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30132 discussions

Re: [Freesurfer] glmfit-sim FWHM 34?
by Backhausen, Lea 16 Jul '18

16 Jul '18

External Email - Use Caution Hi Doug, thanks for your answer! This particular case is surface area. I thought I was using the FWHM15 smoothed data from outputted by qcache. I have no idea why FS tries to call FWHM34 in the glmfit-sim step. Should I have specified somewhere else in the commands? I will attach the log files again. Yes, I am aware I should be using permutation - I just wanted to run Monte Carlo again to compare results. Permutation was in fact how I came to use dev since mri_surfcluster did not work with my MAC. I downloaded a new patch you linked in a previous post but it produced more errors (maybe was not compiled for MAC?). Then I just tried with dev and it worked for me. But then I ran into the FWHM34 thing with Monte Carlo... Do you maybe have a mri_surfcluster available that will run permutation with MAC (High Sierra) and runs with the stable version? Thanks again, I really appreciate your help! Best, Lea __________________________________________________________________ Date: Tue, 3 Jul 2018 12:07:01 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] glmfit-sim FWHM 34? To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <d081e931-855f-f5fb-62bc-23779c295624(a)mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252"; format=flowed How much did you smooth by? Is this thickness, area, or volume? Also, in general, you should not be using dev since it is an uncontrolled distribution (ie, there are many things in there that have not been tested). Also, I'm encouraging people to use permutation rather than monte-carlo-based correction. On 07/03/2018 11:40 AM, Backhausen, Lea wrote: > > > Dear FreeSurfer experts, > > I am trying to do vertex-wise comparisons for thickness, surface area > and volume between three groups with glmfit. > Currently I am using the dev version (-------- > freesurfer-darwin-OSX-ElCapitan-dev-20180627-4a8f901 --------) on Mac > since I ran into problems with mri_surfcluster when using permutation > for multiple comparison correction. That seems to work fine with the > dev version. > > When running Monte Carlo simulation with glmfit-sim I ran into the > following error message: > ERROR: cannot find > /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm34/abs/th33/mc-z.csd > > When I checked, the folder fm34 did not exist. But now I am wondering > why FreeSurfer is trying to use FWHM34 from the beginning as I used > FWHM15 for smoothing in the preprocession step. I see in the > glmfit.log "ResidualFWHM 33.582634" - did I have to specify the > smoothing kernel anywhere else ecxept from the preprocessing step? > > Please find attached the log files for preprocessing, glmfit and > glmfit-sim. > Thank you so much for any help! > > Best > Lea > > > > Lea Backhausen, B.Sc. > > Student Research Assistant Lea Backhausen, B.Sc. Wissenschaftliche Hilfskraft 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 Lea Backhausen, B.Sc. Wissenschaftliche Hilfskraft 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 Lea Backhausen, B.Sc. Wissenschaftliche Hilfskraft 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 Lea Backhausen, B.Sc. Wissenschaftliche Hilfskraft 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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loading multiple saved points
by Yagmur Ozdemir 19 16 Jul '18

16 Jul '18

External Email - Use Caution Hello Freesurfer experts, I am wondering if there is any way I can load up multiple points I saved in tkmedit, in either viewing software at the same time. Each time I defined a point, I changed the edit.dat file's name so it would save as individual files, but when I try to load there is no option to choose amongst dat files, and I noticed that if there are multiple points saved in edit.dat when you "go to saved point" it will load the last point saved. I think I am able to load these into either freeview or tksurfer because in all GUIs the system looks for edit.dat. I think I can load the last points one by one in tksurfer, delete the last vertex from file and save it on tksurfer surface, but I am really for a more intuitive and portable way. Best Idil

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partial volume correction
by Barletta, Valeria 16 Jul '18

16 Jul '18

Hi Freesurfers, We are trying to apply the PVC process to our PET images. We proceeded through step3 as indicated on fswiki, and obtained the files: - gtm.nii - nopvc.nii - mgx.gm.nii How can we obtain the corrected uptake values from these files? Can we obtain a corrected volume file for voxel based analysis? Thanks for your help, Valeria

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glmfit-sim FWHM 34?
by Backhausen, Lea 15 Jul '18

15 Jul '18

External Email - Use Caution Dear FreeSurfer experts, I am trying to do vertex-wise comparisons for thickness, surface area and volume between three groups with glmfit. Currently I am using the dev version (-------- freesurfer-darwin-OSX-ElCapitan-dev-20180627-4a8f901 --------) on Mac since I ran into problems with mri_surfcluster when using permutation for multiple comparison correction. That seems to work fine with the dev version. When running Monte Carlo simulation with glmfit-sim I ran into the following error message: ERROR: cannot find /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm34/abs/th33/mc-z.csd When I checked, the folder fm34 did not exist. But now I am wondering why FreeSurfer is trying to use FWHM34 from the beginning as I used FWHM15 for smoothing in the preprocession step. I see in the glmfit.log "ResidualFWHM 33.582634" - did I have to specify the smoothing kernel anywhere else ecxept from the preprocessing step? Please find attached the log files for preprocessing, glmfit and glmfit-sim. Thank you so much for any help! 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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recon-all error: I think mri_ca_label problem...
by 김결 15 Jul '18

15 Jul '18

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to recon-all function (input file is sample-001.nii.gz), but for some of my subjects I get the following error when I run the recon-all command: I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 2) Platform: Docker freesurfer/freesurfer tag 6.0 (maybe officialized 3) recon-all.log: see attached 4) recon-all.error.log see attached 5) recon-all-status see attached please help me... Kyul

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Freeview modalSession has been exited prematurely - check for a reentrant call to endModalSession:
by Renew Andrade 14 Jul '18

14 Jul '18

External Email - Use Caution Hello: I attach here the command output of an error that I have while using Freeview. It doesn’t allows me to read any file. sh-3.2# freeview -v \ > good_output/mri/T1.mgz \ > good_output/mri/wm.mgz \ > good_output/mri/brainmask.mgz \ > good_output/mri/aseg.mgz:colormap=lut:opacity=0.2 \ > -f good_output/surf/lh.white:edgecolor=blue \ > good_output/surf/lh.pial:edgecolor=red \ > good_output/surf/rh.white:edgecolor=blue \ > good_output/surf/rh.pial:edgecolor=red mghRead(/Volumes/TOSHIBA_EXT/otros/Acad?mico/Research/image_processing/freesurfer_data_tutorial/buckner_data/tutorial_subjs/good_output/mri/T1.mgz, -1): could not open file MRIread failed: Unable to read from /Volumes/TOSHIBA_EXT/otros/AcadÃ©mico/Research/image_processing/freesurfer_data_tutorial/buckner_data/tutorial_subjs/good_output/mri/T1.mgz mghRead(/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/buckner_data/tutorial_subjs/good_output/mri/T1.mgz, -1): could not open file 2018-07-14 20:54:25.295 Freeview[63733:8866675] modalSession has been exited prematurely - check for a reentrant call to endModalSession:

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Re: [Freesurfer] Euler number as quantitative quality measure
by Backhausen, Lea 14 Jul '18

14 Jul '18

External Email - Use Caution Hi Bruce, Thank you for your input, the paper really helped me to understand the concept of the Euler number. So that means anyone interested in using the Euler number as a quality measure will have to use the ?h.orig.nofix surfaces as input, right? And smaller Euler numbers would mean more topological defects i.e. worse quality? I am confused though as to which extend this number is of relevance as like you pointed out FreeSurfer will correct the topology of the surfaces until Euler number = 2 and thus have fixed the defects. Meaning in the end successfully processed data sets won’t have topological defects no matter how bad the Euler number originally was. Or does it still matter? Would be happy to hear from you again! Best, Lea ------------------------------ Lea Backhausen Research Assistant Department of Child and Adolescent Psychiatry, Faculty of Medicine of the TU Dresden, Germany http://www.uniklinikum-dresden.de<http://www.uniklinikum-dresden.de/> ____________________________________________________________________ Date: Thu, 12 Jul 2018 11:01:36 -0400 (EDT) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Euler number as quantitative quality measure To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <alpine.LRH.2.20.1807121100190.28012(a)gate.nmr.mgh.harvard.edu<mailto:alpine.LRH.2.20.1807121100190.28012@gate.nmr.mgh.harvard.edu>> Content-Type: text/plain; charset="windows-1252" Hi Lea the Euler number is an integer, so it will never be 2.5. In fact, in our reconstructed surfaces it will always be exactly 2, except for the *nofix* surfaces, as we explicitly correct the topology of the surfaces (see the Automated Manifold Surgery paper if you are interested in the details) cheers Bruce On Thu, 12 Jul 2018, Backhausen, Lea wrote: > > ????????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

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missing ribbon.mgz
by Aaron Tanenbaum 13 Jul '18

13 Jul '18

External Email - Use Caution I am a bit puzzled. I am running freesurfer 5.3 HCP on ubuntu 14.04. I am getting an error, see below I am using the command recon-all -s BOLD-52_v1 -mprage -autorecon2 This has happened before. What did I do wrong. #@# ASeg Stats Fri Jul 13 12:55:02 CDT 2018 > > INFO: mri_segstats will not calculate Supratentorial > due to missing ribbon.mgz file > /data/nil-bluearc/ances/Aaron/FreeSurfers/BOLD-52_v1 > > mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz > --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 > --excl-ctxgmwm --subcortgray --in mri/norm.mgz --in-intensity-name norm > --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray > --euler --ctab /data/ances/FreeSurfer/freesurfer_5_3_HCP//ASegStatsLUT.txt > --subject BOLD-52_v1 > > > $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ > cwd > cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv > mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg > --excludeid 0 --excl-ctxgmwm --subcortgray --in mri/norm.mgz > --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol > --surf-ctx-vol --totalgray --euler --ctab > /data/ances/FreeSurfer/freesurfer_5_3_HCP//ASegStatsLUT.txt --subject > BOLD-52_v1 > sysname Linux > hostname brahms > machine x86_64 > user tanenbauma > UseRobust 0 > atlas_icv (eTIV) = 1714974 mm^3 (det: 1.135939 ) > mghRead(/data/nil-bluearc/ances/Aaron/FreeSurfers/BOLD-52_v1/mri/ribbon.mgz, > -1): could not open file > Computing euler number > orig.nofix lheno = -70, rheno = -38 > orig.nofix lhholes = 36, rhholes = 20 > Loading mri/aseg.mgz > Getting Brain Volume Statistics > Linux brahms 3.19.0-80-generic #88~14.04.1-Ubuntu SMP Fri Jan 13 14:54:07 > UTC 2017 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s BOLD-52_v1 exited with ERRORS at Fri Jul 13 12:55:11 CDT 2018 > > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >

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fthresh function in tksurfer
by srishti goel 13 Jul '18

13 Jul '18

External Email - Use Caution Hello, I am trying to view network based maps produced from a meta-analysis using neuroelf on the surface in freesurfer. The meta-analytic maps are thresholded maps that represent the proportion of contrasts that activated at each voxel I projected my maps on the surface using: mri_vol2surf --src negative_allsocial_proportion.img --regheader mni152_subject --hemi lh --o ./neg_allsocial_lh.nii --projfrac 0.5 Then to view it used: tksurfer mni152_subject lh inflated -overlay ./neg_allsocial_lh.nii -fthresh 0.05 The issue I have is with the fthresh value. I read the wiki and some stuff on archive about the fthresh value but I am unsure what it exactly means and does. My issue is that the display of my maps changes when I change the fthresh value even though the maps have been k-thresholded using neuroelf before exporting them to freesurfer. More area is marked up when I decrease the threshold value from 0.1 to 0.05 and nothing is visible above 0.1 Does anyone have any thoughts about what might be going on there and how I can fix it? Do I need to do something totally different from what I am doing? Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig(a)email.unc.edu skype: srishti.goel12

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(no subject)
by Muscas Giovanni 13 Jul '18

13 Jul '18

External Email - Use Caution Hi everybody, I was wondering if you could help me. I run a hyppocampal segmentation in a subject and it seemed to work. Now when I'm trying to extract the infos and run "quantifyHippocampalSubfields.sh" I just get this message: Gathering results from subjects in: /home/giovanni/Schreibtisch/freesurfer/subjects Using the suffix name: T1 And writing them to: hippo.txt but actually there's no file at all in the computer. Do you have any idea what I'm doing wrong? Thank you, Giovanni

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