Freesurfer May 2016

freesurfer@nmr.mgh.harvard.edu

135 participants
197 discussions

Using customized stats code for mass-univariate approach in freesurfer for structural data
by Chung, Yoonho 24 May '16

24 May '16

Hi - If I would like to try to perform mass-univariate statistics at the vertex level (thickness, area, vol at each vertex) without using the mri_glmfit, is this order a sound step (in general) for mapping stats parameter of choice (p-val or t s or weights for example) to the surface? 1. Use mris_preproc and surf2surf to get the data to common space and smooth. 2. Load the data to matlab using fs_read_Y() or MRIread 3. Perform stats at each vertex using stats toolbox to apply modeling approach of your choice (e.g., machine learning, linear mixed model etc.) 4. Extract P-values (or other parameters) for each vertex for the variable of primary interest 5. Use MRIwrite to create mgh file 6. Perform multiple comparison using freesurfer functions (e.g., FDR or monte carlo sim) 7. view corrected maps using tksufer? Any steps I should consider adding or avoid? Thank you!

3 2

Intensity stats file for new ROI
by Sabrina Yu 24 May '16

24 May '16

Hello, I have created my own subcortical ROI in freesurfer (saved as .label file), and am trying to generate an intensity stats file for this ROI. Reading the mailing list, I think that the best way to do this is to: 1) mri_label2vol to convert my ROI to a volume file 2) mri_label_volume to generate stats on this volume I was able to achieve the first step, but am unable to generate a stats file with intensity info for the volume. This is the command I tried to use: cd /freesurfer/subjects/<subjectname>/mri mri_label_volume -s <subjectname> stroke_area.mgz label 1 Any help would be much appreciated! Thank you in advance. Sabrina

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Post-doc opening in Neuroinformatics
by Gregory Book 24 May '16

24 May '16

The Olin Neuropsychiatry Research Center has an opening for a post-doc specializing in neuroinformatics, big-data analysis, and machine learning. The Olin Center is the neuropsychiatric research center within Hartford Hospital’s Institute of Living campus, in Hartford, CT. We house a Siemens Skyra 3T whole-body MRI, multiple EEG, TMS, and eye tracking systems, an internal historical database of nearly 13,000 MRI sessions, and a 400-core Linux compute cluster. The candidate will contribute to the development of neuroimaging databases in support of multiple NIH funded projects and with several primary investigators on large scale analyses. The candidate will contribute to the development of the Neuroinformatics Database ( http://github.com/gbook/nidb) to archive data, automate data analysis using new and existing pipelines, and publish journal articles on their own research. MS degree in engineering, science, neuroscience, or psychology is required, PhD preferred. Candidate is expected to have experience in SQL programming and at least one programming language. Proficiency in multiple programming languages such as Perl, C, C++, Javascript, PHP, Matlab, and Python is highly desirable. Contact Greg Book at gregory.book(a)hhchealth.org

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Significant clusters from mri_glmfit
by sabin khadka 24 May '16

24 May '16

Hi all, I used FDR correction method to correct for multiple comparison after mri_glmfit. And I have a cluster covering multiple regions. I want to extract the thickness, surface area, lgi values for local maxima (or, multiple regions covered by the big significant cluster). I see it is not straightforward as when monte-carlo cluster correction is applied. Can anyone suggest me if there is a work around for this apart from manually creating a ROI masks and extracting values? Thanks for help! Cheers, Sabin Khadka

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Problems viewing significant clusters on qdec display
by Vikas Bandalli 24 May '16

24 May '16

Dear Freesurfers, I have come across a problem with viewing the significant clusters on qdec display tab. When a particular query is selected after analyzing for a selected design there are multiple clusters of varying size which appear. This query when run (corrected) with Monte carlo simulation (at particular selected threshold ex;- 1.3 ),the display tab shows an inflated image with significant cluster at selected threshold and also there is an output in the terminal as well which gives data about the size,number of vertices etc of the output cluster Please correct me if I am following the procedure for multiple comparisons wrongly or going wrong in any part of analysis and correction for multiple comparisons. However I have observed that sometimes,even though there is an output in the terminal (sometimes the cluster having almost as 1900-200 vtxs),there is no display of the cluster on the inflated image on the display tab. I dont know why this is happening,But I have seen this to be the case in a number of situations. I would also be interested to know if there is any other alternate method for viewing clusters.Since the clusters on display images are absolute necessity for all reporting purposes . I hope to hear from you soon. Regards , Vikas Bandalli Raju -- Vikas B. R. Medical student Bangalore Medical College and Research Institute (BMCRI), Bangalore,India,

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Freeview error
by 김현호 24 May '16

24 May '16

Dear all I installed freesurfer as supposed for linux of centos 7. I have a problem with freeview error. After install was copleteted, Tying the command : "freeview" -> freeview.bin: error while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or directory So, Installed libXScrnsaver-1.1.2.2-6.1.el7.i686.rpm (libXss.so.1) but the result wasn't changed. Searching for libXss.so.1 file, finded in 'usr/lib' not 'usr/lib64' I want to Install libXss.so.1 usr/lib64 and solve the problem. How can I get freeview to run? Help would be appreciated gushkr.

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Re: [Freesurfer] The results of your email commands
by Dave Yas 23 May '16

23 May '16

Dear Doug, I'm getting mri_segstats error [mghread(...ribbon.mgz) at the end of -autorecon2. I saw your answer for others about this Q before and i know how to solve this IF i was able to access to the links you posted. ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.… ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.… I thought that these should give me some kind of a pop up to prompt me to enter as a guest and get the file to put it in bin/mrisegstats But its not doesin anything. Also im running OSX El capitan. Is there any link that i can visit to download the missing mrisegstats file? Thanks, Yas

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Re: [Freesurfer] ERROR: cannot unpack mosiacs without ASCII header
by Aloi, Joseph 23 May '16

23 May '16

Hi Doug, I've attached the recon-all log for an analysis on a research subject that I successfully ran a few weeks ago and then the recon-all log when I try to run the exact same analysis on the exact same subject now. Thanks so much for taking a look at these. The log files you can just attach to the email to the list (or to me directly if there is something in there that you don't want to post) On 05/20/2016 04:02 PM, Aloi, Joseph wrote: > Excellent, thank you! To do that, do I send an e-mail to the listserv > with the log files attached or do I use the filedrop? > > yea, can you post the log file of both the successful and failing runs? > > On 05/19/2016 11:28 AM, Aloi, Joseph wrote: > > > > Hi Doug, > > > > No that’s not how I usually store my files- I have a folder for the > > particular study that I am working on then the dicoms for each subject > > in that study are stored in individual subject folders within the > > study folder. > > > > I got a chance to look around the recon-all logs this morning for a > > subject that I had successfully processed in the past (but that I get > > the error when I try to process this same dataset now). From > > comparing the recon-all log from when recon-all ran successfully > > versus now, things are running fine up until it gets to MRI_convert. > > However, it looks like things are actually starting to go haywire > > during MRI_convert even before I get the warning about the ASCII > > header and recon-all exits. It appears that MRI_convert is having > > some trouble with extracting some of the information it needs from the > > dicom file, resulting in the error that I posted. I know you guys are > > busy, but would you be able to take a look at the log files? I’ve > > only been using freesurfer a few weeks, so I would definitely > > appreciate any insights you might have from looking at the log files. > > > > Thank you! > > > > I don't have any idea what is going wrong. I noticed that the file > > that it is having problems with is here > > /Users/alojos/Applications/freesurfer/subjects/sub_9999.dcm > > Do you really keep all your dicom files in that location? > > > > > > > > On 05/17/2016 11:47 PM, Aloi, Joseph wrote: > > > Hi Doug, > > > Sorry- I've added entire correspondence onto the end of this > > e-mail. I don't think the disk filled up as I am on a 3 TB hard drive > > and I still have ~2 TB of free space on my disk. Anything else you > > think it could be? > > > Thanks! > > > Joseph Aloi > > > Please remember to include previous correspondence otherwise we can't > > > keep track of the problem! > > > Eg, I don't have the previous email to see what the error was. Is it > > > possible that the disk filled up? > > > On 05/17/2016 09:49 AM, Aloi, Joseph wrote: > > > > Hi Doug, > > > > > > > > Yes, you are correct- data I have previously processed without any > > > > problems is no longer being processed. > > > > > > > > My version of freesurfer is 5.3.0; I only downloaded it a few weeks > > > > ago so I have not changed my freesurfer version recently. > > > > > > > > Thanks! > > > > > > > > Joseph Aloi > > > > Graduate Student, MD/PhD Scholars Program > > > > Department of Pharmacology and Experimental Neuroscience > > > > University of Nebraska Medical Center > > > > > > > > Neurobehavioral Research Assistant, Center For Neurobehavioral > > Research > > > > Boys Town National Research Hospital > > > So the exact same data set is now generating an error whereas it ran > > > smoothly before? What version of FS are you using? Did you change > > versions? > > > doug > > > On 05/16/2016 09:49 AM, Aloi, Joseph wrote: > > > > > > > > Hi freesurfer experts, > > > > > > > > I have recently begun to use freesurfer to do structural MRI > > > > analyses. I have been able to successfully process about 40 > > > > structural scans with recon-all thus far, but starting a few days ago, > > > > I started getting this error whenever I run recon-all: > > > > > > > > WARNING: file > > > > /Users/alojos/Applications/freesurfer/subjects/sub_9999.dcm does not > > > > contain a Siemens ASCII header > > > > > > > > has this file been anonymized? > > > > > > > > ERROR: cannot unpack mosiacs without ASCII header > > > > > > > > Darwin nerc130622.local 14.5.0 Darwin Kernel Version 14.5.0: Mon Jan > > > > 11 18:48:35 PST 2016; root:xnu-2782.50.2~1/RELEASE_X86_64 x86_64 > > > > > > > > recon-all -s sub_9999 exited with ERRORS at Mon May 16 08:43:24 > > CDT 2016 > > > > > > > > Here are a few of the troubleshooting steps I’ve tried to track down > > > > the cause of the error: > > > > > > > > -- Re-run recon-all with a couple of scans from my dataset that I have > > > > already successfully processed > > > > > > > > - - Re-run recon-all the same datasets but on a different computer > > > > > > > > - - Re-convert the scans from .ima files to dicoms in osirix, then > > > > run recon-all > > > > > > > > > > > > For all of these steps, I have gotten the exact same error message. > > > > The files should be anonymized, since I used osirix’s “anonymize and > > > > convert” function to generate the dicom files (the scans were given to > > > > me as .ima files). > > > > > > > > Any suggestions on what to try next? > > > > > > > > Thank you! > > > > > > > > > > > > Joseph Aloi > > > > > > > > The information in this e-mail may be privileged and confidential, > > > > intended only for the use of the addressee(s) above. Any unauthorized > > > > use or disclosure of this information is prohibited. If you have > > > > received this e-mail by mistake, please delete it and immediately > > > > contact the sender. > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > The information in this e-mail may be privileged and confidential, > > > intended only for the use of the addressee(s) above. Any unauthorized > > > use or disclosure of this information is prohibited. If you have > > > received this e-mail by mistake, please delete it and immediately > > > contact the sender. > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...(a)nmr.mgh.harvard.edu > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > <file://localhost/transfer/outgoing/flat/greve> > > > > > > > > The information in this e-mail may be privileged and confidential, > > intended only for the use of the addressee(s) above. Any unauthorized > > use or disclosure of this information is prohibited. If you have > > received this e-mail by mistake, please delete it and immediately > > contact the sender. > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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. > > > Joseph Aloi > Graduate Student, MD/PhD Scholars Program > Department of Pharmacology and Experimental Neuroscience > University of Nebraska Medical Center > > Neurobehavioral Research Assistant, Center For Neurobehavioral Research > Boys Town National Research Hospital > > > > The information in this e-mail may be privileged and confidential, > intended only for the use of the addressee(s) above. Any unauthorized > use or disclosure of this information is prohibited. If you have > received this e-mail by mistake, please delete it and immediately > contact the sender. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Joseph Aloi Graduate Student, MD/PhD Scholars Program Department of Pharmacology and Experimental Neuroscience University of Nebraska Medical Center Neurobehavioral Research Assistant, Center For Neurobehavioral Research Boys Town National Research Hospital The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.

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freeview, tkmedit won't start
by Julian Jäckle 23 May '16

23 May '16

Dear all I installed freesurfer as supposed for linux (ubuntu). When I tried to run freeview an error for tcsh occured. Apparenty I fixed that one but still freeview doesn't start. Typing the command: "freeview" nothing happens (I did export and source freesurfer correctly). Further trying to run tkmedit it says command not found. How can I get freeview and tkmedit to run? Help would be appreciated Julian

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Re: [Freesurfer] ERROR: cannot unpack mosiacs without ASCII header
by Aloi, Joseph 23 May '16

23 May '16

Excellent, thank you! To do that, do I send an e-mail to the listserv with the log files attached or do I use the filedrop? yea, can you post the log file of both the successful and failing runs? On 05/19/2016 11:28 AM, Aloi, Joseph wrote: > > Hi Doug, > > No that’s not how I usually store my files- I have a folder for the > particular study that I am working on then the dicoms for each subject > in that study are stored in individual subject folders within the > study folder. > > I got a chance to look around the recon-all logs this morning for a > subject that I had successfully processed in the past (but that I get > the error when I try to process this same dataset now). From > comparing the recon-all log from when recon-all ran successfully > versus now, things are running fine up until it gets to MRI_convert. > However, it looks like things are actually starting to go haywire > during MRI_convert even before I get the warning about the ASCII > header and recon-all exits. It appears that MRI_convert is having > some trouble with extracting some of the information it needs from the > dicom file, resulting in the error that I posted. I know you guys are > busy, but would you be able to take a look at the log files? I’ve > only been using freesurfer a few weeks, so I would definitely > appreciate any insights you might have from looking at the log files. > > Thank you! > > I don't have any idea what is going wrong. I noticed that the file > that it is having problems with is here > /Users/alojos/Applications/freesurfer/subjects/sub_9999.dcm > Do you really keep all your dicom files in that location? > > > > On 05/17/2016 11:47 PM, Aloi, Joseph wrote: > > Hi Doug, > > Sorry- I've added entire correspondence onto the end of this > e-mail. I don't think the disk filled up as I am on a 3 TB hard drive > and I still have ~2 TB of free space on my disk. Anything else you > think it could be? > > Thanks! > > Joseph Aloi > > Please remember to include previous correspondence otherwise we can't > > keep track of the problem! > > Eg, I don't have the previous email to see what the error was. Is it > > possible that the disk filled up? > > On 05/17/2016 09:49 AM, Aloi, Joseph wrote: > > > Hi Doug, > > > > > > Yes, you are correct- data I have previously processed without any > > > problems is no longer being processed. > > > > > > My version of freesurfer is 5.3.0; I only downloaded it a few weeks > > > ago so I have not changed my freesurfer version recently. > > > > > > Thanks! > > > > > > Joseph Aloi > > > Graduate Student, MD/PhD Scholars Program > > > Department of Pharmacology and Experimental Neuroscience > > > University of Nebraska Medical Center > > > > > > Neurobehavioral Research Assistant, Center For Neurobehavioral > Research > > > Boys Town National Research Hospital > > So the exact same data set is now generating an error whereas it ran > > smoothly before? What version of FS are you using? Did you change > versions? > > doug > > On 05/16/2016 09:49 AM, Aloi, Joseph wrote: > > > > > > Hi freesurfer experts, > > > > > > I have recently begun to use freesurfer to do structural MRI > > > analyses. I have been able to successfully process about 40 > > > structural scans with recon-all thus far, but starting a few days ago, > > > I started getting this error whenever I run recon-all: > > > > > > WARNING: file > > > /Users/alojos/Applications/freesurfer/subjects/sub_9999.dcm does not > > > contain a Siemens ASCII header > > > > > > has this file been anonymized? > > > > > > ERROR: cannot unpack mosiacs without ASCII header > > > > > > Darwin nerc130622.local 14.5.0 Darwin Kernel Version 14.5.0: Mon Jan > > > 11 18:48:35 PST 2016; root:xnu-2782.50.2~1/RELEASE_X86_64 x86_64 > > > > > > recon-all -s sub_9999 exited with ERRORS at Mon May 16 08:43:24 > CDT 2016 > > > > > > Here are a few of the troubleshooting steps I’ve tried to track down > > > the cause of the error: > > > > > > -- Re-run recon-all with a couple of scans from my dataset that I have > > > already successfully processed > > > > > > - - Re-run recon-all the same datasets but on a different computer > > > > > > - - Re-convert the scans from .ima files to dicoms in osirix, then > > > run recon-all > > > > > > > > > For all of these steps, I have gotten the exact same error message. > > > The files should be anonymized, since I used osirix’s “anonymize and > > > convert” function to generate the dicom files (the scans were given to > > > me as .ima files). > > > > > > Any suggestions on what to try next? > > > > > > Thank you! > > > > > > > > > Joseph Aloi > > > > > > The information in this e-mail may be privileged and confidential, > > > intended only for the use of the addressee(s) above. Any unauthorized > > > use or disclosure of this information is prohibited. If you have > > > received this e-mail by mistake, please delete it and immediately > > > contact the sender. > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > The information in this e-mail may be privileged and confidential, > > intended only for the use of the addressee(s) above. Any unauthorized > > use or disclosure of this information is prohibited. If you have > > received this e-mail by mistake, please delete it and immediately > > contact the sender. > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > <file://localhost/transfer/outgoing/flat/greve> > > > > The information in this e-mail may be privileged and confidential, > intended only for the use of the addressee(s) above. Any unauthorized > use or disclosure of this information is prohibited. If you have > received this e-mail by mistake, please delete it and immediately > contact the sender. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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. Joseph Aloi Graduate Student, MD/PhD Scholars Program Department of Pharmacology and Experimental Neuroscience University of Nebraska Medical Center Neurobehavioral Research Assistant, Center For Neurobehavioral Research Boys Town National Research Hospital The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.

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Freesurfer May 2016