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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Huang, Yujing
<yhuan...@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-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
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Huang, Yujing
<yhuan...@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-boun...@nmr.mgh.harvard.edu
<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
*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:
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/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.html
<https://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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
