[Freesurfer] Freesurfer and singularity container (bash script)

2020-07-08 Thread Bahrani, Ahmed A. 
External Email - Use Caution

Hello,



I have a question related to the singularity container to run a bash script 
that includes freesurfer commends.




The issue is

I have built a singularity container and included the freesurfer license in the 
container.



Recalling and executing the script were run successfully as a root user login 
(without any errors), while as a general user (non-root) login, it showed an 
error with nu_correct; however, mri_convert seems to run fine as a step before 
nu_correct. The nu_correct used in the script four times. For the first to 
third nu_correct, it showed a full iteration (50/50) for each one and showed 
the following error:



---Error message---


evaluate_field: posixio.c:210: px_pgin: Assertion `*posp == ((off_t)(-1)) || 
*posp == lseek(nciop->fd, 0, 1)' failed.


nu_evaluate: crashed while running evaluate_field (termination status=134)

nu_correct: crashed while running nu_evaluate (termination status=65280)





Then, at the fourth  nu_correct it stopped after 48 iterations then showed the 
following error:



---Error message---

ncvarput: ncid 4: No space left on device
mivarput1: MINC package entry point
nu_evaluate: crashed while running minccalc (termination status=768)
nu_correct: crashed while running nu_evaluate (termination status=768)





Note: I am using

Linux Redhat 7.9 and the singularity installed using YUM command.

Singularity version 3.6.0



For generating the container, I have used the following:

singularity build -F xxx.sif xxx.def



For running the container, I have used the following:

singularity run -e -C -H /home/Ahmed/aaa/s:/opt/data xxx.sif bash 
/opt/s/s1_WMH.sh





Would you advise please, I want to run the container on other computers, but in 
this case, it will not work.



Thanks,

Ahmed
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] nu_correct error

2020-07-16 Thread Bahrani, Ahmed A. 
External Email - Use Caution

Hello Freesurfer experts,

I have a question related to the singularity container to run a bash script 
that contains a freesurfer's commend "nu_correct".

The singularity container only runs as a root user login and gives error as 
shown below with a general user login.

==

---Error message---
evaluate_field: posixio.c:210: px_pgin: Assertion `*posp == ((off_t)(-1)) || 
*posp == lseek(nciop->fd, 0, 1)' failed.
nu_evaluate: crashed while running evaluate_field (termination status=134)
nu_correct: crashed while running nu_evaluate (termination status=65280)


---Error message---
ncvarput: ncid 4: No space left on device
mivarput1: MINC package entry point
nu_evaluate: crashed while running minccalc (termination status=768)
nu_correct: crashed while running nu_evaluate (termination status=768)


Would you advise, please?

Thanks,
Ahmed
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] nu_correct error {Disarmed}

2020-07-17 Thread Bahrani, Ahmed A. 
External Email - Use Caution

Hi Douglas,

I am using the following:

Linux Redhat version 7.9
Singularity version 3.6.0
Freesurefer version 6.0.0-min (for containers)

I checked all the recon-all.log, and it looks like all of the old reports and I 
could not find where the error report of the freesurefer save from the 
container. I have checked the file output, and it does not have a 
recall-all.log.

Thanks,
Ahmed

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

Sent: Friday, July 17, 2020 10:12 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] nu_correct error

CAUTION: External Sender

What version are you running? Can you send the recon-all.log file?

On 7/16/2020 3:40 PM, Bahrani, Ahmed A. wrote:

External Email - Use Caution

Hello Freesurfer experts,

I have a question related to the singularity container to run a bash script 
that contains a freesurfer's commend "nu_correct".

The singularity container only runs as a root user login and gives error as 
shown below with a general user login.

==

---Error message---
evaluate_field: posixio.c:210: px_pgin: Assertion `*posp == ((off_t)(-1)) || 
*posp == lseek(nciop->fd, 0, 1)' failed.
nu_evaluate: crashed while running evaluate_field (termination status=134)
nu_correct: crashed while running nu_evaluate (termination status=65280)


---Error message---
ncvarput: ncid 4: No space left on device
mivarput1: MINC package entry point
nu_evaluate: crashed while running minccalc (termination status=768)
nu_correct: crashed while running nu_evaluate (termination status=768)


Would you advise, please?

Thanks,
Ahmed



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7Cahmed.bahrani%40uky.edu%7C1beb056d3cbd43038ab808d82a5b9396%7C2b30530b69b64457b818481cb53d42ae%7C0%7C0%7C637305920089095415&sdata=4UHLpStFVSuBTY825%2BGFsYs0yubW13L0Xnf4Fwn5wTA%3D&reserved=0>

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] nu_correct error {Disarmed}

2020-07-23 Thread Bahrani, Ahmed A. 
External Email - Use Caution

Hi Douglas,

For the container, I am using version 6.0.0-min
The freesurfer on my computer is 
freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

Thanks,
Ahmed

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

Sent: Thursday, July 23, 2020 10:31 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] nu_correct error {Disarmed}

CAUTION: External Sender

what version of freesurfer are you running?

On 7/17/2020 2:24 PM, Bahrani, Ahmed A. wrote:

External Email - Use Caution

Hi Douglas,

I am using the following:

Linux Redhat version 7.9
Singularity version 3.6.0
Freesurefer version 6.0.0-min (for containers)

I checked all the recon-all.log, and it looks like all of the old reports and I 
could not find where the error report of the freesurefer save from the 
container. I have checked the file output, and it does not have a 
recall-all.log.

Thanks,
Ahmed

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>
Sent: Friday, July 17, 2020 10:12 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] nu_correct error

CAUTION: External Sender

What version are you running? Can you send the recon-all.log file?

On 7/16/2020 3:40 PM, Bahrani, Ahmed A. wrote:

External Email - Use Caution

Hello Freesurfer experts,

I have a question related to the singularity container to run a bash script 
that contains a freesurfer's commend "nu_correct".

The singularity container only runs as a root user login and gives error as 
shown below with a general user login.

==

---Error message---
evaluate_field: posixio.c:210: px_pgin: Assertion `*posp == ((off_t)(-1)) || 
*posp == lseek(nciop->fd, 0, 1)' failed.
nu_evaluate: crashed while running evaluate_field (termination status=134)
nu_correct: crashed while running nu_evaluate (termination status=65280)


---Error message---
ncvarput: ncid 4: No space left on device
mivarput1: MINC package entry point
nu_evaluate: crashed while running minccalc (termination status=768)
nu_correct: crashed while running nu_evaluate (termination status=768)


Would you advise, please?

Thanks,
Ahmed



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
MailScanner has detected a possible fraud attempt from 
"nam04.safelinks.protection.outlook.com" claiming to be 
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7Cahmed.bahrani%40uky.edu%7C8ccc16ce8337445c523f08d82f154d3b%7C2b30530b69b64457b818481cb53d42ae%7C0%7C0%7C63735843673608&sdata=KOeICSZ7RtGeKiuiTizFIxtpeIvA62lq9R7279nULiQ%3D&reserved=0>




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7Cahmed.bahrani%40uky.edu%7C8ccc16ce8337445c523f08d82f154d3b%7C2b30530b69b64457b818481cb53d42ae%7C0%7C0%7C63735843673608&sdata=KOeICSZ7RtGeKiuiTizFIxtpeIvA62lq9R7279nULiQ%3D&reserved=0>

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] ERROR- input(s) cannot have multiple frames on Recon-all

2021-08-03 Thread Bahrani, Ahmed A. 
External Email - Use Caution

Maybe for post-processing in case you have multi frames, you can merge all of 
them (multi-echo MPRages) and then take the RMS to get one 3D volume.
Ahmed



Ahmed A. Bahrani, Ph.D.,
Sanders-Brown Center on Aging
University of Kentucky




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

Sent: Tuesday, August 3, 2021 9:26 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] ERROR- input(s) cannot have multiple frames on 
Recon-all

CAUTION: External Sender

But do you know why it has multiple frames? We collect multi-echo T1 MPRAGEs 
that will have multiple frames. We then reduce it to one frame by computing the 
RMS across frames (actually the scanner can output a separate RMS series). 
Check to see whether you got an RMS series in their. If not, check with whoever 
collected the data to find out why it has multiple frames.

On 8/2/2021 4:08 PM, Frank Chau wrote:

External Email - Use Caution

Dear Bruce,


I have briefly read a article about multiple frames DICOM. As my understanding, 
it can reduce the amount of data repetition and decreases the time required to 
read and parse DICOM studies.


Yes, I want to use T1-weighted series as input. I have converted a DICOM 
series, which the name of the series is "SAG T1 MPRAGE (INC UPPERCX AS MUCH)",  
to Nifti format. When I input the Nifti T1 file. The multiple frames error 
occurred.


Below are log record:

---

PFCs-MacBook-Pro:T1 PFC$ recon-all -all -i  101.nii -s  101

Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c

Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c

INFO: SUBJECTS_DIR is /Users/PFC/SPM12/T1

Actual FREESURFER_HOME /Applications/freesurfer

Darwin PFCs-MacBook-Pro.local 18.7.0 Darwin Kernel Version 18.7.0: Mon May  3 
20:41:19 PDT 2021; root:xnu-4903.278.68~1/RELEASE_X86_64 x86_64

/Users/PFC/SPM12/T1/101

\n mri_convert /Users/PFC/SPM12/T1/101.nii 
/Users/PFC/SPM12/T1/101/mri/orig/001.mgz \n

mri_convert.bin /Users/PFC/SPM12/T1/101.nii 
/Users/PFC/SPM12/T1/101/mri/orig/001.mgz

 $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $

reading from /Users/PFC/SPM12/T1/101.nii...

TR=7.24, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (0.135649, -0.98975, -0.0446586)

j_ras = (0.0870012, -0.0330015, 0.995661)

k_ras = (0.98693, 0.138946, -0.0816328)

writing to /Users/PFC/SPM12/T1/101/mri/orig/001.mgz...

#

#@# MotionCor Sat Jul 31 18:01:46 HKT 2021

Found 1 runs

/Users/PFC/SPM12/T1/101/mri/orig/001.mgz

Checking for (invalid) multi-frame inputs...

ERROR: input(s) cannot have multiple frames!

/Users/PFC/SPM12/T1/101/mri/orig/001.mgz has 2 frames

Darwin PFCs-MacBook-Pro.local 18.7.0 Darwin Kernel Version 18.7.0: Mon May  3 
20:41:19 PDT 2021; root:xnu-4903.278.68~1/RELEASE_X86_64 x86_64



recon-all -s 101 exited with ERRORS at Sat Jul 31 18:01:48 HKT 2021



For more details, see the log file /Users/PFC/SPM12/T1/101/scripts/recon-all.log

To report a problem, see 
http://secure-web.cisco.com/1ARLUAXWFpvPqkvHHhdhgZfwGYwa-W5rxZHYll2077_CtHzn4d_6hBEuO3ZWQUgAnSWkO3E9qzZZrIqyej4JAVVzPdvW5iOXjGRRWYGeANpAodjc6jG79stflXvsXT0OWMDmWIK1qL8676vNOKc8DrBgJqGtoXjvaIzozG4leYit5HqAj76nrWbnaLM3kJ_XJTNpecG5pBVwUMGmmj98fZpiSF3Wjz68CZkKEF0JxVVxtM22nXj1Rm5azd8Pm4PvLBoKpZq5o2rIY2ExdmXof5g/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

---


Regards


Frank


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Fischl, Bruce 

Sent: 03 August 2021 03:56:31
To: freesurfer@nmr.mgh.harvard.edu
Cc: Jacky Lee; Jacky LEE
Subject: Re: [Freesurfer] ERROR- input(s) cannot have multiple frames on 
Recon-all


Hi Frank



Do you know why there are multiple frames? What kind of MRI acquisition are you

Re: [Freesurfer] recon-all Longitudinal processing (baseline on 1.5T; followup on 3T)

2021-09-02 Thread Bahrani, Ahmed A. 
External Email - Use Caution

Depends on the data analysis that you want to do, the magnetic field strength 
between the two scanners may be a problem that affects the intensity 
distribution of the image overall that lead to under- or over-estimation. See, 
the following paper as an example of longitudinal studies.

https://secure-web.cisco.com/1kuKpr8oUx5I2iJ2rXAjhzY3dtnZ4sGJaDJBmg4nk6qbhDV_eCKt9RquU-RNLJphtIX6pxvzRnrdgDOORmU-Z6OQkvw0dYAcurFAj8i8FJvKIeDLT22bV0e-mVGztS0wy6TTReNp8oU5JHGS1Bya0l00nQxK3YQ8VhxrR4EG1NKNnIzDmmddrW3ibCmdQZrPXJrUiIcdfrIMgTuq9xLS2uiiKHHbuL1zbCLd8mM4r8y5WzfgtIUaA4M1OrOhl87Hhc6oZCbj9iTj9JPc5yYYNsQ/https%3A%2F%2Fdoi.org%2F10.1016%2Fj.jneumeth.2021.109270


Best,
Ahmed,
U of Kentucky






From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Reuter, Martin,Ph.D. 

Sent: Thursday, September 2, 2021 10:54 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] recon-all Longitudinal processing (baseline on 1.5T; 
followup on 3T)

CAUTION: External Sender


Hi Jay,

that would be possible, but we have no experience with such a setting.

The problem is that you will never know if any detected  longitudinal change is 
due to the field strength/scanner/head coil chances or the changes in the way 
it is processed or real anatomical changes.
This is why such a longitudinal study design is problematic. You could look at 
group differences (given that e.g. both groups are acquired/processed the same 
way and under the assumption that there is no interaction with group).
However, the second assumption is probably not true, e.g. motion artefacts 
would be correlated with age and with disease and may affect downstream 
measurements differently across the two scanners.

Best, Martin


> On 31. Aug 2021, at 11:15, Jayachandra Raghava  
> wrote:
>
> Hello Experts,
>
> I am planning to run the longitudinal processing pipeline (Freesurfer version 
> 7.1.1). But I have a few subjects who were scanned on different scanner field 
> strengths at baseline and followup.
>
> For example :
>
> Baseline was scanned on a 1.5T Siemens Scanner
> Followup was scanned on a 3.0T Siemes Trio Scanner
>
> I am planning to
> 1) run the cross-sectional processing for baseline without the 3T flag
> 2) run the cross-sectional processing for followup with the 3T flag
> 3) then generate the unbiased template and longitudinally process all the 
> time points without any special flags.
>
> Is this the best way to process such data? Please let me know if there are 
> any additional flags in the longitudinal processing pipeline to accommodate 
> Scanner/Field strength changes.
>
> Best wishes
> Jay
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1K0bU9j6hOxwCq_4W8YJJk_xZ5VJjWpTdIW0znHa0_V1-g2_H23bcr8C0QJSI1tjBcDvdw1-5A9mCjE-uIp7Y7fkhB3xnYtXWO18o1AWPatmfDmT9unYvF70KQDo2GZQCZ1QWhWDHkGuCJaC2iNJb5yyFwoQI6YWoxKyLMyEQ6HMpHrWoy7j3DAo7Xfxt39hZ9Cj50tDBaTJ9fQC2aWgMFLS2Yy_k-b6uyYFe85AxHuHjeeVRa2c_lKHNrvtilOGGpJevti6dNNgRD8-i2fEB3g/https%3A%2F%2Fnam04.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fmail.nmr.mgh.harvard.edu%252Fmailman%252Flistinfo%252Ffreesurfer%26data%3D04%257C01%257Cahmed.bahrani%2540uky.edu%257Cfa2f980147a142ea79e008d96e21a656%257C2b30530b69b64457b818481cb53d42ae%257C0%257C0%257C637661913079171552%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3DTKY9kKYgLcw0SGjW8iT2wn%252FWumKpE9Q2eXWbKG7YiJc%253D%26reserved%3D0


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1K0bU9j6hOxwCq_4W8YJJk_xZ5VJjWpTdIW0znHa0_V1-g2_H23bcr8C0QJSI1tjBcDvdw1-5A9mCjE-uIp7Y7fkhB3xnYtXWO18o1AWPatmfDmT9unYvF70KQDo2GZQCZ1QWhWDHkGuCJaC2iNJb5yyFwoQI6YWoxKyLMyEQ6HMpHrWoy7j3DAo7Xfxt39hZ9Cj50tDBaTJ9fQC2aWgMFLS2Yy_k-b6uyYFe85AxHuHjeeVRa2c_lKHNrvtilOGGpJevti6dNNgRD8-i2fEB3g/https%3A%2F%2Fnam04.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fmail.nmr.mgh.harvard.edu%252Fmailman%252Flistinfo%252Ffreesurfer%26data%3D04%257C01%257Cahmed.bahrani%2540uky.edu%257Cfa2f980147a142ea79e008d96e21a656%257C2b30530b69b64457b818481cb53d42ae%257C0%257C0%257C637661913079171552%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3DTKY9kKYgLcw0SGjW8iT2wn%252FWumKpE9Q2eXWbKG7YiJc%253D%26reserved%3D0
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://secure-web.cisco.com/1D6wVFsSH8o-bYq7sPe4p33JlC80Jkkr0vaOkpoLTtvi2TnoYSY52BLobqb8r2VSJMAGyC033RK-Xryg95i5BGwqAK5nsvnqj1ETU-EXdG7nhn0FFF-4RG7HA2B6vt2I8dD-_UsXZcUvoWoulTgr5Ux5b2KEMrgoYoM3kTg9913CXlaoNEY7LswuF_NlwgKBBcLl94_Nq18GpSSkqK9OGnur