Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

FreeSurfer License issue
by Carolina Bonivento 20 Jul '18

20 Jul '18

External Email - Use Caution Dear Sir/Madame, I recently subscribed the FS license (attached) but when I tried to run the 'recon-all’ (actually one of its steps, i.e. the MRI_ca_register) I received the following error message: ERROR: Invalid FreeSurfer license key found in license file /root/freesurfer/license.txt Following some instruction that I got previously, I replaced the .license with the license.txt in the $FREESURFER_HOME directory (in my case root/freesurfer) but I still get the same error message. Note that I’m running FreeSurfer through a Docker container running Ubuntu14 that is linked to the ‘freesurfer' folder on the' /User/home' of a macOS High Sierra (of course, Docker and the freesurfer folder are on the same machine). When I filled the license request form I’ve selected Linux/Intel as 'Operating System/Platform', as this is the OS of the Docker container. Is it possible that the issue is due to this? In that case, can I ask for a second license? Thank you in advance for your attention. Looking forward to hearing from you, I’m sending you my best regards, Carolina

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mri_binarize
by John Anderson 20 Jul '18

20 Jul '18

External Email - Use Caution Dear Freesurfer experts, I would like to inquire about the flag --subcort-gm in mri_binarize. It seems that the final product of this flag create a mask include the brain stem which is largely white matter. Why it was included in the subcortical gray matter structures? Thanks for any clarification, john

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Exporting results from QDEC
by Avi Gharehgazlou 20 Jul '18

20 Jul '18

External Email - Use Caution Hi experts, I want to make plots of my results that I have from QDEC, however, I'm having difficulty exporting values from QDEC. I examined LGI differences between groups, and I want to export my results, so the LGI values of significant between-group differences. Will you please tell me how I can do this? Thanks, Avi

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Euler number as quantitative quality measure
by Backhausen, Lea 20 Jul '18

20 Jul '18

External Email - Use Caution Hey Freesurfer Experts, I would like to use the Euler number as a quantitative quality measure of my reconstructed data as Rosen et al. (2017) recommend in their recently published paper. https://www.sciencedirect.com/science/article/pii/S1053811917310832 I figured I can use: mris_euler_number [<options>] insurf to get the euler number for each data set. Which surface should I use though? The white or pial surface area or is there no preference? Does anybody have experience with what range of Euler number would be acceptable? I read that 2 would be perfect but is 2.5 still ok? Or 1? Somehow I could not find any recommendation in the Rosen paper about thresholds or something similar. Did I miss something? Any advice would be highly appreciated! Thanks! Best, Lea _______________________________________ Lea Backhausen, B.Sc. Student Research Assistant Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und –psychotherapie Tel. +49 (0)351 458-7166 Fax +49 (0)351 458-5754 Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://www.uniklinikum-dresden.de<https://deref-web-02.de/mail/client/kXc4jbFBtdU/dereferrer/?redirectUrl=htt…> Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer Vorsitzender des Aufsichtsrates: Prof. Dr. med. Peter C. Scriba USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113

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Question about Freeview, 20% threshold
by Daumail, Loic Jean 20 Jul '18

20 Jul '18

Dear FreeSurfer experts, I am currently using TRACULA( from freeSurfer 6.0), and on the freeview visualization of merged files of the probability distributions of the tracts, I don't understand the thing about the "20% threshold". Indeed, on the tracula tutorial, it is written that the tracts are displayed in a way that they are at 20% of their maximum threshold. However, what does this mean? Is it the 20% of the most probable paths for each tracts? The adjustment bar on the side of the screen permits to vary this threshold, but when we reduce the level of the threshold, the size of the tracts increase, which seems in contradiction with the previous statements... I then suppose that my guess must be wrong? Thank you for your time and consideration! Sincerely, Loïc

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Re: [Freesurfer] Label numbers for thalamic nuclei
by Iglesias Gonzalez, Eugenio 20 Jul '18

20 Jul '18

External Email - Use Caution Dear KT, They range from 8100 to 8300. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of ?? ? <kytak1123(a)hotmail.com> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Friday, 20 July 2018 at 08:17 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Label numbers for thalamic nuclei External Email - Use Caution Dear Freesurfer Team, I have been using segmentation of thalamic nuclei from the Freesurfer dev version(freesurfer-linux-centos7_x86_64-dev). I see some thalamus labels in FreeSurferColorLUT.txt(#8001-8014), but I can't find label numbers for 25 different nuclei. Where could I find those numbers? Thanks in advance, Kayeong Tak

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Why I have to set the environment every time
by 王子谦 20 Jul '18

20 Jul '18

External Email - Use Caution Hi, Every time I wanna use the command of freesufer I have to reset the environment again, otherwise it will remind me “not found the command”. Only after I write “export FREESURFER_HOME=/Applications/freesurfer; source $FREESURFER_HOME/SetUpFreeSurfer.sh” Then I can use it smoothly. But after I close the terminal, I have to rewrite it again. Any suggestion is acceptable. Thanks a lot Ziqian

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Label numbers for thalamic nuclei
by ?? ? 20 Jul '18

20 Jul '18

External Email - Use Caution Dear Freesurfer Team, I have been using segmentation of thalamic nuclei from the Freesurfer dev version(freesurfer-linux-centos7_x86_64-dev). I see some thalamus labels in FreeSurferColorLUT.txt(#8001-8014), but I can't find label numbers for 25 different nuclei. Where could I find those numbers? Thanks in advance, Kayeong Tak

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parallel openmp
by John Absher 19 Jul '18

19 Jul '18

External Email - Use Caution We are trying to run many subjects through recon-all in batches on an 8 core Windows Server on which we have virtualBox running CentOS7 and freesurfer 6. Can you tell me if this command will utilize all 8 cores effectively to process all 8 subjects simultaneously? recon-all -subjid TBI1_002 -i TBI1_002_v1.nii.gz \ -subjid TBI1_003 -i TBI1_003_v1.nii.gz \ -subjid TBI1_005 -i TBI1_005_v1.nii.gz \ -subjid TBI1_006 -i TBI1_006_v1.nii.gz \ -subjid TBI1_007 -i TBI1_007_v1.nii.gz \ -subjid TBI1_009 -i TBI1_009_v1.nii.gz \ -subjid TBI1_012 -i TBI1_012_v1.nii.gz \ -subjid TBI1_013 -i TBI1_013_v1.nii.gz \ -all -parallel -openmp 8 Thanks, John John R. Absher, MD, FAAN GHS Neurosciences jabsher(a)ghs.org<mailto:jabsher@ghs.org> 864-350-6655 (mobile)

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How to obtain sulcal depth in raw mm?
by Jacob Miller 19 Jul '18

19 Jul '18

External Email - Use Caution Hi Freesurfer team, I have a quick question regarding the output of *.sulc* values in Freesurfer: From previous messages on the list, it seems as though the *.sulc* values in each hemisphere are 0-median and unit standard deviation of the original mm sulcal depth. Is this correct? Namely, I'm wondering the best way to obtain vertex-wise values for *raw sulcal depth (**mm)* from a subject's Freesurfer (recon-all) output. Perhaps this may just entail un-standardizing the .sulc values? Thank you! Jacob -- Jacob Miller Graduate Student, D'Esposito Lab Helen Wills Neuroscience Institute (HWNI) University of California, Berkeley https://despolab.berkeley.edu/

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