Re: [Freesurfer] I've tried what to do. But, still freeview doesn't work

[Dicamillo, Robert]

You’re running MacOS Sonoma (14.X) which was not out when 7.3.2 was released in 
2022, i.e., 7.3.2 was not tested on anything newer than MacOS 12.X as listed on 
the download page under https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads.
7.3.2 release

Linux OS: CentOS7, CentOS8, Ubuntu18, Ubuntu20, Ubuntu22
Mac OS: 10.14, 10.15, 11.X, 12.X (Intel binaries).

Since you are running on a Silicon Mac with an M1 chip, you can try downloading 
and installing the following development build from March 2024, however it is 
not a release and so may be unstable,

https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-macOS-darwin_arm64-dev-20240327.pkg

I would not expect freesurfer commands like recon-all to work since your 
machine has 8G of RAM to run both the OS and then any applications on top of 
that.

- R.


On Apr 14, 2024, at 07:28, 이준하 
mailto:dlwnsgk1...@naver.com>> wrote:

External Email - Use Caution

I've put in my license.txt file in the freesurfer file but, freeview doesn't 
work

'Freesurfer quits unexpectedly'

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Re: [Freesurfer] recon-all nu_correct error

[Dicamillo, Robert]

In our cluster testing, we allocate at least 16G to each recon-all command (see 
below).  We run about 150 of those commands in parallel on the cluster during 
off-peak usage and it takes about 12 hours for them to complete.

$ jobsubmit -A fsm -p basic -t 1-00:00:00 -m 16G "recon-all -all -s 0042 -I 
/path_to_subject_0042/001.mgz

The system requirements, 
https://surfer.nmr.mgh.harvard.edu/fswiki/SystemRequirements, stating 8G for 
recon all is intended for a users stand alone machine where memory is limited, 
there are no time/job resource limits - and so it might take 15 hours for a 
single recon-all to run.

- R.

On Mar 28, 2024, at 15:37, Dong, Yilei 
mailto:yid...@health.ucsd.edu>> wrote:

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Hi Yujing,

For context, the way how I have the recon-all set-up is we have a recon-all job 
submission script that runs recon-all for 1 image. Given the folder of 100 MRI 
images, we have another script that calls upon the recon-all script for each 
image within the folder via a for loop. The result is 100 jobs running in 
parallel on the cluster.

I have attached a screenshot of the parameters we set whenever we submit each 
recon-all job for each image by SLURM to UCSD's cluster. The maximum time we 
are allowed for each job is 48 hours. However, my recon-all for all 100 
subjects takes on average 4.5 to 6 hours to run. Each image is also allocated 8 
GB of memory. Our jobs are also shared-node jobs, which means we run more than 
1 job on a single node.

Should we allocate more memory to each job than 8 GB or just reduce the number 
of jobs we submit at a time if 100 is a lot? We were able to successfully run 
through the entire recon-all for 5 subjects in parallel in the past.

Sincerely,
Yilei

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Sent: Thursday, March 28, 2024 11:53 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] recon-all nu_correct error

Hi Yilei,



I think "nu_correct: Command not found. FREESURFER: Undefined variable." is 
unrelated to your recon-all didn’t finish. That error happens in the beginning 
of recon-all and recon-all uses ANTS N4BiasFieldCorrection for nu correct 
instead. We have addressed this error in our dev version.



I’m wondering if your cluster computer enforces some time, memory … limit on 
your job.



Best,



Yujing





From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Dong, Yilei
Sent: Thursday, March 28, 2024 2:18 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] recon-all nu_correct error



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Hi Freesurfer support,



Recently, I submitted a script to run recon-all on 100 MRI images on UCSD's 
computing cluster. I get an error file that says "nu_correct: Command not 
found. FREESURFER: Undefined variable." I previously emailed this problem and 
was told to send my recon-all.log if running the recon-all did not work a 2nd 
time. I was also told previously that my cluster's Freesurfer can't locate the 
minc toolkit binaries on my system. How can this error be troubleshooted? 
Please let me know if you need any other information.



Freesurfer version: 7.2.0, but already available as module
Platform: Rocky Linux release 8.8 (Green Obsidian)
uname -a: Linux login01 4.18.0-477.15.1.el8_8.x86_64 #1 SMP Wed Jun 28 15:04:18 
UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
Recon-all log: see attached



Sincerely,
Yilei
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Re: [Freesurfer] Freeview on WSL in Windows 10

[Dicamillo, Robert]

Hello Monica,

The login page you display is not accessible to the public.   We have 
information about how to get started with WSL on the public wiki pages, e.g., 
https://surfer.nmr.mgh.harvard.edu/fswiki/FS7_wslWe talk about installing 
WSL version 1 and WSL version 2, though it reads like you already have a 
version of WSL up and running and a version of Linux installed.

With WSL running Linux, you should download the appropriate freesurfer binary 
linux .rpm or .deb installer and use that to install freesurfer.  Those are 
available per OS (CentOS 7, 8 and Ubuntu 18, 20, 22) via a link on the WSL 
pages above to here, https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads.

For Freeview to display graphics, you need to install a 3rd party X windows 
server on your windows host.  We demonstrate using Xming but some users have 
not been able to get Xming to work but have had success with MobaXterm.

WSL is a work in progress and can change without notice when Microsoft 
automatically updates your Windows machine.  We cannot guarantee the current 
version of WSL, the 3rd party X-servers, and the specifics graphics 
card/hardware in your computer are all going to cooperate to allow X-windows 
graphics to work.

If WSL does not work for you, an alternative its to use a different 
virtualization technology like VirtualBox instead of WSL.   We have a 
pre-installed version of Freesurfer 7.2.0 inside an Ubuntu 18 VM that runs 
under Virtualbox.  That eliminates having to use/install an X-server on your 
Windows machine.  Information about installing VierualBox and running the 
Freesurfer Ubuntu 18 VM can be found under, https://freesurfer.net/fswiki/VM_67

- R.

On Nov 3, 2022, at 04:11, Monica Crotti 
mailto:monica.cro...@kuleuven.be>> wrote:

External Email - Use Caution

Dear Freesurfer developers,

I am writing to you with regard to two issue I would like to address:

1. I subscribe to the email list but when I am trying to access the page 
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://mail.nmr.mgh.harvard.edu/NMRAuth/GLOBAL/LOGIN
 I got the following error


2. I installed Freesurfer on a WSL2 environment on my computer Windows 10. 
Neverthless, I am unable to run the freeview command. I looked into web for 
solutions related to the error I got which is the following

freeview.bin: error while loading shared libraries: libvtkverdict.so.5.6: 
cannot open shared object file: No such file or directory

Following what I found on the web, I run the following commands

$sudo add-apt-repository ppa:ubuntuhandbook1/ppasudo

apt-get install qt4-dev-tools libqt4-dev libqtcore4 libqtgui4

and I get the following errors

base) root@GBW-L-W3359:/usr/local/KUL_apps/freesurfer# cd bin/
(base) root@GBW-L-W3359:/usr/local/KUL_apps/freesurfer/bin# ldd 'freeview.bin' 
| grep not
libvtkverdict.so.5.6 => not found
libvtkGraphics.so.5.6 => not found
libvtkmetaio.so.5.6 => not found
libvtkpng.so.5.6 => not found
libvtkzlib.so.5.6 => not found
libvtksqlite.so.5.6 => not found
libvtkImaging.so.5.6 => not found
libvtkFiltering.so.5.6 => not found
libvtkCommon.so.5.6 => not found
libvtksys.so.5.6 => not found
libvtkGenericFiltering.so.5.6 => not found
libvtkexoIIc.so.5.6 => not found
libvtkNetCDF.so.5.6 => not found
libvtkVolumeRendering.so.5.6 => not found
libvtkRendering.so.5.6 => not found
libvtkftgl.so.5.6 => not found
libvtkWidgets.so.5.6 => not found
libvtkHybrid.so.5.6 => not found
libvtkIO.so.5.6 => not found
libvtkDICOMParser.so.5.6 => not found

I was wondering if you could help me in solving this issue.

Thank you in advance,
Best regards

Monica
Monica Crotti, M.Sc. | PhD Student
Locomotor and Neurological Disorders Group
Department of Development and Regeneration
KU Leuven, Belgium

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[Freesurfer] Freesurfer Ubuntu VM updated

[Dicamillo, Robert]

The Freesurfer Ubuntu VM has been updated:
- Freesurfer 7.2.0 release from July 2021 is installed
- download image size now ~8G
- expanded image size now ~29G
- documentation updated for installing VirtualBox and running the VM image
- not much should be needed to do in order to start running freesurfer apart 
from adding your license file
- option to run the Freesurfer course tutorial data

See https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67

I would especially be interested in receiving feedback from anyone trying the 
VM for the first time and/or who is new to using VirtualBox.  You can send me 
questions/feedback directly.

- R.
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Re: [Freesurfer] Freesurfer commands not found - unable to install

[Dicamillo, Robert]

Hello Ashesh,

You need someone with admin or root privileges to install tcsh (and I would do 
csh as well) shells on your machine so those scripts can run, i.e.

$ sudo apt-get install tcsh
$ sudo apt-get install csh

On Oct 25, 2018, at 13:35, Thaker, Ashesh A 
mailto:ashesh.tha...@ucdenver.edu>> wrote:

External Email - Use Caution

Dear Freesurfer team,

Surely there is a simple fix to my problem, but I've been unable to succesfully 
run Freesurfer commands after many attempts (with my very basic bash knowledge) 
and searching prior archives.

I'm running Freesurfer on a 64-bit machine, Ubuntu 18.04 LTS.

No Freesurfer commands work (files not found), except the "freesurfer" command. 
I've included some pertinent output below. All of the installation files seem 
to be in the right place and the path seems to be correct, so I'm perplexed. 
Any help very much appreciated.

Kind regards,



Ashesh Thaker, MD | Assistant Professor
School of Medicine, Department of Radiology
University of Colorado Anschutz Medical Campus

720 848 6568 (office) | 
ashesh.tha...@ucdenver.edu

---



ashesh@ashesh-gpu:~$ export FREESURFER_HOME=/usr/local/freesurfer
ashesh@ashesh-gpu:~$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
 freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME   /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer/subjects
MNI_DIR   /usr/local/freesurfer/mni
FSL_DIR   /usr/local/fsl
ashesh@ashesh-gpu:~$ recon-all
bash: /usr/local/freesurfer/bin/recon-all: /bin/tcsh: bad interpreter: No such 
file or directory
ashesh@ashesh-gpu:~$ freeview
bash: /usr/local/freesurfer/bin/freeview: /bin/tcsh: bad interpreter: No such 
file or directory
ashesh@ashesh-gpu:~$ freesurfer

FreeSurfer is a set of tools for the analysis and visualization
of structural and functional brain imaging data. FreeSurfer
also refers to the structural imaging stream within the
FreeSurfer suite.

Users should consult the online documentation available at:

  http://surfer.nmr.mgh.harvard.edu

Alternatively, the 'recon-all' command help-text provides
adequate information to begin processing subject data, such
as the sample subject 'bert' found in the 'freesurfer/subjects'
directory.  Type 'recon-all --help' to view this help-text.

Direct comments and questions to:

  freesurfer@nmr.mgh.harvard.edu

You are running this version of FreeSurfer:

  freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

ashesh@ashesh-gpu:~$ echo $PATH
/usr/local/freesurfer/bin:/usr/local/freesurfer/fsfast/bin:/usr/local/freesurfer/tktools:/usr/local/fsl/bin:/usr/local/freesurfer/mni/bin:/usr/local/fsl/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin



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Re: [Freesurfer] Difference between 6.0.1 and 6.0.0

[Dicamillo, Robert]

Hello Haakon,

I don’t there are significant functionality changes in the 6.0.1 patch release. 
i think  there are however changes to fix some run time errors with respect to 
system libraries found/used on the system running Freesurfer.  Someone else who 
mentors the help list might chime in, but I don’t know of a reason to use 6.0.0 
instead of the 6.0.1 release.

- rob

On Oct 8, 2018, at 9:46 AM, Haakon Ramsland Hol 
mailto:haakon.ramsland@sshf.no>> wrote:


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Dear Experts.

I just happened to stumble across version 6.0.1, what is the main difference 
from 6.0.0?  And I read in a post from 2017 that the flairpial wasn’t optimized 
in v6.0.0 compared to 5.3, and that this would be optimized in version 6.1. Any 
news with regards to flair pial? Is it recommended to use 5.3 if you have flair 
images as well?

Kind regards.

Haakon R. Hol
Radiologist.
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Re: [Freesurfer] QAtools for Freesurfer version6?

[Dicamillo, Robert]

Hello Seonjoo,

Could you send along a link to what you ran/tweaked for “QA tools” on 
freesurfer ?

- rob

On Oct 4, 2018, at 8:31 PM, Lee, Seonjoo 
mailto:sl3...@cumc.columbia.edu>> wrote:


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I tired to use QA tools for freesurfer version6, but did not have much success. 
Is anyone know how to tweak QA tools for freesurfer version 6?
Thank you.
-Seonjoo Lee
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Re: [Freesurfer] Mac OS free surfer instalation (Vasile, Eduard)

[Dicamillo, Robert]

Sure - or if you want to let us know your office number, I could stop by as 
well.

- rob

> On Oct 4, 2018, at 12:10 PM, Vasile, Eduard  wrote:
> 
> Hi Rob, 
> 
> I have matlab installed on my laptop. I am based in South Central, 149, is 
> there anywhere I can come to talk to you guys? I am in need of the software.
> 
> Kind regards
> Eduard
> 
> On 10/4/18, 12:00 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
> freesurfer-requ...@nmr.mgh.harvard.edu" 
>  freesurfer-requ...@nmr.mgh.harvard.edu> wrote:
> 
> Mac OS free surfer instalation (Vasile, Eduard)
> 
> 
> ___
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Re: [Freesurfer] Mac OS free surfer instalation (Vasile, Eduard)

[Dicamillo, Robert]

Hello Eduard,

It looks to me like the application 
freesurfer/BrainstemSS/mac_osx/segmentSubject.app needs to be run via the 
script  freesurfer/BrainstemSS/mac_osx/run_SegmentSubject.sh which sets the 
path to pick up the Matlab library libmwcpp11compat.dylib.

While I think we have that library in house because we have a Matlab license, 
you would need to have a Matlab distribution or download  their runtime 
environment in order to get that library for segmentSubject.app to run.

- rob

> On Oct 3, 2018, at 3:50 PM, Vasile, Eduard  wrote:
> 
> Hi, 
> 
> Coming back with an update from the previous email. I installed it but it 
> tells me that it cannot be open because of a problem and then I get the above 
> error. The version is 6.0. Is there a place where I can come with my laptop 
> and see what is the problem?
> 
> Process:   prelaunch [1300]
> Path:  
> /Applications/freesurfer/*/segmentSubject.app/Contents/MacOS/prelaunch
> Identifier:segmentSubject
> Version:   1
> Code Type: X86-64 (Native)
> Parent Process:??? [1]
> Responsible:   prelaunch [1300]
> User ID:   501
> 
> Date/Time: 2018-10-03 15:47:11.569 -0400
> OS Version:Mac OS X 10.13.6 (17G2307)
> Report Version:12
> Bridge OS Version: 3.0 (16P375)
> Anonymous UUID:C3615BC6-2956-15B2-00D8-9F435B158DB0
> 
> Sleep/Wake UUID:   2988BAC2-9FC2-422B-AF82-6F0576A1E894
> 
> Time Awake Since Boot: 3200 seconds
> 
> System Integrity Protection: enabled
> 
> Crashed Thread:0
> 
> Exception Type:EXC_CRASH (SIGABRT)
> Exception Codes:   0x, 0x
> Exception Note:EXC_CORPSE_NOTIFY
> 
> Termination Reason:DYLD, [0x1] Library missing
> 
> Application Specific Information:
> dyld: launch, loading dependent libraries
> 
> Dyld Error Message:
>  Library not loaded: @rpath/libmwcpp11compat.dylib
>  Referenced from: 
> /Applications/freesurfer/*/segmentSubject.app/Contents/MacOS/prelaunch
>  Reason: image not found
> 
> Binary Images:
>   0x1 -0x10ff7 +segmentSubject (1) 
>  
> /Applications/freesurfer/*/segmentSubject.app/Contents/MacOS/prelaunch
>   0x105013000 -0x10505dacf  dyld (551.4) 
> <8A72DE9C-A136-3506-AA02-4BA2B82DCAF3> /usr/lib/dyld
> 
> 
> 
> Kind regards
> Eduard 
> 
> 
> On 10/3/18, 12:00 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
> freesurfer-requ...@nmr.mgh.harvard.edu" 
>  freesurfer-requ...@nmr.mgh.harvard.edu> wrote:
> 
>Send Freesurfer mailing list submissions to
>   freesurfer@nmr.mgh.harvard.edu
> 
>To subscribe or unsubscribe via the World Wide Web, visit
>   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>or, via email, send a message with subject or body 'help' to
>   freesurfer-requ...@nmr.mgh.harvard.edu
> 
>You can reach the person managing the list at
>   freesurfer-ow...@nmr.mgh.harvard.edu
> 
>When replying, please edit your Subject line so it is more specific
>than "Re: Contents of Freesurfer digest..."
> 
> 
>Today's Topics:
> 
>   1. Re: Error during decompression of DICOM JPEG compressed
>  series (Greve, Douglas N.,Ph.D.)
>   2. Re: Error during decompression of DICOM JPEG compressed
>  series (Dicamillo, Robert)
>   3. Re: Error during decompression of DICOM JPEG compressed
>  series (Greve, Douglas N.,Ph.D.)
>   4. Mac OS free surfer instalation (Vasile, Eduard)
>   5. Re: Mac OS free surfer instalation (Hoopes, Andrew)
>   6. Re: amygdala segmentation atlas influence
>  (Iglesias Gonzalez, Eugenio)
>   7. Deadline approaching: PhD in visual perceptual learning at
>  the Neural Circuits and Cognition lab @ ENI & German Primate
>  Center G?ttingen (Caspar M. Schwiedrzik)
>   8. Re: Overlay electric field distribution on pial surface
>  (Meusen -  Klooster, D.C.W.)
>   9. Re: Overlay electric field distribution on pial surface
>  (Bruce Fischl)
>  10. output values of vertices on surface into a textfile
>  (Sims, Sara A)
> 
> 
>--
> 
>Message: 1
>Date: Tue, 2 Oct 2018 17:00:09 +
>From: "Greve, Douglas N.,Ph.D." 
>Subject: Re: [Freesurfer] Error during decompression of DICOM JPEG
>   compressed series
>To: "freesurfer@nmr.mgh.harvard.edu" 
>Message-ID: <9b313c16-98ba-9434-e1a9-85febbbd2...@mgh.harvard.edu>
>

Re: [Freesurfer] Error during decompression of DICOM JPEG compressed series

[Dicamillo, Robert]

It may be complaining about >& for redirection.  Try using 2>&1 instead.

On Oct 2, 2018, at 4:56 AM, k3...@free.fr wrote:

sh: 1: Syntax error: Bad fd number

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Re: [Freesurfer] Dead Links to 3rd Party Libraries

[Dicamillo, Robert]

Hello Joseph,

Try this link for the 3rd party libs (to use with the cmake build)

http://surfer.nmr.mgh.harvard.edu/pub/data/fspackages/prebuilt/

- rob

On Sep 20, 2018, at 8:39 PM, Moon, Joseph Young-Joon 
mailto:moo...@llnl.gov>> wrote:


External Email - Use Caution

Hi,

I’m trying to build Freesurfer according to the instructions 
athttp://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page

However, the FTP link to prebuilt 3rd party libraries seems to be down. The 
directory “ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt” 
is no longer being hosted.

Please let me know if I misunderstood something!

Thanks,
Joseph Moon

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Re: [Freesurfer] MacOS high Sierra, freesurfer development versiyon build problem! tar.gz

[Dicamillo, Robert]

Hello Emre,

In the terminal window, try at the $ prompt,

$ tar zxpf freesurfer-darwin-OSX-ElCapitan-dev.tar.gz

On Sep 14, 2018, at 8:12 PM, emre mailto:z...@hotmail.com>> 
wrote:

tar.gz

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Re: [Freesurfer] LGI without Matlab license?

[Dicamillo, Robert]

The Mathworks offers runtime distribution that contains the libraries you can 
build your code against w/o needing a Matlab license; you just cannot 
re-distirbute the files from the distribution w/o permission from The 
Mathworks.  I’ve used it to build code that links against libmat etc.   You can 
get it from here,

https://www.mathworks.com/products/compiler/matlab-runtime.html

- rob

On Sep 6, 2018, at 3:45 PM, Thomas, Adam (NIH/NIMH) [E] 
mailto:ad...@nih.gov>> wrote:


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We’d like to calculate the Local Gyrification Index (LGI) on several thousand 
scans, but our HPC cluster does not have the necessary Matlab licenses to do 
this in a reasonable amount of time.

Has anyone managed to compile the LGI code such that it could be run without a 
Matlab license? Or is anyone working on this? Our HPC staff tried to compile 
it, but did not succeed.

Ref: https://surfer.nmr.mgh.harvard.edu/fswiki/LGI


Best Regards,
-Adam Thomas


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Re: [Freesurfer] Unable to copy the license.txt file into $FREESURFER_HOME

[Dicamillo, Robert]

Sent you a reply to your direct email, as attachment I wanted to send is too 
large for list.

- rob

On Aug 24, 2018, at 12:40 PM, Tsz Wai (Bentley) Lo 
mailto:lo...@smh.ca>> wrote:


External Email - Use Caution

Hi FreeSurfer Developers,

I am attempting to copy my license.txt into $FREESURFER_HOME. I have already 
open a terminal window and define and environment variable called 
freesurfer_home but I am not sure where FreeSurfer home is. I am not sure how 
to source the set up script as well. I am on macOS high Sierra.

Bentley




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Re: [Freesurfer] Stats2table_bash.sh script

[Dicamillo, Robert]

Hello K,

If you type

$ asegstats2table --help

you will see that you can specify subjects on the command line as, e.g., for 
bert as

—subjects bert
or apparently
-s bert

It looks like the subjects option expects the name for at least one subjects 
(data),
but the help output says you can list more than one subjects name as the 
argument to
—subjects

On Aug 12, 2018, at 12:31 PM, Schumman Resonance 
mailto:schumm...@gmail.com>> wrote:


External Email - Use Caution


Hi,

I'm trying to run the Stats2table_bash.sh script from Jamaan Alghamdi & Dr. 
Vanessa Sluming.

And I get This error:

  File "/Applications/freesurfer/bin/asegstats2table", line 195
print 'ERROR: subjects are not specified (use --subjects SUBJECTS)'
  ^
SyntaxError: invalid syntax
  File "/Applications/freesurfer/bin/asegstats2table", line 195
print 'ERROR: subjects are not specified (use --subjects SUBJECTS)'
  ^
SyntaxError: invalid syntax
  File "/Applications/freesurfer/bin/aparcstats2table", line 156
print 'ERROR: atleast 1 subject must be provided'
.
.
.



This is my set up:


_


 freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer
FSFAST_HOME   /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /Users/schumman/data
MNI_DIR   /Applications/freesurfer/mni
FSL_DIR   /usr/local/fsl

_


This is the line from SetUpFreeSurfer.sh for my subjects directory


# Set this to your subjects/ dir, usually freesurfer/subjects/
if [ -z $SUBJECTS_DIR ]; then
export SUBJECTS_DIR=/Users/schumman/data


__

And I modified in their script to my FREESURFER_HOME as below


#!/bin/bash
path=`dirname $0`
sleep 1
cd $path
echo "This bash script will create table from ?.stats files"
echo "Written by Jamaan Alghamdi & Dr. Vanessa Sluming"
echo "University of Liverpool"
echo "jamaan.algha...@gmail.com"
echo "http://www.easyneuroimaging.com"
echo "20/12/2010

"


export FREESURFER_HOME=/Applications/freesurfer
sleep 1
source $FREESURFER_HOME/SetUpFreeSurfer.sh
sleep 1

export SUBJECTS_DIR=$PWD
list="`ls -d */`"
asegstats2table --subjects $list --meas volume --skip --statsfile wmparc.stats 
--all-segs --tablefile wmparc_stats.txt
.
.
.


I run the script from my_subject_directory.

I suspect this is something very obvious I'm not able to see and I apologize 
for such a basic question, any help would be much appreciated.

Thanks,
K



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Re: [Freesurfer] Stats2table_bash.sh script

[Dicamillo, Robert]

Hello K,

If you type

$ asegstats2table --help

you will see that you can specify subjects on the command line as, e.g., for 
bert as

—subjects bert
or apparently
-s bert

It looks like the subjects option expects the name for at least one subjects 
(data),
but the help output says you can list more than one subjects name as the 
argument to
—subjects

On Aug 12, 2018, at 12:31 PM, Schumman Resonance 
mailto:schumm...@gmail.com>> wrote:


External Email - Use Caution


Hi,

I'm trying to run the Stats2table_bash.sh script from Jamaan Alghamdi & Dr. 
Vanessa Sluming.

And I get This error:

  File "/Applications/freesurfer/bin/asegstats2table", line 195
print 'ERROR: subjects are not specified (use --subjects SUBJECTS)'
  ^
SyntaxError: invalid syntax
  File "/Applications/freesurfer/bin/asegstats2table", line 195
print 'ERROR: subjects are not specified (use --subjects SUBJECTS)'
  ^
SyntaxError: invalid syntax
  File "/Applications/freesurfer/bin/aparcstats2table", line 156
print 'ERROR: atleast 1 subject must be provided'
.
.
.



This is my set up:


_


 freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer
FSFAST_HOME   /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /Users/schumman/data
MNI_DIR   /Applications/freesurfer/mni
FSL_DIR   /usr/local/fsl

_


This is the line from SetUpFreeSurfer.sh for my subjects directory


# Set this to your subjects/ dir, usually freesurfer/subjects/
if [ -z $SUBJECTS_DIR ]; then
export SUBJECTS_DIR=/Users/schumman/data


__

And I modified in their script to my FREESURFER_HOME as below


#!/bin/bash
path=`dirname $0`
sleep 1
cd $path
echo "This bash script will create table from ?.stats files"
echo "Written by Jamaan Alghamdi & Dr. Vanessa Sluming"
echo "University of Liverpool"
echo "jamaan.algha...@gmail.com"
echo "http://www.easyneuroimaging.com"
echo "20/12/2010

"


export FREESURFER_HOME=/Applications/freesurfer
sleep 1
source $FREESURFER_HOME/SetUpFreeSurfer.sh
sleep 1

export SUBJECTS_DIR=$PWD
list="`ls -d */`"
asegstats2table --subjects $list --meas volume --skip --statsfile wmparc.stats 
--all-segs --tablefile wmparc_stats.txt
.
.
.


I run the script from my_subject_directory.

I suspect this is something very obvious I'm not able to see and I apologize 
for such a basic question, any help would be much appreciated.

Thanks,
K



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Re: [Freesurfer] Untar and sh files in dev version

[Dicamillo, Robert]

Hello K,

Can you try downloading the 6.0.0 release archive from the web site (please 
note it is 4.8G),

freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz<ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz>

Then you will need 5 GB of space to uncompress it.  I would add the v option so 
you can see the expansion in progress,

$ tar zxvpf  freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz

- Rob


On Aug 11, 2018, at 2:55 AM, Schumman Resonance 
mailto:schumm...@gmail.com>> wrote:


External Email - Use Caution

Thanks for your response.
I run the command you suggested and this is what I got:
freesurfer/average/mult-comp-cor/fsaverage_sym/rh/cortex/fwhm04/pos/th33/mc-z.csd:
 (Empty error message)
tar: Error exit delayed from previous errors.

Also, still no .sh files...

Best,
K

On Fri, Aug 10, 2018 at 7:52 PM, Dicamillo, Robert 
mailto:rdicami...@mgh.harvard.edu>> wrote:
Hello Schumman,

Try the following command on the tar archive (cut and paste it if you like)

$ tar zxpf freesurfer-linux-centos6_x86_64-dev.tar.gz

and then take a look at the files.

- Rob

On Aug 10, 2018, at 10:25 PM, Schumman Resonance 
mailto:schumm...@gmail.com>> wrote:


External Email - Use Caution

Hi,

Couple of newbie questions. I downloaded the dev version of freesurfer  and did:
tar xvzf
freesurfer-linux-centos6_x86_64-dev.tar.gz

to get



gzip: stdin: unexpected end of file
tar: Unexpected EOF in archive
tar: Unexpected EOF in archive
tar: Error is not recoverable: exiting now



Also, when I ls the folder I couldn't see the SetUpFreesurfer.sh and 
SurferEnv.sh only the csh files.

Any pointers how to solve these would be appreciated.

Thanks,
S
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Re: [Freesurfer] Untar and sh files in dev version

[Dicamillo, Robert]

Hello Schumman,

Try the following command on the tar archive (cut and paste it if you like)

$ tar zxpf freesurfer-linux-centos6_x86_64-dev.tar.gz

and then take a look at the files.

- Rob

On Aug 10, 2018, at 10:25 PM, Schumman Resonance 
mailto:schumm...@gmail.com>> wrote:


External Email - Use Caution

Hi,

Couple of newbie questions. I downloaded the dev version of freesurfer  and did:
tar xvzf
freesurfer-linux-centos6_x86_64-dev.tar.gz

to get



gzip: stdin: unexpected end of file
tar: Unexpected EOF in archive
tar: Unexpected EOF in archive
tar: Error is not recoverable: exiting now



Also, when I ls the folder I couldn't see the SetUpFreesurfer.sh and 
SurferEnv.sh only the csh files.

Any pointers how to solve these would be appreciated.

Thanks,
S
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Re: [Freesurfer] A Help Request for Freesurfer Installing

[Dicamillo, Robert]

… I forgot to add that the build process listed on the help pages should 
basically work on Ubuntu, if you want to try building it form source; the 
instructions there list Ubuntu 14.

http://freesurfer.net/fswiki/freesurfer_linux_developers_page

- rob

On Jul 18, 2018, at 2:46 AM, Maedeh Khalilian 
mailto:m.khalil...@sutech.ac.ir>> wrote:


External Email - Use Caution

Hello;
This is Maedeh Khalilian, a master student at Shiraz University of Technology.
I have ubuntu 18.04 LTS installed on my laptop. I have already installed 
Freesurfer package but it is the version for CentOS.
I wonder if I can use it with ubuntu.
I would appreciate if you could help me.
Best regards;
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Re: [Freesurfer] A Help Request for Freesurfer Installing

[Dicamillo, Robert]

Hello Maedeh,

I recall building Freesurfer on Ubuntu 16.04, but I don’t have access to that 
machine right now.   I will check to see if I have binaries I can send along, 
and if so, you could try running them on Ubuntu 18.

- rob

On Jul 18, 2018, at 2:46 AM, Maedeh Khalilian 
mailto:m.khalil...@sutech.ac.ir>> wrote:


External Email - Use Caution

Hello;
This is Maedeh Khalilian, a master student at Shiraz University of Technology.
I have ubuntu 18.04 LTS installed on my laptop. I have already installed 
Freesurfer package but it is the version for CentOS.
I wonder if I can use it with ubuntu.
I would appreciate if you could help me.
Best regards;
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Re: [Freesurfer] lazy symbol binding errors

[Dicamillo, Robert]

Hello David,

Please try downloading the following archive, unzip it, and follow the 
instructions in the README to update the files that have the lazy symbol issue.

https://drive.google.com/open?id=1w0vZyWTY0HrbcDiP1jWsmGl_GMUSh7tR

-rob

On Jul 12, 2018, at 4:48 AM, Davide Momi 
mailto:momi.david...@gmail.com>> wrote:


External Email - Use Caution

Dear experts,

I was running mri2mesh command and I got this error:


mris_convert /Users/davidemomi/Desktop/DAVE/sim_fem/fs_subj60/surf/rh.white 
/Users/davidemomi/Desktop/DAVE/sim_fem/m2m_subj60/tmp/wm.rh.stl
dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ___emutls_get_address
  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib


So I've tried to source Freesurfer and run

sudo -E fs_update

But I got another error

rsync -zbrlv --progress --suffix=.1531384527_bak 
rsync://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c/*
 /Applications/freesurfer
rsync: failed to connect to 
surfer.nmr.mgh.harvard.edu: Operation timed 
out (60)
rsync error: error in socket IO (code 10) at 
/BuildRoot/Library/Caches/com.apple.xbs/Sources/rsync/rsync-52/rsync/clientserver.c(106)
 [receiver=2.6.9]


Could you please help me with both errors?

Thanks in advance

Davide
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Re: [Freesurfer] lazy symbol binding errors

[Dicamillo, Robert]

Hello David,

Please try downloading the following archive, unzip it, and follow the 
instructions in the README to update the files that have the lazy symbol issue.

https://drive.google.com/open?id=1w0vZyWTY0HrbcDiP1jWsmGl_GMUSh7tR

-rob

On Jul 12, 2018, at 4:48 AM, Davide Momi 
mailto:momi.david...@gmail.com>> wrote:


External Email - Use Caution

Dear experts,

I was running mri2mesh command and I got this error:


mris_convert /Users/davidemomi/Desktop/DAVE/sim_fem/fs_subj60/surf/rh.white 
/Users/davidemomi/Desktop/DAVE/sim_fem/m2m_subj60/tmp/wm.rh.stl
dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ___emutls_get_address
  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib


So I've tried to source Freesurfer and run

sudo -E fs_update

But I got another error

rsync -zbrlv --progress --suffix=.1531384527_bak 
rsync://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c/*
 /Applications/freesurfer
rsync: failed to connect to 
surfer.nmr.mgh.harvard.edu: Operation timed 
out (60)
rsync error: error in socket IO (code 10) at 
/BuildRoot/Library/Caches/com.apple.xbs/Sources/rsync/rsync-52/rsync/clientserver.c(106)
 [receiver=2.6.9]


Could you please help me with both errors?

Thanks in advance

Davide
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Re: [Freesurfer] recon-all fatal error

[Dicamillo, Robert]

Hello Daniel,

The docker container may not be properly supporting symbolic links, i.e., 
apparently you can write files inside the container, but in your log that error 
 is the first instance of the ln command.

Could you try running it w/o using a container and see if it gets past the ln 
command?   If so, then I would ask someone at your facility to look at the 
docker configuration.  The fix for that error message in some docker postings 
is to upgrade to a newer version of docker.

- rob

On Jul 11, 2018, at 11:06 AM, Daniel Kimmel 
mailto:danielkim...@gmail.com>> wrote:


External Email - Use Caution

Hello,

I'm attempting to run basic preprocessing with reconstruction using 
fmriprep-docker.py and freesurfer. The fmriprep process completes when 
excluding freesurfer, but encounters a fatal error when including freesurfer. 
There error is:

recon-all -s sub-18042401 exited with ERRORS at Wed Jul 11 01:39:47 UTC 2018

For more details, see the log file 
/out/freesurfer/sub-18042401/scripts/recon-all-rh.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Standard error:
ln: failed to create symbolic link 'rh.white.H': Operation not supported
Return code: 1

180711-01:39:51,447 workflow ERROR:
could not run node: 
fmriprep_wf.single_subject_18042401_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon_surfs
180711-01:39:51,452 workflow ERROR:
could not run node: 
fmriprep_wf.single_subject_18042401_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon_surfs
180711-01:39:54,738 cli WARNING:
Errors occurred while generating reports for participants: 18042401 (2).

The call to freesurfer is made by fmriprep, which is doing so within a docker 
container, so unfortunately I don't know the exact version of freesurfer. I'm 
using fmriprep version 1.0.13. I make the call to fmriprep from a CentOS Linux 
box:
uname -a:  Linux xxx.xxx.xxx.columbia.edu 
3.10.0-862.2.3.el7.x86_64 #1 SMP Wed May 9 18:05:47 UTC 2018 x86_64 x86_64 
x86_64 GNU/Linux

I've attached:
1) the complete terminal output from fmriprep (which is reporting the output of 
freesurfer)
2) recon-all-status-rh.log
3) recon-all.log

Thanks very much for your help!
Best,
Daniel




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Re: [Freesurfer] recon-all fatal error

[Dicamillo, Robert]

Hello Daniel,

The docker container may not be properly supporting symbolic links, i.e., 
apparently you can write files inside the container, but in your log that error 
 is the first instance of the ln command.

Could you try running it w/o using a container and see if it gets past the ln 
command?   If so, then I would ask someone at your facility to look at the 
docker configuration.  The fix for that error message in some docker postings 
is to upgrade to a newer version of docker.

- rob

On Jul 11, 2018, at 11:06 AM, Daniel Kimmel 
mailto:danielkim...@gmail.com>> wrote:


External Email - Use Caution

Hello,

I'm attempting to run basic preprocessing with reconstruction using 
fmriprep-docker.py and freesurfer. The fmriprep process completes when 
excluding freesurfer, but encounters a fatal error when including freesurfer. 
There error is:

recon-all -s sub-18042401 exited with ERRORS at Wed Jul 11 01:39:47 UTC 2018

For more details, see the log file 
/out/freesurfer/sub-18042401/scripts/recon-all-rh.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Standard error:
ln: failed to create symbolic link 'rh.white.H': Operation not supported
Return code: 1

180711-01:39:51,447 workflow ERROR:
could not run node: 
fmriprep_wf.single_subject_18042401_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon_surfs
180711-01:39:51,452 workflow ERROR:
could not run node: 
fmriprep_wf.single_subject_18042401_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon_surfs
180711-01:39:54,738 cli WARNING:
Errors occurred while generating reports for participants: 18042401 (2).

The call to freesurfer is made by fmriprep, which is doing so within a docker 
container, so unfortunately I don't know the exact version of freesurfer. I'm 
using fmriprep version 1.0.13. I make the call to fmriprep from a CentOS Linux 
box:
uname -a:  Linux xxx.xxx.xxx.columbia.edu 
3.10.0-862.2.3.el7.x86_64 #1 SMP Wed May 9 18:05:47 UTC 2018 x86_64 x86_64 
x86_64 GNU/Linux

I've attached:
1) the complete terminal output from fmriprep (which is reporting the output of 
freesurfer)
2) recon-all-status-rh.log
3) recon-all.log

Thanks very much for your help!
Best,
Daniel




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Re: [Freesurfer] questions about freeview quit unexpectly

[Dicamillo, Robert]

Hello Shize,

Try downloading the following zip archive, and double click on it to uncompress 
it
https://drive.google.com/file/d/1w0vZyWTY0HrbcDiP1jWsmGl_GMUSh7tR/view?usp=sharing

There is a README file in the archive describing how to update a couple of 
files.  Please try to
apply the updates, and then re-run.

- rob

On Jun 26, 2018, at 4:33 PM, 姜时泽 
mailto:jiangshize1...@163.com>> wrote:


External Email - Use Caution

Hi Rob,
Thank you for your kindly help. This is the log file from terminal. could you 
helps me to figure out what was wrong with it. Many thanks.
Shize

Jun 26 16:31:33 Jiang-Shizes-MacBook-Pro loginwindow[95]: 
-[SFLListManager(ServiceReplyProtocol) notifyChanges:toListWithIdentifier:] 
Notified of item changes to list with identifier 
com.apple.LSSharedFileList.RecentApplications
Jun 26 16:31:33 Jiang-Shizes-MacBook-Pro Freeview[38452]: WARNING: The Gestalt 
selector gestaltSystemVersion is returning 10.9.3 instead of 10.11.3. This is 
not a bug in Gestalt -- it is a documented limitation. Use NSProcessInfo's 
operatingSystemVersion property to get correct system version number.
Call location:
Jun 26 16:31:33 Jiang-Shizes-MacBook-Pro Freeview[38452]: 0   CarbonCore
  0x7fff88942c9b ___Gestalt_SystemVersion_block_invoke + 113
Jun 26 16:31:33 Jiang-Shizes-MacBook-Pro Freeview[38452]: 1   libdispatch.dylib 
  0x7fff872e133f _dispatch_client_callout + 8
Jun 26 16:31:33 Jiang-Shizes-MacBook-Pro Freeview[38452]: 2   libdispatch.dylib 
  0x7fff872e1237 dispatch_once_f + 67
Jun 26 16:31:33 Jiang-Shizes-MacBook-Pro Freeview[38452]: 3   CarbonCore
  0x7fff888ceb47 _Gestalt_SystemVersion + 987
Jun 26 16:31:33 Jiang-Shizes-MacBook-Pro Freeview[38452]: 4   CarbonCore
  0x7fff888cdddb Gestalt + 139
Jun 26 16:31:33 Jiang-Shizes-MacBook-Pro Freeview[38452]: 5   QtCore
  0x00011dfdae46 _Z8qWarningPKcz + 214
Jun 26 16:31:33 Jiang-Shizes-MacBook-Pro Freeview[38452]: 6   ???   
  0x7fff684b5f8b 0x0 + 140734943158155
Jun 26 16:31:33 Jiang-Shizes-MacBook-Pro launchservicesd[80]: 
SecTaskLoadEntitlements failed error=22
Jun 26 16:31:33 --- last message repeated 1 time ---
Jun 26 16:31:33 Jiang-Shizes-MacBook-Pro appleeventsd[51]: 
SecTaskLoadEntitlements failed error=22
Jun 26 16:31:38 Jiang-Shizes-MacBook-Pro launchservicesd[80]: 
SecTaskLoadEntitlements failed error=22
Jun 26 16:31:39 --- last message repeated 1 time ---
Jun 26 16:31:39 Jiang-Shizes-MacBook-Pro WindowServer[166]: 
_CGXRemoveWindowFromWindowMovementGroup: window 0xfe6b is not attached to 
window 0xfe6f
Jun 26 16:31:39 Jiang-Shizes-MacBook-Pro Freeview[38452]: modalSession has been 
exited prematurely - check for a reentrant call to endModalSession:
Jun 26 16:31:39 Jiang-Shizes-MacBook-Pro Freeview[38452]: dyld: lazy symbol 
binding failed: Symbol not found: ___emutls_get_address
  Referenced from: 
/Applications/freesurfer/Freeview.app/Contents/MacOS/../Frameworks/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib
Jun 26 16:31:39 Jiang-Shizes-MacBook-Pro Freeview[38452]: dyld: Symbol not 
found: ___emutls_get_address
  Referenced from: 
/Applications/freesurfer/Freeview.app/Contents/MacOS/../Frameworks/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib
Jun 26 16:31:39 Jiang-Shizes-MacBook-Pro com.apple.xpc.launchd[1] 
(com.yourcompany.Freeview.19232[38452]): Service exited with abnormal code: 59





At 2018-06-27 02:33:31, "Dicamillo, Robert" 
mailto:rdicami...@mgh.harvard.edu>> wrote:
Hi Shize,

You could try looking at the system log.  Before you launch Freeview open a 
terminal window and do,

$  tail -f /var/log/system.log

There will be some output there already from the last recorded system events.

Then launch Freeview, load your file, and when it crashes, see if anything 
relating to Freeview was output to the log file.
If so, you can cut and paste it from the terminal window and send it along.

- rob

On Jun 26, 2018, at 1:30 PM, 姜时泽 
mailto:jiangshize1...@163.com>> wrote:


External Email - Use Caution


Hi Rob
Many thanks for your feedback. There is no notification pop up. The GUI of 
freeview just quit. I am not sure what was wrong with this. DO you have any 
ideas about this? Thank you .
Best wishes
Shize




At 2018-06-27 00:54:45, "Dicamillo, Robert" 
mailto:rdicami...@mgh.harvard.edu>> wrote:
Hello Shize,

Did you see the Finder bring up a window with a notification that Freeview quit 
unexpectedly, with some choices to
click on for “ignore”, “report”, or “reopen” Freeview?If so, it could help 
if you select report, cut and paste (or take a screenshot)
of the first page of the crash report and send it along.

- rob

On Jun 26, 2018, at 12:39 PM, 姜时泽 
mailto:jiangshize1...@163.com>> wrote:


External Email - Use Caution

Dear fresurfer expert

Re: [Freesurfer] questions about freeview quit unexpectly

[Dicamillo, Robert]

Hi Shize,

You could try looking at the system log.  Before you launch Freeview open a 
terminal window and do,

$  tail -f /var/log/system.log

There will be some output there already from the last recorded system events.

Then launch Freeview, load your file, and when it crashes, see if anything 
relating to Freeview was output to the log file.
If so, you can cut and paste it from the terminal window and send it along.

- rob

On Jun 26, 2018, at 1:30 PM, 姜时泽 
mailto:jiangshize1...@163.com>> wrote:


External Email - Use Caution


Hi Rob
Many thanks for your feedback. There is no notification pop up. The GUI of 
freeview just quit. I am not sure what was wrong with this. DO you have any 
ideas about this? Thank you .
Best wishes
Shize




At 2018-06-27 00:54:45, "Dicamillo, Robert" 
mailto:rdicami...@mgh.harvard.edu>> wrote:
Hello Shize,

Did you see the Finder bring up a window with a notification that Freeview quit 
unexpectedly, with some choices to
click on for “ignore”, “report”, or “reopen” Freeview?If so, it could help 
if you select report, cut and paste (or take a screenshot)
of the first page of the crash report and send it along.

- rob

On Jun 26, 2018, at 12:39 PM, 姜时泽 
mailto:jiangshize1...@163.com>> wrote:


External Email - Use Caution

Dear fresurfer experts,
I am currently using freeview 2.0 to check some data. I am not sure why it 
always quit unexpectedly when I try to load a volume. my freeview is installed 
on OS 10.11.3 system. Would you please help me to solve this problem. Thank you.
Best wishes
Shize




--

Shize Jiang
Fudan University,
Department of neurosurgery, Huashan Hospital, Shanghai Medical College
Shanghai,200032,P.R.China
Mobile: (86)18317079839
E-Mail: sjian...@fudan.edu.cn<mailto:sjian...@fudan.edu.cn>












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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 Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] questions about freeview quit unexpectly

[Dicamillo, Robert]

Hello Shize,

Did you see the Finder bring up a window with a notification that Freeview quit 
unexpectedly, with some choices to
click on for “ignore”, “report”, or “reopen” Freeview?If so, it could help 
if you select report, cut and paste (or take a screenshot)
of the first page of the crash report and send it along.

- rob

On Jun 26, 2018, at 12:39 PM, 姜时泽 
mailto:jiangshize1...@163.com>> wrote:


External Email - Use Caution

Dear fresurfer experts,
I am currently using freeview 2.0 to check some data. I am not sure why it 
always quit unexpectedly when I try to load a volume. my freeview is installed 
on OS 10.11.3 system. Would you please help me to solve this problem. Thank you.
Best wishes
Shize




--

Shize Jiang
Fudan University,
Department of neurosurgery, Huashan Hospital, Shanghai Medical College
Shanghai,200032,P.R.China
Mobile: (86)18317079839
E-Mail: sjian...@fudan.edu.cn












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Re: [Freesurfer] Recon-all exited with errors

[Dicamillo, Robert]

I followed up with Ryan off the list one this one yesterday, i.e., he tried one 
of the later dev
builds which fixes those lib issues.  I think recon-all runs for him now w/o 
the lib errors, but
he is getting a non-zero exit from something else.

- rob

On Jun 19, 2018, at 11:00 AM, Hoopes, Andrew 
mailto:ahoo...@mgh.harvard.edu>> wrote:

Hi Ryan, this issue should be fixed in the freesurfer development version, but 
as a temporary fix to get things working in v6, I would suggest disabling SIP 
and rerunning:
http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/
best
Andrew


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Ryan Flores mailto:rya...@stanford.edu>>
Reply-To: FS Help 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Monday, June 18, 2018 at 1:07 PM
To: FS Help 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Recon-all exited with errors


External Email - Use Caution

Dear FS developers,

I tried running recon-all using the -parallel flag over the weekend, but to my 
surprise they all exited with errors. I’m hoping the problem is something 
subtle, but I’m having trouble understanding the error log (please see 
attached). Can someone point out the issue? Thank you for your help.

Best,

Ryan

--
Ryan Flores
Clinical Research Coordinator
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Re: [Freesurfer] crypt_gkey = (null)

[Dicamillo, Robert]

Hello Aaron,

The build timestamp from the output below shows mri_convert is from 8/2014.  
When I look at the build timestamp on our stable 5.3 version of mri_convert I 
see it is from 5/2013.  So the version that you listed is about 1 year newer 
than the 5.3 release I can see.  It is possible that someone downloaded a 
daily/dev build of freesurfer at that time.

You might want to consider running the latest 6.0 release of Freesurfer 
(released in January 2017), which should be fine on CentOS 7.  It can be 
downloaded from, https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall

I also suggest that you start out in a default/clean shell,  set 
FREESURFER_HOME, and then source the setup script for linux,  You can see the 
instructions on that same web page under “Setup and Configuration”.  The setup 
steps should work for version 5 or 6.

- rob

On Jun 12, 2018, at 2:43 PM, Aaron Tanenbaum 
mailto:aaron.b.tanenb...@gmail.com>> wrote:


External Email - Use Caution

I checked my system is not encrypted. I had someone else run the command on the 
same machine. It worked for them. So I changed my BASH environment to a default 
environment. I still get the same error.

I tried this again but with a different FreeSurfer 5.3. turns out the one I was 
using has been altered version of FreeSurfer.  I do not know how it was 
altered. It worked. so it has to do with the altered FreeSurfer.
I ran the command mri_convert -version  on both FreeSurfer.

for the unaltered i get the out put
mri_convert -version
stable5
altered version i get
mri_convert -version
dev build (use --all-info flag for full version info)

with this output i type in mri_convert --all-info
mri_convert  ProgramArguments: --all-info  ProgramVersion: $Name:  $  
TimeStamp: 2018/06/12-18:32:17-GMT  BuildTimeStamp: Aug 22 2014 21:04:47  CVS: 
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $  User: tanenbauma  
Machine: rocky  Platform: Linux  PlatformVersion: 3.10.0-862.el7.x86_64  
CompilerName: GCC  CompilerVersion: 40400
Wondering is this version of mri_convert a developmental version?
Also both version are the CentOS 6 build.


On Tue, Jun 12, 2018 at 1:01 PM Dicamillo, Robert 
mailto:rdicami...@mgh.harvard.edu>> wrote:
Hello Aaron,

You could check to see if the CentOS 7 system is using disk encryption, e.g., 
if the
following command return 1, then it would mean encryption is in use (which can 
be
an issue with FreeSurfer).

$ cat /proc/sys/crypto/fips_enabled

If it returns zero, it could be an issue with a system library like glibc on 
CentOS 7.5
(that does not happen on older versions of  CentOS).

Either way, this is not your doing ;-)


On Jun 12, 2018, at 11:51 AM, Aaron Tanenbaum 
mailto:aaron.b.tanenb...@gmail.com>> wrote:


External Email - Use Caution

I am currently running CentOS 7.5 and attempting to run FreeSurfer 5.3. When i 
get to the part where MRI_convert is creating the the orig001.mgz its gives me 
a segmentation fault. if i run this on a centos 6 system it works fine. below 
is the output of the program.


/data/gizmo/data1/freesurfer5.3/bin/mri_convert 
/data/anlab/Aaron/JoEtzl_testing/Test1/DICOMS/study7/MOCC_AG_002.MR.CCIR-00900_CCIR-0987_Braver.7.27.20180405.144706.1fg9cq4.dcm
 /data/anlab/Aaron/JoEtzl_testing/FreeSurfer/Test1/mri/orig/001.mgz
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
reading from 
/data/anlab/Aaron/JoEtzl_testing/Test1/DICOMS/study7/MOCC_AG_002.MR.CCIR-00900_CCIR-0987_Braver.7.27.20180405.144706.1fg9cq4.dcm...
crypt_gkey = (null)
Segmentation fault (core dumped)



Did I do anything wrong?
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Re: [Freesurfer] crypt_gkey = (null)

[Dicamillo, Robert]

Hello Aaron,

You could check to see if the CentOS 7 system is using disk encryption, e.g., 
if the
following command return 1, then it would mean encryption is in use (which can 
be
an issue with FreeSurfer).

$ cat /proc/sys/crypto/fips_enabled

If it returns zero, it could be an issue with a system library like glibc on 
CentOS 7.5
(that does not happen on older versions of  CentOS).

Either way, this is not your doing ;-)


On Jun 12, 2018, at 11:51 AM, Aaron Tanenbaum 
mailto:aaron.b.tanenb...@gmail.com>> wrote:


External Email - Use Caution

I am currently running CentOS 7.5 and attempting to run FreeSurfer 5.3. When i 
get to the part where MRI_convert is creating the the orig001.mgz its gives me 
a segmentation fault. if i run this on a centos 6 system it works fine. below 
is the output of the program.


/data/gizmo/data1/freesurfer5.3/bin/mri_convert 
/data/anlab/Aaron/JoEtzl_testing/Test1/DICOMS/study7/MOCC_AG_002.MR.CCIR-00900_CCIR-0987_Braver.7.27.20180405.144706.1fg9cq4.dcm
 /data/anlab/Aaron/JoEtzl_testing/FreeSurfer/Test1/mri/orig/001.mgz
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
reading from 
/data/anlab/Aaron/JoEtzl_testing/Test1/DICOMS/study7/MOCC_AG_002.MR.CCIR-00900_CCIR-0987_Braver.7.27.20180405.144706.1fg9cq4.dcm...
crypt_gkey = (null)
Segmentation fault (core dumped)



Did I do anything wrong?
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Re: [Freesurfer] Installing different versions of FreeSurfer on Same computer (error)

[Dicamillo, Robert]

Hello Paul,

By default, the mac installer will install freesurfer under 
/Applications/freesurfer.  There is an
option to change the install location however, see the screenshots under,

https://surfer.nmr.mgh.harvard.edu/fswiki/MacOsInstall

It sounds like you ran the 5.3 installer - did not use the “change install 
location” option,
and got 5.3 under /Applications/freesurfer

Then it sounds like you ran the 6.3 installer, but used the “change install 
location” option - which
clobbered your 5.3 installation under /Applications/fressrufer ?  (I have not 
tried this yet, so
I don’t know what happens).

- rob

On May 29, 2018, at 10:03 PM, miracle ozzoude 
mailto:miracooloz@gmail.wrote>:

   External Email - Use Caution

Hello,

My Mac has v5.3 installed in the default location ( application). However, 
whenever I try to install v6.0 in a different location ( desktop) it deletes 
the existing v5.3 from application. Any solution to this? I’m trying to run the 
brainstem and hippo subfields on v5.3 processed data. Thank you.

Best,
Paul

Sent from my iPhone

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Re: [Freesurfer] Errors are occurring after FreeSurfer Installation

[Dicamillo, Robert]

Hello Stefano,

It looks like you do not have permission to write to
/usr/local/freesurfer/subjects/bert

If multiple people will be using the data there at
the same time, then it is probably not a good idea
for everyone not to be writing to the same location.

An alternative is to set the environment variable
SUBJECTS_DIR to point to a copy of the ./bert
subdirectory under a path you can both read from and write to.

I think the ./bert subdir is about 400M, so you could
try copying it somewhere, e.g., to your $HOME
directory.  So if you ended up with $HOME/bert
as the path to the data, then you would set
SUBJECTS_DIR to $HOME in your shell.

- rob

On May 9, 2018, at 1:20 PM, std...@virgilio.it wrote:


External Email - Use Caution


This errors are occurring when we test FreeSurfer Installation on our server:

1) ubuntu01:/usr/local/freesurfer/subjects> mri_convert sample-001.mgz 
sample-001.nii.gz
mri_convert.bin sample-001.mgz sample-001.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from sample-001.mgz...
TR=7.25, TE=3.22, TI=600.00, flip angle=7.00
i_ras = (-0, -1, -0)
j_ras = (-0, 0, -1)
k_ras = (-1, 0, 0)
writing to sample-001.nii.gz...
niiWrite(): error opening file sample-001.nii.gz
ERROR: failure writing sample-001.nii.gz

2) ubuntu01:/usr/local/freesurfer/subjects> recon-all -i sample-001.nii.gz -s 
bert -all
mkdir: cannot create directory '/usr/local/freesurfer/subjects/bert': 
Permission denied
mkdir: cannot create directory '/usr/local/freesurfer/subjects/bert': 
Permission denied
mkdir: cannot create directory '/usr/local/freesurfer/subjects/bert': 
Permission denied
cp: cannot create regular file 
'/usr/local/freesurfer/subjects/bert/scripts/build-stamp.txt': No such file or 
directory
cat: /usr/local/freesurfer/subjects/bert/scripts/build-stamp.txt: No such file 
or directory
INFO: FreeSurfer build stamps do not match
Subject Stamp:
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
/usr/local/freesurfer/subjects/bert/scripts/patchdir.txt: No such file or 
directory.

3) ubuntu01:/usr/local/freesurfer/subjects> freeview -v sample-001.mgz
freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open 
shared object file: No such file or directory


Thanks

Stefano

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Re: [Freesurfer] Trouble getting git-annex files

[Dicamillo, Robert]

Hello Ruy - sending you a followup off list to your email.

- rob

On May 3, 2018, at 3:16 PM, Ricardo Valle 
<ruyval...@gmail.com<mailto:ruyval...@gmail.com>> wrote:


External Email - Use Caution

Thank you for your help Rob. Could you walk me through how you ran 
setup_configure and configure on Mac?

I ran (from the root of the tree):

  *   ./setup_configure
  *   ./configure F77=/usr/local/bin/gfortran-4.9 CC=/usr/local/bin/gcc-4.9 
CXX=/usr/local/bin/g++-4.9 --with-pkgs-dir=/Users/ruyvalle/Documents/fs-deps/ 
--disable-Werror --prefix=$HOME/fsdev_install --disable-kww-apps
  *   make clean
  *   make -r

Importantly, make -r said:
"Making all in trc
make[2]: Nothing to be done for `all’.”

I’ve tried using --disable-GUI-build instead of --disable-kww-apps with 
configure before as well, as instructed 
here<https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_mac_developers_page>.

I also tried:

  *   cd trc
  *   make dmri_train

The end of make dmri_train’s output is:
ld: entry point (_main) undefined. for architecture x86_64
collect2: error: ld returned 1 exit status
make: *** [dmri_train] Error 1

I believe the --disable-kww-apps causes the Makefile in freesurfer/trc to 
comment out the instructions that would make it build anything. For instance:
#bin_PROGRAMS = dmri_spline$(EXEEXT) \
# dmri_trk2trk$(EXEEXT) \
# dmri_vox2vox$(EXEEXT) \
# dmri_train$(EXEEXT) \
# dmri_paths$(EXEEXT) \
# dmri_pathstats$(EXEEXT) \
# dmri_mergepaths$(EXEEXT) \
# dmri_motion$(EXEEXT) \
# dmri_group$(EXEEXT) \
# dmri_forrest$(EXEEXT)

I tried uncommenting all the dmri_train settings in the Makefile and running 
make dmri_train again, and get the following:
In file included from blood.h:26:0,
 from dmri_train.cxx:26:
vial.h:36:17: fatal error: mpi.h: No such file or directory
 #include 
 ^
compilation terminated.
make: *** [dmri_train.o] Error 1

My guess is that something is not happening properly during ./setup_configure 
or ./configure.

By the way, do you know what the am_* options are in the Makefile?

Ruy
On May 3, 2018, at 1:35 PM, Dicamillo, Robert 
<rdicami...@mgh.harvard.edu<mailto:rdicami...@mgh.harvard.edu>> wrote:

Hello Ruy,

The -r flag to will cause the build to skip some dependencies, e.g., sometimes 
makefiles
will rebuild the world when you don’t need them to, so if you are building only 
1
file, then it can be useful.

It works for me to cd to  ./freesurfer/trc and do the same thing without using
-r, i.e.,

$ cd ./freesurfer/trc
$ rm -f dmri_train dmri_train.o
$ make dmri_train

But I’m doing this in a freesurfer tree where I have already built everything 
once, or I’ve
run the preconfigure, configure steps, and done a make from the top of the tree 
(./freesurfer).

If you see a Makefile in a directory where you want to build, then you can look 
for
the program name in the Makefile.  In this case, if you search for dmi_train in
./freesurfer/trc/Makefile you will see at line 819,

dmri_train$(EXEEXT): $(dmri_train_OBJECTS) $(dmri_train_DEPENDENCIES) 
$(EXTRA_dmri_train_DEPENDENCIES)

This is the rule to build dmri_train, or the target to build 
(dmri_train$(EXEEXT)) is on the left hand side of a colon,
its dependencies are on the right hand side of the colon, and the commands to 
build it are what follows underneath.

The variable $(EXEEXT) gets set to be whatever the executable extension is for 
the OS you are building on; in the
case of linux this is set to an empty string, so for linux the rule could be 
written as,

dmri_train: $(dmri_train_OBJECTS) $(dmri_train_DEPENDENCIES) 
$(EXTRA_dmri_train_DEPENDENCIES)

So you can expect that telling make to build the target “dmri_train” should do 
something, i.e., “make dmri_train”.

But the dependencies for dmri_train include some libraries, which do not get 
built just by typing
“make dmri_train” under ./freesurfer/trc when nothing else has been built in 
the tre.  We can look at trying
to remedy this, but I think the expectation has been that people build from the 
top of the tree
(or at least do that once).

- rob


On May 2, 2018, at 7:16 PM, Ricardo Valle 
<ruyval...@gmail.com<mailto:ruyval...@gmail.com>> wrote:


External Email - Use Caution

Hello Rob,

No, I mean the dmri_train binary that is part of Tracula. The main source file 
is ./freesurfer/trc/dmri_train.cxx. I don’t mind building the whole tree if 
necessary, but I haven’t been able to do so either. Do you know what the -r 
flag to make does?

Thank you,
Ruy
On May 2, 2018, at 6:51 PM, Dicamillo, Robert 
<rdicami...@mgh.harvard.edu<mailto:rdicami...@mgh.harvard.edu>> wrote:

Hello Ruy,

Do you mean the mri_train binary that gets built under ./freesurfer/mri_train ?
(I see a ./freesurfer/dmri_poistats, ./freesurfer/dmri_tensroreig but not a 
./freesurfer/dmri_train).

Things are not necessarily setup so you can cd to ./freesurfer/ and 
just build
what is there in isolation from 

Re: [Freesurfer] Trouble getting git-annex files

[Dicamillo, Robert]

Hello Ruy,

The -r flag to will cause the build to skip some dependencies, e.g., sometimes 
makefiles
will rebuild the world when you don’t need them to, so if you are building only 
1
file, then it can be useful.

It works for me to cd to  ./freesurfer/trc and do the same thing without using
-r, i.e.,

$ cd ./freesurfer/trc
$ rm -f dmri_train dmri_train.o
$ make dmri_train

But I’m doing this in a freesurfer tree where I have already built everything 
once, or I’ve
run the preconfigure, configure steps, and done a make from the top of the tree 
(./freesurfer).

If you see a Makefile in a directory where you want to build, then you can look 
for
the program name in the Makefile.  In this case, if you search for dmi_train in
./freesurfer/trc/Makefile you will see at line 819,

dmri_train$(EXEEXT): $(dmri_train_OBJECTS) $(dmri_train_DEPENDENCIES) 
$(EXTRA_dmri_train_DEPENDENCIES)

This is the rule to build dmri_train, or the target to build 
(dmri_train$(EXEEXT)) is on the left hand side of a colon,
its dependencies are on the right hand side of the colon, and the commands to 
build it are what follows underneath.

The variable $(EXEEXT) gets set to be whatever the executable extension is for 
the OS you are building on; in the
case of linux this is set to an empty string, so for linux the rule could be 
written as,

dmri_train: $(dmri_train_OBJECTS) $(dmri_train_DEPENDENCIES) 
$(EXTRA_dmri_train_DEPENDENCIES)

So you can expect that telling make to build the target “dmri_train” should do 
something, i.e., “make dmri_train”.

But the dependencies for dmri_train include some libraries, which do not get 
built just by typing
“make dmri_train” under ./freesurfer/trc when nothing else has been built in 
the tre.  We can look at trying
to remedy this, but I think the expectation has been that people build from the 
top of the tree
(or at least do that once).

- rob


On May 2, 2018, at 7:16 PM, Ricardo Valle 
<ruyval...@gmail.com<mailto:ruyval...@gmail.com>> wrote:


External Email - Use Caution

Hello Rob,

No, I mean the dmri_train binary that is part of Tracula. The main source file 
is ./freesurfer/trc/dmri_train.cxx. I don’t mind building the whole tree if 
necessary, but I haven’t been able to do so either. Do you know what the -r 
flag to make does?

Thank you,
Ruy
On May 2, 2018, at 6:51 PM, Dicamillo, Robert 
<rdicami...@mgh.harvard.edu<mailto:rdicami...@mgh.harvard.edu>> wrote:

Hello Ruy,

Do you mean the mri_train binary that gets built under ./freesurfer/mri_train ?
(I see a ./freesurfer/dmri_poistats, ./freesurfer/dmri_tensroreig but not a 
./freesurfer/dmri_train).

Things are not necessarily setup so you can cd to ./freesurfer/ and 
just build
what is there in isolation from the rest of the tree.

But for ./freesiurfer/mri_train, you could try the following, which worked for 
me on a Mac, e.g.,
after changing mri_train.c,

$ cd ./freesurfer/mri_train
$ rm -f mri_train mri_train.o
$ make -r mri_train

- rob




On May 2, 2018, at 5:37 PM, Ricardo Valle 
<ruyval...@gmail.com<mailto:ruyval...@gmail.com>> wrote:


External Email - Use Caution

Hello,

I need help recompiling dmri_train for Mac. It seems like the instructions in 
the Mac Developer’s don’t work.

When I cd to the trc subdirectory and run make, I am told there is nothing to 
do. I tried editing the Makefile, adding bin_PROGRAMS = dmri_train, at which 
point I got a different error. I then uncommented some other lines in the 
Makefile and managed to start compiling dmri_train, but I’ve been getting a 
never-ending sequence of errors, essentially telling me that the compiler can’t 
find various dependencies (boost/program_options.h, itk*.h, etc.). I’ve tried 
running ./configure with various flags that disable or enable various build 
options, copying over .h files from other locations, adding -I  
directives for the compiler in the Makefile, etc. etc. to no avail.

Thank you,
Ruy
On Apr 30, 2018, at 5:19 PM, Ricardo Valle 
<ruyval...@gmail.com<mailto:ruyval...@gmail.com>> wrote:

Dear Freesurfer community,

I am trying to recompile Freesurfer in order to get a binary of the latest 
version of dmri_train. I have been following the instructions in the Freesurfer 
Mac Developer’s 
page<https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_mac_developers_page> 
and am stuck at the following:
git annex get --metadata fstags=makeinstall .

I am attaching the output (stdout and stderr) from this command to this email. 
Please note that I called the git-annex repository mgh rather than datasrc. The 
purpose of running this is so I can run make install.

Is there a way of recompiling only dmri_train or only the dmri_* programs? If 
not, do you know why git-annex might be giving me problems and how to solve 
this?

Thank you,
Ruy


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Re: [Freesurfer] Trouble getting git-annex files

[Dicamillo, Robert]

Hello Ruy,

Do you mean the mri_train binary that gets built under ./freesurfer/mri_train ?
(I see a ./freesurfer/dmri_poistats, ./freesurfer/dmri_tensroreig but not a 
./freesurfer/dmri_train).

Things are not necessarily setup so you can cd to ./freesurfer/ and 
just build
what is there in isolation from the rest of the tree.

But for ./freesiurfer/mri_train, you could try the following, which worked for 
me on a Mac, e.g.,
after changing mri_train.c,

$ cd ./freesurfer/mri_train
$ rm -f mri_train mri_train.o
$ make -r mri_train

- rob




On May 2, 2018, at 5:37 PM, Ricardo Valle 
> wrote:


External Email - Use Caution

Hello,

I need help recompiling dmri_train for Mac. It seems like the instructions in 
the Mac Developer’s don’t work.

When I cd to the trc subdirectory and run make, I am told there is nothing to 
do. I tried editing the Makefile, adding bin_PROGRAMS = dmri_train, at which 
point I got a different error. I then uncommented some other lines in the 
Makefile and managed to start compiling dmri_train, but I’ve been getting a 
never-ending sequence of errors, essentially telling me that the compiler can’t 
find various dependencies (boost/program_options.h, itk*.h, etc.). I’ve tried 
running ./configure with various flags that disable or enable various build 
options, copying over .h files from other locations, adding -I  
directives for the compiler in the Makefile, etc. etc. to no avail.

Thank you,
Ruy
On Apr 30, 2018, at 5:19 PM, Ricardo Valle 
> wrote:

Dear Freesurfer community,

I am trying to recompile Freesurfer in order to get a binary of the latest 
version of dmri_train. I have been following the instructions in the Freesurfer 
Mac Developer’s 
page 
and am stuck at the following:
git annex get --metadata fstags=makeinstall .

I am attaching the output (stdout and stderr) from this command to this email. 
Please note that I called the git-annex repository mgh rather than datasrc. The 
purpose of running this is so I can run make install.

Is there a way of recompiling only dmri_train or only the dmri_* programs? If 
not, do you know why git-annex might be giving me problems and how to solve 
this?

Thank you,
Ruy


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Re: [Freesurfer] Freesurfer and crypt

[Dicamillo, Robert]

Hi Bennet,

I’m attaching a compressed tar file, chklc_fips.tgz, that is an attempt at 
creating a binary
(chklc_fips) that uses its own local version of crypt.  See the README file 
when you
untar the archive.   This is not officially supported in any way, and while it 
can read
my license file in a non-FIPS environment, I cannot say if it will actually 
work for you.

- -rob


On Apr 19, 2018, at 10:14 AM, Bennet Fauber 
<ben...@umich.edu<mailto:ben...@umich.edu>> wrote:


Hi, Rob,

The call to crypt() appears to be in FreeSurfer's license validation routine, 
since it is immediately after reading the license file.  In the sense that 
FreeSurfer cannot run without some sort of license, and that license validation 
is using the native Unix crypt() function to validate, it's not quite 
OpenSource.  I think someone at FreeSurfer would need to replace the single 
call to the crypt() function with some other function that isn't marked as 
'insecure' to bypass this.

I thought I saw something earlier on the mailing list about this, and that 
there was a workaround, but I am unable to locate it again.  Any chance this 
could get passed to the developer who maintains the license validation code?  
Depending on the code and their willingness to share, we might be able to 
contribute an alternative for systems with the elevated security.

This currently may not be a bit issue, but we are seeing increasing strictness 
on our end to comply with federal security guidelines, and it may not just be 
our Medical Center and local VA that are pushing these security measures.

This is what it looks like when it succeeds.

11527 open("/sw/arcts/centos7/freesurfer/6.0.0/license.txt", O_RDONLY) = 3
11527 fstat(3, {st_mode=S_IFREG|0644, st_size=52, ...}) = 0
11527 mmap(NULL, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) 
= 0x2b4bcc176000
11527 read(3, "ben...@umich.edu<mailto:ben...@umich.edu>\n6925\n *CpU.rbF6"..., 
8192) = 52
11527 read(3, "", 8192) = 0
11527 open("/proc/sys/crypto/fips_enabled", O_RDONLY) = 4
11527 read(4, "0\n", 31)= 2
11527 close(4)  = 0
11527 close(3)  = 0
11527 munmap(0x2b4bcc176000, 8192)  = 0
11527 getcwd("/home/bennet/tmp/freesurfer", 4096) = 28
11527 open("/home/bennet/tmp/freesurfer/sample-001.mgz", O_RDONLY) = 3

I do not believe that this is something that can be 'whitelisted', as this is 
set in the Linux kernel at boot time.

Thanks,-- bennet


On Thu, Apr 12, 2018 at 11:29 AM, Dicamillo, Robert 
<rdicami...@mgh.harvard.edu<mailto:rdicami...@mgh.harvard.edu>> wrote:
Hello Bennet,

Maybe someone else can chime in on this, as I have not worked on a system
with FIPS, but perhaps there is a way for the FIPS administrator to white list
all the Freesurfer binaries (and the license file), as security exempt.

I know some Enterprise/business applications like Adobe’s Acrobat, etc.,
(closed source) are built with code to work on FIPS compliant systems, but
I don’t see there is currently anything in Freesurfer (essentially open source),
code that knows about cryptographic modules, digital signatures, etc. to work on
a secure system.  Even turning on SElinux for linux OS can be an
issue for some programs.

Another thing to inquire about is if the IT folks maintain any non-secure 
servers,
, i.e., I would not assume that any application will just work in a secure 
environment.

- rob

> On Apr 12, 2018, at 10:51 AM, Bennet Fauber 
> <ben...@umich.edu<mailto:ben...@umich.edu>> wrote:
>
> It appears that FreeSurfer is not compatible with systems for which
> FIPS level security is mandated.  In our case, I am told this is part
> of our data use agreement with the VA.
>
> We tried to run it, and I get the following stack trace showing what
> appears to be license validation using the crypt() function, which is
> blacklisted by the Linux kernel by the FIPS configuration.
>
> 28063 open("/opt/apps/freesurfer-6.0/freesurfer/license.txt", O_RDONLY) = 3
> 28063 fstat(3, {st_mode=S_IFREG|0644, st_size=59, ...}) = 0
> 28063 mmap(NULL, 4096, PROT_READ|PROT_WRITE,
> MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x7fa319883000
> 28063 read(3, 
> "issc-sysad...@umich.edu<mailto:issc-sysad...@umich.edu>\n23098\n*C"..., 
> 4096) = 59
> 28063 read(3, "", 4096) = 0
> 28063 open("/proc/sys/crypto/fips_enabled", O_RDONLY) = 4
> 28063 read(4, "1\n", 31)= 2
> 28063 close(4)  = 0
> 28063 write(1, "ERROR: crypt() returned null wit"..., 46) = 46
> 28063 exit_group(1)
>
> Is there a workaround so we can run FreeSurfer FIPS-enabled systems?
>
> Appreciate your consideration of this question,
>
> -- bennet
>
>
&

Re: [Freesurfer] mri_deface keeps seg faulting

[Dicamillo, Robert]

Can you ls /usr/local/freesurfer/stable6/bin

If so, you could put that at the start of your path to get the release 6
binaries.

-rob

On Apr 17, 2018, at 11:39 AM, Warner, Graham Cary 
> wrote:

Hi,

I'm trying to deface an MEMPRAGE dataset using the following command:


[jazz:test_deface] (nmr-stable53-env) mri_deface outSubDir/mri/orig/001.mgz  
talairach_mixed_with_skull.gca face.gca sample_T1_input_defaced.mgz

and am getting the output:


logging results to sample_T1_input_defaced.log
reading 'talairach_mixed_with_skull.gca'...
reading 'outSubDir/mri/orig/001.mgz'...
changing type of input volume to 8 bits/voxel...
MRIchangeType: Building histogram
Segmentation fault (core dumped)

I'm using the Martinos center's default version of mri_deface located at 
/usr/local/freesurfer/stable5_3_0/bin/mri_deface. I'm using the 
talairach_mixed_with_skull.gca and face.gca sample files found 
onhttps://surfer.nmr.mgh.harvard.edu/fswiki/mri_deface but the actual input mgz 
came from a scanner here at the center. Maybe this is a CentOS 7 compatibility 
problem? Please let me know if there is any other information I can provide.

Thank you,
Graham
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Re: [Freesurfer] Freesurfer and crypt

[Dicamillo, Robert]

Hello Bennet,

Maybe someone else can chime in on this, as I have not worked on a system
with FIPS, but perhaps there is a way for the FIPS administrator to white list 
all the Freesurfer binaries (and the license file), as security exempt.

I know some Enterprise/business applications like Adobe’s Acrobat, etc.,
(closed source) are built with code to work on FIPS compliant systems, but
I don’t see there is currently anything in Freesurfer (essentially open source),
code that knows about cryptographic modules, digital signatures, etc. to work on
a secure system.  Even turning on SElinux for linux OS can be an
issue for some programs.

Another thing to inquire about is if the IT folks maintain any non-secure 
servers,
, i.e., I would not assume that any application will just work in a secure 
environment.

- rob

> On Apr 12, 2018, at 10:51 AM, Bennet Fauber  wrote:
> 
> It appears that FreeSurfer is not compatible with systems for which
> FIPS level security is mandated.  In our case, I am told this is part
> of our data use agreement with the VA.
> 
> We tried to run it, and I get the following stack trace showing what
> appears to be license validation using the crypt() function, which is
> blacklisted by the Linux kernel by the FIPS configuration.
> 
> 28063 open("/opt/apps/freesurfer-6.0/freesurfer/license.txt", O_RDONLY) = 3
> 28063 fstat(3, {st_mode=S_IFREG|0644, st_size=59, ...}) = 0
> 28063 mmap(NULL, 4096, PROT_READ|PROT_WRITE,
> MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x7fa319883000
> 28063 read(3, "issc-sysad...@umich.edu\n23098\n*C"..., 4096) = 59
> 28063 read(3, "", 4096) = 0
> 28063 open("/proc/sys/crypto/fips_enabled", O_RDONLY) = 4
> 28063 read(4, "1\n", 31)= 2
> 28063 close(4)  = 0
> 28063 write(1, "ERROR: crypt() returned null wit"..., 46) = 46
> 28063 exit_group(1)
> 
> Is there a workaround so we can run FreeSurfer FIPS-enabled systems?
> 
> Appreciate your consideration of this question,
> 
> -- bennet
> 
> 
> 
> On Thu, Mar 29, 2018 at 5:05 PM, Bennet Fauber  wrote:
>> I have a couple of users here who are reporting that on machines with
>> FIPS enabled, which in turn disables certain cryptographic functions,
>> FreeSurfer core dumps with a call to the crypt() function, which FIPS
>> disables.
>> 
>> Someone speculated based on output from strace that this is FreeSurfer
>> possibly attempting to validate its license.
>> 
>> Is this a known problem?  Is there a solution?
>> 
>> We have a university compliance office and possibly similar people
>> from our local VA who are insisting that FIPS be enabled.
>> 
>> If you need more information, please let me know and I will try to
>> obtain it for you.
>> 
>> Thanks,-- bennet
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Re: [Freesurfer] -make all error

[Dicamillo, Robert]

Hello Carissa,

There have been some changes to the files related to the “—make all” option.  
You can try downloading an updated version of the
 recon-all.makefile from the list of files under,

ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/centos7_x86_64/

and replace the existing one in $FREESURFER_HOME/bin with the downloaded one.

One way to do this from the terminal would be,

… move aside the old recon-all.makefile.OLD ...

$ mv  $FREESURFER_HOME/bin/recon-all.makefile  
$FREESURFER_HOME/bin/recon-all.makefile.OLD

… and if you downloaded the new one into your home directory downloads folder, 
then you would copy it in from
the path, e.g., if saved to $HOME/Downloads,

$ cp  -f  $HOME/Downloads/recon-all.makefile  
$FREESURFER_HOME/bin/recon-all.makefile

… check they files now the same - you should get no output from the diff 
command …

$ diff  $HOME/Downloads/recon-all.makefile  
$FREESURFER_HOME/bin/recon-all.makefile

The try running  your rein-all again.

- rob


On Apr 11, 2018, at 11:53 AM, Carissa Nicole Weis 
> wrote:

Hello,

I am running recon-all for several subjects’ 7T data using Freesurfer version 
6.0 and currently trying to ensure appropriate skull stripping and pial/wm 
surface generation. For a few participants that needed some control points 
added and for which I reran them through the –autorecon2-cp option, I was 
unable to open the pial surfaces for review. I’ve seen on some of the other 
posts that you guys recommend running “recon-all –make all” to rebuild the 
files. I’ve tried to run the -make all command but have been running into the 
same error in the “Jacobian white lh” step:

#@# Jacobian white lh Wed Apr 4 12:07:37 CDT 2018
/bigraid-03/LS/Data/7T_fall2017/6315/6315_fs/scripts

mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg 
../surf/lh.jacobian_white

reading surface from ../surf/lh.white.preaparc…
mrisReadTriangleFile(../surf/lh.sphere.reg): surface doesn’t match 
../surf/lh.white.preaparc

No such file or directory
mrisReadTriangleFile failed.

No such file or directory
mris_jacobian: could not read target surface ../surf/lh.sphere.reg
No such file or directory

recon-all –s 6315_fs exited with ERRORS at Wed Apr 4 12:07:40 CDT 2018


All of the output in the log file up until this point appears to have finished 
without error. I can now open the surfaces for review, but am wondering what is 
affected by –make all not finishing completely.


Carissa N. Weis, B.S.
Graduate Student
Affective Neuroscience Laboratory
University of Wisconsin-Milwaukee
cnw...@uwm.edu

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Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

[Dicamillo, Robert]

If you are running on Ubuntu, I have a build of the freesurfer source checked
out from about one month ago (March 9th) that I did on an Ubuntu 16.04 system 
using gcc 4.9.

However,  I did not have the test data to run tests, so I must add the 
disclaimer that the binaries
have not gone thru the usual tests.  But if you want to try it, you can download
the compressed ~2G archive from the link below.  It is an archive of the 
./install
tree with ./bin, ./lib, etc.

https://drive.google.com/file/d/1hWs3gdfVExRMW5nl-aufQyMX8yWSHi8Y/view?usp=sharing

- rob

On Apr 9, 2018, at 2:31 PM, Hoopes, Andrew 
> wrote:

Hi Anna,

Unfortunately, we’re not able to build the dev code right now due to a compile 
error, but this should get sorted out within the next day or two, so I can help 
you out with getting this new mri_normalize then

best
Andrew

From: 
>
 on behalf of Anna Daniels 
>
Reply-To: FS Help 
>
Date: Monday, April 9, 2018 at 1:10 PM
To: FS Help 
>
Subject: Re: [Freesurfer] recon-all: exited with errors (white matter peak at 
110, cannot allocate memory)

Hi Bruce,
thank you for the quick reply!
Ubuntu 16.04 LTS 64-bit
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Please let me know how to incorporate the new version into the installation.
Thank you very much and best,
Anna


Hi Anna

no attachments :<

Srishti's issue stemmed from control points outside of the head. The
current (dev) version of mri_normalize detects and removes them. Can you
grab a new version of mri_normalize and see if it fixes your problem? Let
us know your hardware/software environment and we will get it to you

cheers
Bruce


On Fri, 6 Apr 2018, Anna Daniels wrote:

> Hi Bruce, hi Srishti,
>
> I have exactly the same problem with several subjects rerunning recon-all
> and there was sufficient memory available. I also tried out the last command
> directly which resulted in the same error log.
>
> ?mri_normalize 
> -f/home/anna/FREESURFER/00_DATA_MABT1T2/02a_MABT1T2_cross_edits_transfer/rrer
> uncrosstest_cp17/22275_T1_fs_edit/tmp/control.dat -mprage -aseg
> aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz
>
> Attached you can find the input file.
>
> Thank you and best,
> Anna?[icon_10_generic_list.png] ?22275_T1_fs_edit.zip[IMAGE]
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Re: [Freesurfer] Building from source #3 -- dynamic binding

[Dicamillo, Robert]

Hello Yaroslav,

I believe there is already an option that can be set at configure time to build 
dynamical;ly, though
I have not tried it. e.g., maybe it causes the libraries that
Freesurfer builds internally to be built as shared instead of static.

However, at least in out nightly builds, the freesurfer binaries link
dynamically with the linux system libs.  It looks like there are about 130
linux system libraries referenced by all the ELF files in a built freesurfer 
tree.

By comparison I think there may be no more then 15 static libs built and linked
against inside the freesurfer tree.  While these could be built shared, I’m
not sure there is an expectation that end users should be able to replace/update
these libs within a release of Freesiurfer.

- rob


> On Mar 29, 2018, at 4:36 PM, Yaroslav Halchenko 
>  wrote:
> 
> Dear FreeSurfer developers,
> 
> I would like to pick up on this elderly theme by wondering:
> 
> Would you be philosophically opposed against patches/pull requests
> which introduce dynamic linking for freesurfer build?  
> 
> Would anyone from the FreeSurfer team be interested to pursue such
> an effort?
> 
> The idea is to try to reincarnate the effort of pulling
> functionality/binary-code which is now spread/duplicated across many
> distributed statically linked binaries, into a set of (internal)
> libraries.  Benefits IMHO are numerous, starting from
> 
> - smaller binary distribution
> 
> - consistency (replacing one patched binary copy but leaving the
>  other copies which linked statically unpatched)
> 
> - ...
> 
> 
> Cheers,
> 
> On Sun, 21 Feb 2016, Yaroslav Halchenko wrote:
>> On Sun, 21 Feb 2016, zkauf...@nmr.mgh.harvard.edu wrote:
> 
>>> This topic gets brought up occasionally and their are valid arguments
>>> to both sides. One reason we have hesitated to use dynamic libs is the
>>> partly due to freesurfers long release cycle (all subjects that are
>>> part of a study need to be performed all on the same version). This
>>> long release cycle sometimes necessitates fixes to a particular binary
>>> in the stream, which users are then free to use. Although this is a
>>> less than ideal release strategy, it is the reality of the situation.
>>> And if we linked against dynamic libs than any time a binary was
>>> updated, ALL those libs, would need to be updated,
>>> which in turn would affect all binaries which link against them. 
> 
>> AFAIK it is exactly the other way around ;) Please correct me if I
>> am wrong.
> 
>> With static inclusion of code, if the fix is in the code which is shared
>> among binaries, you will need  to provide new copies for all those
>> effected binaries so they come with new copies of that code.   Only if
>> the fix is within code specific to the binary -- only that binary
>> indeed.
> 
>> In case if that 'fixed' code being a part of an internal dynamic library
>> [*], you would need to provide only a copy of that library, and binaries
>> linked against it can stay original since they just dynamically load
>> that code from the library and do not carry broken code.   If it
>> is a fix to the code specific to the binary -- situation is just the
>> same as with static linking.
> 
>> [*] under assumption that the fix doesn't entail changing  API/ABI.  In
>> case if those change -- indeed adjustment/rebuild of dependent binaries
>> would be necessary.  BUT such situations come much less often than just
>> fixes of the code without changing data structures and function
>> interfaces. And in your case, even if that happens, it is just a matter
>> again of uploading all those affected binaries (as you would do with
>> static linking) + the dynamic library.  And again, I think, even if a
>> binary uses some functionality of the library, but not a 'fixed'
>> function, it could as well stay without 'update' while linking to
>> the new dyn library.
> 
>> That is the primary reason why Linux distributions rely on dynamic
>> libraries and reusing system-wide installed artifacts (e.g. java script
>> "libraries", Python modules, etc) as often as possible -- to fix a
>> vulnerability in the code of a core library/artifact requires just
>> upload of the fixed library/artifact without rebuilding all binaries (or
>> replacing all copies of artifacts) which could have potentially absorbed
>> that code via static "linking".  Could you imagine the chaos if
>> libc was statically included in every binary and then security fix
>> was needed to propagate to all 30,000 packages? ;)
> 
> 
>>> I suppose only newly released binaries could be static,
>>> but their may be unintended consequences that Im not thinking of at the
>>> moment.
> 
>>> Im open to conversing about this, and appreciate any constructive feedback
>>> on improving our release model. 
> 
>> Well -- I can't recommend anything new really, and just repeat my
>> whining: modularize just a bit (e.g. separate package for heavy data
>> pieces which rarely change + dynamic 

Re: [Freesurfer] Problem running mri_convert

[Dicamillo, Robert]

Hello Jay,

I think this undefined reference has been fixed in the builds of the freesurfer
source for the Mac since the 6.0.0 release.  I am just not sure how to get
an update to you.  But stay tuned.

- rob

On Mar 22, 2018, at 10:02 PM, Jay Edelman 
> wrote:

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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