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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Huang, Yujing
<yhuan...@mgh.harvard.edu<mailto:yhuan...@mgh.harvard.edu>>
Date: Tuesday, March 5, 2024 at 4:25 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto: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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Ariko, Taylor
Sent: Tuesday, March 5, 2024 2:35 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto: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/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.html<https://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.html<https://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
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