Freesurfer

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30088 discussions

Getting stats from stats files. rh.w-g.pct. asegstatsdiff
by Троицкий Антон Александ рович 24 Oct '19

24 Oct '19

External Email - Use Caution Dear free surfer developers, 1. I processed several items of data. And I have rh.w-g.pct file in my stats folders. How can I get process this file to get table reading file? I tried to use asegstats2table and aparcstats2table but it didn’t work. I tried to find appropriate script in $FREESUFER_HOME/bin folder. But it doesn’t help. Could you provide me with necessary information about getting of stats from rh.w-g.pct to table file like asegstats2table? 2. I try to execute asegstatsdiff script from the command line (Mac Os). There is a message appears «if: Expression Syntax.» In the header of this script the string «#! /bin/tcsh -f» is written. So, How I understand I need to use something else instead of bash, isn’t it? Best regards, Anton Troitskii.

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subcortical volume-based pet analysis
by miracle ozzoude 24 Oct '19

24 Oct '19

External Email - Use Caution Hello Experts, I do have couple questions about using mri_glmfit and mri_glmfit-sim for this analysis based on the tutorial page. https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer 1) Do i have to add any other flags when using mri_glmfit for this analysis? mri_glmfit --y ${results_dir}/all.mgx.subctxgm.mni305.sm05.nii.gz --fsgd $pet_fsgd --C $matrix1 \ --mask ${SUBJECTS_DIR}/fsaverage/mri.2mm/subcort.mask.mgz --glmdir ${results_dir}/sub.pet.B6.glmdir 2) When correcting for multiple comparisons, should i use --2spaces or --3spaces? 3) I ran a paired ttest analysis using age as regressor of no interest for amyloid uptake. My contrast is "1 0" based on the tutorial https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis. How do i interpret the direction of contrast if I get a result from mri_glmfit-sim (see below)? This is because it doesn't have the Max column for surface based analysis # Cluster Size(n) Size(mm^3) MNIX MNIY MNIZ Max CWP CWPLow CWPHi 1 12709 101672.0 26.00 -69.00 -41.00 5.46844 0.01037 0.00798 0.01316 Right-Cerebellum-White-Matter Thank you. best, Paul

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

24 Oct '19

External Email - Use Caution Dear FreeSurfer experts: I am trying to use my own data so I don’t have the same tutorial structure. I do keep the folder structure as similar as possible in order for FreeSurfer to run but I cannot have different sessions for example I just have resting or bold but not both. Is it a problem when running this analysis? This is my directory structure ➜ ~ cd /Users/andraderenew/Downloads/2 ➜ 2 git:(master) ✗ ls rest ➜ 2 git:(master) ✗ cd rest ➜ rest git:(master) ✗ ls dti_FA.nii.gz dti_L2.nii.gz dti_MD.nii.gz dti_S0.nii.gz dti_V2.nii.gz dti_L1.nii.gz dti_L3.nii.gz dti_MO.nii.gz dti_V1.nii.gz dti_V3.nii.gz ➜ rest git:(master) ✗ Sincerely, Andrade. look in sess01/bold, you should see 001 and 002. Do you? On 10/22/2019 9:40 AM, Renew Andrade wrote: 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. _______________________________________________ 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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Re: [Freesurfer] can´t open an image in Freeview {Disarmed}
by fsbuild 24 Oct '19

24 Oct '19

External Email - Use Caution Hello Adam, I’m doing some work with a VirtualBox VM running Ubuntu 18.04 -but hosted from Mac OS instead of Windows.  I will install the 6.0.0 freesurfer release in the Ubuntu VM and run some of the freeview command tests we use, but so far I have not seen the graphics behavior you describe.    The VirtualBox software has some guest extensions to install in the Ubuntu OS that can help with performance and graphics.  On the Mac I have seen that w/o additions like that installed, the entire VM window will flicker.  I might also be able to try the Ubuntu VM on a Windows 10 machine. - R. On Oct 24, 2019, at 15:27, Adam Rytina <adam.rytina(a)outlook.cz> wrote:        External Email - Use Caution        Hello,Yes sure, I checked my setup of Freesurfer enviroment - the same as the wiki page I guess.I loaded an image from the freesurfer distribution directly from the command line - the same problem (the grey windows popping out).The strange thing is I´m running also FSL on Ubuntu VM without any problem, thereby I don´t think the issue is related to the Ubuntu VM. Moreover, I succesfully opened some images few days ago and the program was running without any problem. However, it took just a while and then this issued appeared again. There is just a grey window popping out (choosing all options run very quickly without any problem).Well, I´m totally helpless. I tried to download it again, run Freesurfer on Ubuntu 16. and 18. version but the problem still persists. RegardsAdamOd: fsbuild <fsbuild@contbay.com>Odesláno: středa 23. října 2019 7:30Komu: 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,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/DownloadAndInstallIt looks like you would do (using sh or bash),$ export FREESURFER_HOME=/usr/local/freesurfer$ source $FREESURFER_HOME/SetUpFreeSurfer.sh… output showing your settings ......You could try loading to see if the graphics look any different.$ freeview $FRESURFER_HOME/subjects/bert/mri/brain.mgzThe 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(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "mail.nmr.mgh.harvard.edu" claiming to behttps://mail.nmr..mgh.harvard.edu/mailman/listinfo/freesurfer____________… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/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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