Freesurfer

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30071 discussions

fthresh documentation
by srishti goel 16 Jul '18

16 Jul '18

External Email - Use Caution Hello, I am trying to decide what fthresh values should I be using for viewing my mkda maps on surface. Where could I find some theoretical explanation of how to figure that out the freesurfer wiki? I have read a lot of different things on the archive but didn't figure out my answer. It's great appreciated. 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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recon-all -s 1 exited with ERRORS
by Bernardo Regal 16 Jul '18

16 Jul '18

External Email - Use Caution Hello FreeSurfer Developers, I have a problem to convert the files using the recon-all. It appears, recon-all -s 1 exited with ERRORS. Before I had the last version (stable v6.0.0). As I did not find a solution of how to fix this problem, so I decided to make a downgrade to the previous version (5.3.0 stable). I thought that maybe the oldest version of this program was solved. But no, I still have the same problem. How I can fix this problem permanently? My code is: $ export SUBJECTS_DIR=/home/regal/Data/Subjects/test_old_version $ recon-all -s 1 /home/regal/Data/Subjects/test_old_version/01C_dislebi_T1.nii -autorecon-all than: " ERROR: Flag /home/regal/Data/Subjects/test_old_version/01C_dislebi_T1.nii unrecognized. -s 1 /home/regal/Data/Subjects/test_old_version/01C_dislebi_T1.nii -autorecon-all Linux genedys2 4.15.0-2-amd64 #1 SMP Debian 4.15.11-1 (2018-03-20) x86_64 GNU/Linux recon-all -s 1 exited with ERRORS at Tue Jul 3 18:47:19 CEST 2018 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting " 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 2) Platform: Linux genedys2 4.15.0-2-amd64 #1 SMP Debian 4.15.11-1 (2018-03-20) x86_64 GNU/Linux Thank you for your help, Best regards -- Bernardo Regal [image: Mailtrack] <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=sig…> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=sig…> 07/03/18, 7:27:54 PM

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Visualization of surface based analysis results
by John Anderson 16 Jul '18

16 Jul '18

External Email - Use Caution Dear Freesurfer experts, I ran surface based analysis between two groups using PET surfer to study the difference in PET signal between two groups. I followed the same steps as in wiki and everything went fine. To visualize the final statistical maps, I used the command: tksurfer fsaverage lh pial -overlay -overlay cache.th20.pos.sig.cluster.mgh The report "cache.th20.pos.sig.cluster.summary" shows two significant structures (attached figure 1). Looking at the figure from the output of tksurfer (attached figure 2). I see significant results in the frontal lobe. Please what I am doing wrong? Your guidance is highly appreciated John

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Monte Carlo threshold p-values
by Dincer, Aylin 16 Jul '18

16 Jul '18

External Email - Use Caution Hello FreeSurfer experts, In the FreeSurfer wiki page regarding multiple comparisons (<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecMultipleComparisons ) under "Simulation", it mentions the common Monte Carlo thresholds and their associated p-values. Would you be able to explain how the associated p values for each z threshold was calculated? (Ex. The associated p-value for z=1.3 is 0.05) Thank you! Aylin ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Extract Value from pcc.nii.gz
by Wang, Zhuonan 16 Jul '18

16 Jul '18

Hi FS Experts, I am doing the FAST analysis. After I finished the isxconcat-sess and got PCC.nii.gz, how can I extract the value from PCC.nii.gz file? Meanwhile, if I want to make group comparisons by using mri_glmfit, how to extract the values? Looking forward to your response Thank you. Zhuonan

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Matched analysis with 2 controls 1 case weighting
by Dowling, Kevin Francis 16 Jul '18

16 Jul '18

Hello Freesurfer Experts, I'm writing with a quick question about matched analysis. We have a cohort of MRI data collected such that there are two controls for each case, and these 2 controls are each matched to a specific case using a propensity score algorithm (~400 subjects total). For our analysis, we would like to try to implement a matched (or paired difference) analysis of cortical thickness (across the whole surface, not .aparcs) in Freesurfer. However, based all the documentation I have been able to find it seems that FS permits only paired difference analyses using matched pairs. Is this correct? Might there any way to implement such an analysis in Freesurfer using matched trios instead? We are open to using any Freesurfer version for this analysis, including dev, though the scans are currently reconned with FS 5.3. Thank you so much for your consideration! With kind regards, Kevin Kevin F. Dowling Clinical Research Coordinator Brain Genomics Laboratory Division of Psychiatric Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street Charlestown, MA, 02129 (p) 617.643.3215 Pronouns: He / Him / His

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Monte Carlo simulation - vertex wise threshold question
by Dincer, Aylin 16 Jul '18

16 Jul '18

External Email - Use Caution Hi FreeSurfer experts, I am trying to understand the Monte Carlo Z simulation in FreeSufer (mri_glmfit-sim) and have a question about the vertex wise /cluster forming threshold. In the simulation, a vertex wise threshold (ex. -cache 3 abs) is set and the threshold is applied to a z map. Is the 3 threshold (p value of 0.001) converted to a z score using the z table before it is applied to the map? Thanks! Aylin ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Re: [Freesurfer] non-stationarity in CTh maps
by Antonin Skoch 16 Jul '18

16 Jul '18

External Email - Use Caution Dear experts, following on this old thread, do you have any new knowledge on the possible severity of non-stationarity in cortical-thickness maps and its effect on permutation-based cluster-extent inference? Given current status of development, is here a possibility to estimate it/correct for it? Regards, Antonin Skoch Hi Hugo, they are assumed to be stationary. I've never tried to figure out how much of a problem this is.doug On 7/25/12 6:03 PM, Hugo Baggio wrote: Dear all,I have been performing cortical thickness analyses and as far as I understand the thickness maps are non-stationary (please correct me if I'm wrong). I have two questions: 1. How susceptible is Monte Carlo clusterwise correction to this(should I expect clusters at smoother areas to be bigger?)? 2. Does FS perform some sort of correction to this non-stationarity or are images assumed to be stationary at statistical analyses?Thanks a lot for your help! Hugo

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Petsurfer: Longitudinal GTM stats?
by Elijah Mak 16 Jul '18

16 Jul '18

External Email - Use Caution Hi Freesurfer Team and Doug, Is there any way to derive the gtmstats from Petsurfer within a longitudinal design? Could I get your take on the steps below? 1. Extract GTM stats from each PET time-point (registered to the closest structural MRI in time). 2. Manually compute the percent change per region across time-points. Alternatively, would it be more ideal to resample the PET data to the surfaces at each time point before extracting the MGX-based ROI PET data with mri_segstats? With this approach, it would be possible to use the longitudinal commands, right? Thanks! Elijah

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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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