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Hello, These two logs are from the same subject but with slightly different preprocesses. The initial images are a 90 axial slides (512*512). I also have her images with 30 slides (with 5mm gaps in between). All these got the same error message with freesurfer. she has multiple lesions (but very small size) in the cerebellum and cerebral cortex, and also in the white matter.

I hope these information may be useful.

Thanks Zhen

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Huang, Yujing Sent: Wednesday, March 12, 2025 8:09 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [EXTERNAL] Re: [Freesurfer] autorecon1_norm.mgz not found

Can you attach your recon-all.log?

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 Ni, Zhen (NIH/NINDS) [C] Sent: Wednesday, March 12, 2025 7:56 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] autorecon1_norm.mgz not found

External Email - Use Caution Hello, I'm using the command "recon-all -autorecon1 -subjid $SUBJECTNAME". After about 2 hours, there are a few mgz and other files generated in the /mri directory, however, I got an error message:

WARNING: entowm has very low volumes so not using it to edit GA of cortex label

#--------------------------------------

#@# CC Seg Mon Mar 10 19:13:32 EDT 2025

\n seg2cc --s sub-002 \n

ERROR: cannot find /Applications/freesurfer/8.0.0/subjects/sub-002/mri/norm.mgz

Darwin nzs-MacBook-Air.local 23.6.0 Darwin Kernel Version 23.6.0: Fri Jul 5 17:54:20 PDT 2024; root:xnu-10063.141.1~2/RELEASE_X86_64 x86_64

recon-all -s sub-002 exited with ERRORS at Mon Mar 10 19:13:33 EDT 2025

I wonder if you have any idea to fix the problem.

Zhen

CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.

External Email - Use Caution

Thanks a lot. It moved a bit forward but new errors occurred, seems like co-registration to Talairach space?

Zhen

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Huang, Yujing Sent: Wednesday, March 12, 2025 11:58 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [EXTERNAL] Re: [Freesurfer] autorecon1_norm.mgz not found

Can you try to add '-canorm' to your 'recon-all -autorecon1' command line?

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 Ni, Zhen (NIH/NINDS) [C] Sent: Wednesday, March 12, 2025 10:28 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] autorecon1_norm.mgz not found

External Email - Use Caution Hello, These two logs are from the same subject but with slightly different preprocesses. The initial images are a 90 axial slides (512*512). I also have her images with 30 slides (with 5mm gaps in between). All these got the same error message with freesurfer. she has multiple lesions (but very small size) in the cerebellum and cerebral cortex, and also in the white matter.

I hope these information may be useful.

Thanks Zhen

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 Sent: Wednesday, March 12, 2025 8:09 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [EXTERNAL] Re: [Freesurfer] autorecon1_norm.mgz not found

Can you attach your recon-all.log?

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 Ni, Zhen (NIH/NINDS) [C] Sent: Wednesday, March 12, 2025 7:56 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] autorecon1_norm.mgz not found

External Email - Use Caution Hello, I'm using the command "recon-all -autorecon1 -subjid $SUBJECTNAME". After about 2 hours, there are a few mgz and other files generated in the /mri directory, however, I got an error message:

WARNING: entowm has very low volumes so not using it to edit GA of cortex label

#--------------------------------------

#@# CC Seg Mon Mar 10 19:13:32 EDT 2025

\n seg2cc --s sub-002 \n

ERROR: cannot find /Applications/freesurfer/8.0.0/subjects/sub-002/mri/norm.mgz

Darwin nzs-MacBook-Air.local 23.6.0 Darwin Kernel Version 23.6.0: Fri Jul 5 17:54:20 PDT 2024; root:xnu-10063.141.1~2/RELEASE_X86_64 x86_64

recon-all -s sub-002 exited with ERRORS at Mon Mar 10 19:13:33 EDT 2025

I wonder if you have any idea to fix the problem.

Zhen

CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.

CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.

Can you also add '-gcareg' to your command line?

I'm not sure if any other steps are needed. If that doesn't work, can you run the full recon-all pipeline? Use directive '-all' instead of '-autorecon1'.

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Ni, Zhen (NIH/NINDS) [C] Sent: Wednesday, March 12, 2025 12:56 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] autorecon1_norm.mgz not found

External Email - Use Caution Sorry, I think I attached a wrong log moment ago. Please refer to this one.

Thanks Zhen

From: Ni, Zhen (NIH/NINDS) [C] Sent: Wednesday, March 12, 2025 12:46 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: RE: autorecon1_norm.mgz not found

Thanks a lot. It moved a bit forward but new errors occurred, seems like co-registration to Talairach space?

Zhen

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 Sent: Wednesday, March 12, 2025 11:58 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [EXTERNAL] Re: [Freesurfer] autorecon1_norm.mgz not found

Can you try to add '-canorm' to your 'recon-all -autorecon1' command line?

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 Ni, Zhen (NIH/NINDS) [C] Sent: Wednesday, March 12, 2025 10:28 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] autorecon1_norm.mgz not found

External Email - Use Caution Hello, These two logs are from the same subject but with slightly different preprocesses. The initial images are a 90 axial slides (512*512). I also have her images with 30 slides (with 5mm gaps in between). All these got the same error message with freesurfer. she has multiple lesions (but very small size) in the cerebellum and cerebral cortex, and also in the white matter.

I hope these information may be useful.

Thanks Zhen

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 Sent: Wednesday, March 12, 2025 8:09 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [EXTERNAL] Re: [Freesurfer] autorecon1_norm.mgz not found

Can you attach your recon-all.log?

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 Ni, Zhen (NIH/NINDS) [C] Sent: Wednesday, March 12, 2025 7:56 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] autorecon1_norm.mgz not found

External Email - Use Caution Hello, I'm using the command "recon-all -autorecon1 -subjid $SUBJECTNAME". After about 2 hours, there are a few mgz and other files generated in the /mri directory, however, I got an error message:

WARNING: entowm has very low volumes so not using it to edit GA of cortex label

#--------------------------------------

#@# CC Seg Mon Mar 10 19:13:32 EDT 2025

\n seg2cc --s sub-002 \n

ERROR: cannot find /Applications/freesurfer/8.0.0/subjects/sub-002/mri/norm.mgz

Darwin nzs-MacBook-Air.local 23.6.0 Darwin Kernel Version 23.6.0: Fri Jul 5 17:54:20 PDT 2024; root:xnu-10063.141.1~2/RELEASE_X86_64 x86_64

recon-all -s sub-002 exited with ERRORS at Mon Mar 10 19:13:33 EDT 2025

I wonder if you have any idea to fix the problem.

Zhen

CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.

CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.