Freesurfer

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Re: [Freesurfer] can´t open an image in Freeview {Disarmed}
by fsbuild 24 Oct '19

24 Oct '19

External Email - Use Caution Hello Adam, It’s not clear to me that the vtk libs are the issue. Please check that you setup your FREESURFER environment as listed on the freesurfer help/wiki pages,https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall It looks like you would do (using sh or bash), $ export FREESURFER_HOME=/usr/local/freesurfer$ source $FREESURFER_HOME/SetUpFreeSurfer.sh… output showing your settings ...... You could try loading an image from the freesurfer distribution directly from the command line to see if the graphics look any different. $ freeview $FRESURFER_HOME/subjects/bert/mri/brain.mgz The grey boxes could be from the VM not having enough CPU or video memory resources allocated to it and so the graphics refresh is slow.  You could try running some other graphics applications in the VM to see if you get the same greyed out effect. If you run freeview from the command line with no args, $ freeview - then you should get an empty window with just some icons at the top.  Is it sluggish trying to drag around the empty freesurfer window?  If so, I would ask whoever setup the VM to try and improve its performance. You could also try setting this on the command line for the vtk libs - but it may not fix the graphics getting greyed out.$ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$FREESURFER_HOME/lib/vtk/lib/vtk5.6 - R. On Oct 22, 2019, at 14:46, Adam Rytina <adam.rytina(a)outlook.cz> wrote:        External Email - Use Caution        Hello,thanks for your answer. Please see attached the screenshot.I typed "$ which freeview.bin" --> the output: "/usr/local/freesurfer/bin/freeview.bin"I typed "$ ldd `which freeview..bin` | grep not" --> the output: 20 files "libvtk...so.5.6 are not found" Please see the attached screenshot.While trying to install the packages (eg. "sudo apt-get install libvtkverdict.so.5.6"), the output is: Reading package lists... DoneBuilding dependency treeReading state information... DoneE: Unable to locate package libvtkverdict.so.5.6E: Couldn't find any package by glob 'libvtkverdict.so.5.6'E: Couldn't find any package by regex 'libvtkverdict.so.5.6'What´s wrong? Please, could you advise me? I tried to run freeview on Ubuntu 16.04 and 18.04 as well but the problem still remains the same.Thanks a lot for your helpRegardsAdamOd: fsbuild <fsbuild@contbay.com>Odesláno: pondělí 21. října 2019 4:28Komu: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Kopie: adam.rytina@outlook.cz <adam.rytina@outlook.cz>Předmět: Re: [Freesurfer] can´t open an image in Freeview Hello Adam,Please check if you have a “freeview.bin” program.$ which freeview.binIf you get a path back with freeview.bin in it, e.g. something like/usr/local/freesurfer/bin/freeview.bin- then try the ldd command on freeview.bin,$ ldd `which freeview.bin` | grep not- then see if it lists that something is not found.- R.On Oct 19, 2019, at 03:27, Adam Rytina <adam.rytina(a)outlook.cz> wrote:        External Email - Use Caution        Hello,I run the command "$ ldd `which freeview` | grep not" and the result is "not a dynamic executable". Do you know where the problem is?What I read there could be the problem regarding 32bit or 64bit system I´m working on. I am running on Windows 10 64bit, 64 bit CPU, 64bit Ubuntu 16.04. I downloaded the 6.0.0. Freesurfer version from the official page:https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstallPlease, could you help me?Thanks a lotAdamOd: fsbuild <fsbuild@contbay.com>Odesláno: pátek 18.. října 2019 22:05Komu: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Kopie: adam.rytina@outlook.cz <adam.rytina@outlook.cz>Předmět: Re: [Freesurfer] can´t open an image in Freeview Hello Adam,See if you can run the following command, and if it reports anything is not found (you can cut and paste the command)- R.$ ldd `which freeview` | grep notAdam Rytina   October 18, 2019 at 14:31        External Email - Use Caution        Hello all,I´m new to Freesurfer and I´m struggling with loading an image in FreeView. I am running the Freesurfer 6..0.0. on Ubuntu 16.04. Virtual Machine. While opening FreeView (typing "freeview" in the shell) just some empty grey windows will pop out (please see attached the screenshot). Besides this, everything is OK, I successfully tested Freesurfer installation. I haven´t found any simmilar issue on the Internet. Thus, please, could you help me to address this issue?Thanks a lotAdamBez virů. www.avast.com_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh..harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<freeview.png>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Learning dti processing tutorial
by Renew Andrade 24 Oct '19

24 Oct '19

External Email - Use Caution In other words I cannot process TRACULA without the T1w images of my subjects? Because this Parkinson database is from NITRC and I only have the diffusion images not the T1. I can practice on other subjects that I have both the T1 and diffusion images but I was expecting on using this Parkinson tractography and do the analysis. In case you want to know is this https://www.nitrc.org/projects/parktdi/ <https://www.nitrc.org/projects/parktdi/>. Sincerely, Andrade. Hi, you need to run recon-all on the T1, not on the diffusion scan. This will produce an anatomical segmentation of each subject based on the T1s, which TRACULA will then use to extract anatomical priors on white matter tracts, to aid tractography. When you run trac-all to do the actual tractography, then you run it on the diffusion scan. ________________________________ From: freesurfer-boun...(a)nmr.mgh.harvard.edu <freesurfer-boun...(a)nmr.mgh.harvard.edu> on behalf of Renew Andrade <andradere...(a)yahoo.com> Sent: Friday, October 18, 2019 5:02:35 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Learning dti processing tutorial External Email - Use Caution I am using a database of NITRC repository https://www.nitrc.org/projects/parktdi/ <https://www.nitrc.org/projects/parktdi/> . This images have a nifti file for 1000s/mm^2 and 2500s/mm^2. I don’t know if it is MPRAGE or not. Can you help me? What is the input file that you are supplying? Often this happens when the input it a multi-echo MPRAGE. If so, you can run mri_concat multi-echo-mprage.mgz --rms --o mprage.mgz then use mprage.mgz as the input to recon-all On 10/12/2019 4:48 PM, Renew Andrade wrote: > External Email - Use Caution > > Dear freesurfer experts: > I am trying to learn dti processing. For using Tracula it appears there is a > need for running "recon-all -all -i -s” on every subject before starting to > run Tracula. But there seems to be a problem. I have a Parkinson dwi images > database and every subject gives me an error of the type “input(s) cannot > have multiple frames!”. I am a little bit stuck on this step. Is it a problem > of the file as input? Am I putting the wrong file? Can it be done a recon-all > analysis to a dwi image? With trackvis I can obtain the results without any > problem. My doubt comes from FreeSurfer only and may be my little knowledge > about it. > Thanks for your help! > Sincerely, > Andrade. > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>

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LME model contrast matrix
by Liu Guodong 24 Oct '19

24 Oct '19

External Email - Use Caution Hello FreeSurfer Developers, I'm doing the LME tutorial, and I have some questions . 1. Why don’t we need to put the healthy controls in the designed matrix X? 2. What’s the interpretation of the first row of the contrast matrix [1 0 0 0 0], does it mean first group minus healthy group? 3. There is a pvalue and a vector sgn from the result of F-test, I know the interpretation of the sgn, but I don’t know the hypothesis of the pvalue, could you please help me with that? Thanks in advance! Best regards, Guodong

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Learning fsfast tutorial
by Renew Andrade 23 Oct '19

23 Oct '19

External Email - Use Caution Dear experts: I am trying to run preproc-sess -s sess01 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run But the outcome is ERROR: no run directories found. What could be wrong? If you need more information let me know! Sincerely, Andrade.

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time point exlusion file exceed nframes
by Lauri Tuominen 23 Oct '19

23 Oct '19

External Email - Use Caution Dear Freesurfers, I am running resting state analysis. I have TR 2.3, and 209 time points/frames, total length of the scan 483 seconds. I don’t drop any frames from the beginning ( nskip = 0 ). For one subject, the last two time points are motion outliers. So my tpef file includes numbers 478.4 and 480.7. When I run selxavg3-sess, I get the error time point exlusion file exceed nframes. I can’t figure out where the bug might be. So once again I would really appreciate your help! Thanks Lauri Tuominen

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Problem with hippocampal / amygdala and brainstem modules
by Iglesias Gonzalez, Juan E. 23 Oct '19

23 Oct '19

Dear all, If you have downloaded the development version of FreeSurfer any time during the last 3 weeks, you may have experienced problems with the modules that segment the hippocampal subfields, nuclei of the amygdala, and substructures of the brainstem. This is due to a very small bug that we will sort out immediately; I expect it to be fixed in tonight’s build. However, if you have downloaded the development version during these 3 weeks, you don’t need to download the whole thing again. You can simply edit the following two files: $FREESURFER_HOME/average/HippoSF/atlas/compressionLookupTable.txt $FREESURFER_HOME/average/BrainstemSS/atlas/compressionLookupTable.txt and replace “Left-Thalamus” by “Left-Thalamus-Proper”. Apologies for the inconvenience, Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com

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Re: [Freesurfer] can´t open an image in Freeview
by fsbuild 22 Oct '19

22 Oct '19

External Email - Use Caution Hello Adam, Please check if you have a “freeview.bin” program. $ which freeview.bin If you get a path back with freeview.bin in it, e.g. something like/usr/local/freesurfer/bin/freeview.bin - then try the ldd command on freeview.bin, $ ldd `which freeview.bin` | grep not - then see if it lists that something is not found. - R. On Oct 19, 2019, at 03:27, Adam Rytina <adam.rytina(a)outlook.cz> wrote:        External Email - Use Caution        Hello,I run the command "$ ldd `which freeview` | grep not" and the result is "not a dynamic executable". Do you know where the problem is?What I read there could be the problem regarding 32bit or 64bit system I´m working on. I am running on Windows 10 64bit, 64 bit CPU, 64bit Ubuntu 16.04. I downloaded the 6.0.0. Freesurfer version from the official page:https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstallPlease, could you help me?Thanks a lotAdamOd: fsbuild <fsbuild@contbay.com>Odesláno: pátek 18. října 2019 22:05Komu: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Kopie: adam.rytina@outlook.cz <adam.rytina@outlook.cz>Předmět: Re: [Freesurfer] can´t open an image in Freeview Hello Adam,See if you can run the following command, and if it reports anything is not found (you can cut and paste the command)- R.$ ldd `which freeview` | grep notAdam Rytina October 18, 2019 at 14:31        External Email - Use Caution        Hello all,I´m new to Freesurfer and I´m struggling with loading an image in FreeView. I am running the Freesurfer 6.0.0. on Ubuntu 16.04. Virtual Machine. While opening FreeView (typing "freeview" in the shell) just some empty grey windows will pop out (please see attached the screenshot). Besides this, everything is OK, I successfully tested Freesurfer installation. I haven´t found any simmilar issue on the Internet. Thus, please, could you help me to address this issue?Thanks a lotAdamBez virů. www.avast.com_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 1

segmentation tablet
by Lilla Zollei 22 Oct '19

22 Oct '19

Hi All, We are looking into replacing our old Wacom segmentation tablet and the two options that I have found so far are the * Wacom Cintiq Pro 32 and * Microsoft Surface Studio 2 Neither of these are linux compatible, which has created some issues in the past. Are there any groups out there who have any experience with the above (esp related to performance with FreeView) and / or any other interactive display solutions? Best, Lilla

1 0

trac-all error
by nayan wadhwani 22 Oct '19

22 Oct '19

External Email - Use Caution Hello Freesurfer, After running recon all script which completed successfully, I ran trac-all command which exited with error and tried running it with dicom files. 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 Abort ERROR: input file must be in NIfTI format Darwin EPILEPSY 16.7.0 Darwin Kernel Version 16.7.0: Mon Nov 13 21:56:25 PST 2017; root:xnu-3789.72.11~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Fri Oct 18 22:13:02 PDT 2019 And please help me the correct config the one I created, I am attaching it below to try it with .nii files Thanks and Regards Nayan Wadhwani

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tracula FA question - 2 cohorts/2 scanners
by Krieger, Donald N. 21 Oct '19

21 Oct '19

External Email - Use Caution I have tracula runs on two cohorts whose imaging was obtained on different scanners with slightly different beta's and other parameters. Would the differences in the scanners and scanning parameters be expected to produce large cohort-wide differences in the FA's? Can you point to a reference? Thanks - Don

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