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Download 2021 CRNL Rar

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/feed _forum.php?forum_id=4441 Full instructions for installing and using the RSS app with Slack feed to Slack can be found in the Slack Help Center. Close function confirmDel() var agree=confirm("Proceed with deletion? ");if (agree) return true ;else return false ;function manageattachments(url,del) var newwindow;if (del=="yes") if (!confirmDel())return;newwindow =, 'Attach', 'statusbar=no,menubar=no,toolbar=no,scrollbars=yes,resizable=yes,width=600,height=480');if (window.focus) newwindow.focus()Showing 1-75 of 177 postsStart New Topic Display: Threaded PostsFlat PostsThreaded TitlesActive TopicsjQuery(".hide-with-javascript").css("display","none");Results per page: Show 25Show 50Show 75Show 100jQuery(".hide-with-javascript").css("display","none");1 2 3 Next >Oct 7, 2014 08:10 PM Chris RordenWelcome to Open-DiscussionWelcome to Open-DiscussionQuote & Reply Reply Oct 30, 2014 03:10 PM Bastian ChengWhite Matter AtlasHi!First of all: what a great tool! I've been looking for an intuitivevisualization program for a long time.One questions: Are the overlays from a standard white mattertractography atlas available?I found them in the connectivity explorer by denis ducreux and waswondering if one could use them in this software.My aim would be to compare own tracking results to locations ofwhite matter regards,BastianQuote & Reply Reply Nov 22, 2014 12:11 PM Chris RordenRE: White Matter AtlasThanks for your comments. I think you have a couple of options forwhite matter tractsConnectopedia is a fantastic tool from Denis Ducreux that uses theMRIcroGL engine for rendering. You can use it on its own or use theimages with other tools. You can use the images withinConnectopedia or with other tools (as I recall, with OSX you haveto 'show package contents' to see the images). These are highquality maps from a single individual: Marco Catani and his team have created some nice probabilisticwhite matter maps based on a group of indiviuals. & Reply Reply Nov 22, 2014 03:11 PM Bastian Cheng RE: White Matter AtlasHi Chris! Those are excellent suggestions! Thank you again for yourhelp!BastianQuote & Reply Reply Dec 28, 2014 11:12 PM Xiaowei SongDoes MRIcroGL have a cmd interface?Hi, Chris,thanks for the great 3D displaying tool.Does or will MRIcroGL have a cmd interface like caret andcaret_command?Best,XiaoweiQuote & Reply Reply Sep 5, 2015 01:09 PM Chris RordenRE: Does MRIcroGL have a cmd interface?Hello- MRIcroGL has a full scripting language, you can see examples here You can have MRIcroGL run these scripts when it launches, and thisallows other programs to control MRIcroGL (for example havingMatlab batch a large set of images). In particular, with Matlab youwould use the "system" function to launch MRIcroGL. There are twomethods:1.) If you place a text file named 'startup.gls' in MRIcroGL'sscript folder it will run this script when the program launches.2.) You can pass the name of a script file to MRIcroGL at launch,for example "MRIcroGL /myDir/myScript.gls". This will causeMRIcroGL to run the specified script. a.) A very useful function for these scripts is the "quit;"command. Put this in the last line of your script and MRIcroGL willshut down once it has completed running your script. This is usefulif you want to save a batch of bitmaps and do not want any userinteraction. However, be aware that if a user opens and runs ascript from the graphical user interface with a "quit" the programwill shut down as soon as it is done. In particular, if you make a"startup.gls" script with "quit" in it and do not delete this fileafter it is executed users will not be able to run MRIcroGLgraphically: whenever it is launched it will auotmatically run thestartup script and then quit.3.) Be aware that with OSX the script and application files areboth hidden in the application package, and in general OSX is morefinicky about running items (the interface may give you a warning).In any case, with OSX you would call the script like this"/osx/ "Quote & Reply Reply Sep 5, 2015 01:09 PM Chris RordenBeta test for new releaseI am about to release a new version of MRIcroGL. If anyone wishesto test this, you can download it from and find out about the new features here unless bugs are reported, this will be the new stable release.-cQuote & Reply Reply Dec 18, 2015 07:12 PM Sirous Nekooei - MUMSRE: Beta test for new releaseDear ChrisFirst of all, I'd like to thank you so much for this usefulsoftware.I want to use it for presentation of fMRI overlays.As you know, physicians are used to view images in radiologicorientation. So I'd like to print them like that.In the previous versions, there was an R/L flip option (in MRIcroand MRIcron) but in MRIcroGL, which has a better interface topresent mosaic visualization, the R/L option is missing.Is there a specific reason for that?SirousQuote & Reply Reply Mar 8, 2016 04:03 PM gaeljDeeper activationsHi,I've been unsuccessfully looking for the 'search depth' setting ofmricron in mricroGL. I love the quality of the render in mricroGL,but have not yet found a satisfactory way of displaying activationsthat are slightly under the brain surface.I join an illustration of what I can do with mricron and the best Ican achieve with mricroGL. Note that the parietal activations arenot easy to see on the mricroGL rendering, do you have a way ofimproving this that I did not see ?Thank you for your help.Gaël.Attachment: render.png Quote & Reply Reply Apr 5, 2016 09:04 PM Andre Peres - Brain Institute - Federal University of Rio Grande do Norte - UFRNMRIcroGL issuesHello,I'm using the last version of MRIcroGL on iMac OS X 10.9.5, and onLubuntu 14.4. However, I found some problems running on bothsystems: On Mac, when I try to run a script, the mac crashes, and Ineed to reboot pressing the power button. On linux, it's happeningsomething weird, when I type something in the interface (max/minIntensity) or in the script window the letters are typedtwice,i.e., if I press just one time the letter A, it's typed AA,the same occur with the numbers.I have tried all the three versions available on the website, butdoesn't work.Please, could you help me?Quote & Reply Reply May 10, 2016 09:05 PM rachelnakoShowing ovarlay withsignificant t-values onlyDear all,I am just a student and quite new to this software (I'm noteven sure if this is the right place to ask). I also use SPM and Iwas wondering if it is possible to show the significantly differentvoxels, after bonferroni correction in MRIcroGL like I can in SPM ? And is it possible to show this in the ROIs as well? Putdifferently: how can I reduce the presence of type I errors inimages in MRIcroGL? Is that what the Min / Max values are for?I would like to show these clusters in 3D, as MRIcroGL offers.Many thanks in advance & Kind Regards,RachelQuote & Reply Reply Jun 19, 2016 05:06 PM Sebastian UrchsTrojan flagged on most recent windows zipHi,I just downloaded the windows zipfrom got a warning from my antivir (360 security) that the filecontained a trojan:Type:Threat detected in compressed filesDescription:C:\Users\Sebastian\Downloads\>mricrogl\dcm2niix.exe: Win32/Trojan.97aScan Engine:360 Cloud Scan EngineLocation:C:\Users\Sebastian\Downloads\windows.zipSuggestion:Quarantined filesPretty sure it's a false flag but in any case I'd like to let youknow.Best,SebastianQuote & Reply Reply Jun 30, 2016 08:06 PM Carl Helmick - Dalhousie University, Psychiatry Deptdcm2niix-5May2016 ignores -o flagThe command-line program dcm2niix does not respect the "-o flag. Would it be possible to compile and release a new version ofdcm2niix?Thanks!CarlQuote & Reply Reply Aug 30, 2016 04:08 PM Niels FockeRE: dcm2niix-5May2016 ignores -o flagI can confirm this behaviour - the -o flag seems to be ignored bythe May05 version (Linux, 64bit). A fix would be appreaciated,since I would like to use this software in a batched/automated way.Thanks. NielsQuote & Reply Reply Oct 3, 2016 01:10 PM Benjamin Wagner - UT Southwestern Medical CenterRE: dcm2niix-5May2016 ignores -o flagI hope a fixed release of this will come out soon. I need the5 May version for handle some Philips data but also need the -o forbatch processing. If not a release of the whole MRIcroGLmaybe just the affected dcm2niix binaries?BenQuote & Reply Reply Oct 12, 2016 02:10 PM Benjamin Wagner - UT Southwestern Medical Center30-Sept-2016 dcm2niix requires GLIBC_2.14The dcm2niix included with the referenced release will not run onRHEL 6.6. It fails with the error:dcm2niix: /lib64/ version 'GLIBC_2.14' not found(required by dcm2niix)MRIcroGL does work. I looks as if the two executables werecompiled on different machines:[]$ file 'which dcm2niix'/project/software/mricron/20160930gl/dcm2niix: ELF 64-bit LSBexecutable, x86-64, version 1 (SYSV), dynamically linked (usesshared libs), for GNU/Linux 2.6.32, stripped[]$ file 'which MRIcroGL'/project/software/mricron/20160930gl/MRIcroGL: ELF 64-bit LSBexecutable, x86-64, version 1 (SYSV), dynamically linked (usesshared libs), for GNU/Linux 2.4.0, strippedAny chance of dcm2niix being compiled for a lower GLIBC?BenQuote & Reply Reply Oct 14, 2016 04:10 PM Mo BenMIRcroGL Absolute Intensity Calculation?Hello All,I'm working on a virtual reality NIfTI viewer and I'm usingsome of the color scheme look up tables from this project asreference.The LUT files in the source use an absolute value for min and maxintensity, matching the values displayed in the top left corner ofthe MIRcroGL viewer. For example, CT_Lungs uses the followingvalues: [FLT] min=-902 max=-305I'm not sure how these values are calculated, or how the NIfTIfiles are mapped to this scale. I did some analyzing of the headerfile and data. It seems they are encoded from [0,255] and theheader files' glmin and glmax values match those values. Meanwhilecl_min and cl_max are unused.How are these absolute values calculated? Am I missing somethingobvious here?Quote & Reply Reply Oct 14, 2016 04:10 PM Mo BenRE: MIRcroGL Absolute Intensity Calculation?Did some more digging and figured it out. Using the scl_slopand scl_inter values you can find the scaled values.Quote & Reply Reply Oct 16, 2016 07:10 AM Mo BenRE: MIRcroGL Absolute Intensity Calculation?Ok, opening this back up.Some of the .clut (Color scheme source look up tables) files havemin and max set to 0. I expected those color schemes to use thelowest and highest intensity for each file they were used on, butit turns out it is determining a seemingly arbitrary range ofintensity, which is different for each file.Does anyone know how the minimum and maximum intensity for thosecolor schemes is calculated? For example the default grayscale whenused on the ch256.nii file uses a minimum of 40 and maximum of120, even though the intensity can go down to 0.Quote & Reply Reply Oct 27, 2016 03:10 PM Javier Juan-Albarracín - Universitat Politècnica de València (UPV)dcm2niix ignores compresion flagdcm2niix seems to ignore the -z compression flag (at least inwindows). I have also checked that pigz.exe is in the same folderthan dcm2niix.exe but the output is always a .nii file. I haveproved with "-z y" and without explicitly setting the flag but theoutput is always an uncompressed NIfTI. Any idea?Thanks! JavierQuote & Reply Reply Oct 31, 2016 04:10 PM Cecil YenRE: 30-Sept-2016 dcm2niix requires GLIBC_2.14I also found the same issue here. Our institute was still using RedHat/CentOS 6 as our working hose. So, we can't upgrade to RedHat/CentOS 7 soon. Is there any reason that dcm2niix has to bebuilt against newer GLIBC?CecilQuote & Reply Reply Nov 1, 2016 03:11 PM Chris RordenRE: 30-Sept-2016 dcm2niix requires GLIBC_2.14You can download a version of dcm2niix compiled on Centos 6.6(kernel 2.6.18; GCC 4.4.7) dcm2niix and MRIcroGL were compiled on the same machine, butgenerated with different compilers (dcm2niix = gcc, MRIcroGL =fpc). GLIBC 2.14 was released in 2011 and Linux 2.6.32 in 2009, somy compiled software should work on most modern Linux systems. Icompiled the project on NeuroDebian 8.0 (kernel 2.6.32; GCC 4.9.2).I think there will always be a tradeoff in distributing compiledLinux software between maximum compatibility versus benefits of newversions. If you want a version optimized for your system you can alwayscompile your own by getting the code from GitHub ( ), and running the "make" command in the "console" folder.Quote & Reply Reply Nov 1, 2016 03:11 PM Chris RordenRE: Deeper activationsWith the latest version of MRIcroGL (30Sept2016) you controloverlay depth with the "overDistance" and "overAlpha" sliders(assuming you are using the "Default" shader). You may also want toswitch the shader from "Default" to one of the "overlay_*" shaders(e.g. overlay_shell or overlay_glass).For visualizing deep activations, a surface renderer (e.g. SurfIce) displaying a mesh may be nicer than a volume renderer(MRIcroGL): :MainPage#Overlay_a_normalized_SPM_or_FSL_statistical_map_that_has_been_converted_to_an_iso-surface_mesh :MainPage#Scripting_a_mesh_overlayQuote & Reply Reply Nov 1, 2016 03:11 PM Chris RordenRE: MRIcroGL issuesCan I suggest you download the latest versions (30Sept2016) andtell me if your issues persist?Quote & Reply Reply Nov 1, 2016 03:11 PM Chris RordenRE: Showing ovarlay withsignificant t-values onlySure, just adjust the minimum and maximum values in the "Overlay"panel (see the "Overlays" section of the manual).Attachment: threshold.jpg Quote & Reply Reply Nov 1, 2016 04:11 PM Chris RordenRE: Trojan flagged on most recent windows zipAppears to be a false positive - my machine hasSymantec ProtectionSuite and I compile straight from cygwin. Furthermore, a scan ofthat file with the 56 virus detection tools usedby does not find any problems. Iassume your 360 security will have an update to resolve this.Quote & Reply Reply Nov 3, 2016 03:11 PM Chris RordenRE: dcm2niix ignores compresion flagMake sure the executable pigz.exe is in the same folder as thedcm2niix.exe. Both executables are included with MRIcroGL. dcm2niixgenerates a warning if you request gzipped output but it can notfind pigz. By the way, future versions of the Windows software willuse the internal compressor if it can not find pigz, similar to thecurrent Linux/OSX releases. In general, the multithreaded pigz ismuch faster than the single-threaded internal compressor, but ifyou are storing data to a slow (networked) disk, you may find theinternal compressor faster (since using pigz requires the softwareto first save the uncompressed data to disk and then compress thatfile, while the internal compressor saves the data compressed in asingle pass). This explains why Linux/OSX versions of dcm2niixallow you to specify three options for gzip: "-z y", "-z i", "-zn", that will (respectively) gzip output (using pigz if found),gzip output (using internal compressor) or not gzip the output.--------- Example 1 : pigz found ---------c:\mricrogl>dcm2niix -z Y c:\tst_t1Chris Rorden's dcm2niiX version 10oct2016 (32-bit Windows)Found 192 DICOM image(s)Convert 192 DICOM asc:\tst_t1\20140228152127_T1_mprage_ns_sag_p2_iso_1.0mm__4 (256x256x192x1)compress: ".\pigz" -n -f"c:\tst_t1\20140228152127_T1_mprage_ns_sag_p2_iso_1.0mm__4.nii"Conversion required 1.781000 seconds.--------- Example 2 : pigz not found ---------c:\mricrogl>dcm2niix -z Y c:\tst_t1Compression requires pigz.exe in the same folder as the executableChris Rorden's dcm2niiX version 10oct2016 (32-bit Windows)Found 192 DICOM image(s)Convert 192 DICOM asc:\tst_t1\20140228152127_T1_mprage_ns_sag_p2_iso_1.0mm__4 (256x256x192x1)Conversion required 0.234000 seconds.Quote & Reply Reply Nov 27, 2016 12:11 PM Christian KaufmannDicom to Nifti / dcm2niix / Slice timingDear all,is it possible to include DICOM slice time information (fromSiemens MR) in Nifti file header? It might be possible withdcm2niix but I might have missed the right flag. Any advice ishighly appreciated, thank you.ChristianQuote & Reply Reply May 27, 2017 11:05 AM Chris RordenRE: Dicom to Nifti / dcm2niix / Slice timingHello- dcm2niix with put the Siemens slice order information intothe NIfTI slice_order tag. An exception to this is if your data wasacquired with multiband, where the slice order can not becompletely described by the 6 slice order options In this case, you can look at the "SliceTiming" field of the BIDSjson header to determine the order.Quote & Reply Reply May 27, 2017 06:05 PM SUDHAKAR MISHRA - Indian Institute of Information Technology AllahabadMRIcroGL with RIs it possible to use MRIcroGL with R.Quote & Reply Reply May 28, 2017 05:05 AM SUDHAKAR MISHRA - Indian Institute of Information Technology AllahabadOverlayload in MRIcroGLWhat is this overlayload in MRIcroGL. In the example scripts'Motor' is given. If I put some other brain region it throws error.If anyone has any clue about how to put this entry, please postit. Any help would be great.Quote & Reply Reply Jun 1, 2017 12:06 AM Chris RordenRE: MRIcroGL with RMRIcroGL is a standalone executable, so you can not wrap it R.However, it does have a scripting language that you can use tolaunch it, open images, save bitmaps and even quit. This allows youto control it with any programming language that allows you toexecute an external program - I provide samples for shell scripts,Matlab and Python. A web search for "R execute external program"will show you how to do this. :MainPage#Scripting_from_the_command_line_and_other_programsQuote & Reply Reply Jun 1, 2017 12:06 AM Chris RordenRE: Overlayload in MRIcroGLYou can find out what MRIcroGL scripting functions do by readingthe included PDF manual, or by selecting the command in thescripting window. When you insert a command using the scriptingwindow you will see usage notes appear at the bottom of the window.For example, if you choose the Insert/Overlay/Overlayload menu itemyou will see:OVERLAYLOAD (lFilename: string): integer; Will add the overlaynamed filename and return the number of the overlay.The software comes with a sample NIfTI image named "motor.nii.gz"which shows motor activation as observed in an fMRI task. If youwant to load a different image you will need to provide its name,for example OverlayLoad('c:\mydir\myimg.nii'). You could shortenthis to OverlayLoad('myimg') if the image is in the same folder asthe MRIcroGL executable.Quote & Reply Reply Jun 15, 2017 03:06 PM Lars Kasper - Translational Neuromodeling Unit, IBT, University of Zurich and ETH ZurichBitmap-saving and image smoothing optionsDear Chris,I am a big fan of the whole MRIcro*-series


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