[Freesurfer] mri_synthsr with CT images

2023-03-17 Thread Gonzalo Rojas Costa
External Email - Use Caution

Dear Juan:

  I tested mri_synthsr using three different CT images with the threshold
(80 value) that you told me some days ago. The first works ok, but with the
other 2, I got the following error:

developer@developer-VirtualBox:~$ mri_synthseg --i
/home/developer/Documents/OAS31367/sub-OAS31367_sess-d0142_run-01_CT_0_80.nii.gz
--o /home/developer/Documents/OAS31367 --cpu
SynthSeg 2.0
using CPU, hiding all CUDA_VISIBLE_DEVICES
using 1 thread
predicting 1/1
Killed

  What does "Killed" mean? Any log file?

  Sincerely,




Gonzalo Rojas Costa
Department of Radiology
Clínica las Condes
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel: 56-9-97771785
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Re: [Freesurfer] Error When Running Recon-all- "Segmentation Fault"

2023-03-17 Thread Huang, Yujing
Hi Annie,

It looks like you are using an older release - 
freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0.

See compatibility issues discussed in this post:

https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg74552.html

Best,

Yujing


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Annie Cooper
Sent: Friday, March 17, 2023 2:18 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Error When Running Recon-all- "Segmentation Fault"


External Email - Use Caution
Hi there,
I am currently trying to run recon-all using a supercomputer at my university 
and am running into more errors than usual.
When trying to run recon-all from my terminal, I ran into this error message:

[asurite@agave1:~/Desktop/T1_IMAGE]$ recon-all -s ATN001v1 -i 
T1-MPRAGE-8min_Series0301_T1-MPRAGE-8min_20211223085844_301.nii.gz -all

Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0

Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0

INFO: SUBJECTS_DIR is /home/asurite/Desktop/subjects

Actual FREESURFER_HOME /packages/freesurfer-5.0.0

Linux 
agave1.agave.rc.asu.edu
 3.10.0-693.21.1.el7.x86_64 #1 SMP Wed Mar 7 19:03:37 UTC 2018 x86_64 x86_64 
x86_64 GNU/Linux

/home/asurite/Desktop/subjects/ATN001v1

 mri_convert 
/home/asurite/Desktop/T1_IMAGE/T1-MPRAGE-8min_Series0301_T1-MPRAGE-8min_20211223085844_301.nii.gz
 /home/asurite/Desktop/subjects/ATN001v1/mri/orig/001.mgz

mri_convert 
/home/asurite/Desktop/T1_IMAGE/T1-MPRAGE-8min_Series0301_T1-MPRAGE-8min_20211223085844_301.nii.gz
 /home/asurite/Desktop/subjects/ATN001v1/mri/orig/001.mgz

Segmentation fault

Linux 
agave1.agave.rc.asu.edu
 3.10.0-693.21.1.el7.x86_64 #1 SMP Wed Mar 7 19:03:37 UTC 2018 x86_64 x86_64 
x86_64 GNU/Linux

recon-all -s ATN001v1 exited with ERRORS at Fri Mar 17 10:44:47 MST 2023

Any tips on why I might be receiving a "Segmentation fault" when trying to run 
recon-all? I've tried utilizing the mail archive to find an answer and haven't 
found anything that helped. Thank you!

Best,
Annie
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[Freesurfer] Error When Running Recon-all- "Segmentation Fault"

2023-03-17 Thread Annie Cooper
External Email - Use Caution

Hi there,
I am currently trying to run recon-all using a supercomputer at my
university and am running into more errors than usual.
When trying to run recon-all from my terminal, I ran into this error
message:

[asurite@agave1:~/Desktop/T1_IMAGE]$ recon-all -s ATN001v1 -i
T1-MPRAGE-8min_Series0301_T1-MPRAGE-8min_20211223085844_301.nii.gz -all

Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0

Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0

INFO: SUBJECTS_DIR is /home/asurite/Desktop/subjects

Actual FREESURFER_HOME /packages/freesurfer-5.0.0

Linux agave1.agave.rc.asu.edu 3.10.0-693.21.1.el7.x86_64 #1 SMP Wed Mar 7
19:03:37 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

/home/asurite/Desktop/subjects/ATN001v1

 mri_convert
/home/asurite/Desktop/T1_IMAGE/T1-MPRAGE-8min_Series0301_T1-MPRAGE-8min_20211223085844_301.nii.gz
/home/asurite/Desktop/subjects/ATN001v1/mri/orig/001.mgz

mri_convert
/home/asurite/Desktop/T1_IMAGE/T1-MPRAGE-8min_Series0301_T1-MPRAGE-8min_20211223085844_301.nii.gz
/home/asurite/Desktop/subjects/ATN001v1/mri/orig/001.mgz

Segmentation fault

Linux agave1.agave.rc.asu.edu 3.10.0-693.21.1.el7.x86_64 #1 SMP Wed Mar 7
19:03:37 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s ATN001v1 exited with ERRORS at Fri Mar 17 10:44:47 MST 2023

Any tips on why I might be receiving a "Segmentation fault" when trying to
run recon-all? I've tried utilizing the mail archive to find an answer and
haven't found anything that helped. Thank you!

Best,
Annie
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[Freesurfer] head in a bad position in scanner

2023-03-17 Thread Aaron Tanenbaum
External Email - Use Caution

We acquired some data this morning where the participant's head was in an
unusual orientation. The participant has cervical dystonia. I have
processed data like this before and freesurfer always fails. I am assuming
Freesurfer is unable to register the image.  I have not even run this image
through freesurfer yet. Is there a way to deal with this without altering
the image?
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[Freesurfer] Job posting: Research assistant Z-lab @OSU

2023-03-17 Thread Saygin, Zeynep M.
External Email - Use Caution

Dear all,
I'm hiring a full-time research assistant. Please see below!


The Ohio State University, Dept. of Psychology – Dr. Zeynep Saygin’s Lab, to 
assist with neuroscience research on the functional and structural architecture 
of the human brain in adults and children.  The Z-lab studies the functional 
and structural differentiation of the human brain across early development and 
adulthood, and the plasticity of the brain in response to disorders and injury 
(see 
zeynepsaygin.com
 for recent publications).


Please apply here:

https://secure-web.cisco.com/1sWjkkfC4POCU7eVOCKoEI1dfwLHm5ZVKy_C14DQGA1Q3rJwqYCNLVHpB0-0c5KdENj-utMsiQGytOl2ugcoX0fAmVMFvox6n10kJSmAF3gUZx0ZAqbfhzfjwgr_AM6y6KbKl9JTA5k4YkT9kjXpqXyXmfrLUToOWWNBxoQb6Ng3Jmj8dhCGxOo11OOMfkc_swV9VFxbOglOFR5NxIxarjMeGH_KfuwVd-M8mPUG0w6mrCUY0deaI_QNe6Jos6P0gW7IcudL2qcugfABYnU21jPlTkkYBi1mHKrM1oH-Qxi4Wq8j_1f2ZwgnL9ctGVbijI1zeQw3Oa_k35dRFcrINDA/https%3A%2F%2Fosu.wd1.myworkdayjobs.com%2FOSUCareers%2Fjob%2FColumbus-Campus%2FResearch-Senior-Technician_R73458-1


Review of applications will continue on a rolling basis until the position is 
filled. The target start date is July 2023 but this is negotiable. This is a 
1-year position with the possibility for renewal contingent on performance and 
funding.



The Project Coordinator will oversee and execute data collection for ongoing 
studies in the lab, hire and oversee undergraduate research assistants, manage 
administrative study materials, and helping analyze study data. This position 
is an excellent opportunity for an enthusiastic individual looking to gain 
research experience on related topics (development, cognitive neuroscience, 
psychology, brain injury) before applying to graduate or medical school.



Responsibilities will include:

  *   Overseeing and executing recruitment and retention of infant, child, and 
adult participants
  *   Overseeing and executing data collection (including neuroimaging & 
behavioral assessments & experiments)
  *   Managing lab materials, including: preparing and managing IRB protocols, 
study protocols, training materials; conducting literature reviews; maintaining 
and supporting website and github pages (including updating with datasets and 
analysis scripts/software).
  *   Working with lab members and collaborators to collect and analyze data; 
hiring and overseeing undergraduate research assistants; training new staff 
members on study protocols; organizing progress meetings; cultivating diverse, 
inclusive, and collaborative workplace.
  *   Attending and presenting at research conferences and co-authoring 
manuscripts.

REQUIRED QUALIFICATIONS:

  *   Bachelor's degree (preferably in psychology, neuroscience, cognitive 
science or related field).
  *   Exceptional interpersonal skills and cultural sensitivity for interacting 
with infants, children, and parents from diverse backgrounds.
  *   Candidate must be able to travel for recruitment, meetings, and data 
collection.
  *   Strong organizational and time management skills, motivation to learn new 
skills, and determination to achieve study enrollment targets.



PREFERRED QUALIFICATIONS:

  *   Previous experience interacting with infants or families from diverse 
backgrounds.
  *   Previous research experience (working with human subjects data; 
behavioral or neuroimaging) and/or coding experience (e.g., MATLAB, Python, 
shell scripting).



Interested individuals should contact saygi...@osu.edu with a CV and names of 
2-3 references.


--
Zeynep M. Saygin, Ph.D.
Assistant Professor of Psychology
The Ohio State University
205 Psychology Bldg. 1835 Neil Ave
Columbus, OH 43210
zlab
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Re: [Freesurfer] Transparency issue in FreeView

2023-03-17 Thread Wighton, Paul
Great, thanks R!

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of fsbuild 

Sent: Friday, March 17, 2023 1:00 AM
To: freesurfer@nmr.mgh.harvard.edu
Cc: anthony.gala...@nih.gov
Subject: Re: [Freesurfer] Transparency issue in FreeView

External Email - Use Caution

My guess is remote rendering via ssh uses a different set of drivers compared 
to rendering done sitting at the console of the CentOS8 machine.  Usually it is 
remote rendering that is broken more often than not because of differences in 
OpenGL drivers or the graphics card on the machine ssh’ing in receiving X11 
forwarding, e.g. OpenGL trying to work in headless mode.

Either way, you can try setting  LIBGL_DEBUG=verbose to see what’s reported 
and/or different between the local and remote environments.
$ export LIBGL_DEBUG=verbose
… or just on the command line when you run the command …
$ LIBGL_DEBUG=verbose  freeview 

Graphics card drivers from vendors like NVIDIA can modify system libGL 
libraries and some people have found that for (remote) rendering to work those 
drivers need to be uninstalled.  I have not heard of that adversely affecting 
rending from the host machine’s console however.  But you might want to check 
you have the latest OpenGL drivers installed on the CentOS8 machine, e.g., 
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://www.linuxquestions.org/questions/linux-software-2/how-can-i-check-if-i-have-installed-opengl-on-my-centos-server-4175583741/

This article is more geared towards remote debugging, but might give you some 
insight, https://www.scm.com/doc/Installation/Remote_GUI.html

- R.

On Mar 16, 2023, at 19:19, Wighton, Paul  wrote:

Hi All,

I have a colleague who is trying to use FreeView on Red Hat Enterprise Linux 8, 
and there seems to be a transparency issue where windows behind the viewer are 
being displayed.  See attached screenshot.

This only happens when using FreeView on the desktop.  When using freeview over 
`ssh -X` everything looks good.

Any ideas, or debugging info we could pass along?

Thanks,

-Paul___
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[Freesurfer] Help passcode

2023-03-17 Thread Isra RM
External Email - Use Caution

Hello FreeSurfer,
Where can I find a passcode to unzip the VW
file FS_7_2_0_ubuntu_18_04_06.ova.7z I have just downloaded?
Thanks
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Re: [Freesurfer] mri_synthseg ERROR 'std::bad_alloc'

2023-03-17 Thread fsbuild
External Email - Use Caution

Various postings reference it’s related to the application failing to obtain 
memory.  That does not necessarily mean virtual/physical memory is 
exhausted, but rather the memory management scheme used by the application is 
unable to provide a big enough chunk of memory to be allocated in time for use. 
  Some people suggest monitoring the process, e.g., “ps” command, to look 
at either system memory usage or GPU memory usage in the case of using GPU, 
e.g., NVIDIA command “nvidia-smi” while things are running.  One post 
seems to indicate memory is not physically underrun from a graph of memory 
consumption when the error occurs.

- R.
https://secure-web.cisco.com/1lQSEMDdo1ulf5k6B_UJrBUyBSDW206IbKCm6lAKEaSvRWBvvtCIkwcvvbT4vQmnUGPqI1YwqFo_B--SqgvbcRZuIszhkH6bV01SbhZv0YTrKgH8Qi4wLgEz7zCHCEZcaaKrUUhpGkgSw7dKp4tVASrUBWkuGngCsKvZieru2WwqG_JQRHqn4sO6seG37pb-olykWntGAHoiOjxfhIERmq9uB24dxIGUE_3R2uqs47rtg1F1YZ2HmsOUdvKP7IXyTGzB0pHuYl4a7YaxoAIO6-Z4tam_T7IBwlZWSG9K_9WTjXu0yN7eA3uo3ME3aNsRX/https%3A%2F%2Fgithub.com%2Ftensorflow%2Ftensorflow%2Fissues%2F9487
https://secure-web.cisco.com/167ERnV8gwZmPGQneh48CAQ4nbl0Jx8bfLYgpOKuUmdUIeNOa-RicfdvesRINPxn8Vkfixw62ZIvIqhHEUhjFPUJPY_EsK4lR3cBata4EjKap-MQUFDoFBDI6WMMhVRnT9NJDH2g15FGKN4Er7H-HgJc14t-TkWX_Txf3BLYm7eIrQK0sv-1jyJa52_-p4StPspsEC6Xc_LP6h6IqHj_h4sf7VUL5d7L16AsnZTDbSx-3SRKutDRKIUvRwZuMOora8Qb3WEBeKTg5qjDJ3C5IVvCL4weyE8IGkxeML9hxvrzLzxtx5AF_qtiig6adEb2w/https%3A%2F%2Fgithub.com%2Fawentzonline%2Fimage-analogies%2Fissues%2F28
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https://secure-web.cisco.com/1CxLDSwk7AAkcqahJRoHD9KM8_J8VZB04y-dz5oD-weCfrJ_k5kxqmy_qavLLoXSaEVTSoezeYqh8d7Wix6wBpHXWLYZ1dkp7WBO_gbVxks7Xia_yMgievHym3MTkQjOltUbVDqPOG83YO0RMar-okoo9lcR_DFlRhb4b5hyoEBf9UMzYNcnq--riVPNzL8RtLHQG1NIy4l4kz4YNmDF2NLioa6NjU-n3tJ2c90uwQbOETZxVcfn_9lPJs5p-DAUsbr-rAEUpFAnbIJ-avnuYVM38v1e6p8z_BP-E6h2kyPBmGrn0flK-2Eg8B8IY0v4H/https%3A%2F%2Fstackoverflow.com%2Fquestions%2F58450942%2Fhow-to-solve-what-stdbad-alloc-error-with-cleverhans-on-gpu

On Mar 17, 2023, at 05:37, Steinbacher Jürgen  
wrote:External Email - Use 
CautionDear Freesurfer 
team, I have now fs 7.3.2 installed on ubuntu 22.04.2 on a 8 core i7-4790 
CPU (supporting AVX instructions)  with 28.0Gb  fs works fine 
now,  but I had a patient where the segmentation did not work  well, 
so I wanted to try  mri_synthseg.I have tensorflow 2.4.1 (python 3.7.13) 
installed and running on a gtx 1650 gpu. So running mri_synthseg first time did 
not prompt to install it again.When I run mri_synthseg  it tells 
predicting 1/1 and after about 25 sec it terminates telling: „terminate called 
after throwing an instance of ‚std::bad_alloc‘“  what(): 
std::bad_alloc  Abort(core dumped)?? (memory problem??)It 
terminates independent of using other patients, or gpu – cpu or more or less 
cores..I also tried „synthstrip“ to test the tensorflow installation working 
with fs and this works well!Do you have an idea, & 
solution??? Greetings 
Jürgen ___Freesurfer mailing 
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[Freesurfer] mri_synthseg ERROR 'std::bad_alloc'

2023-03-17 Thread Steinbacher Jürgen
External Email - Use Caution

Dear Freesurfer team,

I have now fs 7.3.2 installed on ubuntu 22.04.2 on a 8 core i7-4790 CPU 
(supporting AVX instructions)  with 28.0Gb  fs works fine now,  but I had a 
patient where the segmentation did not work  well, so I wanted to try  
mri_synthseg.
I have tensorflow 2.4.1 (python 3.7.13) installed and running on a gtx 1650 
gpu. So running mri_synthseg first time did not prompt to install it again.
When I run mri_synthseg  it tells predicting 1/1 and after about 25 sec it 
terminates telling: "terminate called after throwing an instance of 
'std::bad_alloc'"  what(): std::bad_alloc  Abort(core dumped)
?? (memory problem??)
It terminates independent of using other patients, or gpu - cpu or more or less 
cores..
I also tried "synthstrip" to test the tensorflow installation working with fs 
and this works well!
Do you have an idea, & solution???
Greetings Jürgen

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