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: -0.00, -0.00,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: 0.00 ras xform present xform info: x_r = -1., y_r = 0., z_r = 0., c_r = -18770011487391973376. : x_a = 0., y_a = 0., z_a = 1., c_a =nan : x_s = 0., y_s = -1., z_s = 0., c_s =-0. Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: 0. -0. nannan -0. -0. nannan -0. 0. nannan 0. 0. 0. 1. 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 on behalf of Huang, Yujing Date: Tuesday, March 5, 2024 at 4:25 PM To: Freesurfer support list 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 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/1YEiKrKcbgSdrDxUh7Jnp3JDZTJ2pl3aYMzWocJZCv7iRtCy9Dav5iNiVgpHlMiH28i0zNAvXbSOaLD2KDrpXsQP7DebQsMkLuaekXYGlbATO_iDpNQsM_Xx1UWwZsEk6IJIzddHZOtKCk4kcbD5wJa4S-k9UZIsGkDt9NGqFRaXiMn1Ifl85WCU_D0R-hY79NchLHFbNli3H0mnZLby_KAIdqrkoz00BNFpgG0TN20r0_uXYsKlrCtxHS1Jr60-SnLBqdKWVJ0-Xk9b6WfWPkslbqA5QM-K20BlK4U1kVdNeCTgcJAxosVioja_0_H4nz7SYzstvCw3qM7LI5rBiOw/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting<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_SZY3tfGjNWqrLPpayxctYehni827EcLH8K0R
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-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Date: Thursday, March 7, 2024 at 9:05 AM To: 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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Ariko, Taylor Sent: Wednesday, March 6, 2024 9:47 AM To: Freesurfer support list <mailto: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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Huang, Yujing mailto:yhuan...@mgh.harvard.edu>> Date: Wednesday, March 6, 2024 at 8:37 AM To: Freesurfer support list mailto: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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Ariko, Taylor Sent: Tuesday, March 5, 2024 7:24 PM To: Freesurfer support list mailto: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: -0.00, -0.00,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: 0.00 ras xform present xform info: x_r = -1., y_r = 0., z_r = 0., c_r = -18770011487391973376. : x_a = 0., y_a = 0., z_a = 1., c_a =nan : x_s = 0., y_s = -1., z_s = 0., c_s =-0. Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: 0. -0. nannan -0. -0. nannan -0. 0. nannan 0. 0. 0. 1. 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> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Huang, Yujing mailto:yhuan...@mgh
Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could not establish read access to rh.area
External Email - Use Caution Hello Yujing, It works! Thank you so much for your help!! Best, Taylor From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Huang, Yujing Date: Tuesday, March 12, 2024 at 3:58 PM To: Freesurfer support list 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-boun...@nmr.mgh.harvard.edu On Behalf Of Ariko, Taylor Sent: Tuesday, March 12, 2024 9:53 AM To: Freesurfer support list 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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Douglas N. Greve mailto:dgr...@mgh.harvard.edu>> Date: Thursday, March 7, 2024 at 9:05 AM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> mailto: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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Ariko, Taylor Sent: Wednesday, March 6, 2024 9:47 AM To: Freesurfer support list <mailto: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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Huang, Yujing mailto:yhuan...@mgh.harvard.edu>> Date: Wednesday, March 6, 2024 at 8:37 AM To: Freesurfer support list mailto: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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Ariko, Taylor Sent: Tuesday, March 5, 2024 7:24 PM To: Freesurfer support list mailto: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: -0.00, -0.00,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,
