subject:"\[Freesurfer\] mris

Re: [Freesurfer] mris_preproc error: cannot allocate memory

2023-08-01 Thread Huang, Yujing

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It looks like it is corrupted.

Can you try ‘mris_info 
/media/sf_T1/freesurfer_results/HCA9679715_V1_MR/surf/lh.sphere.reg’?  I think 
it probably will fail the same way.

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of MANSSOUR Wassima
Sent: Tuesday, August 1, 2023 4:49 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] mris_preproc error: cannot allocate memory


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Hello M.Yujing,

I’m using the HCP-A cohort (Human Connectome Project – Aging), where the 
structural MRIs were preprocessed. So, I’m working directly with the FreeSurfer 
outputs provided.
Is it possible that the lh.sphere.reg of this subject is corrupted?

Thank you,

Wassima

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
Sent: Tuesday, August 1, 2023 10:14 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] mris_preproc error: cannot allocate memory


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This is the error from log:

Reading source surface reg 
/media/sf_T1/freesurfer_results/HCA9679715_V1_MR/surf/lh.sphere.reg
error: Cannot allocate memory
error: TAGskip: tag=116798, failed to calloc 116799 bytes!

The TAG number looks wrong. I’m wondering how you created 
/media/sf_T1/freesurfer_results/HCA9679715_V1_MR/surf/lh.sphere.reg?

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 MANSSOUR Wassima
Sent: Tuesday, August 1, 2023 2:52 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] mris_preproc error: cannot allocate memory


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Hello M.Douglas,

I’m running the following command: mris_preproc --fsgd FSGD2.fsgd --target 
fsaverage --hemi lh --meas thickness --out lh.uci_nuci.thikness.00.mgh.
Please find attached the log file.

Thank you,

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
Sent: Tuesday, August 1, 2023 3:52 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mris_preproc error: cannot allocate memory


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That should be enough RAM. What is your command line? Can you send the log file?
On 8/1/2023 7:52 AM, MANSSOUR Wassima wrote:

External Email - Use Caution
Hello FreeSurfer Developers,

I'm conducting the Surface Based Group Analysis explained on the tutoriel 
(MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://secure-web.cisco.com/1EYOnYsnqtH8mgegInJXTbyCBVBFMmjDFwDrh0Tp_xV4VKbUepWhpjl241CG6gyi8quceHen_qwmeBVVtEDGwKzWWYn41rWlLra4BInEk1jSo1P14Oblp-Tq3rnLm1M3DJHnUjxEalyU-obwMc1KLYHMEFQN6EvE-YDPz08F97q4WaZ2kCCkSNxomGLfslH6j_uuvOtnPFvc3R9OK45qYrqyjwW3Qov2JLdvwIZSUf-rglcvHULyNAUxoiXv4RS-W/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysisV6.0<https://secure-web.cisco.com/1_YynvwS-dkAnt9HfkAib_JfSy9UZxarfHbzK2t54zb7qCQJxUZZt_Vc0ZIEwqIkD7F27OVUNpLeyNZde-aYgOenPT2_ckqjlYPJrCvQk1NftmX9tjie43cnqsBx4LdigIwZDM-b4v8G_ni6Ejmxmt5RrR5FvxVRnilvDjf241utdgvvHDoBVhnmkoaKzRHeBB_hDZqH0hV_cWvaAaHUtdkqONm6sm-wQzdoTTjg5gjgl6LoFmUCN0VW3p1RPOneDtlJhlP40jjialruPa8d6ByiaS7LGnKxKzxk8PWDLZwBXMiOa1ROzLXIKyVPcBy17YNLC1ex_wY2_4xHhz2cm3Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysisV6.0>)
but I keep getting the error: "Cannot allocate memory" while running the 
mris_preproc  command.

I'm using the data of 355 subjects stored on an external hard drive, and a pc 
of 23G RAM, but it stops at the 334 subject.
I've already tried with a windows and mac of 16G RAM and got the error, so 
moved to the other one but still getting the same issue.
Does anyone have any thoughts on how to trouble-shoot this? or any other 
alternative solution to run the mris_preproc on all the subjects?

FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0
Platforme: Debian 3.16.7


Thank you for your help,
--
Wassima MANSSOUR
Master Student at INSEA Rabat
M2SI - Information Systems & Intelligent Systems
IMRB intern-France
wmanss...@insea.ac.ma<mailto:wmanss...@insea.ac.ma>
wassima.manss...@u-pec.fr<mailto:wassima.manss...@u-pec.fr>



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Re: [Freesurfer] mris_preproc error: cannot allocate memory

2023-08-01 Thread Huang, Yujing

External Email - Use Caution

This is the error from log:

Reading source surface reg 
/media/sf_T1/freesurfer_results/HCA9679715_V1_MR/surf/lh.sphere.reg
error: Cannot allocate memory
error: TAGskip: tag=116798, failed to calloc 116799 bytes!

The TAG number looks wrong. I’m wondering how you created 
/media/sf_T1/freesurfer_results/HCA9679715_V1_MR/surf/lh.sphere.reg?

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of MANSSOUR Wassima
Sent: Tuesday, August 1, 2023 2:52 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] mris_preproc error: cannot allocate memory


External Email - Use Caution
Hello M.Douglas,

I’m running the following command: mris_preproc --fsgd FSGD2.fsgd --target 
fsaverage --hemi lh --meas thickness --out lh.uci_nuci.thikness.00.mgh.
Please find attached the log file.

Thank you,

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
Sent: Tuesday, August 1, 2023 3:52 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mris_preproc error: cannot allocate memory


External Email - Use Caution
That should be enough RAM. What is your command line? Can you send the log file?
On 8/1/2023 7:52 AM, MANSSOUR Wassima wrote:

External Email - Use Caution
Hello FreeSurfer Developers,

I'm conducting the Surface Based Group Analysis explained on the tutoriel 
(MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://secure-web.cisco.com/1eTzROZW5NnwIZ7dOLDlWK54X1VqXBxL4yRUMo2AvE8lWZDHregJu1Xv4OFYXUrt84KywWWnXfnpSBrJoRi0g1ErcX_-bcIjZO9uZYd_elpUIf2vm437b3_NvPbrCSbJ7cQNzlddT2f4Rxgy8BEYfxs0eS_Xi97NqySPi7mfJj14_zOJRr52Jb4wtgzGAsou6TP3kbkYCZenE8Cix-DHpjtGAmVRf3D1hcxw6wbU6l1TgsMoLA6OcFKYoy-2lK-8M/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysisV6.0<https://secure-web.cisco.com/1_YynvwS-dkAnt9HfkAib_JfSy9UZxarfHbzK2t54zb7qCQJxUZZt_Vc0ZIEwqIkD7F27OVUNpLeyNZde-aYgOenPT2_ckqjlYPJrCvQk1NftmX9tjie43cnqsBx4LdigIwZDM-b4v8G_ni6Ejmxmt5RrR5FvxVRnilvDjf241utdgvvHDoBVhnmkoaKzRHeBB_hDZqH0hV_cWvaAaHUtdkqONm6sm-wQzdoTTjg5gjgl6LoFmUCN0VW3p1RPOneDtlJhlP40jjialruPa8d6ByiaS7LGnKxKzxk8PWDLZwBXMiOa1ROzLXIKyVPcBy17YNLC1ex_wY2_4xHhz2cm3Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysisV6.0>)
but I keep getting the error: "Cannot allocate memory" while running the 
mris_preproc  command.

I'm using the data of 355 subjects stored on an external hard drive, and a pc 
of 23G RAM, but it stops at the 334 subject.
I've already tried with a windows and mac of 16G RAM and got the error, so 
moved to the other one but still getting the same issue.
Does anyone have any thoughts on how to trouble-shoot this? or any other 
alternative solution to run the mris_preproc on all the subjects?

FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0
Platforme: Debian 3.16.7


Thank you for your help,
--
Wassima MANSSOUR
Master Student at INSEA Rabat
M2SI - Information Systems & Intelligent Systems
IMRB intern-France
wmanss...@insea.ac.ma<mailto:wmanss...@insea.ac.ma>
wassima.manss...@u-pec.fr<mailto:wassima.manss...@u-pec.fr>



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https://secure-web.cisco.com/1w9QkqXlTuUI7DQ718kEQT4K_LS3XkOhnfRt91OTYyIv5ffVSmS0JMjYjZ5K8P6sUYyrt8FtGAHBhmckCJ690cADVWkqrqTaYQpIdZvEgTMhP7eT-qUzMWYnv_xotpCTZZuVLpBZySdHBPR1-6A8OkPAR-XpHKdXnpeauL6XXPNAbG7R3UIUYqnQKLSna0JgMPlXg5twyLbCXrNyyVHjvc1V-GbiwECutyqvAvFUZwkGxlGI_MwYlvFCVDQx0v-WO/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<https://secure-web.cisco.com/1XWcS2l5SicrnDgN4gbTQZt1Nd_cVEWf0etLF5oIpmmmKJs9gwOJvEqy1EbB2fYqaB_TSaMqF-yvzSuh7OGdmU9slvknwXY5PA3sx0ke-37UuFEUPfd75knhtpdzf324gWx7BrDZ711CANLz_duLhFUfVITkflAX9O2Rxd7JcdS2Gk5Le-koV7gjM6kt8ux9WnYzXh7nh0wk8nbIFeeHC9zzXLAAtaA5ThMo8-FltWXsHSj0RRqEtAeJYLDH8lXQsIPHgKs7NpLE_kyAXSe3DqA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>

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Re: [Freesurfer] mris_preproc error: cannot allocate memory

2023-08-01 Thread Douglas N. Greve

   External Email - Use Caution

That should be enough RAM. What is your command line? Can you send the 
log file?


On 8/1/2023 7:52 AM, MANSSOUR Wassima wrote:


External Email - Use Caution

Hello FreeSurfer Developers,


I'm conducting the *Surface Based Group Analysis* explained on the 
tutoriel (*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://secure-web.cisco.com/1SYbVLlm03vwDvlNfoqpcp8WG_cRgKP3SgXW6SVF_rrwzLXF4U4qzBWw1moNMisSlbq8gZRJodQ63vDzMtYf9omXiXJptq-mdifK-tHaszmvGUE72bceDbUBiYtjsn0Y1Zkdx2d5dXQ8rqgsKPRg8TVyu4OKwq67hDUWMlG6LZy1MAYcN-wO3vAnOzJYVo89fYIjMRA0MaLaafO6Qzpeht14gEIqrSP772fHBq7TKCXmhfX5wVWa1hv1x0DZ6sYkzcTJDVbGo-2v7w-fiHshrig/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysisV6.0 
)


but I keep getting the error: *"Cannot allocate memory"*while running 
the /mris_preproc ///command.



I'm using the data of 355 subjects stored on an external hard drive, 
and a pc of 23G RAM, but it stops at the 334 subject.


I've already tried with a windows and mac of 16G RAM and got the 
error, so moved to the other one but still getting the same issue.


Does anyone have any thoughts on how to trouble-shoot this? or any 
other alternative solution to run the /mris_preproc /on all the subjects?



/FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0
/

/Platforme: Debian 3.16.7/



Thank you for your help,

--

*Wassima MANSSOUR*

Master Student at INSEA Rabat

M2SI - Information Systems & Intelligent Systems

IMRB intern-France

wmanss...@insea.ac.ma

wassima.manss...@u-pec.fr__




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The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
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Re: [Freesurfer] mris_preproc read error

2022-06-14 Thread Joanna L Eckhardt

External Email - Use Caution

Dear FS team,

There was indeed a problem with recon-all and I reran the subject and did what 
you said, and now there is no mris_preproc read error. Thank you very much for 
your assistance!

All my best,
Joanna


--

Joanna Eckhardt

Neurosciences Graduate Program

University of California, San Diego


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Thursday, June 9, 2022 1:27 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] mris_preproc read error

It looks like something might have gone wrong during recon-all for that 
subject. Does recon-all.log say it completed successfully? Try deleting the 
lh.sphere.reg (and any other file with 0 size) and running recon-all 
-autorecon2-surfonly -autorecon3, then do -qcache

On 6/7/2022 12:41 PM, Joanna L Eckhardt wrote:

External Email - Use Caution

Dear FS team,

I am emailing to check in on the status of this issue. Any insights on how to 
move forward with this error? I can try rerunning this subject in the meantime 
to see if that fixes the problem.

Thank you very much your assistance!

Best wishes,
Joanna


--

Joanna Eckhardt

Neurosciences Graduate Program

University of California, San Diego


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Joanna L Eckhardt 
<mailto:jeckha...@health.ucsd.edu>
Sent: Friday, June 3, 2022 10:37 AM
To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mris_preproc read error


External Email - Use Caution

Dear FreeSurfer team,

I reran -qcache for sub-101 (also, I had specified -qcache processing for all 
subjects during initial recon-all so it should have already occurred), and it 
exited with errors. Below is the output from the -qcache rerun, with the error 
being:

ERROR: reading 
/home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/surf/lh.sphere.reg
Read 0 bytes, expected 1
error: No such file or directory
error: mri_surf2surf: could not read surface 
/home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/surf/lh.sphere.reg
Command exited with non-zero status 1

Let me know if you have any insights, or if I need to rerun the recon-all for 
this subject.

Thank you for your assistance!
Joanna


developer@developer-VirtualBox:~/FreeSurfer/osg-outputs/cannabis-BL$ recon-all 
-s sub-101 -qcache
INFO: FreeSurfer build stamps do not match
Subject Stamp:
Current Stamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
INFO: SUBJECTS_DIR is /home/developer/FreeSurfer/osg-outputs/cannabis-BL
Actual FREESURFER_HOME /usr/local/freesurfer/7.2.0
-rw-rw-r-- 1 developer developer 35431 Jun  3 13:28 
/home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/scripts/recon-all.log
Linux developer-VirtualBox 5.4.0-113-generic #127~18.04.1-Ubuntu SMP Wed May 18 
15:40:23 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
~/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri/transforms 
~/FreeSurfer/osg-outputs/cannabis-BL/sub-101
~/FreeSurfer/osg-outputs/cannabis-BL/sub-101
#@# white curv lh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv
   Update not needed
#@# white area lh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --area-map ../surf/lh.white ../surf/lh.area
   Update not needed
#@# pial curv lh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial
   Update not needed
#@# pial area lh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial
   Update not needed
#@# thickness lh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 
../surf/lh.thickness
   Update not needed
#@# area and vertex vol lh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 
../surf/lh.thickness
   Update not needed
#@# white curv rh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv
   Update not needed
#@# white area rh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --area-map ../surf/rh.white ../surf/rh.area
   Update not needed
#@# pial curv rh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-out

Re: [Freesurfer] mris_preproc read error

2022-06-09 Thread Douglas N. Greve

It looks like something might have gone wrong during recon-all for that 
subject. Does recon-all.log say it completed successfully? Try deleting 
the lh.sphere.reg (and any other file with 0 size) and running recon-all 
-autorecon2-surfonly -autorecon3, then do -qcache


On 6/7/2022 12:41 PM, Joanna L Eckhardt wrote:


External Email - Use Caution

Dear FS team,

I am emailing to check in on the status of this issue. Any insights on 
how to move forward with this error? I can try rerunning this subject 
in the meantime to see if that fixes the problem.


Thank you very much your assistance!

Best wishes,
Joanna

*--*

*Joanna Eckhardt***

Neurosciences Graduate Program

University of California, San Diego


*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Joanna L 
Eckhardt 

*Sent:* Friday, June 3, 2022 10:37 AM
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] mris_preproc read error

External Email - Use Caution

Dear FreeSurfer team,

I reran -qcache for sub-101 (also, I had specified -qcache processing 
for all subjects during initial recon-all so it /should/ have already 
occurred), and it exited with errors. Below is the output from the 
-qcache rerun, with the error being:


ERROR: reading 
/home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/surf/lh.sphere.reg

Read 0 bytes, expected 1
error: No such file or directory
error: mri_surf2surf: could not read surface 
/home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/surf/lh.sphere.reg

Command exited with non-zero status 1

Let me know if you have any insights, or if I need to rerun the 
recon-all for this subject.


Thank you for your assistance!
Joanna

*developer@developer-VirtualBox*:*~/FreeSurfer/osg-outputs/cannabis-BL*$ 
recon-all -s sub-101 -qcache
INFO: FreeSurfer build stamps do not match
Subject Stamp:
Current Stamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
INFO: SUBJECTS_DIR is /home/developer/FreeSurfer/osg-outputs/cannabis-BL
Actual FREESURFER_HOME /usr/local/freesurfer/7.2.0
-rw-rw-r-- 1 developer developer 35431 Jun  3 13:28 
/home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/scripts/recon-all.log
Linux developer-VirtualBox 5.4.0-113-generic #127~18.04.1-Ubuntu SMP Wed May 18 
15:40:23 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
~/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri/transforms 
~/FreeSurfer/osg-outputs/cannabis-BL/sub-101
~/FreeSurfer/osg-outputs/cannabis-BL/sub-101
#@# white curv lh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv
    Update not needed
#@# white area lh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --area-map ../surf/lh.white ../surf/lh.area
    Update not needed
#@# pial curv lh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial
    Update not needed
#@# pial area lh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial
    Update not needed
#@# thickness lh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 
../surf/lh.thickness
    Update not needed
#@# area and vertex vol lh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 
../surf/lh.thickness
    Update not needed
#@# white curv rh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv
    Update not needed
#@# white area rh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --area-map ../surf/rh.white ../surf/rh.area
    Update not needed
#@# pial curv rh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial
    Update not needed
#@# pial area rh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial
    Update not needed
#@# thickness rh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 
../surf/rh.thickness
    Update not needed
#@# area and vertex vol rh Fri Jun  3 13:29:48 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --thickness ../surf

Re: [Freesurfer] mris_preproc read error

2022-06-07 Thread Joanna L Eckhardt

External Email - Use Caution

Dear FS team,

I am emailing to check in on the status of this issue. Any insights on how to 
move forward with this error? I can try rerunning this subject in the meantime 
to see if that fixes the problem.

Thank you very much your assistance!

Best wishes,
Joanna


--

Joanna Eckhardt

Neurosciences Graduate Program

University of California, San Diego


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Joanna L Eckhardt 

Sent: Friday, June 3, 2022 10:37 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] mris_preproc read error


External Email - Use Caution

Dear FreeSurfer team,

I reran -qcache for sub-101 (also, I had specified -qcache processing for all 
subjects during initial recon-all so it should have already occurred), and it 
exited with errors. Below is the output from the -qcache rerun, with the error 
being:

ERROR: reading 
/home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/surf/lh.sphere.reg
Read 0 bytes, expected 1
error: No such file or directory
error: mri_surf2surf: could not read surface 
/home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/surf/lh.sphere.reg
Command exited with non-zero status 1

Let me know if you have any insights, or if I need to rerun the recon-all for 
this subject.

Thank you for your assistance!
Joanna


developer@developer-VirtualBox:~/FreeSurfer/osg-outputs/cannabis-BL$ recon-all 
-s sub-101 -qcache
INFO: FreeSurfer build stamps do not match
Subject Stamp:
Current Stamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
INFO: SUBJECTS_DIR is /home/developer/FreeSurfer/osg-outputs/cannabis-BL
Actual FREESURFER_HOME /usr/local/freesurfer/7.2.0
-rw-rw-r-- 1 developer developer 35431 Jun  3 13:28 
/home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/scripts/recon-all.log
Linux developer-VirtualBox 5.4.0-113-generic #127~18.04.1-Ubuntu SMP Wed May 18 
15:40:23 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
~/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri/transforms 
~/FreeSurfer/osg-outputs/cannabis-BL/sub-101
~/FreeSurfer/osg-outputs/cannabis-BL/sub-101
#@# white curv lh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv
   Update not needed
#@# white area lh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --area-map ../surf/lh.white ../surf/lh.area
   Update not needed
#@# pial curv lh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial
   Update not needed
#@# pial area lh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial
   Update not needed
#@# thickness lh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 
../surf/lh.thickness
   Update not needed
#@# area and vertex vol lh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 
../surf/lh.thickness
   Update not needed
#@# white curv rh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv
   Update not needed
#@# white area rh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --area-map ../surf/rh.white ../surf/rh.area
   Update not needed
#@# pial curv rh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial
   Update not needed
#@# pial area rh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial
   Update not needed
#@# thickness rh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 
../surf/rh.thickness
   Update not needed
#@# area and vertex vol rh Fri Jun  3 13:29:48 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 
../surf/rh.thickness
   Update not needed
#
#@# Qdec Cache preproc lh thickness fsaverage Fri Jun  3 13:29:48 EDT 2022
/home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/surf

 mris_preproc --s sub-101 --hemi lh --meas thickness --target fsaverage --out 
lh.thickness.fsaverage.mgh

nsubjects = 1
tmpdir

Re: [Freesurfer] mris_preproc read error

2022-06-03 Thread Joanna L Eckhardt

-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
tmpdir is ./tmp.mris_preproc.3286
Src lh sphere.reg
Trg lh sphere.reg




---
#@# 1/1 sub-101 Fri Jun  3 13:29:48 EDT 2022 --
---
mri_surf2surf --srcsubject sub-101 --srchemi lh --srcsurfreg sphere.reg 
--trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval 
./tmp.mris_preproc.3286/sub-101.1.mgh --sval 
/home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/surf/lh.thickness 
--sfmt curv --noreshape --cortex
Source registration surface changed to sphere.reg
Target registration surface changed to sphere.reg

7.2.0

setenv SUBJECTS_DIR /home/developer/FreeSurfer/osg-outputs/cannabis-BL
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/surf
mri_surf2surf --srcsubject sub-101 --srchemi lh --srcsurfreg sphere.reg 
--trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval 
./tmp.mris_preproc.3286/sub-101.1.mgh --sval 
/home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/surf/lh.thickness 
--sfmt curv --noreshape --cortex

sysname  Linux
hostname developer-VirtualBox
machine  x86_64
user developer
srcsubject = sub-101
srcval = 
/home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/surf/lh.thickness
srctype= curv
trgsubject = fsaverage
trgval = ./tmp.mris_preproc.3286/sub-101.1.mgh
trgtype=
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
srchemi= lh
trghemi= lh
frame  = 0
fwhm-in= 0
fwhm-out   = 0
label-src  = lh.cortex.label
label-trg  = lh.cortex.label
OKToRevFaceOrder  = 1
UseDualHemi = 0
Reading source surface reg 
/home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/surf/lh.sphere.reg
ERROR: reading 
/home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/surf/lh.sphere.reg
Read 0 bytes, expected 1
error: No such file or directory
error: mri_surf2surf: could not read surface 
/home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/surf/lh.sphere.reg
Command exited with non-zero status 1
@#@FSTIME  2022:06:03:13:29:48 mris_preproc N 10 e 0.09 S 0.01 U 0.07 P 92% M 
6600 F 0 R 7976 W 0 c 69 w 146 I 0 O 8 L 0.00 0.00 0.08
@#@FSLOADPOST 2022:06:03:13:29:48 mris_preproc N 10 0.00 0.00 0.08
Linux developer-VirtualBox 5.4.0-113-generic #127~18.04.1-Ubuntu SMP Wed May 18 
15:40:23 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-101 exited with ERRORS at Fri Jun  3 13:29:48 EDT 2022

For more details, see the log file 
/home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/scripts/recon-all.log
To report a problem, see 
http://secure-web.cisco.com/1-76aEy05df7D8YaI6eF1TTSi7PfbpgqGmxvrpopTG6UzZ7P40sSPn5R3RwkUZE7hFtfctC9AC1-Z2R2HcRYGkbJyzCwRgbUtDBZlQDZNgEL_vfHufyLL6n1XMRKx4KqUpAgoORgGfcE4yPAEUVPM2x5QShNwp5ejbnzr5ljflQjJjfWwexQ9GEyNYdobNhu_LqMgsTROsB_kC_MHGExMsMP4GdSite4jvAV_PC52XJAl6a50hAB-8lGEiofO7qnBqbf4qflLEjoX35haIYRi9_IVHd3GeaE7wIp3IV_Y0tzfo0Y3h6pG1tLi41LQguIrFH4J8U0g1J6SpRdeYlFYpQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting



--

Joanna Eckhardt

Neurosciences Graduate Program

University of California, San Diego


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Friday, June 3, 2022 10:03 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] mris_preproc read error

Try running recon-all -s subject -qcache for that subject

On 6/2/2022 7:55 PM, Joanna L Eckhardt wrote:

External Email - Use Caution

Dear FreeSurfer Help Team,

I am working through the FreeSurfer tutorial on cannabis using Ubuntu VM on 
windows (FS version 7.1.1). I am on the group analysis portion of the tutorial 
attempting to run mris_preproc. However, I am receiving the following error 
upon running the script:


error: No such file or directory
error: 
mghRead(/home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/surf/rh.thickness.fwhm10.fsaverage.mgh,
 -1): read error


I wonder if something has been going wrong with recon-all as I believe it is 
saying that there is an error with one of the outputs in sub-101? Recon-all has 
been running in a suspiciously short time (~5 hours), but I do not know enough 
about the processing steps to know what might be occurring wrong in recon-all 
or in trying to run mris_preproc.

Please let me know if I can send you anything else to provide more information 
on the issue.

Thank you for your time and assistance.

Best wishes,
Joanna



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://secure-web.cisco.com/1HiAV9lBi1iMxMH3MhVMXWab6BUBnO-Q74GyygNnfL784hWo46npOxlilhlB1cAlf9HlIkTFmFnmdtMa6saZmGVJBxTf4g0tEHr_0PraiumQ9Ebb0ndZ6gVZz1KGNhNbuAIN0ROYY-N6qRNeqElt8kWxRyiOaBfweXga642BD-Fe1FskyHsSiwliEgx3JMbr15OiHpR-sWAx5QtN3mxByuAfCOL9qP0O7ZRuUP5GTrF_GR60nZnp4xga_9kABlmOXafCnclYuh1avA_o9VJFo7E_d4-KrnAXJDoEH3Pwt3TirUBhMZM417p2-k93hs8BxPp7aZaK7EHjHyzDhXgHNKQ/https%3A%2F%2Fmail.nmr.mgh.harva

Re: [Freesurfer] mris_preproc read error

2022-06-03 Thread Douglas N. Greve

Try running recon-all -s subject -qcache for that subject

On 6/2/2022 7:55 PM, Joanna L Eckhardt wrote:

External Email - Use Caution

Dear FreeSurfer Help Team,

I am working through the FreeSurfer tutorial on cannabis using Ubuntu
VM on windows (FS version 7.1.1). I am on the group analysis portion
of the tutorial attempting to run mris_preproc. However, I am
receiving the following error upon running the script:

error: No such file or directory
error:
mghRead(/home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/surf/rh.thickness.fwhm10.fsaverage.mgh,
-1): read error
I wonder if something has been going wrong with recon-all as I believe
it is saying that there is an error with one of the outputs in
sub-101? Recon-all has been running in a suspiciously short time (~5
hours), but I do not know enough about the processing steps to know
what might be occurring wrong in recon-all or in trying to run
mris_preproc.

Please let me know if I can send you anything else to provide more
information on the issue.

Thank you for your time and assistance.

Best wishes,
Joanna

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Mass General Brigham
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline
.
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.

[Freesurfer] mris_preproc read error

2022-06-02 Thread Joanna L Eckhardt

External Email - Use Caution

Dear FreeSurfer Help Team,

I am working through the FreeSurfer tutorial on cannabis using Ubuntu VM on
windows (FS version 7.1.1). I am on the group analysis portion of the tutorial
attempting to run mris_preproc. However, I am receiving the following error
upon running the script:

error: No such file or directory
error:
mghRead(/home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/surf/rh.thickness.fwhm10.fsaverage.mgh,
-1): read error

I wonder if something has been going wrong with recon-all as I believe it is
saying that there is an error with one of the outputs in sub-101? Recon-all has
been running in a suspiciously short time (~5 hours), but I do not know enough
about the processing steps to know what might be occurring wrong in recon-all
or in trying to run mris_preproc.

Please let me know if I can send you anything else to provide more information
on the issue.

Thank you for your time and assistance.

Best wishes,
Joanna
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Mass General Brigham
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline
.
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.

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