Re: [Freesurfer] freeview crash

[Fischl, Bruce]

Hi Yusheng
lh.area is not a surface. It is a scalar overlay that can be loaded onto a 
surface. Try loading lh.inflated or lh.white then load area or thickness on top 
of it using file load overlay or curvature
Cheers
Bruce

> On Mar 22, 2021, at 10:30 PM, 超级无敌  wrote:
> 
> Yusheng

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[Freesurfer] Hippocampal Suubfields Segmentation Violation

[WON JONG CHWA]

External Email - Use Caution

Dear FreeSurfer experts,

I am trying to compute hippocampal subfields with
https://secure-web.cisco.com/1f2QJwnqjis6w0KTpz2gk4AyWSMQmrO3JmYGqPPbxpD5JmmDwbJUxZvvKKZq6qt2Y3hoFg8_CcTB_QmP5hdXEqByKvJoyiipEKvwvEhB1aLd1_SovZI6F7-sjY9ZMjQxIGngrN1ZEtMTF9y2YNZbAr0nNvcskDaNW803jSZ1y3CFGTbRdm8MnVa6zDdc-DRz-982-ay8UM0Nv5zKpFqHzvNzFn0X-R-xuf3nNYTxWe2mSo_3dRDrKI_abtuVjWSmZJNlJ3R8JwY2gsSF5XqaT4w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldsAndNucleiOfAmygdala.
I have tried this with multiple subjects multiple times but the following
error persists. Any help would be greatly appreciated. Thank you.

--
Fitting mesh to image data took 959.4679 seconds
Transforming points
Transforming points
Wrote image to file image.mgz
Constructing image-to-world transform from header information (asmr1.mgz)
Constructing image-to-world transform from header information
(/Users/rajilab/Documents/CHS_IMAGING_DATA/97-2002/03638/FS/tmp/hippoSF_T1_v21_left/imageDump.mgz)
Wrote image to file asmr2.mgz
This file does not contain MRI parameters
Caught unexpected exception of unknown type.


   Segmentation violation detected at Mon Mar 22 21:39:10 2021


Configuration:
  Crash Decoding : Disabled
  Current Visual : Quartz
  Default Encoding   : ISO-8859-1
  MATLAB Architecture: maci64
  MATLAB Root: /Applications/freesurfer/7.1.1/MCRv84
  MATLAB Version : 8.4.0.150421 (R2014b)
  Operating System   : Darwin 20.3.0 Darwin Kernel Version 20.3.0: Thu Jan
21 00:07:06 PST 2021; root:xnu-7195.81.3~1/RELEASE_X86_64 x86_64
  Processor ID   : x86 Family 6 Model 85 Stepping 4, GenuineIntel
  Software OpenGL: 0
  Virtual Machine: Java 1.7.0_55-b13 with Oracle Corporation Java
HotSpot(TM) 64-Bit Server VM mixed mode
  Window System  : Quartz

Fault Count: 1


Abnormal termination:
Segmentation violation

Register State (from fault):
  RAX = 0003  RBX = 00010a71e080
  RCX = 7fea4a20  RDX = 71207180
  RSP = 7fea4a20  RBP = 7fff2030195e
  RSI = 7000  RDI = 7fff203031f9

   R8 = 4a9295e0   R9 = 71207180
  R10 = 7fff202f0002  R11 = 7fea4a2d9e60
  R12 = 71207498  R13 = 
  R14 = 000124484d9b  R15 = 0060

  RIP = 71207498  RFL = 712071e0

   CS = 00012431b27b   FS = 712071c0   GS = 0001

Stack Trace (from fault):
[  0] 0x00010c970e64
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00028260
_ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+0052
[  1] 0x00010c974a2a
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00043562
_ZN2fl4test17terminate_handledEv+0906
[  2] 0x00010c974477
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00042103
_ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+0119
[  3] 0x00012405eb7a
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00387962
_Z32mnRunPathDependentInitializationv+3146
[  4] 0x00012405ee58
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00388696
_Z32mnRunPathDependentInitializationv+3880
[  5] 0x00012405c733
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00378675
mnFatalSignalHandler+0275
[  6] 0x7fff2051cd7d
/usr/lib/system/libsystem_platform.dylib+00015741 _sigtramp+0029
[  7] 0x
+
[  8] 0x00012431b27b
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01782395
_Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+00010667
[  9] 0x000124274a17
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01100311
_Z15inRunFinalizers7opcodesPS_Pi+0119
[ 10] 0x00012431929d
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01774237
_Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+2509
[ 11] 0x000124edec55
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_dispatcher.dylib+00400469
_ZN8Mfh_file11dispatch_fhEiPP11mxArray_tagiS2_+0645
[ 12] 0x0001242bc48b
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01393803
_Z23inEvalPcodeHeaderToWordP15_memory_contextiPP11mxArray_tagP12_pcodeheaderP6Mfh_mpj+0219
[ 13] 0x00012426ef4b
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01077067
_Z25in_local_call_with_setjmpIN5boost3_bi6bind_tIvPFvP15_memory_contextPiPP11mxArray_tagP12_pcodeheaderjENS1_5list5INS1_5valueIS4_EENS0_3argILi1EEENSG_ILi2EEENSE_ISA_EENSE_IiEEEN6mlutil14cmddistributor17inExecutionStatusET_S5_S8_b+0171
[ 14] 0x00012426a221
/Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01057313

Re: [Freesurfer] VirtualBox Ubuntu login

[fsbuild]

External Email - Use Caution

Hello Sarah,
I will send the information to your email shortly.
- R.

On Mar 22, 2021, at 22:35, Bick, Sarah sarah.b...@vumc.org 
wrote:External Email - Use 
CautionExternal
 Email - Use CautionI am 
attempting to login to ubuntu via VirtualBox but am required to input a 
password for the “Developer” account. Could you please help me with what this 
is or how I can login?___Freesurfer 
mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer​
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[Freesurfer] VirtualBox Ubuntu login

[Bick, Sarah]

External Email - Use Caution

I am attempting to login to ubuntu via VirtualBox but am required to input a 
password for the “Developer” account. Could you please help me with what this 
is or how I can login?
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[Freesurfer] License Agreement for re-distribution

[Ezequiel Mikulan]

External Email - Use Caution

Hi All, I've developed an open-source software for MRI pseudonymization that 
uses Freesurfer so I wanted to check that I'm correctly handling the licenses. 
In Freesurfer's License Agreement it says that: "If you distribute Software (as 
defined below) downloaded from FreeSurfer, all of the paragraphs of Part B of 
this Agreement must be included with and apply to such Software".
It is not clear to me if we should copy the relevant part into our license or 
if it is ok if we add a text file in the software with Freesurfer's license. In 
other words, should Part B be included inside our license or inside the 
software as a file?
How should I proceed? Thanks,
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Re: [Freesurfer] Which pial surface to trust

[Jones, Richard]

External Email - Use Caution

A couple of questions:-
1) Do you experience similar variability with the T2 and FLAIR options or is 
FLAIR more variable due to it's generally lower SNR?
2) Should the spatial resolution of the T2/FLAIR scan match that of the T1 scan?

Richard

Message: 8
Date: Wed, 17 Mar 2021 17:51:51 -0400
From: "Douglas N. Greve" 
Subject: Re: [Freesurfer] Which pial surface to trust, with or without
-FLAIR option
To: 
Message-ID: <3c789103-dad7-974a-0d76-58a02cba2...@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

We get a lot of variable results with FLAIR. Sometimes it helps,
sometimes it hurts. FLAIR scans themselves can be very variable across
sites. If it is looking like it is hurting your results, then just run
without it.

On 3/12/2021 11:07 AM, Xiaojiang Yang wrote:
>
> External Email - Use Caution
>
> Dear FS developers,
>
> I have run FS?s recon-all on many cases, with and without -FLAIR
> options. I found the pial? surface results (?h.pial) I obtained
> without -FLAIR option fit to the original image
> (subjected/mri/orig.mgz) much better than those with -FLAIR option, at
> least from my visual judgment. See *MailScanner has detected a
> possible fraud attempt from "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/1kdfPWDTAquCY3qAKfDNtc8TRiBI5hNHL96VYA9_mTvUn4qpO75SL3h5c4SdXB7ViTEwQr3qvBdcNSLFjdejtW60w8ivtHhUzNRG8q3lZ1xbTIeqmxzu5UakhOAKktPA6QRnwdwkJndw3FM8BTgEY5zvq8wxfJDDr0yrIvj-8mnF4PHlJi1y3SfCiVWPakRs0mSeQjRO-dRiFpl7IoDxugFH1C4OHRgZGkARvy-KxV4pKw_0ubMRqVmKUV5rqXP3m0SDssF44schYVSa5wqU_Bg/https%3A%2F%2Fimgur.com%2Fa%2FwrY0HTY
> ?for
> one example.
>
> I know -FLAIR option was introduced to improve the quality of pial
> surface segmentation. Now for many cases, my intuition is that -FLAIR
> option decreases the pial quality. My questions are:
>
>   * Is this intuition correct?
>   * Should I trust the pial surface that?s obtained with or without
> -FLAIR option in general?
>
> In addition, when I use the -FLAIR option, I sometimes get failed when
> running recon-all. After I did some manual edits to the brainmask
> image, and re-run the recon-all:
>
> recon-all -autorecon-pial -subjid 
>
> I can get recon-all successful. But if I run recon-all without -FLAIR
> option, I can get successful results without needing to manually edit
> the brainmask image.
>
> So my last question is:
>
>   * Should I just run recon-all without -FLAIR option, or, with -FLAIR
> option + manual edit + re-run with -autorecon-pial? Which is better?
>
> Thank you very much!
>
> John
>


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[Freesurfer] "ERROR: crypt() returned null with 4-line file" when running via Singularity

[Zoner, Katja]

External Email - Use Caution

Hi all,


I am trying to run a single subject through FreeSurfer 7.1.1 via Singularity 
image (pulled from the FreeSurfer DockerHub) like this:

export SINGULARITYENV_FS_LICENSE=/mnt/22Q/images/license.txt
export SINGULARITYENV_SUBJECTS_DIR=/mnt/22Q/data/freesurfer

singularity exec --cleanenv -B /project/bbl_projects/22Q/:/mnt/22Q \
/project/bbl_projects/22Q/images/freesurfer_7.1.1.sif \
recon-all -s sub-17867 -i 
/mnt/22Q/data/bids_directory/sub-17867/ses-22Q1/anat/sub-17867_ses-22Q1_T1w.nii.gz
 -all


But it fails quickly with error message:

ERROR: crypt() returned null with 4-line file

Do you know what might be causing this error message? How can I address this?

Additional info:

  1.  FreeSurfer version: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551
  2.  uname -a: Linux singularity01 3.10.0-1127.8.2.el7.x86_64 #1 SMP Tue May 
12 16:57:42 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
  3.  recon-all.log: see attached

See GitHub issue: 
https://secure-web.cisco.com/1ut10r0i0QuSlDil5z36vyz9khjKfY1Scbdqd9hofmPnzDpnN0bPBmojSGjIHi7yzY-uAiR9TwSegSq34pGGazlC4w7PY2qro7tebqzKCIDwTGzo0b7dGo_5WJsUXpEF8pnoBxLzE5qyK-Ip4LxSG2qYpeYTUe26cjH1b7slOniWz6RSxWjdwFtHm84K-HRyUCV5fxm82SyHP7wdwOdwxAVCjfNMXBfZFnqjbhknEIVYKcFpKgXkTKuzl2SdmuJhOfFiYNxkixGTo_DisMo8Qiw/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fissues%2F848

[https://secure-web.cisco.com/1TDcdfVeSPTzDeg0asgP7Yy7WKhWmvgHB9T_fyDNBmSSR44igxbFcjkvEBwioJUXRaWvFZHtoGPQqrUbSlBypgDgQbDuBWjvd-22zMLp_ozjhIwKQzVLJKCp0yPoqA5Jl_pFvhR-3OKlIQ9D5gOx-1rSy9WaziDl1r-sKmOwEbyWlYPXOi1GYxFF_5VZ3ElEqF1XxMvU2JxTpTowEWPoVTRECmtbmBdJhnEkKiBKV2AlSQcbm-ZEJyL2cL-lSnLuPDlXjKSBdlNZgzeMLSL51ug/https%3A%2F%2Favatars.githubusercontent.com%2Fu%2F6330653%3Fs%3D400%26v%3D4
`ERROR: crypt() returned null with 4-line file` when running via Singularity 
image · Issue #848 · 
freesurfer/freesurfer
I am trying to run a single subject through FreeSurfer 7.1.1 via Singularity 
image like this: export SINGULARITYENV_FS_LICENSE=/mnt/22Q/images/license.txt 
export SINGULARITYENV_SUBJECTS_DIR=/mnt/22...
github.com


Thank you for any assistance!

Katja Zoner



recon-all.log
Description: recon-all.log
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[Freesurfer] Research Assistant Positions at Washington University School of Medicine

[Dincer, Aylin]

External Email - Use Caution

The Benzinger Imaging Core Laboratory at 
Washington University School of Medicine is looking for full-time Research 
Assistants (multiple openings available!) to work with us on magnetic resonance 
imaging and positron emission tomography studies of Alzheimer disease.

Your responsibilities will include:

1. Processing of imaging data using neuroimaging software 
toolkits (FreeSurfer, MATLAB, R, SAS, SPSS)

2.Performing QC / QA on imaging data and preliminary analyses

3.Opportunities to work on your own research projects and perform 
statistical analyses.

4.Assisting with research studies, collection of data, set-up and 
maintenance of equipment.

The ideal candidate will be able to work independently, communicate with 
laboratory staff and investigators, and maintain complete and organized 
records/reports.  They'll have working knowledge of computer software and a 
familiarity with command line interface computer processing (Linux). They are 
interested in psychology and/or neuroscience.

Apply with one of the links below interested!
RTII Posting 
50550
RTII Posting 
50947

All the best,
Aylin

Aylin Dincer, Neuroimaging Engineer
Benzinger Lab | Mallinckrodt Institute of Radiology | Neuroimaging Laboratory
Pronouns: she/her/hers

Washington University School of Medicine
4525 Scott Ave.
St. Louis, MO 63110
aylin.din...@wustl.edu





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Re: [Freesurfer] License Agreement for re-distribution

[Hoopes, Andrew]

Hi Ezequiel,

Just including the FS license in the software as a separate text file is fine.

Best,
Andrew

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

Date: Monday, March 22, 2021 at 12:48 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] License Agreement for re-distribution

External Email - Use Caution
Hi All, I've developed an open-source software for MRI pseudonymization that 
uses Freesurfer so I wanted to check that I'm correctly handling the licenses.

In Freesurfer's License Agreement it says that: "If you distribute Software (as 
defined below) downloaded from FreeSurfer, all of the paragraphs of Part B of 
this Agreement must be included with and apply to such Software".

It is not clear to me if we should copy the relevant part into our license or 
if it is ok if we add a text file in the software with Freesurfer's license. In 
other words, should Part B be included inside our license or inside the 
software as a file?

How should I proceed? Thanks,

Ezequiel
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Re: [Freesurfer] Some brain area missing after running recon-all

[Fischl, Bruce]

Hi Stef

This is usually the result of a incorrectly fixed topological defect. You can 
confirm this if the area is present in the ?h.orig.nofix and not in the 
?h.orig.  The fix depends on the source of the defect. It might be as simple as 
drawing a single voxel back into the wm.mgz, but might need more. Look at the 
wm and see if it is  mostly accurate or not and whether the intensities in the 
white matter are near where they should be (target is 110, so ideally mostly 
above 100)

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Stef Meliss
Sent: Monday, March 22, 2021 10:37 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Some brain area missing after running recon-all


External Email - Use Caution

External Email - Use Caution
Dear FreeSurfer Experts

I am using FreeSurfer on my anatomical data to use segmentations and 
parcellations in my fMRI analyses in AFNI. After reviewing the output from 
recon-all -all (FreeSurfer version 6.0.0), I noticed that one subject is 
missing some occipital areas in the output (e.g. aparc+aseg.mgz). Please see 
attached for a screenshot of the output from

   freeview -v mri/brainmask.mgz \
   mri/wm.mgz:colormap=heat:opacity=0.4 \
   -f surf/lh.white:edgecolor=yellow \
   surf/lh.pial:edgecolor=red \
   surf/rh.white:edgecolor=yellow \
   surf/rh.pial:edgecolor=red \
   surf/rh.inflated:visible=0 \
   surf/lh.inflated:visible=0

From what I read in the information on troubleshooting the output, I understand 
that manual editing is necessary to fix this – is this correct? I have verified 
that the missing areas are included in the brainmask as well as aseg.presurf. I 
am not sure though how to determine whether I am dealing with a segmentation 
error or a normalization error or maybe even a combination of both.

If you could give me some pointers on which steps to take, that would be highly 
appreciated.

Many thanks in advance for your help.

Best regards,

Stef

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Re: [Freesurfer] Freesurfer 6.0.0 Container & MCR

[Hoopes, Andrew]

Hi Ursula,

I was just reminded that we purposely don’t include MCR in the container due to 
redistribution-restrictions by the MCR license. So, it’s up to the user to 
install or provide the MCR library if needed.

best
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Hoopes, Andrew 

Date: Friday, March 19, 2021 at 1:06 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freesurfer 6.0.0 Container & MCR
Hi Ursula,

Thanks for pointing this out. I think it’s just the case that MCR wasn’t 
installed in that container. I’m surprised this hasn’t been brought up before. 
We’ll update the container with it.

best
Andrew

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

Date: Friday, March 19, 2021 at 12:23 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Freesurfer 6.0.0 Container & MCR

External Email - Use Caution
Hi Freesurfer experts,

I’m trying to use the official FS 6.0.0 container from Dockerhub on a new HPC 
(for consistency with previous pipelines), and got the error below about not 
finding the Matlab Compiler Runtime in the container. I have worked around it 
by explicitly binding the mcr on the HPC to the container with “-B 
/cbica/software/external/matlab/mcr/v711/:/opt/freesurfer/MCRv80”, but is this 
the expected behavior? Or is there some issue? My understanding was that one of 
the advantages of mcr was that you could include it in containers and 
distribute compiled code, so was surprised to find this come up.

Thanks in advance,
Ursula
---
Ursula Tooley
Ph.D. Candidate
Neuroscience Graduate Group
University of Pennsylvania
she/her/hers
utoo...@gmail.com
202.413.5627




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Re: [Freesurfer] Problem with freesurfer measures

[Alberto Del Cerro Leon]

External Email - Use Caution

Thanks!, how can I obtain the white matter volume stats using my annotation
file?

El mar, 16 mar 2021 a las 16:59, Douglas N. Greve ()
escribió:

> I think they will give very similar results, but my guess is that #1 is a
> little better
>
> On 3/8/2021 11:40 AM, Alberto Del Cerro Leon wrote:
>
> External Email - Use Caution
> I want to use the annotation file created by myself in fsaverage to
> calculate the anatomical stats, but i dont know what is the best workflow.
>
> 1. Convert the annotation file to each subject space using mri_sur2surf
> and using mri_anatomical_stats in each subject
> 2. Convert the surface of each subject to fsaverage space and use
> mri_segstats to obtain the data, in this case i dont know what surface i
> have to convert to fsaverage space to do it (i can see thickness
> (lh/rh.thickness) and volume (lh/rh.volume) but not folding index and white
> matter volume)
>
> Any idea?
>
> El lun, 8 mar 2021 a las 16:04, Fischl, Bruce ()
> escribió:
>
>> Hi Alberto
>>
>>
>>
>>1. And 4. Are not properties of single surfaces – they are computed
>>from the white and the pial. For 2 and 3 that is really up to you
>>
>> Cheers
>> Bruce
>>
>>
>>
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Alberto Del Cerro
>> Leon
>> *Sent:* Monday, March 8, 2021 7:02 AM
>> *To:* Freesurfer support list 
>> *Subject:* [Freesurfer] Problem with freesurfer measures
>>
>>
>>
>> *External Email - Use Caution*
>>
>> Hello Freesurfer team, I am using an annotation file that i've created
>> previously to obtain the measures of some ROIs. To do that i am using de
>> commands mri_surf2surf and mri_segstats. I want to obtain the following
>> measures:
>>
>> 1. Gray and White Matter Volume
>>
>> 2. Folding Index
>>
>> 3. Curvature measures
>>
>> 4. Thickness
>>
>> However I don't know what surface in the surf folder of each subject I
>> have to use. Could u help me?
>> ___
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Re: [Freesurfer] Freesurfer 7.1 recon-all -long exits with erros

[Yakupov, Renat /DZNE]

External Email - Use Caution

Dear Douglas,


thank you for confirmation.

My initial suspicion that fs_time caused the error was because of this part of 
the script:


if($#outfile == 0)  set outfile = /dev/stdout


where it explicitly uses /dev/stdout when no output file is provided. fs_time 
from Freesurfer 6 doesnt do that.


And it was pretty much confirmed when I rewrote that part of fs_time:


if($#outfile == 0)  set outfile = /dev/stdout; # time default is stderr, which 
is annoying
set cmd = ($cmd -o $outfile)

changed to:

if($#outfile == 0) then
  set cmd = ($cmd 2>&1) # time default is stderr, which is annoying
else
  set cmd = ($cmd -o $outfile)
endif

and it worked.


>From what I was able to find, it looks like '/dev/stdout` might not work on 
>all file systems, and the one our HPC cluster is using might be one of them.


Best regards,

Renat.



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

Sent: Friday, March 19, 2021 5:13 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Freesurfer 7.1 recon-all -long exits with erros

fs_time will not affect any processing, so you could replace it with a stub. 
But why do you think it is fs_time?

On 3/19/2021 10:54 AM, Yakupov, Renat /DZNE wrote:

External Email - Use Caution

Dear Freesurfer developers,


I am trying to run the longitudinal processing pipeline of our data on our HPC 
cluster (SGE based) and it crashes at the 3rd step - generating the 
longitudinal runs. The exact command is 'recon-all -long tp1dir basedir -all'. 
There is no error message on the screen, it just says that it exited with 
errors.


The recon-all.log file has no error information either, other than the 
statement that it exited with errors. It seems to have stopped after 
mri_nu_correct.mni step and looking further it looks like it crashed at the 
beginning of orig_nu step, since orig_nu.log has this error message:


/usr/bin/time: /dev/stdout: Not a directory

Please see attached log files.


Additional information:


Freesurfer version: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551


uname -a:

Linux compute-0-2.local 2.6.32-504.16.2.el6.x86_64 #1 SMP Wed Apr 22 06:48:29 
UTC 2015 x86_64 x86_64 x86_64 GNU/Linux

lsb_release -a:
LSB Version:
:base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch
Distributor ID:CentOS
Description:CentOS release 6.6 (Final)
Release:6.6
Codename:Final

What is interesting is that running it on the headnode directly without qsub 
works fine. The headnode has the same OS and tcsh versions.

In my rather poorly informed opinion, it looks like fs_time is the culprit. For 
a quick fix, is it safe to assume that using fs_time from Freesurfer 6 wont 
affect the processing pipeline in any way?

Thank you!

Best regards,
Renat.




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