQ-lAzdm9SS0VD1FTbz45enl8IaOWz6IRp_KLvd-O07tGlRWlew0e-tEz_uiSd7h7vjXFLqsJ43sz_QtFlRODTxSyXDZGJH-L2KeK1nXuICROZ0fCFy4KhTJxJ3haAuYRWOZcUa5BBA0fS4iGoh92xzUyORn8wvcaGQ3GMrAFxd-bI-V_SZY3tfGjNWqrLPpayxctYehni827EcLH8K0REtJUxl1SPpG6Pe3Emtor75zz-0Hm9qjm0-uKKTYgh6I5B9-s-Y0K05FI459LrA6nQEDmQc7Af7uhtsjN1f1kK5Ejciw7kqOfhnQ*2Fhttp*2A3A*2A2F*2A2Fsurfer.nmr.mgh.harvard.edu*2A2Ffswiki*2A2FBugReporting__*3BJSUlJSU*21*21KVu0SnhVq1hAFvslES2Y*21IF_PyIoN46gdEwAovSOrLvwK3TfosortPgW4RoFCW1D0uGc53eu3quu-JN8Jgna7cnZtnrrNAAZ4Th2md4U5n7NY7g_I*24__;JSUlJSUlJSUlJSUlJSUlJSUlJQ!!KVu0SnhVq1hAFvslES2Y!InYluqAPKNvYpM9tWOlA5ofPrAM-h-wkDOXsARfqcxhK-TXgMa09Cda9ZPb1NZKAuXrd50xWIfeHXufMCvjArvc12mGl$
The recon-all.error file contains:
------------------------------ SUBJECT p03_8 DATE Tue Aug 1 15:58:13 EDT 2023 USER taylorariko HOST C02F10PVPN5W.local PROCESSOR x86_64 OS Darwin Darwin C02F10PVPN5W.local 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:56 PDT 2023; root:xnu-8796.141.3~6/RELEASE_X86_64 x86_64 7.2.0 (freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b) /Applications/freesurfer/7.2.0/bin/recon-all PWD /Volumes/Beta/Carmen/t1/p03_8/p03_8/mri CMD vertexvol --s p03_8 --rh --th3
I have made sure that I have read, write, and execute access to the folder /path/to/subject/surf and the file rh.area. I can successfully run the command to make rh.area (mris_place_surface --area-map ../surf/rh.white ../surf/rh.area), but the error persists in using rh.area. I have disk space and can run other commands such as this fake one (mris_calc -o rh.area.Test rh.area.pial add rh.area.pial), but not if it contains rh.area. I have tried to rerun the command from root and get the same error message.
I found 2 similar threads of the mail-archive, though I didn’t find any remedies:
1. MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1EdSflXLCbUMqRstSPe_nuwk8u66dpoC-awtedCjcJEbkJa...https://secure-web.cisco.com/1hN6rqk2XZSbzb3F50XqJEb03I-YaAPxJboKdBP6UcFnq4HhfIEpAZzhvgakabXU5v4-ol0_JTkvyf4aSPATbOCFFxeW79fniZruGf_gP81bl9Qd-HflhrgidJQcnRcW41vqLhELvvzX_TYtNegUTHBehQyCLLGmo5ereg3rWNq-HVayO23alXBgHl8RW3DvJQkvWu0a-exjtRawSSDujJL7vB37rl89wFKOuEoydkXc65lt5gPYdM9nYB_iv4GeXj2ttiEl3-azuskATzYAKumjM7Edlz1lE0ANQ2oSGtDS6YYfOodEtuHwWonuju0S-VeAzd-PtOVwqqBSNpw2I-Q/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1E6jIKLSpw7NluXRn2D-isCeIzODPsiH3Jo9Vn7j1NkSzEdgQFqIT-yFUk40J8xiqLyQ4x_Y-RZaw5Qaxs1jNi3GT0PDsMI3-1lAhOZwAqLQokIDS8eGVG8WkKccEyR3UQkKVKZvtyTme9bufG_TtMM4ThQ9jnFYOyRa6v9ATrUQ8bi0wuLfAL5SfQN2moagVYcvVEuAQuavwcQOnM37pGTqBD_tsEUghyFNAGMCw7s6w-Jyz88PXMchP4wUb7Snok2Y7uzRLa3e8MJ1S1brOJYa7Bd27riu_krNV26r6R74z7XICgwmILuLsVi6wfEV3xrALAbkeZhVCdteqBhGRug%2Fhttps*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fsecure-web.cisco.com*2F1s_8L81vMyC0-KdGicsKrUniSkh4Egg5_LxXz-_YnmsgL0Gm5kE9GJdy_R08c77fGYQTPDdQWTXx7zHH94KsUkxY5QpVUmicO4epJQCmrRk9qMFABnrFnqeMNWHf8BMzYZT9-_q55fpDjwdwtbSup33zXWmZ7_Qaxd-4Z5VhTLIcQnzdH1PATkHpAO-TTMDS2pwJXoqBJWfCdjq5iu6ZD_6K0lrHqWnH3JudltTqMg3oGYhVXWbXscFSmN__-ZRnNfVJ8CDc90XN86oLWU105NH4AaObyV0lLfIM82_MyoJeAcNXkfuOpxqrOcWWH_mbDB5W0KbiD_DVkA4CTMYOqPQ*2Fhttps*2A3A*2A2F*2A2Fwww.mail-archive.com*2A2Ffreesurfer*2A40nmr.mgh.harvard.edu*2A2Fmsg44230.html__*3BJSUlJSUl*21*21KVu0SnhVq1hAFvslES2Y*21IF_PyIoN46gdEwAovSOrLvwK3TfosortPgW4RoFCW1D0uGc53eu3quu-JN8Jgna7cnZtnrrNAAZ4Th2md4U5n7lbwM4K*24__;JSUlJSUlJSUlJSUlJSUlJSUlJSU!!KVu0SnhVq1hAFvslES2Y!InYluqAPKNvYpM9tWOlA5ofPrAM-h-wkDOXsARfqcxhK-TXgMa09Cda9ZPb1NZKAuXrd50xWIfeHXufMCvjArjnHczWH$ 2. MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1l3Jg7aj_iGcAxHGm3qW8MhoW899Cng8SxyypP25lihblRd...https://secure-web.cisco.com/1he-c9QMm8pHXrf1qWbFuGAFRvVHK5uJLXaFH4Euh0WnFYsyoiDtlStu_EbG2quPo7OA1XfwFWnmKJ-sRC8KtWBqQejam98TkOORrSk68qq1FafMZl7q1ntDhGH22-HNr1X-dCkNRQx5V5S56KaASpVOoCrcHtYxSJR1iTtFzR7_Z9RScZtwLHsWBT0sbvtDt7FGBocf_a1o_kfqa9CK7FRwnYiKW8KGpPcJmSIH6gtxE9_J_uIq53x57sIvBYvF3RdFm-HxBanltJxUp81oHwZ5xqYlz30XeYChQOYAUh96QtaRSccndmbsw8o-bksGzbzX8u2Cdut7MWndEQQYHlw/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1hv_iWDGNbq3Dw5TXCTGVNYP7K-1AejQF4PsF7SwERE6z4zX6BWyPDvAfpegjx9pMz4kxqOemvJDo9Ykz041NnNwKpfe_sK4VTXDeNE_H_JFGiZ7vkBbiTuk5LWP3CMYt8pvtVaPCUvQuzfCnmz3tvZ1kr_7728ysSbcT0NX6Ms6PcI5yE2JzbhBi5dhWRytXVe6Dn1fJX4CeTHqPFBXccDefHmalE2xRO8WbyOAGEbG7iODT8IEHjguLHAGQtgfpNzXEmwH32gIx6nomosNn7YIcKFYD63x8Q0Pvm6anhUoRE6fHjO3NSt74t9FrDoUoXO7AC2Olk0KYSNF6jP7axA%2Fhttps*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fsecure-web.cisco.com*2F1MW6Y468pIeNLaB3ruN22mzrkJIjqalKQmsNncuNqyZW9S97Lqt_NIPp9ILpSPWI1wipv6Yr0BpbNmGPSoS-nDLaWTSHWRvXjPBhx6OWaUG3ykAth8rcrPy56gCpMo8EJHuhvxzkr3J5a8gg_8hfpQn3rWeGwxvT0rbc0ADxMrz98-mzO1bI4_zT80IcHOH6lIka2UdyAuC6gQplfb_eWpXafHuJDUR-JbSxIKSJcWIraGWK6JhoVQfgB3PNWSVgFkCVarUhylVDULGGQwPvt8XCNNPOC-bX_PoKwRMM7irjngRXBU0TPYBqY3QjiI4O9FrPJMQEQNW3NadmyXb4uhQ*2Fhttps*2A3A*2A2F*2A2Fwww.mail-archive.com*2A2Ffreesurfer*2A40nmr.mgh.harvard.edu*2A2Fmsg51444.html__*3BJSUlJSUl*21*21KVu0SnhVq1hAFvslES2Y*21IF_PyIoN46gdEwAovSOrLvwK3TfosortPgW4RoFCW1D0uGc53eu3quu-JN8Jgna7cnZtnrrNAAZ4Th2md4U5n5i6wwN6*24__;JSUlJSUlJSUlJSUlJSUlJSUlJSU!!KVu0SnhVq1hAFvslES2Y!InYluqAPKNvYpM9tWOlA5ofPrAM-h-wkDOXsARfqcxhK-TXgMa09Cda9ZPb1NZKAuXrd50xWIfeHXufMCvjArhcJqcW-$
Does anyone have any thoughts on how to trouble-shoot this? I have included my recon-all.log in the case it is of any use.
1. Freesurfer version: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b 2. Platform: macOS Sonoma 14.3.1 3. uname -a: Darwin C02F10PVPN5W.local 23.3.0 Darwin Kernel Version 23.3.0: Wed Dec 20 21:28:58 PST 2023; root:xnu-10002.81.5~7/RELEASE_X86_64 x86_64 4. recon-all.log: see attached
Thanks in advance!
Taylor Ariko
Hi Taylor,
Thanks for sharing the data.
I see the problem now. The first 14336 bytes of your rh.area fit SIGNA_FILE criteria. So, it is read as SIGNA_FILE instead of MRI_CURV_FILE.
We will have a fix in dev version. But I’m not sure how to get around this in FS 7.2.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Ariko, Taylor Sent: Wednesday, March 6, 2024 9:47 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could not establish read access to rh.area
External Email - Use Caution Hello Yujing,
If I rerun this command:
mris_place_surface --area-map ../surf/rh.white ../surf/rh.area
It says it is writing curvature file in the command line output:
writing curvature file ../surf/rh.area
Though the problem persists (mri_info says same thing as before). I have attached rh.white and rh.area for your review.
Many thanks, Taylor
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Date: Wednesday, March 6, 2024 at 8:37 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could not establish read access to rh.area It doesn’t look like rh.area is recognized correctly. ‘mri_info rh.area’ should show it is a ‘curv’ file with nvertices x 1 x 1 dimensions.
I’m not sure where exactly the area values are calculated. What happen if you re-run this step? mris_place_surface --area-map ../surf/rh.white ../surf/rh.area
Can you share the ?h.white and ?h.area?
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Ariko, Taylor Sent: Tuesday, March 5, 2024 7:24 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could not establish read access to rh.area
External Email - Use Caution Hello Yujing,
Thank you for your quick response!
When I run:
mris_calc -o rh.area.mid /path/to/subject/surf/rh.area add /path/to/subject/surf/rh.area.pial
I get the following error:
error: No such file or directory error: read_signa(/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/I.001): could not open file error: No such file or directory error: mris_calc: could not establish read access to '/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/rh.area'.
But when I run:
mri_info rh.area
I get the following output:
Volume information for rh.area type: unknown dimensions: 831 x 10015 x 25953 voxel sizes: -0.000000, -0.000000, nan type: SHORT (4) fov: 1016.473 dof: 1 xstart: 0.0, xend: 990983162970892849632569550308376576.0 ystart: -0.0, yend: 3079152361728581627851833344.0 zstart: -0.0, zend: -3815443229699337177012458129513775104.0 TR: 0.00 msec, TE: -0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -18770011487391973376.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = nan : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -0.0000 Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: 0.0000 -0.0000 nan nan -0.0000 -0.0000 nan nan -0.0000 0.0000 nan nan 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant nan
ras to voxel transform: error: mat = NULL!
It appears that this is where the issue is coming from. Any ideas on why this is occurring? The brain is normal and has good rh.white and rh.pial surfaces.
Many thanks, Taylor
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Date: Tuesday, March 5, 2024 at 4:25 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [EXTERNAL] Re: [Freesurfer] recon-all hard error: mris_calc could not establish read access to rh.area CAUTION: This email originated from outside the organization. DO NOT CLICK ON LINKS or OPEN ATTACHMENTS unless you know and trust the sender. Hi Taylor,
I don’t understand how you could get that error. It seems to me that read_signa() is for reading .signa files.
Can you try ‘mris_calc -o rh.area.mid rh.area add rh.area.pial’ directly? Pass full path to your rh.area and rh.area.pial.
What does ‘mri_info rh.area’ report?
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Ariko, Taylor Sent: Tuesday, March 5, 2024 2:35 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] recon-all hard error: mris_calc could not establish read access to rh.area
External Email - Use Caution Hello FreeSurfer Developers,
I am attempting to run the recon-all pipeline on one subject using the following code:
recon-all -all -i t1.nii -s p03_1
Although, I get the following error in the command line:
mris_calc -o rh.area.mid rh.area add rh.area.pial error: No such file or directory error: read_signa(/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/I.001): could not open file error: No such file or directory error: mris_calc: could not establish read access to 'rh.area'.
Tue Aug 1 15:58:13 EDT 2023 ERROR: vertexvol mris_calc -o rh.area.mid rh.area add rh.area.pial Darwin C02F10PVPN5W.local 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:56 PDT 2023; root:xnu-8796.141.3~6/RELEASE_X86_64 x86_64
recon-all -s p03_8 exited with ERRORS at Tue Aug 1 15:58:13 EDT 2023
To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttps://secure-web.cisco.com/1RZ-Xt7gXypFuea8NNkn6obmcMVwrPaQYiPZ0zTdmhY2IC1Zolyisw7eyh88qchNHlmxGH_5BQL_nq1-gfMY6vsFsU18cl8aNqEWD4ZO34wjXXfRScEKv88avY6poKRQxDUE0oM7aKFh_PyA9V0m9Ao6b8JuaMZV5AYeuHMNsdDLZ4V7cOuY0B5LnVfqZzF0vuiKJJ8xBWJLc6QjlzLzxU_ELraZ4wfCEWrR-Gba2NR7HHyBAm09i9655jGUOFI6zdvd51yqZk5zvPLWRMAAxCeEPCR_X3GzHd3ROvbE_nZp3HTb84BSxTYyB9pdm4AlGdOcMJlPCJJtox5uykZpSxQ/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1jPGfvEBFLG40bsU54UXs7wMCIp3C8zH7DpuFNxTMYcjl-sVJRX-_aLyLuGndGPWZVt9BS5c6qE7Ec_SFuNMDiQEsLM13mSxNH8JZdOiEsFCBb7otWnSANHdoam-CFMvwHH2hW6fpR1lNkOLCrAjWoOuEjE4RFiC_LZHPOCyvhfx01Lu2p1JcialLX_-bHtZq55Upe0GiY_sfOInNMp__KAE98N6nJAVI8k7ino9WC1uOZ6u-fUoCz7gesDsnzK2Za9jdm-HBAp2v_3YQz8mWlhQaTCBkKivWJgFqVjadKzcj7OeVU3QeptI7IaQhTMRXgjxd69R77-389ZRcdil8dw%2Fhttps%2A3A%2A2F%2A2Furldefense.com%2A2Fv3%2A2F__http%2A3A%2A2Fsecure-web.cisco.com%2A2F1dFtz9tfZWpoyZVj7mXFMLhzADOYxytPQ-lAzdm9SS0VD1FTbz45enl8IaOWz6IRp_KLvd-O07tGlRWlew0e-tEz_uiSd7h7vjXFLqsJ43sz_QtFlRODTxSyXDZGJH-L2KeK1nXuICROZ0fCFy4KhTJxJ3haAuYRWOZcUa5BBA0fS4iGoh92xzUyORn8wvcaGQ3GMrAFxd-bI-V_SZY3tfGjNWqrLPpayxctYehni827EcLH8K0REtJUxl1SPpG6Pe3Emtor75zz-0Hm9qjm0-uKKTYgh6I5B9-s-Y0K05FI459LrA6nQEDmQc7Af7uhtsjN1f1kK5Ejciw7kqOfhnQ%2A2Fhttp%2A2A3A%2A2A2F%2A2A2Fsurfer.nmr.mgh.harvard.edu%2A2A2Ffswiki%2A2A2FBugReporting__%2A3BJSUlJSU%2A21%2A21KVu0SnhVq1hAFvslES2Y%2A21IF_PyIoN46gdEwAovSOrLvwK3TfosortPgW4RoFCW1D0uGc53eu3quu-JN8Jgna7cnZtnrrNAAZ4Th2md4U5n7NY7g_I%2A24__%3BJSUlJSUlJSUlJSUlJSUlJSUlJQ%21%21KVu0SnhVq1hAFvslES2Y%21InYluqAPKNvYpM9tWOlA5ofPrAM-h-wkDOXsARfqcxhK-TXgMa09Cda9ZPb1NZKAuXrd50xWIfeHXufMCvjArvc12mGl%24
The recon-all.error file contains:
------------------------------ SUBJECT p03_8 DATE Tue Aug 1 15:58:13 EDT 2023 USER taylorariko HOST C02F10PVPN5W.local PROCESSOR x86_64 OS Darwin Darwin C02F10PVPN5W.local 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:56 PDT 2023; root:xnu-8796.141.3~6/RELEASE_X86_64 x86_64 7.2.0 (freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b) /Applications/freesurfer/7.2.0/bin/recon-all PWD /Volumes/Beta/Carmen/t1/p03_8/p03_8/mri CMD vertexvol --s p03_8 --rh --th3
I have made sure that I have read, write, and execute access to the folder /path/to/subject/surf and the file rh.area. I can successfully run the command to make rh.area (mris_place_surface --area-map ../surf/rh.white ../surf/rh.area), but the error persists in using rh.area. I have disk space and can run other commands such as this fake one (mris_calc -o rh.area.Test rh.area.pial add rh.area.pial), but not if it contains rh.area. I have tried to rerun the command from root and get the same error message.
I found 2 similar threads of the mail-archive, though I didn’t find any remedies:
1. MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg44230.htmlhttps://secure-web.cisco.com/1jMJLq9IWeIRjXwk3A82x_IsCGmCpTS-a7xyYNAmL4y2YW0NObYC1h3is0t6ALiBUXmrSF-ejvBaW_hJmEXIhWe3n7sVgGwDO_h133T2ZfcDoYf63i6GkTbWQ1VElHtkdIedKc1LArRENxthRwIs3lD-eHg5C_kayIY63WUmUF6wD4Ggtj6jQCXIvVIWj1KYeyD1IKmRkFRuxzaphKzg-S9olvhcDKTBQAkwegOVEzKCT8DI7sCR7UuJ-wpfiY3HN7DNJNZ-J8bcocx-pARRqbPX6DNqgQySLXEwaEbouWyhLMUxkn3Y-FFtjR9MLkQAgZu7O4Zo2pI7SZYm8UE3d3w/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1E6jIKLSpw7NluXRn2D-isCeIzODPsiH3Jo9Vn7j1NkSzEdgQFqIT-yFUk40J8xiqLyQ4x_Y-RZaw5Qaxs1jNi3GT0PDsMI3-1lAhOZwAqLQokIDS8eGVG8WkKccEyR3UQkKVKZvtyTme9bufG_TtMM4ThQ9jnFYOyRa6v9ATrUQ8bi0wuLfAL5SfQN2moagVYcvVEuAQuavwcQOnM37pGTqBD_tsEUghyFNAGMCw7s6w-Jyz88PXMchP4wUb7Snok2Y7uzRLa3e8MJ1S1brOJYa7Bd27riu_krNV26r6R74z7XICgwmILuLsVi6wfEV3xrALAbkeZhVCdteqBhGRug%2Fhttps%2A3A%2A2F%2A2Furldefense.com%2A2Fv3%2A2F__https%2A3A%2A2Fsecure-web.cisco.com%2A2F1s_8L81vMyC0-KdGicsKrUniSkh4Egg5_LxXz-_YnmsgL0Gm5kE9GJdy_R08c77fGYQTPDdQWTXx7zHH94KsUkxY5QpVUmicO4epJQCmrRk9qMFABnrFnqeMNWHf8BMzYZT9-_q55fpDjwdwtbSup33zXWmZ7_Qaxd-4Z5VhTLIcQnzdH1PATkHpAO-TTMDS2pwJXoqBJWfCdjq5iu6ZD_6K0lrHqWnH3JudltTqMg3oGYhVXWbXscFSmN__-ZRnNfVJ8CDc90XN86oLWU105NH4AaObyV0lLfIM82_MyoJeAcNXkfuOpxqrOcWWH_mbDB5W0KbiD_DVkA4CTMYOqPQ%2A2Fhttps%2A2A3A%2A2A2F%2A2A2Fwww.mail-archive.com%2A2A2Ffreesurfer%2A2A40nmr.mgh.harvard.edu%2A2A2Fmsg44230.html__%2A3BJSUlJSUl%2A21%2A21KVu0SnhVq1hAFvslES2Y%2A21IF_PyIoN46gdEwAovSOrLvwK3TfosortPgW4RoFCW1D0uGc53eu3quu-JN8Jgna7cnZtnrrNAAZ4Th2md4U5n7lbwM4K%2A24__%3BJSUlJSUlJSUlJSUlJSUlJSUlJSU%21%21KVu0SnhVq1hAFvslES2Y%21InYluqAPKNvYpM9tWOlA5ofPrAM-h-wkDOXsARfqcxhK-TXgMa09Cda9ZPb1NZKAuXrd50xWIfeHXufMCvjArjnHczWH%24 2. MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51444.htmlhttps://secure-web.cisco.com/1kzbC-1TGfknjZatLqrkie9mDrwseuKFvB8BOYwkca3ISUcixUkNUSuuAus7RHM1NJM5BL-r0Lw3GnliSehfiY0mu99LfE1WuMlBWXUdkuk347c1qF_UACb9Ff5hBRS44O8Tr17iDVyvX2IegIMR58VIdF2-clN2nhiNrwKENMp9B9U3-YXDkGdlrkNcgW4r5sLMTNyPurdQJ40qtqxPuW708I8QqzE19sceuZKgl0bSejz4KOu5L_8D1Ayi-MavIoQIAkFV5yt3Hq-FC8yK3up31dHT5uAdTaK1MOpndTrGm2GiEktL6OMDXZC-9WaBcKxjxmdVl3Y5xZ0oU9e86jA/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1hv_iWDGNbq3Dw5TXCTGVNYP7K-1AejQF4PsF7SwERE6z4zX6BWyPDvAfpegjx9pMz4kxqOemvJDo9Ykz041NnNwKpfe_sK4VTXDeNE_H_JFGiZ7vkBbiTuk5LWP3CMYt8pvtVaPCUvQuzfCnmz3tvZ1kr_7728ysSbcT0NX6Ms6PcI5yE2JzbhBi5dhWRytXVe6Dn1fJX4CeTHqPFBXccDefHmalE2xRO8WbyOAGEbG7iODT8IEHjguLHAGQtgfpNzXEmwH32gIx6nomosNn7YIcKFYD63x8Q0Pvm6anhUoRE6fHjO3NSt74t9FrDoUoXO7AC2Olk0KYSNF6jP7axA%2Fhttps%2A3A%2A2F%2A2Furldefense.com%2A2Fv3%2A2F__https%2A3A%2A2Fsecure-web.cisco.com%2A2F1MW6Y468pIeNLaB3ruN22mzrkJIjqalKQmsNncuNqyZW9S97Lqt_NIPp9ILpSPWI1wipv6Yr0BpbNmGPSoS-nDLaWTSHWRvXjPBhx6OWaUG3ykAth8rcrPy56gCpMo8EJHuhvxzkr3J5a8gg_8hfpQn3rWeGwxvT0rbc0ADxMrz98-mzO1bI4_zT80IcHOH6lIka2UdyAuC6gQplfb_eWpXafHuJDUR-JbSxIKSJcWIraGWK6JhoVQfgB3PNWSVgFkCVarUhylVDULGGQwPvt8XCNNPOC-bX_PoKwRMM7irjngRXBU0TPYBqY3QjiI4O9FrPJMQEQNW3NadmyXb4uhQ%2A2Fhttps%2A2A3A%2A2A2F%2A2A2Fwww.mail-archive.com%2A2A2Ffreesurfer%2A2A40nmr.mgh.harvard.edu%2A2A2Fmsg51444.html__%2A3BJSUlJSUl%2A21%2A21KVu0SnhVq1hAFvslES2Y%2A21IF_PyIoN46gdEwAovSOrLvwK3TfosortPgW4RoFCW1D0uGc53eu3quu-JN8Jgna7cnZtnrrNAAZ4Th2md4U5n5i6wwN6%2A24__%3BJSUlJSUlJSUlJSUlJSUlJSUlJSU%21%21KVu0SnhVq1hAFvslES2Y%21InYluqAPKNvYpM9tWOlA5ofPrAM-h-wkDOXsARfqcxhK-TXgMa09Cda9ZPb1NZKAuXrd50xWIfeHXufMCvjArhcJqcW-%24
Does anyone have any thoughts on how to trouble-shoot this? I have included my recon-all.log in the case it is of any use.
1. Freesurfer version: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b 2. Platform: macOS Sonoma 14.3.1 3. uname -a: Darwin C02F10PVPN5W.local 23.3.0 Darwin Kernel Version 23.3.0: Wed Dec 20 21:28:58 PST 2023; root:xnu-10002.81.5~7/RELEASE_X86_64 x86_64 4. recon-all.log: see attached
Thanks in advance!
Taylor Ariko
Yujing, you can just send Taylor a binary that can be put in the local version of $FREESURFER/bin
On 3/6/2024 11:45 AM, Huang, Yujing wrote:
Hi Taylor,
Thanks for sharing the data.
I see the problem now. The first 14336 bytes of your rh.area fit SIGNA_FILE criteria. So, it is read as SIGNA_FILE instead of MRI_CURV_FILE.
We will have a fix in dev version. But I’m not sure how to get around this in FS 7.2.
Best,
Yujing
*From:*freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *On Behalf Of *Ariko, Taylor *Sent:* Wednesday, March 6, 2024 9:47 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could not establish read access to rh.area
* External Email - Use Caution *
Hello Yujing,
If I rerun this command:
mris_place_surface --area-map ../surf/rh.white ../surf/rh.area
It says it is writing curvature file in the command line output:
writing curvature file ../surf/rh.area
Though the problem persists (mri_info says same thing as before). I have attached rh.white and rh.area for your review.
Many thanks,
Taylor
*From: *freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Huang, Yujing YHUANG43@mgh.harvard.edu *Date: *Wednesday, March 6, 2024 at 8:37 AM *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could not establish read access to rh.area
It doesn’t look like rh.area is recognized correctly. ‘mri_info rh.area’ should show it is a ‘curv’ file with nvertices x 1 x 1 dimensions.
I’m not sure where exactly the area values are calculated. What happen if you re-run this step?
mris_place_surface --area-map ../surf/rh.white ../surf/rh.area
Can you share the ?h.white and ?h.area?
Best,
Yujing
*From:*freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *On Behalf Of *Ariko, Taylor *Sent:* Tuesday, March 5, 2024 7:24 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could not establish read access to rh.area
* External Email - Use Caution *
Hello Yujing,
Thank you for your quick response!
When I run:
mris_calc -o rh.area.mid /path/to/subject/surf/rh.area add /path/to/subject/surf/rh.area.pial
I get the following error:
error: No such file or directory
error: read_signa(/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/I.001): could not open file
error: No such file or directory
error:
mris_calc: could not establish read access to '/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/rh.area'.
But when I run:
mri_info rh.area
I get the following output:
Volume information for rh.area
type: unknown
dimensions: 831 x 10015 x 25953
voxel sizes: -0.000000, -0.000000, nan
type: SHORT (4)
fov: 1016.473
dof: 1
xstart: 0.0, xend: 990983162970892849632569550308376576.0
ystart: -0.0, yend: 3079152361728581627851833344.0
zstart: -0.0, zend: -3815443229699337177012458129513775104.0
TR: 0.00 msec, TE: -0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees
nframes: 1
PhEncDir: UNKNOWN
FieldStrength: 0.000000
ras xform present
xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -18770011487391973376.0000
: x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = nan
: x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -0.0000
Orientation : LIA
Primary Slice Direction: coronal
voxel to ras transform:
0.0000 -0.0000 nan nan
-0.0000 -0.0000 nan nan
-0.0000 0.0000 nan nan
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant nan
ras to voxel transform:
error: mat = NULL!
It appears that this is where the issue is coming from. Any ideas on why this is occurring? The brain is normal and has good rh.white and rh.pial surfaces.
Many thanks,
Taylor
*From: *freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Huang, Yujing YHUANG43@mgh.harvard.edu *Date: *Tuesday, March 5, 2024 at 4:25 PM *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject: *[EXTERNAL] Re: [Freesurfer] recon-all hard error: mris_calc could not establish read access to rh.area
*CAUTION:*This email originated from outside the organization. *DO NOT CLICK ON LINKS* _or_ *OPEN ATTACHMENTS* unless you know and trust the sender.
Hi Taylor,
I don’t understand how you could get that error. It seems to me that read_signa() is for reading .signa files.
Can you try ‘mris_calc -o rh.area.mid rh.area add rh.area.pial’ directly? Pass full path to your rh.area and rh.area.pial.
What does ‘mri_info rh.area’ report?
Best,
Yujing
*From:*freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *On Behalf Of *Ariko, Taylor *Sent:* Tuesday, March 5, 2024 2:35 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] recon-all hard error: mris_calc could not establish read access to rh.area
* External Email - Use Caution *
Hello FreeSurfer Developers,
I am attempting to run the recon-all pipeline on one subject using the following code:
recon-all -all -i t1.nii -s p03_1
Although, I get the following error in the command line:
mris_calc -o rh.area.mid rh.area add rh.area.pial
error: No such file or directory
error: read_signa(/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/I.001): could not open file
error: No such file or directory
error:
mris_calc: could not establish read access to 'rh.area'.
Tue Aug 1 15:58:13 EDT 2023
ERROR: vertexvol
mris_calc -o rh.area.mid rh.area add rh.area.pial
Darwin C02F10PVPN5W.local 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:56 PDT 2023; root:xnu-8796.141.3~6/RELEASE_X86_64 x86_64
recon-all -s p03_8 exited with ERRORS at Tue Aug 1 15:58:13 EDT 2023
To report a problem, see*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be*http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting https://secure-web.cisco.com/1RZ-Xt7gXypFuea8NNkn6obmcMVwrPaQYiPZ0zTdmhY2IC1Zolyisw7eyh88qchNHlmxGH_5BQL_nq1-gfMY6vsFsU18cl8aNqEWD4ZO34wjXXfRScEKv88avY6poKRQxDUE0oM7aKFh_PyA9V0m9Ao6b8JuaMZV5AYeuHMNsdDLZ4V7cOuY0B5LnVfqZzF0vuiKJJ8xBWJLc6QjlzLzxU_ELraZ4wfCEWrR-Gba2NR7HHyBAm09i9655jGUOFI6zdvd51yqZk5zvPLWRMAAxCeEPCR_X3GzHd3ROvbE_nZp3HTb84BSxTYyB9pdm4AlGdOcMJlPCJJtox5uykZpSxQ/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1jPGfvEBFLG40bsU54UXs7wMCIp3C8zH7DpuFNxTMYcjl-sVJRX-_aLyLuGndGPWZVt9BS5c6qE7Ec_SFuNMDiQEsLM13mSxNH8JZdOiEsFCBb7otWnSANHdoam-CFMvwHH2hW6fpR1lNkOLCrAjWoOuEjE4RFiC_LZHPOCyvhfx01Lu2p1JcialLX_-bHtZq55Upe0GiY_sfOInNMp__KAE98N6nJAVI8k7ino9WC1uOZ6u-fUoCz7gesDsnzK2Za9jdm-HBAp2v_3YQz8mWlhQaTCBkKivWJgFqVjadKzcj7OeVU3QeptI7IaQhTMRXgjxd69R77-389ZRcdil8dw%2Fhttps%2A3A%2A2F%2A2Furldefense.com%2A2Fv3%2A2F__http%2A3A%2A2Fsecure-web.cisco.com%2A2F1dFtz9tfZWpoyZVj7mXFMLhzADOYxytPQ-lAzdm9SS0VD1FTbz45enl8IaOWz6IRp_KLvd-O07tGlRWlew0e-tEz_uiSd7h7vjXFLqsJ43sz_QtFlRODTxSyXDZGJH-L2KeK1nXuICROZ0fCFy4KhTJxJ3haAuYRWOZcUa5BBA0fS4iGoh92xzUyORn8wvcaGQ3GMrAFxd-bI-V_SZY3tfGjNWqrLPpayxctYehni827EcLH8K0REtJUxl1SPpG6Pe3Emtor75zz-0Hm9qjm0-uKKTYgh6I5B9-s-Y0K05FI459LrA6nQEDmQc7Af7uhtsjN1f1kK5Ejciw7kqOfhnQ%2A2Fhttp%2A2A3A%2A2A2F%2A2A2Fsurfer.nmr.mgh.harvard.edu%2A2A2Ffswiki%2A2A2FBugReporting__%2A3BJSUlJSU%2A21%2A21KVu0SnhVq1hAFvslES2Y%2A21IF_PyIoN46gdEwAovSOrLvwK3TfosortPgW4RoFCW1D0uGc53eu3quu-JN8Jgna7cnZtnrrNAAZ4Th2md4U5n7NY7g_I%2A24__%3BJSUlJSUlJSUlJSUlJSUlJSUlJQ%21%21KVu0SnhVq1hAFvslES2Y%21InYluqAPKNvYpM9tWOlA5ofPrAM-h-wkDOXsARfqcxhK-TXgMa09Cda9ZPb1NZKAuXrd50xWIfeHXufMCvjArvc12mGl%24
The recon-all.error file contains:
SUBJECT p03_8
DATE Tue Aug 1 15:58:13 EDT 2023
USER taylorariko
HOST C02F10PVPN5W.local
PROCESSOR x86_64
OS Darwin
Darwin C02F10PVPN5W.local 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:56 PDT 2023; root:xnu-8796.141.3~6/RELEASE_X86_64 x86_64
7.2.0 (freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b)
/Applications/freesurfer/7.2.0/bin/recon-all
PWD /Volumes/Beta/Carmen/t1/p03_8/p03_8/mri
CMD vertexvol --s p03_8 --rh --th3
I have made sure that I have read, write, and execute access to the folder /path/to/subject/surf and the file rh.area. I can successfully run the command to make rh.area (mris_place_surface --area-map ../surf/rh.white ../surf/rh.area), but the error persists in using rh.area. I have disk space and can run other commands such as this fake one (mris_calc -o rh.area.Test rh.area.pial add rh.area.pial), but not if it contains rh.area. I have tried to rerun the command from root and get the same error message.
I found 2 similar threads of the mail-archive, though I didn’t find any remedies:
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Does anyone have any thoughts on how to trouble-shoot this? I have included my recon-all.log in the case it is of any use.
- Freesurfer version: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
- Platform: macOS Sonoma 14.3.1
- uname -a:Darwin C02F10PVPN5W.local 23.3.0 Darwin Kernel Version 23.3.0: Wed Dec 20 21:28:58 PST 2023; root:xnu-10002.81.5~7/RELEASE_X86_64 x86_64
- recon-all.log: see attached
Thanks in advance!
Taylor Ariko
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
That would be wonderful, thank you.
Best, Taylor
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Date: Thursday, March 7, 2024 at 9:05 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could not establish read access to rh.area Yujing, you can just send Taylor a binary that can be put in the local version of $FREESURFER/bin On 3/6/2024 11:45 AM, Huang, Yujing wrote: Hi Taylor,
Thanks for sharing the data.
I see the problem now. The first 14336 bytes of your rh.area fit SIGNA_FILE criteria. So, it is read as SIGNA_FILE instead of MRI_CURV_FILE.
We will have a fix in dev version. But I’m not sure how to get around this in FS 7.2.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Ariko, Taylor Sent: Wednesday, March 6, 2024 9:47 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could not establish read access to rh.area
External Email - Use Caution Hello Yujing,
If I rerun this command:
mris_place_surface --area-map ../surf/rh.white ../surf/rh.area
It says it is writing curvature file in the command line output:
writing curvature file ../surf/rh.area
Though the problem persists (mri_info says same thing as before). I have attached rh.white and rh.area for your review.
Many thanks, Taylor
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Date: Wednesday, March 6, 2024 at 8:37 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could not establish read access to rh.area It doesn’t look like rh.area is recognized correctly. ‘mri_info rh.area’ should show it is a ‘curv’ file with nvertices x 1 x 1 dimensions.
I’m not sure where exactly the area values are calculated. What happen if you re-run this step? mris_place_surface --area-map ../surf/rh.white ../surf/rh.area
Can you share the ?h.white and ?h.area?
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Ariko, Taylor Sent: Tuesday, March 5, 2024 7:24 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could not establish read access to rh.area
External Email - Use Caution Hello Yujing,
Thank you for your quick response!
When I run:
mris_calc -o rh.area.mid /path/to/subject/surf/rh.area add /path/to/subject/surf/rh.area.pial
I get the following error:
error: No such file or directory error: read_signa(/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/I.001): could not open file error: No such file or directory error: mris_calc: could not establish read access to '/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/rh.area'.
But when I run:
mri_info rh.area
I get the following output:
Volume information for rh.area type: unknown dimensions: 831 x 10015 x 25953 voxel sizes: -0.000000, -0.000000, nan type: SHORT (4) fov: 1016.473 dof: 1 xstart: 0.0, xend: 990983162970892849632569550308376576.0 ystart: -0.0, yend: 3079152361728581627851833344.0 zstart: -0.0, zend: -3815443229699337177012458129513775104.0 TR: 0.00 msec, TE: -0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -18770011487391973376.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = nan : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -0.0000 Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: 0.0000 -0.0000 nan nan -0.0000 -0.0000 nan nan -0.0000 0.0000 nan nan 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant nan
ras to voxel transform: error: mat = NULL!
It appears that this is where the issue is coming from. Any ideas on why this is occurring? The brain is normal and has good rh.white and rh.pial surfaces.
Many thanks, Taylor
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Date: Tuesday, March 5, 2024 at 4:25 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [EXTERNAL] Re: [Freesurfer] recon-all hard error: mris_calc could not establish read access to rh.area CAUTION: This email originated from outside the organization. DO NOT CLICK ON LINKS or OPEN ATTACHMENTS unless you know and trust the sender. Hi Taylor,
I don’t understand how you could get that error. It seems to me that read_signa() is for reading .signa files.
Can you try ‘mris_calc -o rh.area.mid rh.area add rh.area.pial’ directly? Pass full path to your rh.area and rh.area.pial.
What does ‘mri_info rh.area’ report?
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Ariko, Taylor Sent: Tuesday, March 5, 2024 2:35 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] recon-all hard error: mris_calc could not establish read access to rh.area
External Email - Use Caution Hello FreeSurfer Developers,
I am attempting to run the recon-all pipeline on one subject using the following code:
recon-all -all -i t1.nii -s p03_1
Although, I get the following error in the command line:
mris_calc -o rh.area.mid rh.area add rh.area.pial error: No such file or directory error: read_signa(/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/I.001): could not open file error: No such file or directory error: mris_calc: could not establish read access to 'rh.area'.
Tue Aug 1 15:58:13 EDT 2023 ERROR: vertexvol mris_calc -o rh.area.mid rh.area add rh.area.pial Darwin C02F10PVPN5W.local 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:56 PDT 2023; root:xnu-8796.141.3~6/RELEASE_X86_64 x86_64
recon-all -s p03_8 exited with ERRORS at Tue Aug 1 15:58:13 EDT 2023
To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1awPkvMGqqe4nOl07-lioFXGBXYKV2IQVLjNCEapAZAFk6lZ...https://secure-web.cisco.com/1z3JI8-8hxe596-2o0_cl3XnGA1GeuXlCs3-sdGVtueW3P8l8w19qmwjUNvkPfr-W4YEu8f8_UjTFFKuOqYXTRqoYgaC9XOox9N44SD3f0dm8rRAS86m20OEMA5wRLz-2zlX0FsL1tHGx36ExLWYFWaaIC4kzaCzr57Y08vlemmR6v1OC3v0zPJW38bA-ix1u6Nk_EwLBKDFKVJHcLsDgOiUqrmMuyeQ1dA6afD8_MPfFzY0sSn6Qm3qDoYnzRNCKa3lutDemnBG56QqA7pT54u7iGI67YK8wAen0afue0oi7xfo2YVktx6Kj5VwBGNTE/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1RZ-Xt7gXypFuea8NNkn6obmcMVwrPaQYiPZ0zTdmhY2IC1Zolyisw7eyh88qchNHlmxGH_5BQL_nq1-gfMY6vsFsU18cl8aNqEWD4ZO34wjXXfRScEKv88avY6poKRQxDUE0oM7aKFh_PyA9V0m9Ao6b8JuaMZV5AYeuHMNsdDLZ4V7cOuY0B5LnVfqZzF0vuiKJJ8xBWJLc6QjlzLzxU_ELraZ4wfCEWrR-Gba2NR7HHyBAm09i9655jGUOFI6zdvd51yqZk5zvPLWRMAAxCeEPCR_X3GzHd3ROvbE_nZp3HTb84BSxTYyB9pdm4AlGdOcMJlPCJJtox5uykZpSxQ%2Fhttps*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fsecure-web.cisco.com*2F1jPGfvEBFLG40bsU54UXs7wMCIp3C8zH7DpuFNxTMYcjl-sVJRX-_aLyLuGndGPWZVt9BS5c6qE7Ec_SFuNMDiQEsLM13mSxNH8JZdOiEsFCBb7otWnSANHdoam-CFMvwHH2hW6fpR1lNkOLCrAjWoOuEjE4RFiC_LZHPOCyvhfx01Lu2p1JcialLX_-bHtZq55Upe0GiY_sfOInNMp__KAE98N6nJAVI8k7ino9WC1uOZ6u-fUoCz7gesDsnzK2Za9jdm-HBAp2v_3YQz8mWlhQaTCBkKivWJgFqVjadKzcj7OeVU3QeptI7IaQhTMRXgjxd69R77-389ZRcdil8dw*2Fhttps*2A3A*2A2F*2A2Furldefense.com*2A2Fv3*2A2F__http*2A3A*2A2Fsecure-web.cisco.com*2A2F1dFtz9tfZWpoyZVj7mXFMLhzADOYxytPQ-lAzdm9SS0VD1FTbz45enl8IaOWz6IRp_KLvd-O07tGlRWlew0e-tEz_uiSd7h7vjXFLqsJ43sz_QtFlRODTxSyXDZGJH-L2KeK1nXuICROZ0fCFy4KhTJxJ3haAuYRWOZcUa5BBA0fS4iGoh92xzUyORn8wvcaGQ3GMrAFxd-bI-V_SZY3tfGjNWqrLPpayxctYehni827EcLH8K0REtJUxl1SPpG6Pe3Emtor75zz-0Hm9qjm0-uKKTYgh6I5B9-s-Y0K05FI459LrA6nQEDmQc7Af7uhtsjN1f1kK5Ejciw7kqOfhnQ*2A2Fhttp*2A2A3A*2A2A2F*2A2A2Fsurfer.nmr.mgh.harvard.edu*2A2A2Ffswiki*2A2A2FBugReporting__*2A3BJSUlJSU*2A21*2A21KVu0SnhVq1hAFvslES2Y*2A21IF_PyIoN46gdEwAovSOrLvwK3TfosortPgW4RoFCW1D0uGc53eu3quu-JN8Jgna7cnZtnrrNAAZ4Th2md4U5n7NY7g_I*2A24__*3BJSUlJSUlJSUlJSUlJSUlJSUlJQ*21*21KVu0SnhVq1hAFvslES2Y*21InYluqAPKNvYpM9tWOlA5ofPrAM-h-wkDOXsARfqcxhK-TXgMa09Cda9ZPb1NZKAuXrd50xWIfeHXufMCvjArvc12mGl*24__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!KVu0SnhVq1hAFvslES2Y!JPULH7FhtAP6Ki_ip5N5UfRcXCtC75Ia8gM2JFeSzPApFGec7yUwJNxF3_24jDFN6WJ0MHl9Ai_yqgm4nE9AkHPu9Q$
The recon-all.error file contains:
------------------------------ SUBJECT p03_8 DATE Tue Aug 1 15:58:13 EDT 2023 USER taylorariko HOST C02F10PVPN5W.local PROCESSOR x86_64 OS Darwin Darwin C02F10PVPN5W.local 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:56 PDT 2023; root:xnu-8796.141.3~6/RELEASE_X86_64 x86_64 7.2.0 (freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b) /Applications/freesurfer/7.2.0/bin/recon-all PWD /Volumes/Beta/Carmen/t1/p03_8/p03_8/mri CMD vertexvol --s p03_8 --rh --th3
I have made sure that I have read, write, and execute access to the folder /path/to/subject/surf and the file rh.area. I can successfully run the command to make rh.area (mris_place_surface --area-map ../surf/rh.white ../surf/rh.area), but the error persists in using rh.area. I have disk space and can run other commands such as this fake one (mris_calc -o rh.area.Test rh.area.pial add rh.area.pial), but not if it contains rh.area. I have tried to rerun the command from root and get the same error message.
I found 2 similar threads of the mail-archive, though I didn’t find any remedies:
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Does anyone have any thoughts on how to trouble-shoot this? I have included my recon-all.log in the case it is of any use.
1. Freesurfer version: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b 2. Platform: macOS Sonoma 14.3.1 3. uname -a: Darwin C02F10PVPN5W.local 23.3.0 Darwin Kernel Version 23.3.0: Wed Dec 20 21:28:58 PST 2023; root:xnu-10002.81.5~7/RELEASE_X86_64 x86_64 4. recon-all.log: see attached
Thanks in advance!
Taylor Ariko
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Hi Taylor,
Attached are mri_info and mris_calc from our dev version for Darwin-x86-64. Make a copy of your current binaries, and copy them into your $FREESURFER_HOME/bin. Make sure they have the execute permission.
Let me know how they work for you!
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Ariko, Taylor Sent: Tuesday, March 12, 2024 9:53 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could not establish read access to rh.area
External Email - Use Caution That would be wonderful, thank you.
Best, Taylor
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu> Date: Thursday, March 7, 2024 at 9:05 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could not establish read access to rh.area Yujing, you can just send Taylor a binary that can be put in the local version of $FREESURFER/bin On 3/6/2024 11:45 AM, Huang, Yujing wrote: Hi Taylor,
Thanks for sharing the data.
I see the problem now. The first 14336 bytes of your rh.area fit SIGNA_FILE criteria. So, it is read as SIGNA_FILE instead of MRI_CURV_FILE.
We will have a fix in dev version. But I’m not sure how to get around this in FS 7.2.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Ariko, Taylor Sent: Wednesday, March 6, 2024 9:47 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could not establish read access to rh.area
External Email - Use Caution Hello Yujing,
If I rerun this command:
mris_place_surface --area-map ../surf/rh.white ../surf/rh.area
It says it is writing curvature file in the command line output:
writing curvature file ../surf/rh.area
Though the problem persists (mri_info says same thing as before). I have attached rh.white and rh.area for your review.
Many thanks, Taylor
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Date: Wednesday, March 6, 2024 at 8:37 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could not establish read access to rh.area It doesn’t look like rh.area is recognized correctly. ‘mri_info rh.area’ should show it is a ‘curv’ file with nvertices x 1 x 1 dimensions.
I’m not sure where exactly the area values are calculated. What happen if you re-run this step? mris_place_surface --area-map ../surf/rh.white ../surf/rh.area
Can you share the ?h.white and ?h.area?
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Ariko, Taylor Sent: Tuesday, March 5, 2024 7:24 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could not establish read access to rh.area
External Email - Use Caution Hello Yujing,
Thank you for your quick response!
When I run:
mris_calc -o rh.area.mid /path/to/subject/surf/rh.area add /path/to/subject/surf/rh.area.pial
I get the following error:
error: No such file or directory error: read_signa(/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/I.001): could not open file error: No such file or directory error: mris_calc: could not establish read access to '/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/rh.area'.
But when I run:
mri_info rh.area
I get the following output:
Volume information for rh.area type: unknown dimensions: 831 x 10015 x 25953 voxel sizes: -0.000000, -0.000000, nan type: SHORT (4) fov: 1016.473 dof: 1 xstart: 0.0, xend: 990983162970892849632569550308376576.0 ystart: -0.0, yend: 3079152361728581627851833344.0 zstart: -0.0, zend: -3815443229699337177012458129513775104.0 TR: 0.00 msec, TE: -0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -18770011487391973376.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = nan : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -0.0000 Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: 0.0000 -0.0000 nan nan -0.0000 -0.0000 nan nan -0.0000 0.0000 nan nan 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant nan
ras to voxel transform: error: mat = NULL!
It appears that this is where the issue is coming from. Any ideas on why this is occurring? The brain is normal and has good rh.white and rh.pial surfaces.
Many thanks, Taylor
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Date: Tuesday, March 5, 2024 at 4:25 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [EXTERNAL] Re: [Freesurfer] recon-all hard error: mris_calc could not establish read access to rh.area CAUTION: This email originated from outside the organization. DO NOT CLICK ON LINKS or OPEN ATTACHMENTS unless you know and trust the sender. Hi Taylor,
I don’t understand how you could get that error. It seems to me that read_signa() is for reading .signa files.
Can you try ‘mris_calc -o rh.area.mid rh.area add rh.area.pial’ directly? Pass full path to your rh.area and rh.area.pial.
What does ‘mri_info rh.area’ report?
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Ariko, Taylor Sent: Tuesday, March 5, 2024 2:35 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] recon-all hard error: mris_calc could not establish read access to rh.area
External Email - Use Caution Hello FreeSurfer Developers,
I am attempting to run the recon-all pipeline on one subject using the following code:
recon-all -all -i t1.nii -s p03_1
Although, I get the following error in the command line:
mris_calc -o rh.area.mid rh.area add rh.area.pial error: No such file or directory error: read_signa(/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/I.001): could not open file error: No such file or directory error: mris_calc: could not establish read access to 'rh.area'.
Tue Aug 1 15:58:13 EDT 2023 ERROR: vertexvol mris_calc -o rh.area.mid rh.area add rh.area.pial Darwin C02F10PVPN5W.local 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:56 PDT 2023; root:xnu-8796.141.3~6/RELEASE_X86_64 x86_64
recon-all -s p03_8 exited with ERRORS at Tue Aug 1 15:58:13 EDT 2023
To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttps://secure-web.cisco.com/1_LzalUtWm2XHzFdPW5ROlTWI-u2J28qOJSoFT3SLzBtHmtfCy-uJewLrLkAjTRxk2SvXt4W8coyHK3oVcShQUc0tK8l31jwK5GapVj-0dPERlkoA_vfmgoItUiNLmwph7rc0lDckL3QXAEeMCOTLOBIBQyxKYFXzbO-k1loLywY82MUNM3WvAxDllCARDcbwttziO_pMhlSfiYysiMv_i9MTMSAH378Dj1Fl4Dmw55tZsdR4e7XWQ6pSMuJOtPYo2aidsscl0HD4kxI8Y1hhiA/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1RZ-Xt7gXypFuea8NNkn6obmcMVwrPaQYiPZ0zTdmhY2IC1Zolyisw7eyh88qchNHlmxGH_5BQL_nq1-gfMY6vsFsU18cl8aNqEWD4ZO34wjXXfRScEKv88avY6poKRQxDUE0oM7aKFh_PyA9V0m9Ao6b8JuaMZV5AYeuHMNsdDLZ4V7cOuY0B5LnVfqZzF0vuiKJJ8xBWJLc6QjlzLzxU_ELraZ4wfCEWrR-Gba2NR7HHyBAm09i9655jGUOFI6zdvd51yqZk5zvPLWRMAAxCeEPCR_X3GzHd3ROvbE_nZp3HTb84BSxTYyB9pdm4AlGdOcMJlPCJJtox5uykZpSxQ%2Fhttps%2A3A%2A2F%2A2Furldefense.com%2A2Fv3%2A2F__https%2A3A%2A2Fsecure-web.cisco.com%2A2F1jPGfvEBFLG40bsU54UXs7wMCIp3C8zH7DpuFNxTMYcjl-sVJRX-_aLyLuGndGPWZVt9BS5c6qE7Ec_SFuNMDiQEsLM13mSxNH8JZdOiEsFCBb7otWnSANHdoam-CFMvwHH2hW6fpR1lNkOLCrAjWoOuEjE4RFiC_LZHPOCyvhfx01Lu2p1JcialLX_-bHtZq55Upe0GiY_sfOInNMp__KAE98N6nJAVI8k7ino9WC1uOZ6u-fUoCz7gesDsnzK2Za9jdm-HBAp2v_3YQz8mWlhQaTCBkKivWJgFqVjadKzcj7OeVU3QeptI7IaQhTMRXgjxd69R77-389ZRcdil8dw%2A2Fhttps%2A2A3A%2A2A2F%2A2A2Furldefense.com%2A2A2Fv3%2A2A2F__http%2A2A3A%2A2A2Fsecure-web.cisco.com%2A2A2F1dFtz9tfZWpoyZVj7mXFMLhzADOYxytPQ-lAzdm9SS0VD1FTbz45enl8IaOWz6IRp_KLvd-O07tGlRWlew0e-tEz_uiSd7h7vjXFLqsJ43sz_QtFlRODTxSyXDZGJH-L2KeK1nXuICROZ0fCFy4KhTJxJ3haAuYRWOZcUa5BBA0fS4iGoh92xzUyORn8wvcaGQ3GMrAFxd-bI-V_SZY3tfGjNWqrLPpayxctYehni827EcLH8K0REtJUxl1SPpG6Pe3Emtor75zz-0Hm9qjm0-uKKTYgh6I5B9-s-Y0K05FI459LrA6nQEDmQc7Af7uhtsjN1f1kK5Ejciw7kqOfhnQ%2A2A2Fhttp%2A2A2A3A%2A2A2A2F%2A2A2A2Fsurfer.nmr.mgh.harvard.edu%2A2A2A2Ffswiki%2A2A2A2FBugReporting__%2A2A3BJSUlJSU%2A2A21%2A2A21KVu0SnhVq1hAFvslES2Y%2A2A21IF_PyIoN46gdEwAovSOrLvwK3TfosortPgW4RoFCW1D0uGc53eu3quu-JN8Jgna7cnZtnrrNAAZ4Th2md4U5n7NY7g_I%2A2A24__%2A3BJSUlJSUlJSUlJSUlJSUlJSUlJQ%2A21%2A21KVu0SnhVq1hAFvslES2Y%2A21InYluqAPKNvYpM9tWOlA5ofPrAM-h-wkDOXsARfqcxhK-TXgMa09Cda9ZPb1NZKAuXrd50xWIfeHXufMCvjArvc12mGl%2A24__%3BJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl%21%21KVu0SnhVq1hAFvslES2Y%21JPULH7FhtAP6Ki_ip5N5UfRcXCtC75Ia8gM2JFeSzPApFGec7yUwJNxF3_24jDFN6WJ0MHl9Ai_yqgm4nE9AkHPu9Q%24
The recon-all.error file contains:
------------------------------ SUBJECT p03_8 DATE Tue Aug 1 15:58:13 EDT 2023 USER taylorariko HOST C02F10PVPN5W.local PROCESSOR x86_64 OS Darwin Darwin C02F10PVPN5W.local 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:56 PDT 2023; root:xnu-8796.141.3~6/RELEASE_X86_64 x86_64 7.2.0 (freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b) /Applications/freesurfer/7.2.0/bin/recon-all PWD /Volumes/Beta/Carmen/t1/p03_8/p03_8/mri CMD vertexvol --s p03_8 --rh --th3
I have made sure that I have read, write, and execute access to the folder /path/to/subject/surf and the file rh.area. I can successfully run the command to make rh.area (mris_place_surface --area-map ../surf/rh.white ../surf/rh.area), but the error persists in using rh.area. I have disk space and can run other commands such as this fake one (mris_calc -o rh.area.Test rh.area.pial add rh.area.pial), but not if it contains rh.area. I have tried to rerun the command from root and get the same error message.
I found 2 similar threads of the mail-archive, though I didn’t find any remedies:
1. MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg44230.htmlhttps://secure-web.cisco.com/1LqWBRkOv2O4jEDKLOJa6ezOmmjY5pX2zbiUafC-UE8-VQce5kt8aZ0DUbnxXPhPaxbutnP5k4GmUVVx_wJIJlNAyHQdY4r4249-pAlVVe1IV6c3WHAfHq63hCmuCUTdqcDH6-7tKFJJc-2x5REYIl4R4sX98LPk_zL21gPOJzkRiTJigydDWdOMM1U0no6zzyUTAyr7Lay9fHzoN_fR9yQtixBl0vL_3JrRx9ktakKhB1_u5TK9NIrqae9XCjJcVdTNlT_cORabUCveu_uJaAQ/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1jMJLq9IWeIRjXwk3A82x_IsCGmCpTS-a7xyYNAmL4y2YW0NObYC1h3is0t6ALiBUXmrSF-ejvBaW_hJmEXIhWe3n7sVgGwDO_h133T2ZfcDoYf63i6GkTbWQ1VElHtkdIedKc1LArRENxthRwIs3lD-eHg5C_kayIY63WUmUF6wD4Ggtj6jQCXIvVIWj1KYeyD1IKmRkFRuxzaphKzg-S9olvhcDKTBQAkwegOVEzKCT8DI7sCR7UuJ-wpfiY3HN7DNJNZ-J8bcocx-pARRqbPX6DNqgQySLXEwaEbouWyhLMUxkn3Y-FFtjR9MLkQAgZu7O4Zo2pI7SZYm8UE3d3w%2Fhttps%2A3A%2A2F%2A2Furldefense.com%2A2Fv3%2A2F__https%2A3A%2A2Fsecure-web.cisco.com%2A2F1E6jIKLSpw7NluXRn2D-isCeIzODPsiH3Jo9Vn7j1NkSzEdgQFqIT-yFUk40J8xiqLyQ4x_Y-RZaw5Qaxs1jNi3GT0PDsMI3-1lAhOZwAqLQokIDS8eGVG8WkKccEyR3UQkKVKZvtyTme9bufG_TtMM4ThQ9jnFYOyRa6v9ATrUQ8bi0wuLfAL5SfQN2moagVYcvVEuAQuavwcQOnM37pGTqBD_tsEUghyFNAGMCw7s6w-Jyz88PXMchP4wUb7Snok2Y7uzRLa3e8MJ1S1brOJYa7Bd27riu_krNV26r6R74z7XICgwmILuLsVi6wfEV3xrALAbkeZhVCdteqBhGRug%2A2Fhttps%2A2A3A%2A2A2F%2A2A2Furldefense.com%2A2A2Fv3%2A2A2F__https%2A2A3A%2A2A2Fsecure-web.cisco.com%2A2A2F1s_8L81vMyC0-KdGicsKrUniSkh4Egg5_LxXz-_YnmsgL0Gm5kE9GJdy_R08c77fGYQTPDdQWTXx7zHH94KsUkxY5QpVUmicO4epJQCmrRk9qMFABnrFnqeMNWHf8BMzYZT9-_q55fpDjwdwtbSup33zXWmZ7_Qaxd-4Z5VhTLIcQnzdH1PATkHpAO-TTMDS2pwJXoqBJWfCdjq5iu6ZD_6K0lrHqWnH3JudltTqMg3oGYhVXWbXscFSmN__-ZRnNfVJ8CDc90XN86oLWU105NH4AaObyV0lLfIM82_MyoJeAcNXkfuOpxqrOcWWH_mbDB5W0KbiD_DVkA4CTMYOqPQ%2A2A2Fhttps%2A2A2A3A%2A2A2A2F%2A2A2A2Fwww.mail-archive.com%2A2A2A2Ffreesurfer%2A2A2A40nmr.mgh.harvard.edu%2A2A2A2Fmsg44230.html__%2A2A3BJSUlJSUl%2A2A21%2A2A21KVu0SnhVq1hAFvslES2Y%2A2A21IF_PyIoN46gdEwAovSOrLvwK3TfosortPgW4RoFCW1D0uGc53eu3quu-JN8Jgna7cnZtnrrNAAZ4Th2md4U5n7lbwM4K%2A2A24__%2A3BJSUlJSUlJSUlJSUlJSUlJSUlJSU%2A21%2A21KVu0SnhVq1hAFvslES2Y%2A21InYluqAPKNvYpM9tWOlA5ofPrAM-h-wkDOXsARfqcxhK-TXgMa09Cda9ZPb1NZKAuXrd50xWIfeHXufMCvjArjnHczWH%2A24__%3BJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJQ%21%21KVu0SnhVq1hAFvslES2Y%21JPULH7FhtAP6Ki_ip5N5UfRcXCtC75Ia8gM2JFeSzPApFGec7yUwJNxF3_24jDFN6WJ0MHl9Ai_yqgm4nE8hWVCnXQ%24 2. MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51444.htmlhttps://secure-web.cisco.com/1wSUPFR-JTOwxpuJ6MVFppxh6vj2VCXOAfm_iBst88MdfiJRK3a7o03g2ukn-vBNIP8XZtl8UKJXlY8BGWgoGs_silvS_Nb-FJpWCfvZe928f7zsVUpeoUKAEGOWu0yQP2pXkNQYb5V7GvHZ7n_ZzE5DbCsJSnttOC_0cua4v07klNvL8JSUWEjNVPDt5JHT0O1La6yYknS0o5JICZnQJh716tiMqkB8xcch0BN81SFOd9IRLrcolcKs6WKXSat7os5sq6Bh-P_lNjH9QmavDmQ/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1kzbC-1TGfknjZatLqrkie9mDrwseuKFvB8BOYwkca3ISUcixUkNUSuuAus7RHM1NJM5BL-r0Lw3GnliSehfiY0mu99LfE1WuMlBWXUdkuk347c1qF_UACb9Ff5hBRS44O8Tr17iDVyvX2IegIMR58VIdF2-clN2nhiNrwKENMp9B9U3-YXDkGdlrkNcgW4r5sLMTNyPurdQJ40qtqxPuW708I8QqzE19sceuZKgl0bSejz4KOu5L_8D1Ayi-MavIoQIAkFV5yt3Hq-FC8yK3up31dHT5uAdTaK1MOpndTrGm2GiEktL6OMDXZC-9WaBcKxjxmdVl3Y5xZ0oU9e86jA%2Fhttps%2A3A%2A2F%2A2Furldefense.com%2A2Fv3%2A2F__https%2A3A%2A2Fsecure-web.cisco.com%2A2F1hv_iWDGNbq3Dw5TXCTGVNYP7K-1AejQF4PsF7SwERE6z4zX6BWyPDvAfpegjx9pMz4kxqOemvJDo9Ykz041NnNwKpfe_sK4VTXDeNE_H_JFGiZ7vkBbiTuk5LWP3CMYt8pvtVaPCUvQuzfCnmz3tvZ1kr_7728ysSbcT0NX6Ms6PcI5yE2JzbhBi5dhWRytXVe6Dn1fJX4CeTHqPFBXccDefHmalE2xRO8WbyOAGEbG7iODT8IEHjguLHAGQtgfpNzXEmwH32gIx6nomosNn7YIcKFYD63x8Q0Pvm6anhUoRE6fHjO3NSt74t9FrDoUoXO7AC2Olk0KYSNF6jP7axA%2A2Fhttps%2A2A3A%2A2A2F%2A2A2Furldefense.com%2A2A2Fv3%2A2A2F__https%2A2A3A%2A2A2Fsecure-web.cisco.com%2A2A2F1MW6Y468pIeNLaB3ruN22mzrkJIjqalKQmsNncuNqyZW9S97Lqt_NIPp9ILpSPWI1wipv6Yr0BpbNmGPSoS-nDLaWTSHWRvXjPBhx6OWaUG3ykAth8rcrPy56gCpMo8EJHuhvxzkr3J5a8gg_8hfpQn3rWeGwxvT0rbc0ADxMrz98-mzO1bI4_zT80IcHOH6lIka2UdyAuC6gQplfb_eWpXafHuJDUR-JbSxIKSJcWIraGWK6JhoVQfgB3PNWSVgFkCVarUhylVDULGGQwPvt8XCNNPOC-bX_PoKwRMM7irjngRXBU0TPYBqY3QjiI4O9FrPJMQEQNW3NadmyXb4uhQ%2A2A2Fhttps%2A2A2A3A%2A2A2A2F%2A2A2A2Fwww.mail-archive.com%2A2A2A2Ffreesurfer%2A2A2A40nmr.mgh.harvard.edu%2A2A2A2Fmsg51444.html__%2A2A3BJSUlJSUl%2A2A21%2A2A21KVu0SnhVq1hAFvslES2Y%2A2A21IF_PyIoN46gdEwAovSOrLvwK3TfosortPgW4RoFCW1D0uGc53eu3quu-JN8Jgna7cnZtnrrNAAZ4Th2md4U5n5i6wwN6%2A2A24__%2A3BJSUlJSUlJSUlJSUlJSUlJSUlJSU%2A21%2A21KVu0SnhVq1hAFvslES2Y%2A21InYluqAPKNvYpM9tWOlA5ofPrAM-h-wkDOXsARfqcxhK-TXgMa09Cda9ZPb1NZKAuXrd50xWIfeHXufMCvjArhcJqcW-%2A24__%3BJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJQ%21%21KVu0SnhVq1hAFvslES2Y%21JPULH7FhtAP6Ki_ip5N5UfRcXCtC75Ia8gM2JFeSzPApFGec7yUwJNxF3_24jDFN6WJ0MHl9Ai_yqgm4nE9miZE1jg%24
Does anyone have any thoughts on how to trouble-shoot this? I have included my recon-all.log in the case it is of any use.
1. Freesurfer version: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b 2. Platform: macOS Sonoma 14.3.1 3. uname -a: Darwin C02F10PVPN5W.local 23.3.0 Darwin Kernel Version 23.3.0: Wed Dec 20 21:28:58 PST 2023; root:xnu-10002.81.5~7/RELEASE_X86_64 x86_64 4. recon-all.log: see attached
Thanks in advance!
Taylor Ariko
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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/1HmjZXMseyySWV_XTgT8pj_v9c5EjoXUfoCHwJozr8AbA2u_evKnMMhWO4xt_IQPdZpT3pY3dKnri_HT4Ow5HcP7Dm-O2aTr4Jse_Tj9E8Ay4H8Wc3iLxJcdHTi-4UaCxmr1OqbgFSZgmmJlr8lYvK8BN5ZeVDar44h3PNsBxt_8U_K6yOO-SaoGLzNTWk3unhc7M0FGgRiAyqRdTu5qTs5CN9Dl0b_IqNJhPwRP3_Dw4Eg2UBFJruuBPNfQ8qu01oW0487pM-URccw6b5atJSXgb2qEi8RKRT-onh4zkzkdH9USIhpCMsmeiDGaeuvkz/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer__%3B%21%21KVu0SnhVq1hAFvslES2Y%21JPULH7FhtAP6Ki_ip5N5UfRcXCtC75Ia8gM2JFeSzPApFGec7yUwJNxF3_24jDFN6WJ0MHl9Ai_yqgm4nE-UICcMdw%24
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I uploaded those two binaries to OneDrive. Let me know if you can access them.
From: Huang, Yujing Sent: Tuesday, March 12, 2024 2:55 PM To: 'Freesurfer support list' freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could not establish read access to rh.area
Hi Taylor,
Attached are mri_info and mris_calc from our dev version for Darwin-x86-64. Make a copy of your current binaries, and copy them into your $FREESURFER_HOME/bin. Make sure they have the execute permission.
Let me know how they work for you!
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Ariko, Taylor Sent: Tuesday, March 12, 2024 9:53 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could not establish read access to rh.area
External Email - Use Caution That would be wonderful, thank you.
Best, Taylor
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu> Date: Thursday, March 7, 2024 at 9:05 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could not establish read access to rh.area Yujing, you can just send Taylor a binary that can be put in the local version of $FREESURFER/bin On 3/6/2024 11:45 AM, Huang, Yujing wrote: Hi Taylor,
Thanks for sharing the data.
I see the problem now. The first 14336 bytes of your rh.area fit SIGNA_FILE criteria. So, it is read as SIGNA_FILE instead of MRI_CURV_FILE.
We will have a fix in dev version. But I’m not sure how to get around this in FS 7.2.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Ariko, Taylor Sent: Wednesday, March 6, 2024 9:47 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could not establish read access to rh.area
External Email - Use Caution Hello Yujing,
If I rerun this command:
mris_place_surface --area-map ../surf/rh.white ../surf/rh.area
It says it is writing curvature file in the command line output:
writing curvature file ../surf/rh.area
Though the problem persists (mri_info says same thing as before). I have attached rh.white and rh.area for your review.
Many thanks, Taylor
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Date: Wednesday, March 6, 2024 at 8:37 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could not establish read access to rh.area It doesn’t look like rh.area is recognized correctly. ‘mri_info rh.area’ should show it is a ‘curv’ file with nvertices x 1 x 1 dimensions.
I’m not sure where exactly the area values are calculated. What happen if you re-run this step? mris_place_surface --area-map ../surf/rh.white ../surf/rh.area
Can you share the ?h.white and ?h.area?
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Ariko, Taylor Sent: Tuesday, March 5, 2024 7:24 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could not establish read access to rh.area
External Email - Use Caution Hello Yujing,
Thank you for your quick response!
When I run:
mris_calc -o rh.area.mid /path/to/subject/surf/rh.area add /path/to/subject/surf/rh.area.pial
I get the following error:
error: No such file or directory error: read_signa(/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/I.001): could not open file error: No such file or directory error: mris_calc: could not establish read access to '/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/rh.area'.
But when I run:
mri_info rh.area
I get the following output:
Volume information for rh.area type: unknown dimensions: 831 x 10015 x 25953 voxel sizes: -0.000000, -0.000000, nan type: SHORT (4) fov: 1016.473 dof: 1 xstart: 0.0, xend: 990983162970892849632569550308376576.0 ystart: -0.0, yend: 3079152361728581627851833344.0 zstart: -0.0, zend: -3815443229699337177012458129513775104.0 TR: 0.00 msec, TE: -0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -18770011487391973376.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = nan : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -0.0000 Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: 0.0000 -0.0000 nan nan -0.0000 -0.0000 nan nan -0.0000 0.0000 nan nan 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant nan
ras to voxel transform: error: mat = NULL!
It appears that this is where the issue is coming from. Any ideas on why this is occurring? The brain is normal and has good rh.white and rh.pial surfaces.
Many thanks, Taylor
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Date: Tuesday, March 5, 2024 at 4:25 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [EXTERNAL] Re: [Freesurfer] recon-all hard error: mris_calc could not establish read access to rh.area CAUTION: This email originated from outside the organization. DO NOT CLICK ON LINKS or OPEN ATTACHMENTS unless you know and trust the sender. Hi Taylor,
I don’t understand how you could get that error. It seems to me that read_signa() is for reading .signa files.
Can you try ‘mris_calc -o rh.area.mid rh.area add rh.area.pial’ directly? Pass full path to your rh.area and rh.area.pial.
What does ‘mri_info rh.area’ report?
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Ariko, Taylor Sent: Tuesday, March 5, 2024 2:35 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] recon-all hard error: mris_calc could not establish read access to rh.area
External Email - Use Caution Hello FreeSurfer Developers,
I am attempting to run the recon-all pipeline on one subject using the following code:
recon-all -all -i t1.nii -s p03_1
Although, I get the following error in the command line:
mris_calc -o rh.area.mid rh.area add rh.area.pial error: No such file or directory error: read_signa(/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/I.001): could not open file error: No such file or directory error: mris_calc: could not establish read access to 'rh.area'.
Tue Aug 1 15:58:13 EDT 2023 ERROR: vertexvol mris_calc -o rh.area.mid rh.area add rh.area.pial Darwin C02F10PVPN5W.local 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:56 PDT 2023; root:xnu-8796.141.3~6/RELEASE_X86_64 x86_64
recon-all -s p03_8 exited with ERRORS at Tue Aug 1 15:58:13 EDT 2023
To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttps://secure-web.cisco.com/1_LzalUtWm2XHzFdPW5ROlTWI-u2J28qOJSoFT3SLzBtHmtfCy-uJewLrLkAjTRxk2SvXt4W8coyHK3oVcShQUc0tK8l31jwK5GapVj-0dPERlkoA_vfmgoItUiNLmwph7rc0lDckL3QXAEeMCOTLOBIBQyxKYFXzbO-k1loLywY82MUNM3WvAxDllCARDcbwttziO_pMhlSfiYysiMv_i9MTMSAH378Dj1Fl4Dmw55tZsdR4e7XWQ6pSMuJOtPYo2aidsscl0HD4kxI8Y1hhiA/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1RZ-Xt7gXypFuea8NNkn6obmcMVwrPaQYiPZ0zTdmhY2IC1Zolyisw7eyh88qchNHlmxGH_5BQL_nq1-gfMY6vsFsU18cl8aNqEWD4ZO34wjXXfRScEKv88avY6poKRQxDUE0oM7aKFh_PyA9V0m9Ao6b8JuaMZV5AYeuHMNsdDLZ4V7cOuY0B5LnVfqZzF0vuiKJJ8xBWJLc6QjlzLzxU_ELraZ4wfCEWrR-Gba2NR7HHyBAm09i9655jGUOFI6zdvd51yqZk5zvPLWRMAAxCeEPCR_X3GzHd3ROvbE_nZp3HTb84BSxTYyB9pdm4AlGdOcMJlPCJJtox5uykZpSxQ%2Fhttps%2A3A%2A2F%2A2Furldefense.com%2A2Fv3%2A2F__https%2A3A%2A2Fsecure-web.cisco.com%2A2F1jPGfvEBFLG40bsU54UXs7wMCIp3C8zH7DpuFNxTMYcjl-sVJRX-_aLyLuGndGPWZVt9BS5c6qE7Ec_SFuNMDiQEsLM13mSxNH8JZdOiEsFCBb7otWnSANHdoam-CFMvwHH2hW6fpR1lNkOLCrAjWoOuEjE4RFiC_LZHPOCyvhfx01Lu2p1JcialLX_-bHtZq55Upe0GiY_sfOInNMp__KAE98N6nJAVI8k7ino9WC1uOZ6u-fUoCz7gesDsnzK2Za9jdm-HBAp2v_3YQz8mWlhQaTCBkKivWJgFqVjadKzcj7OeVU3QeptI7IaQhTMRXgjxd69R77-389ZRcdil8dw%2A2Fhttps%2A2A3A%2A2A2F%2A2A2Furldefense.com%2A2A2Fv3%2A2A2F__http%2A2A3A%2A2A2Fsecure-web.cisco.com%2A2A2F1dFtz9tfZWpoyZVj7mXFMLhzADOYxytPQ-lAzdm9SS0VD1FTbz45enl8IaOWz6IRp_KLvd-O07tGlRWlew0e-tEz_uiSd7h7vjXFLqsJ43sz_QtFlRODTxSyXDZGJH-L2KeK1nXuICROZ0fCFy4KhTJxJ3haAuYRWOZcUa5BBA0fS4iGoh92xzUyORn8wvcaGQ3GMrAFxd-bI-V_SZY3tfGjNWqrLPpayxctYehni827EcLH8K0REtJUxl1SPpG6Pe3Emtor75zz-0Hm9qjm0-uKKTYgh6I5B9-s-Y0K05FI459LrA6nQEDmQc7Af7uhtsjN1f1kK5Ejciw7kqOfhnQ%2A2A2Fhttp%2A2A2A3A%2A2A2A2F%2A2A2A2Fsurfer.nmr.mgh.harvard.edu%2A2A2A2Ffswiki%2A2A2A2FBugReporting__%2A2A3BJSUlJSU%2A2A21%2A2A21KVu0SnhVq1hAFvslES2Y%2A2A21IF_PyIoN46gdEwAovSOrLvwK3TfosortPgW4RoFCW1D0uGc53eu3quu-JN8Jgna7cnZtnrrNAAZ4Th2md4U5n7NY7g_I%2A2A24__%2A3BJSUlJSUlJSUlJSUlJSUlJSUlJQ%2A21%2A21KVu0SnhVq1hAFvslES2Y%2A21InYluqAPKNvYpM9tWOlA5ofPrAM-h-wkDOXsARfqcxhK-TXgMa09Cda9ZPb1NZKAuXrd50xWIfeHXufMCvjArvc12mGl%2A24__%3BJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl%21%21KVu0SnhVq1hAFvslES2Y%21JPULH7FhtAP6Ki_ip5N5UfRcXCtC75Ia8gM2JFeSzPApFGec7yUwJNxF3_24jDFN6WJ0MHl9Ai_yqgm4nE9AkHPu9Q%24
The recon-all.error file contains:
------------------------------ SUBJECT p03_8 DATE Tue Aug 1 15:58:13 EDT 2023 USER taylorariko HOST C02F10PVPN5W.local PROCESSOR x86_64 OS Darwin Darwin C02F10PVPN5W.local 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:56 PDT 2023; root:xnu-8796.141.3~6/RELEASE_X86_64 x86_64 7.2.0 (freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b) /Applications/freesurfer/7.2.0/bin/recon-all PWD /Volumes/Beta/Carmen/t1/p03_8/p03_8/mri CMD vertexvol --s p03_8 --rh --th3
I have made sure that I have read, write, and execute access to the folder /path/to/subject/surf and the file rh.area. I can successfully run the command to make rh.area (mris_place_surface --area-map ../surf/rh.white ../surf/rh.area), but the error persists in using rh.area. I have disk space and can run other commands such as this fake one (mris_calc -o rh.area.Test rh.area.pial add rh.area.pial), but not if it contains rh.area. I have tried to rerun the command from root and get the same error message.
I found 2 similar threads of the mail-archive, though I didn’t find any remedies:
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Does anyone have any thoughts on how to trouble-shoot this? I have included my recon-all.log in the case it is of any use.
1. Freesurfer version: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b 2. Platform: macOS Sonoma 14.3.1 3. uname -a: Darwin C02F10PVPN5W.local 23.3.0 Darwin Kernel Version 23.3.0: Wed Dec 20 21:28:58 PST 2023; root:xnu-10002.81.5~7/RELEASE_X86_64 x86_64 4. recon-all.log: see attached
Thanks in advance!
Taylor Ariko
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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/1HmjZXMseyySWV_XTgT8pj_v9c5EjoXUfoCHwJozr8AbA2u_evKnMMhWO4xt_IQPdZpT3pY3dKnri_HT4Ow5HcP7Dm-O2aTr4Jse_Tj9E8Ay4H8Wc3iLxJcdHTi-4UaCxmr1OqbgFSZgmmJlr8lYvK8BN5ZeVDar44h3PNsBxt_8U_K6yOO-SaoGLzNTWk3unhc7M0FGgRiAyqRdTu5qTs5CN9Dl0b_IqNJhPwRP3_Dw4Eg2UBFJruuBPNfQ8qu01oW0487pM-URccw6b5atJSXgb2qEi8RKRT-onh4zkzkdH9USIhpCMsmeiDGaeuvkz/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer__%3B%21%21KVu0SnhVq1hAFvslES2Y%21JPULH7FhtAP6Ki_ip5N5UfRcXCtC75Ia8gM2JFeSzPApFGec7yUwJNxF3_24jDFN6WJ0MHl9Ai_yqgm4nE-UICcMdw%24
External Email - Use Caution
Hello Yujing,
It works! Thank you so much for your help!!
Best, Taylor
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Huang, Yujing YHUANG43@mgh.harvard.edu Date: Tuesday, March 12, 2024 at 3:58 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could not establish read access to rh.area Hi Taylor,
Attached are mri_info and mris_calc from our dev version for Darwin-x86-64. Make a copy of your current binaries, and copy them into your $FREESURFER_HOME/bin. Make sure they have the execute permission.
Let me know how they work for you!
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Ariko, Taylor Sent: Tuesday, March 12, 2024 9:53 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could not establish read access to rh.area
External Email - Use Caution That would be wonderful, thank you.
Best, Taylor
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu> Date: Thursday, March 7, 2024 at 9:05 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could not establish read access to rh.area Yujing, you can just send Taylor a binary that can be put in the local version of $FREESURFER/bin On 3/6/2024 11:45 AM, Huang, Yujing wrote: Hi Taylor,
Thanks for sharing the data.
I see the problem now. The first 14336 bytes of your rh.area fit SIGNA_FILE criteria. So, it is read as SIGNA_FILE instead of MRI_CURV_FILE.
We will have a fix in dev version. But I’m not sure how to get around this in FS 7.2.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Ariko, Taylor Sent: Wednesday, March 6, 2024 9:47 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could not establish read access to rh.area
External Email - Use Caution Hello Yujing,
If I rerun this command:
mris_place_surface --area-map ../surf/rh.white ../surf/rh.area
It says it is writing curvature file in the command line output:
writing curvature file ../surf/rh.area
Though the problem persists (mri_info says same thing as before). I have attached rh.white and rh.area for your review.
Many thanks, Taylor
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Date: Wednesday, March 6, 2024 at 8:37 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could not establish read access to rh.area It doesn’t look like rh.area is recognized correctly. ‘mri_info rh.area’ should show it is a ‘curv’ file with nvertices x 1 x 1 dimensions.
I’m not sure where exactly the area values are calculated. What happen if you re-run this step? mris_place_surface --area-map ../surf/rh.white ../surf/rh.area
Can you share the ?h.white and ?h.area?
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Ariko, Taylor Sent: Tuesday, March 5, 2024 7:24 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could not establish read access to rh.area
External Email - Use Caution Hello Yujing,
Thank you for your quick response!
When I run:
mris_calc -o rh.area.mid /path/to/subject/surf/rh.area add /path/to/subject/surf/rh.area.pial
I get the following error:
error: No such file or directory error: read_signa(/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/I.001): could not open file error: No such file or directory error: mris_calc: could not establish read access to '/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/rh.area'.
But when I run:
mri_info rh.area
I get the following output:
Volume information for rh.area type: unknown dimensions: 831 x 10015 x 25953 voxel sizes: -0.000000, -0.000000, nan type: SHORT (4) fov: 1016.473 dof: 1 xstart: 0.0, xend: 990983162970892849632569550308376576.0 ystart: -0.0, yend: 3079152361728581627851833344.0 zstart: -0.0, zend: -3815443229699337177012458129513775104.0 TR: 0.00 msec, TE: -0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -18770011487391973376.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = nan : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -0.0000 Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: 0.0000 -0.0000 nan nan -0.0000 -0.0000 nan nan -0.0000 0.0000 nan nan 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant nan
ras to voxel transform: error: mat = NULL!
It appears that this is where the issue is coming from. Any ideas on why this is occurring? The brain is normal and has good rh.white and rh.pial surfaces.
Many thanks, Taylor
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Date: Tuesday, March 5, 2024 at 4:25 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [EXTERNAL] Re: [Freesurfer] recon-all hard error: mris_calc could not establish read access to rh.area CAUTION: This email originated from outside the organization. DO NOT CLICK ON LINKS or OPEN ATTACHMENTS unless you know and trust the sender. Hi Taylor,
I don’t understand how you could get that error. It seems to me that read_signa() is for reading .signa files.
Can you try ‘mris_calc -o rh.area.mid rh.area add rh.area.pial’ directly? Pass full path to your rh.area and rh.area.pial.
What does ‘mri_info rh.area’ report?
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Ariko, Taylor Sent: Tuesday, March 5, 2024 2:35 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] recon-all hard error: mris_calc could not establish read access to rh.area
External Email - Use Caution Hello FreeSurfer Developers,
I am attempting to run the recon-all pipeline on one subject using the following code:
recon-all -all -i t1.nii -s p03_1
Although, I get the following error in the command line:
mris_calc -o rh.area.mid rh.area add rh.area.pial error: No such file or directory error: read_signa(/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/I.001): could not open file error: No such file or directory error: mris_calc: could not establish read access to 'rh.area'.
Tue Aug 1 15:58:13 EDT 2023 ERROR: vertexvol mris_calc -o rh.area.mid rh.area add rh.area.pial Darwin C02F10PVPN5W.local 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:56 PDT 2023; root:xnu-8796.141.3~6/RELEASE_X86_64 x86_64
recon-all -s p03_8 exited with ERRORS at Tue Aug 1 15:58:13 EDT 2023
To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1BaogbkIIUtiT2lWrEZ9ffN5IlMO7MVNR3sFluB_Qsh4M2WC...https://secure-web.cisco.com/1FhulX_b6T5k5fqkVZ0ETCAkzxl53UlrCcjLXmeaHr6RCMrF8lUHPbNjuAGwXwUt2wUa49ohZt8wawSyzVfnoTa7VjuMopnSTodGYjOkkLrYH0FdrjgYxteFfelrjRDaBVR16MimLgPz6jAxB-hI0k-5MeOW6Br_oRxD5vPR4-v-ppLB8AthA8RLAsoSuEpKr7mYrWlVgm1XwRtQTCqbztF6qlAWKNRDh-i7o4LIIXegTHuNVWheHoG1tee1vMpo7F6JwtoE32zMQDLu6oWXe7PvLLaBnCsHYSFPfCvEaotdhe9KxbQf_IdBrj3MzF8Ept_0SmfBGpzJTYEappjD_Kw/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1_LzalUtWm2XHzFdPW5ROlTWI-u2J28qOJSoFT3SLzBtHmtfCy-uJewLrLkAjTRxk2SvXt4W8coyHK3oVcShQUc0tK8l31jwK5GapVj-0dPERlkoA_vfmgoItUiNLmwph7rc0lDckL3QXAEeMCOTLOBIBQyxKYFXzbO-k1loLywY82MUNM3WvAxDllCARDcbwttziO_pMhlSfiYysiMv_i9MTMSAH378Dj1Fl4Dmw55tZsdR4e7XWQ6pSMuJOtPYo2aidsscl0HD4kxI8Y1hhiA%2Fhttps*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fsecure-web.cisco.com*2F1RZ-Xt7gXypFuea8NNkn6obmcMVwrPaQYiPZ0zTdmhY2IC1Zolyisw7eyh88qchNHlmxGH_5BQL_nq1-gfMY6vsFsU18cl8aNqEWD4ZO34wjXXfRScEKv88avY6poKRQxDUE0oM7aKFh_PyA9V0m9Ao6b8JuaMZV5AYeuHMNsdDLZ4V7cOuY0B5LnVfqZzF0vuiKJJ8xBWJLc6QjlzLzxU_ELraZ4wfCEWrR-Gba2NR7HHyBAm09i9655jGUOFI6zdvd51yqZk5zvPLWRMAAxCeEPCR_X3GzHd3ROvbE_nZp3HTb84BSxTYyB9pdm4AlGdOcMJlPCJJtox5uykZpSxQ*2Fhttps*2A3A*2A2F*2A2Furldefense.com*2A2Fv3*2A2F__https*2A3A*2A2Fsecure-web.cisco.com*2A2F1jPGfvEBFLG40bsU54UXs7wMCIp3C8zH7DpuFNxTMYcjl-sVJRX-_aLyLuGndGPWZVt9BS5c6qE7Ec_SFuNMDiQEsLM13mSxNH8JZdOiEsFCBb7otWnSANHdoam-CFMvwHH2hW6fpR1lNkOLCrAjWoOuEjE4RFiC_LZHPOCyvhfx01Lu2p1JcialLX_-bHtZq55Upe0GiY_sfOInNMp__KAE98N6nJAVI8k7ino9WC1uOZ6u-fUoCz7gesDsnzK2Za9jdm-HBAp2v_3YQz8mWlhQaTCBkKivWJgFqVjadKzcj7OeVU3QeptI7IaQhTMRXgjxd69R77-389ZRcdil8dw*2A2Fhttps*2A2A3A*2A2A2F*2A2A2Furldefense.com*2A2A2Fv3*2A2A2F__http*2A2A3A*2A2A2Fsecure-web.cisco.com*2A2A2F1dFtz9tfZWpoyZVj7mXFMLhzADOYxytPQ-lAzdm9SS0VD1FTbz45enl8IaOWz6IRp_KLvd-O07tGlRWlew0e-tEz_uiSd7h7vjXFLqsJ43sz_QtFlRODTxSyXDZGJH-L2KeK1nXuICROZ0fCFy4KhTJxJ3haAuYRWOZcUa5BBA0fS4iGoh92xzUyORn8wvcaGQ3GMrAFxd-bI-V_SZY3tfGjNWqrLPpayxctYehni827EcLH8K0REtJUxl1SPpG6Pe3Emtor75zz-0Hm9qjm0-uKKTYgh6I5B9-s-Y0K05FI459LrA6nQEDmQc7Af7uhtsjN1f1kK5Ejciw7kqOfhnQ*2A2A2Fhttp*2A2A2A3A*2A2A2A2F*2A2A2A2Fsurfer.nmr.mgh.harvard.edu*2A2A2A2Ffswiki*2A2A2A2FBugReporting__*2A2A3BJSUlJSU*2A2A21*2A2A21KVu0SnhVq1hAFvslES2Y*2A2A21IF_PyIoN46gdEwAovSOrLvwK3TfosortPgW4RoFCW1D0uGc53eu3quu-JN8Jgna7cnZtnrrNAAZ4Th2md4U5n7NY7g_I*2A2A24__*2A3BJSUlJSUlJSUlJSUlJSUlJSUlJQ*2A21*2A21KVu0SnhVq1hAFvslES2Y*2A21InYluqAPKNvYpM9tWOlA5ofPrAM-h-wkDOXsARfqcxhK-TXgMa09Cda9ZPb1NZKAuXrd50xWIfeHXufMCvjArvc12mGl*2A24__*3BJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl*21*21KVu0SnhVq1hAFvslES2Y*21JPULH7FhtAP6Ki_ip5N5UfRcXCtC75Ia8gM2JFeSzPApFGec7yUwJNxF3_24jDFN6WJ0MHl9Ai_yqgm4nE9AkHPu9Q*24__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSU!!KVu0SnhVq1hAFvslES2Y!KhGKTjf3Su-wVEnbWkZkqZC27-EMPT7klbf0wcrT2qj8s4AK6w3lKPjwK_IBkfd1RNojt1kaflI-0ZJqVd_xv4YZQ1nW$
The recon-all.error file contains:
------------------------------ SUBJECT p03_8 DATE Tue Aug 1 15:58:13 EDT 2023 USER taylorariko HOST C02F10PVPN5W.local PROCESSOR x86_64 OS Darwin Darwin C02F10PVPN5W.local 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:56 PDT 2023; root:xnu-8796.141.3~6/RELEASE_X86_64 x86_64 7.2.0 (freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b) /Applications/freesurfer/7.2.0/bin/recon-all PWD /Volumes/Beta/Carmen/t1/p03_8/p03_8/mri CMD vertexvol --s p03_8 --rh --th3
I have made sure that I have read, write, and execute access to the folder /path/to/subject/surf and the file rh.area. I can successfully run the command to make rh.area (mris_place_surface --area-map ../surf/rh.white ../surf/rh.area), but the error persists in using rh.area. I have disk space and can run other commands such as this fake one (mris_calc -o rh.area.Test rh.area.pial add rh.area.pial), but not if it contains rh.area. I have tried to rerun the command from root and get the same error message.
I found 2 similar threads of the mail-archive, though I didn’t find any remedies:
1. MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1RWd_NMXfDW2Au-rmA8vNY7MCxrBQ_nNDSyoE-f-DvHLja5...https://secure-web.cisco.com/1B46Y9C__ElIBVXLiBWZz3culh4gTdTyXhdRLCT76lBdCXILB6IkdVfE3aOW-PAj2LCj-WvQ5P3piZkqyDBSNKTZYTiNM6cV8C3VEo646r-hSBUU9mtlJvL1EQ-9HLjaNcmDGv5EX-85ySvIhjqpCMG1hpR_ZqJ2peUwKLD3apQNUM2059heGfQP4aBYm8KroDANwjSrm-pbdvHVXDbqcfcLPSIiNs8H_quEns1dguvsz1DEtMnRQBXcVAbZasrTjO7od1ehnjpwHYi9Ufy_APHg-j6WobjYJPU-_wozfSjQgQxFHU1DHBcd3Y0Cgxi5eBxRFsY8F4pymVNXB06mDdw/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1LqWBRkOv2O4jEDKLOJa6ezOmmjY5pX2zbiUafC-UE8-VQce5kt8aZ0DUbnxXPhPaxbutnP5k4GmUVVx_wJIJlNAyHQdY4r4249-pAlVVe1IV6c3WHAfHq63hCmuCUTdqcDH6-7tKFJJc-2x5REYIl4R4sX98LPk_zL21gPOJzkRiTJigydDWdOMM1U0no6zzyUTAyr7Lay9fHzoN_fR9yQtixBl0vL_3JrRx9ktakKhB1_u5TK9NIrqae9XCjJcVdTNlT_cORabUCveu_uJaAQ%2Fhttps*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fsecure-web.cisco.com*2F1jMJLq9IWeIRjXwk3A82x_IsCGmCpTS-a7xyYNAmL4y2YW0NObYC1h3is0t6ALiBUXmrSF-ejvBaW_hJmEXIhWe3n7sVgGwDO_h133T2ZfcDoYf63i6GkTbWQ1VElHtkdIedKc1LArRENxthRwIs3lD-eHg5C_kayIY63WUmUF6wD4Ggtj6jQCXIvVIWj1KYeyD1IKmRkFRuxzaphKzg-S9olvhcDKTBQAkwegOVEzKCT8DI7sCR7UuJ-wpfiY3HN7DNJNZ-J8bcocx-pARRqbPX6DNqgQySLXEwaEbouWyhLMUxkn3Y-FFtjR9MLkQAgZu7O4Zo2pI7SZYm8UE3d3w*2Fhttps*2A3A*2A2F*2A2Furldefense.com*2A2Fv3*2A2F__https*2A3A*2A2Fsecure-web.cisco.com*2A2F1E6jIKLSpw7NluXRn2D-isCeIzODPsiH3Jo9Vn7j1NkSzEdgQFqIT-yFUk40J8xiqLyQ4x_Y-RZaw5Qaxs1jNi3GT0PDsMI3-1lAhOZwAqLQokIDS8eGVG8WkKccEyR3UQkKVKZvtyTme9bufG_TtMM4ThQ9jnFYOyRa6v9ATrUQ8bi0wuLfAL5SfQN2moagVYcvVEuAQuavwcQOnM37pGTqBD_tsEUghyFNAGMCw7s6w-Jyz88PXMchP4wUb7Snok2Y7uzRLa3e8MJ1S1brOJYa7Bd27riu_krNV26r6R74z7XICgwmILuLsVi6wfEV3xrALAbkeZhVCdteqBhGRug*2A2Fhttps*2A2A3A*2A2A2F*2A2A2Furldefense.com*2A2A2Fv3*2A2A2F__https*2A2A3A*2A2A2Fsecure-web.cisco.com*2A2A2F1s_8L81vMyC0-KdGicsKrUniSkh4Egg5_LxXz-_YnmsgL0Gm5kE9GJdy_R08c77fGYQTPDdQWTXx7zHH94KsUkxY5QpVUmicO4epJQCmrRk9qMFABnrFnqeMNWHf8BMzYZT9-_q55fpDjwdwtbSup33zXWmZ7_Qaxd-4Z5VhTLIcQnzdH1PATkHpAO-TTMDS2pwJXoqBJWfCdjq5iu6ZD_6K0lrHqWnH3JudltTqMg3oGYhVXWbXscFSmN__-ZRnNfVJ8CDc90XN86oLWU105NH4AaObyV0lLfIM82_MyoJeAcNXkfuOpxqrOcWWH_mbDB5W0KbiD_DVkA4CTMYOqPQ*2A2A2Fhttps*2A2A2A3A*2A2A2A2F*2A2A2A2Fwww.mail-archive.com*2A2A2A2Ffreesurfer*2A2A2A40nmr.mgh.harvard.edu*2A2A2A2Fmsg44230.html__*2A2A3BJSUlJSUl*2A2A21*2A2A21KVu0SnhVq1hAFvslES2Y*2A2A21IF_PyIoN46gdEwAovSOrLvwK3TfosortPgW4RoFCW1D0uGc53eu3quu-JN8Jgna7cnZtnrrNAAZ4Th2md4U5n7lbwM4K*2A2A24__*2A3BJSUlJSUlJSUlJSUlJSUlJSUlJSU*2A21*2A21KVu0SnhVq1hAFvslES2Y*2A21InYluqAPKNvYpM9tWOlA5ofPrAM-h-wkDOXsARfqcxhK-TXgMa09Cda9ZPb1NZKAuXrd50xWIfeHXufMCvjArjnHczWH*2A24__*3BJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJQ*21*21KVu0SnhVq1hAFvslES2Y*21JPULH7FhtAP6Ki_ip5N5UfRcXCtC75Ia8gM2JFeSzPApFGec7yUwJNxF3_24jDFN6WJ0MHl9Ai_yqgm4nE8hWVCnXQ*24__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!KVu0SnhVq1hAFvslES2Y!KhGKTjf3Su-wVEnbWkZkqZC27-EMPT7klbf0wcrT2qj8s4AK6w3lKPjwK_IBkfd1RNojt1kaflI-0ZJqVd_xv9-Vzgik$ 2. MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1RZSbxARg0DxDfe8zoJf8ZC89d2XCQRDu8mnTZgUu-y7XuX...https://secure-web.cisco.com/1MPdVemDrmF6TspSzWlNMJS8NNHbg1QVtOpJx9D_5qGlP04PPy7u91Ii9-iqY6veUqhH-2cLoJOYXum7Mxy8dlNHMWDdVgTQHb_hym4C8JwDCIhNvBKrIfytgtjA2SZ8kXGUMRI46tsTyOiBu2ngY211FgYMJ1zaCM5W7o1vxiXQa3PjeuG5ZqsJ222BbU9GBktlh4BUKjFQ51G-Y0_F-z-vw37krlxpJ9Yt4yid-S9tkRCuBnzF9ZPMkgCUibwnu2M1u8RZT0g3Hzug0Pl16FfhpUJPtVFE5qnXeAh57RY5MGkABr3bLZn7rh3ubPIfHr69XsK0bXHkaFNM5IB-Hhw/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1wSUPFR-JTOwxpuJ6MVFppxh6vj2VCXOAfm_iBst88MdfiJRK3a7o03g2ukn-vBNIP8XZtl8UKJXlY8BGWgoGs_silvS_Nb-FJpWCfvZe928f7zsVUpeoUKAEGOWu0yQP2pXkNQYb5V7GvHZ7n_ZzE5DbCsJSnttOC_0cua4v07klNvL8JSUWEjNVPDt5JHT0O1La6yYknS0o5JICZnQJh716tiMqkB8xcch0BN81SFOd9IRLrcolcKs6WKXSat7os5sq6Bh-P_lNjH9QmavDmQ%2Fhttps*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fsecure-web.cisco.com*2F1kzbC-1TGfknjZatLqrkie9mDrwseuKFvB8BOYwkca3ISUcixUkNUSuuAus7RHM1NJM5BL-r0Lw3GnliSehfiY0mu99LfE1WuMlBWXUdkuk347c1qF_UACb9Ff5hBRS44O8Tr17iDVyvX2IegIMR58VIdF2-clN2nhiNrwKENMp9B9U3-YXDkGdlrkNcgW4r5sLMTNyPurdQJ40qtqxPuW708I8QqzE19sceuZKgl0bSejz4KOu5L_8D1Ayi-MavIoQIAkFV5yt3Hq-FC8yK3up31dHT5uAdTaK1MOpndTrGm2GiEktL6OMDXZC-9WaBcKxjxmdVl3Y5xZ0oU9e86jA*2Fhttps*2A3A*2A2F*2A2Furldefense.com*2A2Fv3*2A2F__https*2A3A*2A2Fsecure-web.cisco.com*2A2F1hv_iWDGNbq3Dw5TXCTGVNYP7K-1AejQF4PsF7SwERE6z4zX6BWyPDvAfpegjx9pMz4kxqOemvJDo9Ykz041NnNwKpfe_sK4VTXDeNE_H_JFGiZ7vkBbiTuk5LWP3CMYt8pvtVaPCUvQuzfCnmz3tvZ1kr_7728ysSbcT0NX6Ms6PcI5yE2JzbhBi5dhWRytXVe6Dn1fJX4CeTHqPFBXccDefHmalE2xRO8WbyOAGEbG7iODT8IEHjguLHAGQtgfpNzXEmwH32gIx6nomosNn7YIcKFYD63x8Q0Pvm6anhUoRE6fHjO3NSt74t9FrDoUoXO7AC2Olk0KYSNF6jP7axA*2A2Fhttps*2A2A3A*2A2A2F*2A2A2Furldefense.com*2A2A2Fv3*2A2A2F__https*2A2A3A*2A2A2Fsecure-web.cisco.com*2A2A2F1MW6Y468pIeNLaB3ruN22mzrkJIjqalKQmsNncuNqyZW9S97Lqt_NIPp9ILpSPWI1wipv6Yr0BpbNmGPSoS-nDLaWTSHWRvXjPBhx6OWaUG3ykAth8rcrPy56gCpMo8EJHuhvxzkr3J5a8gg_8hfpQn3rWeGwxvT0rbc0ADxMrz98-mzO1bI4_zT80IcHOH6lIka2UdyAuC6gQplfb_eWpXafHuJDUR-JbSxIKSJcWIraGWK6JhoVQfgB3PNWSVgFkCVarUhylVDULGGQwPvt8XCNNPOC-bX_PoKwRMM7irjngRXBU0TPYBqY3QjiI4O9FrPJMQEQNW3NadmyXb4uhQ*2A2A2Fhttps*2A2A2A3A*2A2A2A2F*2A2A2A2Fwww.mail-archive.com*2A2A2A2Ffreesurfer*2A2A2A40nmr.mgh.harvard.edu*2A2A2A2Fmsg51444.html__*2A2A3BJSUlJSUl*2A2A21*2A2A21KVu0SnhVq1hAFvslES2Y*2A2A21IF_PyIoN46gdEwAovSOrLvwK3TfosortPgW4RoFCW1D0uGc53eu3quu-JN8Jgna7cnZtnrrNAAZ4Th2md4U5n5i6wwN6*2A2A24__*2A3BJSUlJSUlJSUlJSUlJSUlJSUlJSU*2A21*2A21KVu0SnhVq1hAFvslES2Y*2A21InYluqAPKNvYpM9tWOlA5ofPrAM-h-wkDOXsARfqcxhK-TXgMa09Cda9ZPb1NZKAuXrd50xWIfeHXufMCvjArhcJqcW-*2A24__*3BJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJQ*21*21KVu0SnhVq1hAFvslES2Y*21JPULH7FhtAP6Ki_ip5N5UfRcXCtC75Ia8gM2JFeSzPApFGec7yUwJNxF3_24jDFN6WJ0MHl9Ai_yqgm4nE9miZE1jg*24__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!KVu0SnhVq1hAFvslES2Y!KhGKTjf3Su-wVEnbWkZkqZC27-EMPT7klbf0wcrT2qj8s4AK6w3lKPjwK_IBkfd1RNojt1kaflI-0ZJqVd_xv6OMuUUo$
Does anyone have any thoughts on how to trouble-shoot this? I have included my recon-all.log in the case it is of any use.
1. Freesurfer version: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b 2. Platform: macOS Sonoma 14.3.1 3. uname -a: Darwin C02F10PVPN5W.local 23.3.0 Darwin Kernel Version 23.3.0: Wed Dec 20 21:28:58 PST 2023; root:xnu-10002.81.5~7/RELEASE_X86_64 x86_64 4. recon-all.log: see attached
Thanks in advance!
Taylor Ariko
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MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1S9kpaYZ-oi0F4gW93GvGat7UnMRrT9wgVRW1n2ZJ8jcyOc...https://secure-web.cisco.com/1SrngFbadr6_FOgAXjE8OWdg4TfKKtNlvKjH_KeXwZ41B4DRE0-gPKp1HSGP8zZtfOEo2kJ85T4_8i8HBIAZAAPhugJTz78UA49NJyNxJJ5cq38kpBnqYtz34tERdO4bCSCkOvH1WufKu1WrL-TYh178svQut4R3dgWpW6VDLBOwlajhpMIPKkQD5tAFqqHsTCd7WwYYiin4QTw5g3Y_k-ePM6Ayt4uUMeHnEptmxXzwqfhcoC2OiZzwpVWpsE1vT9gImnF-dl9eeYl0qyi17_eyohUpIsO_3xo3vVc6BvfcC-IS27-6BciZbnB9rFPwYfaMEzDKntKi4qWW0ziotBg/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1HmjZXMseyySWV_XTgT8pj_v9c5EjoXUfoCHwJozr8AbA2u_evKnMMhWO4xt_IQPdZpT3pY3dKnri_HT4Ow5HcP7Dm-O2aTr4Jse_Tj9E8Ay4H8Wc3iLxJcdHTi-4UaCxmr1OqbgFSZgmmJlr8lYvK8BN5ZeVDar44h3PNsBxt_8U_K6yOO-SaoGLzNTWk3unhc7M0FGgRiAyqRdTu5qTs5CN9Dl0b_IqNJhPwRP3_Dw4Eg2UBFJruuBPNfQ8qu01oW0487pM-URccw6b5atJSXgb2qEi8RKRT-onh4zkzkdH9USIhpCMsmeiDGaeuvkz%2Fhttps*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fmail.nmr.mgh.harvard.edu*2Fmailman*2Flistinfo*2Ffreesurfer__*3B*21*21KVu0SnhVq1hAFvslES2Y*21JPULH7FhtAP6Ki_ip5N5UfRcXCtC75Ia8gM2JFeSzPApFGec7yUwJNxF3_24jDFN6WJ0MHl9Ai_yqgm4nE-UICcMdw*24__;JSUlJSUlJSUlJSUlJSUl!!KVu0SnhVq1hAFvslES2Y!KhGKTjf3Su-wVEnbWkZkqZC27-EMPT7klbf0wcrT2qj8s4AK6w3lKPjwK_IBkfd1RNojt1kaflI-0ZJqVd_xvwcwaDCg$
freesurfer@nmr.mgh.harvard.edu
-
Ariko, Taylor -
Douglas N. Greve -
Huang, Yujing