Melodic GUI failed to open on qball 1. Sounds like some environment setting issue within FSL.

qball2 has empty /data/qb/
need to map path to Atlanta/ ?

We will need hc-ICA tools installed on all clusters. Anna, myself, and Bruce will need this tool to generate prelim data for upcoming grants and for papers. The download link can be found here : http://web1.sph.emory.edu/users/yguo2/software.html

There is a severe lack of homogeneity across clusters (for example, melodic works on one, but fails on another cluster ; matlab license is updated on one but not on others) that makes it very inconvenient for users to smoothly process data without having to switch (i.e. ssh into different cluster) just to accomplish one specific part of processing . It is understandable that some softwares that require expensive resources (for example, eddy CUDA) cannot be installed across all clusters, but maintaining homogeneity for other generic and relatively inexpensive software is logical and reasonable, and also important from the perspective of keeping our neuroimaging core users happy...after all a lot of them are working hard (without making too many excuses) to generate prelim data to support themselves or other investigators, generate products and papers for the lab and so on... :-)

Hi,
Gateway01 will not open on KSPACE Mac. The windows machine was restarted, so this seems to be an issue with KSPACE.
Best,
LCK

There are at least a couple of lab laptops that need attention. This request is not urgent, urgent, but still important when we need these laptops to work during critical needs such as data collection and webinars.

1. The QED laptop (sitting in my office for Erica's inventory) keeps rebooting. This was the laptop on which I had practiced for Argye's talk, but when I turned it on while setting up for the talk, it would allow me to log-in and while it was configuring the desktop settings, it would reboot. This happened several times, and was no good when I needed it to work especially before a seminar talk.

2. The Dell laptop (Neuro 165LT) sitting in a laptop bag in neuroimaging lab also has some issues. It was used for Argye's talk, but it decided to reboot in the middle of skype talk. It even started making loud sound even after unhooking from all the other A/V setup we have in the conference room.

FSL has been standardized on Ralph to run from the neurodebian version. This is the most updated version, but it complains that it wants fsleyes to be run instead of fslview.

You can still run fslview but you have to type: fslview_deprecated

I am in the midst of installing fsleyes on ralph. Pano is next.

Regarding the server exclusively mounted on Pano (aka "ache" or "simoneroberts"),

When using it for FSL tools such as fsleyes/fslview, flirt, fslmaths, etc, it very often freezes and becomes inaccessible. I rsynced the data I'm actively processing to a local drive and have not had these issues recur since.

I wanted to report that this server might need troubleshooting. Other than server data preservation, this is not high priority if no additional indications of broader Pano problems arise.

Hi Keith,

We've been using multiple iterations of a FIX command to try to run standard classifiers. I get an error message from the very beginning.

This link says that maybe it's something to do with installation of some version of R?
https://www.nitrc.org/forum/forum.php?thread_id=7610&forum_id=2

I know the standard classifiers are working for Stella and others, but she tried to run on my data, and it didn't work.

Not sure if you might be able to help troubleshoot in your "copious free time"? 😉

Thanks,

A

Anna Woodbury, MD, C.Ac
Assistant Professor | Anesthesiology
Associate Program Director | Emory Pain Fellowship
Emory University School of Medicine
VA Pain Clinic | 404-321-6111 x 5563
From: Woodbury, Anna
Sent: Monday, June 11, 2018 7:26 PM
To: Krishnamurthy, Venkatagiri
Subject: Re: Unable to run standard classifiers

Here's the new error message in the attached screenshot after I used what you suggested.

It looks like I need to specify an output directory/output file? where should I do that? Is it "-o...blablabla?"

Anna Woodbury, MD, C.Ac
Assistant Professor | Anesthesiology
Associate Program Director | Emory Pain Fellowship
Emory University School of Medicine
VA Pain Clinic | 404-321-6111 x 5563
From: Krishnamurthy, Venkatagiri
Sent: Monday, June 11, 2018 6:37:25 PM
To: Woodbury, Anna
Subject: RE: Unable to run standard classifiers

Anna,

On lens, you will need to do : /usr/local/fix1.06/fix –c PENFS_blabla.ica /usr/local/fix1.06/training_files/WhII_MB6.RData 15

Also, since your’s is multiband data, you will need to use the ‘WhII_MB6.RData’ classifier and not the one you had in your print screen shot. J

-Giri.

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I am facing a problem to open melview, an image(MRI) viewer software.I have installed all necessary dependencies for tis software. It was working fine with Ubuntu 14.04 LTS. When I have upgraded it to Ubuntu 16.04 LTS, I am facing this problem. It seems like some configuration has to be done for python in Ubuntu 16.04 LTS.

After installing melview and its dependencies I was trying to open melview. But got the following error message.

pc@RB:$ whereis melview
melview: /usr/bin/melview /usr/local/bin/melview/usr/share/man/man1/melview.1.gz
pc@RB:$ melview
No such file: ''
Traceback (most recent call last):
File "/usr/local/bin/melview", line 9, in
load_entry_point('melview==1.0.1', 'console_scripts', 'melview')()
File "build/bdist.linux-x86_64/egg/melview/melodic_traits.py", line 863, in main
File "build/bdist.linux-x86_64/egg/melview/melodic_traits.py", line 514, in init
nibabel.py3k.FileNotFoundError: No such file: ''
pc@RB:$ python melview
python: can't open file 'melview': [Errno 2] No such file or directory
pc@RB:$ python2.7 melview
python2.7: can't open file 'melview': [Errno 2] No such file or directory
pc@RB:~$

software-installation python
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edited Jan 20 '17 at 6:17
d a i s y
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asked Jan 20 '17 at 4:37
Ramesh
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This is accurate. The issue is the updated ni-babel 2.1

This solves the error:

No such file: '' Traceback (most recent call last): File "/usr/local/bin/melview", line 9, in load_entry_point('melview==1.0.1', 'console_scripts', 'melview')() File "build/bdist.linux-x86_64/egg/melview/melodic_traits.py", line 863, in main File "build/bdist.linux-x86_64/egg/melview/melodic_traits.py", line 514, in init nibabel.py3k.FileNotFoundError: No such file: ''

In Xubuntu 14.04 with neurodebian:

to fix:

sudo apt-get update

sudo apt-get install python-nibabel=1.2.2-1

sudo apt-mark hold python-nibabel

Hi,
afni's 3dcopy command cannot be found on Ralph. Print screen below in case I am just using it incorrectly...
Best,
-LCK

The computer in the imaging lab is burping. Please give it the equivalent of an antacid. @kmcgregor123456

Could you please upgrade Rama to support "vim"?? It is easiest for me to teach Nancy when the functionality is equivalent to what I am used to.

Thank you!

In the last several months we have seen a steady increase in number of users (such as Rachael, Lawson, Anna, Kyle, Mehdi, Aarushi, and hopefully many more) of neuroimaging lab. Specifically when they are physically at the VA, I think it will good to have more accessible computers (that supports image analysis) and space in the Neuroimaging lab for our users. Currently, we only have Tasaki on which a lot of users don't have account, and the other mac which has malfunctioning display. I also think it is not reasonable to expect every user of Neuroimaging lab to bring their own laptop to do lab work, and in the process if their personal laptop fails/breaks then they are stuck with days of not having convenient means (and help with fixing any job-related computer issues) to do their job.

I believe this concern will also need Bruce's advice and inputs. I am just putting it out there ...

ubuntu 16 released an SSO (SINGLE SIGN ON) module that has to be properly configured for our machines to work on our LDAP server. This new module is incompatible with our current LDAP/Kerberos authentication system. We have to disable SSO on Ubuntu 16+ to rectify.

Ticket example

Fix fail on qball4:
extract features
/opt/fmrib/matlab/bin/matlab not found!

Hi,
Matlab needs a license update on Pano
Matlab needs to be installed on Rama
All other systems (qball 1-4, lens, and ralph) were checked, and have Matlab working.
Best,
LCK

In qball 1 when we attempt to open Melview, it closes the entire terminal. Not sure about other clusters.

We will need updated spm (on all clusters) to support GIFT analysis. Stella will be an immediate user, and potentially Anna.

Matlab license on qball4 is not updated. Not sure about the other clusters (qball 1, 2, 3, ralph, lens etc)

Can I have a user account and log-in to tasaki, please ?

Keith,

Nancy cannot use her Emory VPN to access the Emory machines, although she has permissions on all ends that I'm aware of and her Emory VPN works. It seems like an authorization may need to be set in place. Giri mentioned something about you being the gatekeeper for this. Is this something you are able to authorize, and if so, what do you need from us? If this is out of the scope of what you maintain, lo siento - who do you suggest we ask (Emory IT?) and what do you suggest we ask them?

Thank you,
Simone

Hi Keith,

The Mac computer at my desk has the same issue as the one in imaging lab. It keeps flashing pink and purple pixels. Is this a graphic card issue ?

Thanks,
Giri.

Hi Keith,
Aarushi and I tried firing up ITKSNAP on lens and ralph, and it does not load correctly, and we are not able to open the images. We tried both Tasaki and the other Mac, and it doesn't work. The error message looks like:

Badvalue (integer parameter out of range for operation ) 0X0
Badvalue (invalid parameter attributes) 0X000006
Badmatch (invalid parameter attributes) 0X0

These error messaged keep looping over and over. We got pretty much the same message for both lens and ralph (using either Tasaki or the other Mac computer).

Thanks.
Giri.

Requests have been made to update our imaging hardware to a Puppet type system for systems management. This means replicating a single computer profile to all computer systems attached to the CVNR. This will take time to implement as puppet requires considerable implementation resources.

Rama will be receiving a new Ryzen processor with 24 threads and 12 cores at 3.5Ghz. This is the 48th most powerful processor on the market, which is notable because the most powerful processor costs over 4000 dollars...

RAMA will receive the following:
512GB SSD drive at 550MB/sec which is 3x the speed of standards HDD drives
64 GB DDR4 RAM which is 1.5x faster than our current 48GB DDR3 RAM
1070 ti graphics card with 2432 CUDA cores at 1.6GHz
10 GigE ethernet

The Mac computer (not Tasaki) in the neuroimaging lab has problems with display. Sometimes it starts flickering colorful pixels, sometimes more than 60-70% of the monitor turns red or some other color, and sometimes it just freezes.

NFS server ache.birc.emory.edu not mounting on pano - can't access any of the work I am currently processing for GABA-L or for the manuscript I'm working on. Help would be greatly appreciated.

Some of the newer options (such as -Xclustsim) within 3dttest++ command does not run on lens. It gives the FATAL ERROR : 3dttest++: don't recognize option '-Xclustsim' (argv[31]). It runs on qball1 though. I think having homogeneity across all machines will be very helpful.

Thanks,
Giri.

Since AROMA may not be the magical ICA answer to all that is motion (especially MB data), more projects may be utilizing FSL FIX. Could we document which nodes have FSL FIX available? If possible, could we also install FSL FIX on more nodes?
Best,
-LCK

Emory medical student who was recently credentialed to work on my fibromyalgia study at the VA.

We have been eagerly awaiting her credentialing over the last 6 months or so, and she’s finally here!

Would you be able to create a login for her on birc so that she can assist with the pre-processing steps? Would you prefer that I enter this information on the site you linked us to for computer questions?

Thanks!

Anna

Pano froze Friday. I wasn't running much (looking at T1s, a few remote terminals with nothing running, and had one reasonably sized trackvis file open), but I believe 3 users were logged in so there may have been more going on in actuality. Since rebooting it manually (I was sitting at the machine) I also can't use X2Go. I tried to X2Go remote into Pano while frozen before rebooting it, and was denied in the same way I would be if the machine was simply off. I don't know if these things are related but temporally they coincided. At minimum perhaps it would be a good idea to talk about Pano and how to avoid it crashing again?

I can still ssh from my mac terminal, but never in X2Go. I've tried restarting Pano, the VMWare client, and my own computer. I've tried to log in more times than I could count, from both Emory's wifi and my own. I could use some help. The error appears then disappears quickly, but I'll update this if I can get a screenshot...

Finally, when sshing into Pano, it seems a bit slow... For example when nothing or minimal things are running, entering a cd command has a lag.

On lens: 'which fix' reports the fix path as /opt/fix/fix, even though updated fix path is usr/local/fix1.066/fix
Need to delete previous fix install?

FSL will not open in ralph or lens.

We tried FSL eyes (Anna, Corinne, Giri) to try to view the images that weren't loading in Afni, but it would not open.

Hi,
ITKsnap3qt4 is not working on the physical lens machine @wmb, even when logged into another terminal (screen shot below shows ssh'd into ralph). The program opens, but the 'invalid context' error appears when attempting to open an image. Must be some sort of display/video card issue, but am not sure.
Best,
-LCK

We need a lab sponsored or CVNR sponsored dedicated and well-maintained laptop for work-related skype and webinar purposes.

Also, we need a step-by-step instruction manual for how to setup for skype and webinar setup in the conference room. Lisa Calas and Erica should have a copy of this manual so that anyone who need to setup for a webinar can independently do their setup without having to waste a lot of their own and others' time. The instructions manual should include the details for windows and mac setup. Especially since mac requires other compatible accessories, we need to have them available somewhere in the conference room. Since I recently gained a bit of experience with the setup, I am more than happy to help making the manual.

When i try to run FNIRT on qball1, it keeps saying that config file cannot be found. I tried providing full path to the config file...fnirt command does not take full path for the config file. however, when I logged in to lens, fnirt runs fine. I guess qball1 needs fsl upgrade or path setup checked.
Thanks,
Giri.

Keith Rebooted the qballs after 600+ days of uptime.

Likely the systems are undergoing a fsck. Should be fixed by April 9.

We are having issues running Tshift. We have different issues depending on the computer used (lens vs. ralph vs. qb1).

On lens and qb1, Tshift will not run (per our earlier discussion). On ralph, the script will run and create an appropriately titled Tshift file with what appears to be 350 volumes in Afni, but in Afni, opens up "empty image" and we cannot see anything.

Here are the error messages we received when running the script:
slice time correction for MB rest fMRI data
extract raw slicetime pattern
extract final slicetime pattern
transpose final slicetime pattern
./Tshift_volreg_rsfcMRI_AW.sh: line 33: 3dTshift: command not found
finish slice time correction for MB task fMRI data
motion correction with reference of the middle volume of rest data
./Tshift_volreg_rsfcMRI_AW.sh: line 37: 3dvolreg: command not found
finish motion correction

installed melview on pano.

Required a number of updates to python.

SMART failures on hard disk. Restoring our DICOMs from BACKUP.

Due to issues with spatnorm and restarting analysis of rsfMRI, I am cleaning up files. To organize, I need permissions to move some files or folders (created by users that have exited the lab):

/data/qb/Atlanta/Crosson_GABA-L/S2105/preprocfiles/MPRAGE/S2105_MPRAGE_dcm2nii.nii.gz

/data/qb/Atlanta/Crosson_GABA-L/S1107/preprocfiles/MPRAGE/segfiles/
/data/qb/Atlanta/Crosson_GABA-L/S1110/preprocfiles/MPRAGE/segfiles/
/data/qb/Atlanta/Crosson_GABA-L/S2005/preprocfiles/MPRAGE/segfiles/
/data/qb/Atlanta/Crosson_GABA-L/S2007/preprocfiles/MPRAGE/segfiles/
/data/qb/Atlanta/Crosson_GABA-L/S2008/preprocfiles/MPRAGE/segfiles/
/data/qb/Atlanta/Crosson_GABA-L/S2011/preprocfiles/MPRAGE/segfiles/
/data/qb/Atlanta/Crosson_GABA-L/S2012/preprocfiles/MPRAGE/segfiles/
/data/qb/Atlanta/Crosson_GABA-L/S2110/preprocfiles/MPRAGE/segfiles/
/data/qb/Atlanta/Crosson_GABA-L/S2113/preprocfiles/MPRAGE/segfiles/
/data/qb/Atlanta/Crosson_GABA-L/S2114/preprocfiles/MPRAGE/segfiles/

Hi,
LINDA on Lens is encountering a problem in one of its 'which' loops (see attached blurry picture). Currently the Ralph version is working fine, so this is not high priority. However, as we collect more stroke data, we may encounter a computational resource issue if we only have LINDA installed on one node.
Best,
LCK

We will need DensParcorr installed on all our clusters. The immediate users for this tool are myself, Anna, and Stella for prelim data for grants, papers and dissertation work. The download link is here: http://web1.sph.emory.edu/users/yguo2/software.html

Hi,
apparently fslview is now deprecated, and fsleyes is the new viewer for the cool kids on the block (see printscreen). Is this something we can install on the server?
Best,
LCK

Can't connect to internet on VMWare and thus can't download/install/use X2Go or troubleshoot, or work remotely on most things.