Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

Thalamic subnuclei color table
by Crawford, Anna 25 Oct '19

25 Oct '19

External Email - Use Caution Hello, Just a quick question. We recently installed the new thalamus segmentation subroutine. It's really wonderful, and much promise to our work. I can't find a lookup table with the numerical labels from the FS output to the thalamic nuclei. The numbers around between 8103-8133 on the right, and 8203 and 8233 on the left. Can you point me in the right direction for this? For other FS segmented volumes I always use the following, but it doesn't include these thalamic subnuclei http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurfe… Thank you, Anna Please consider the environment before printing this e-mail Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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Mri_mask producing only zeros
by Sims, Sara A (Campus) 24 Oct '19

24 Oct '19

External Email - Use Caution Freesurfers, I am trying to use mri_mask using surface overlays. I made a label into a volume and then into a surface with 1s inside the label and 0s outside the label. I want to make a connectivity map surface overlay with values only within my label overlay. However when I run it, it creates a surface overlay with only zeros. There is definitely values within the label surface overlay (I triple checked). Code I used: Mri_mask original_surface_overlay label_mask new_masked_output It doesn’t output any errors. Here is what it looks like in freeview: Original surface overlay (label is outlined in green) [cid:image001.png@01D5821A.1324B130] The label made into a surface overlay (same as the one shown in green above): [cid:image002.png@01D5821A.1324B130] But this is the output: all zeros even though there was data within the mask. [cid:image003.png@01D5821A.1324B130] Help! Sara A. Sims

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Mean p-value of uncorrected cluster in Qdec
by Lucia Batzu 24 Oct '19

24 Oct '19

External Email - Use Caution Dear Freesurfer Developers, I'm running a Qdec analysis in which I'm looking for correlations between cortical thickness and a continuous CSF measurement. I'm interested in a specific area in which a cluster of correlation pops up, but doesn't survive cluster-wise correction for multiple comparisons. The details of the cluster are the following: Contrast: 'rh-Avg-thickness-CSF_protein-Cor', 15fwhm, DOF: 61 ClusterNo: 1 Max: 3.1156 VtxMax: 122763 Size(mm2): 1247.98 TalX: 19.9 TalY: -46.6 TalZ: -9.0 NVtxs: 2022 Annotation: lingual I would like to know if there is a way to extract the mean p-value [or, better, -log10(p)] of the uncorrected cluster. Thank you very much in advance, Best, Lucia

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how to get the full name of cortical segmentation structures?
by chen 24 Oct '19

24 Oct '19

External Email - Use Caution Dear freesurfer experts, I want to know the full name of the cortical segmentation structures. The look up table cannot solve my question. For example, the full name of the rh_bankssts_volume or rh_parsopercularis_volume. Cheers, Chen

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Converting ROIs from MNI152 space to MNI305
by Barbour, Tracy,M.D. 24 Oct '19

24 Oct '19

Hello experts, I am trying to convert insula ROIs that are in MNI 152 2 mm space to MNI305 space. I will eventually this ROI for connectivity analysis. I ran mri_vol2vol: mri_vol2vol --mov $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz --targ /autofs/cluster/neuromod/Insula_ROIs/left/k10/cluster_1.nii.gz --reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --inv --o cluster_1.mni305.mgz When I visualize the results the converted ROI is more caudal than the original. What am I doing wrong? Tracy

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Re: [Freesurfer] Error in glmfit-sim cache
by Renew Andrade 24 Oct '19

24 Oct '19

External Email - Use Caution I have tried all the values it pinpoints to but none seem to work.

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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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