Freesurfer

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30132 discussions

Troubleshooting fix topology lh stall
by Hoang, Ricky 20 Mar '20

20 Mar '20

External Email - Use Caution Hello Freesurfer experts, I am trying to run recon-all to assess cortical thickness on a 3D FSPGR+C scan. The run keeps timing out during the fix topology lh step. I have looked at the resulting images and I am not sure whether I need to fix the white matter, add control points, or do something else entirely to fix the problem. The lh.inflated.nofix does not seem to have anything unwanted still attached and the lh.defect_label will not load. The lh.inflated.nofix does show some areas that have strands/spikes, which I think might be due to the gadolinium contrast. I wanted to ask for opinions on how to proceed. I have attached the recon-all.log. This is also a link to the output folder: https://drive.google.com/drive/folders/14fj1JAGAvuB-DpgLCxQwOXQ08u6-Vfvj?us… Thank you! Ricky

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Permutation simulation produces unexpected results
by Purcell, Juliann 20 Mar '20

20 Mar '20

External Email - Use Caution Hi FreeSurfer Experts, I am running permutation simulations with several smoothing levels and cluster forming thresholds to evaluate the best parameters for our data, since there does not seem to be a consensus in the literature. However, I'm getting an unexpected result at only one smoothing/threshold level. I have run permutations (mri_glmfit-sim) at 0mm, 5mm, 10mm using the following thresholds: 1.3, 2.0, 2.3, and 3.0. Results of permutation at 10mm + threshold 1.3 were not as expected and did not line up with results at the other smoothing and threshold levels. I've re-checked that the command is correctly referencing the data and I've compared the th1.3 log file with the log files at the other thresholds. I could not find any differences that would cause the output of the permutation simulations to be so different between th1.3 and th2.0. There are no errors or failures in the permutation log files. I've searched the message board and didn't see any posts that related to this issue. Although it's possible that these are true results, I want to make sure there isn't a mistake on my end. Any help would be greatly appreciated! Below is information about my FreeSurfer version, platform, and the log files from the permutation simulations: 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: Linux 3) uname -a: Linux c0135 3.10.0-1062.9.1.el7.x86_64 #1 SMP Mon Dec 2 08:31:54 EST 2019 x86_64 x86_64 x86_64 GNU/Linux 4) Perm sim log files: See attached logs for 10mm smoothing at threshold 1.3 and threshold 2.0 Best, Juliann Purcell, MSc Doctoral Candidate Medical/Clinical Psychology Doctoral Program University of Alabama at Birmingham Department of Psychology juliannp(a)uab.edu<mailto:juliannp@uab.edu>

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Re: [Freesurfer] Operating System
by fsbuild 19 Mar '20

19 Mar '20

External Email - Use Caution Hello Stephanie, I already had 6.0.0 installed and did an incremental upgrade from 10.13 to 10.15, and did not run into any serious issues other than having to grant some permissions.   However, other older software already in /Applications may fail to run after the upgrade (which was the case after I did one upgrade). If you must upgrade, I suggest using Disk Utility to make a disk image backup of your entire boot or Macintosh HD partition so you can try to revert back using its restore function if necessary.  I've only put the upgrade on one machine because it is new Apple hardware that cannot run 10.13 or 10.14..  My advice generally is to always stay one revision behind the latest version of Mac OS - which right now would be 10.14 Mojave.  I don’t have or know of any software that only runs on 10.15 but does not run on 10.14.  So all my other machines that can still run 10.14 have not been upgraded. - R. On Mar 19, 2020, at 16:11, Rellick, Stephanie <srellick(a)hsc.wvu.edu> wrote:        External Email - Use Caution        I am needing to upgrade my operating system to Catalina on my Mac, and I am running Freesurfer version 6.0.0.  Is this version compatible with CatalinaOS?Thanks,Stephanie_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Operating System
by Rellick, Stephanie 19 Mar '20

19 Mar '20

External Email - Use Caution I am needing to upgrade my operating system to Catalina on my Mac, and I am running Freesurfer version 6.0.0. Is this version compatible with CatalinaOS? Thanks, Stephanie

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recon-all error
by Mason Wells 19 Mar '20

19 Mar '20

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to run the recon-all command on a Linux machine but it appears to be falling at one of the first hurdles. INFO: extension is mgz #-------------------------------------------- #@# Talairach Wed Mar 18 15:30:51 GMT 2020 /home/masontwells/Documents/Data/freesurfer/subjects/LM/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux masontwells-VIG800S 5.3.0-40-generic #32~18.04.1-Ubuntu SMP Mon Feb 3 14:05:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux recon-all -s LM exited with ERRORS at Wed Mar 18 15:30:53 GMT 2020 For more details, see the log file /home/masontwells/Documents/Data/freesurfer/subjects/LM/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting masontwells@masontwells-VIG800S: 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. I am running freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Thanks in advance, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk> Tel: 02920 879628 Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214-><http://www.cardiff.ac.uk/people/research-students/view/482937-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk> Ffôn: 02920 879628

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Re: [Freesurfer] mri hippocampal subfields:output file
by Iglesias Gonzalez, Juan E. 18 Mar '20

18 Mar '20

Hi Flavia, Did the hippo subfield routine complete successfully? Are the outputs in the mri directories of the subjects? Did you look at the log files of the subfield routine? Cheers, /E Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Loreto, Flavia" <f.loreto(a)imperial.ac.uk> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Wednesday, March 18, 2020 at 08:28 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] mri hippocampal subfields:output file External Email - Use Caution Dear FreeSurfer experts, Version: FreeSurfer 6.0 Platform: Bash remotely through High Performance Computing (HPC) on a MacOS Mojave We have run hippocampal subfields segmentation analyses and we are now having problems exporting the volumetric outputs. We have run Iglesias’ ‘obsolete’ script to obtain hippocampal volumes, as our system does not support the dev version of Freesurfer. recon-all -all -s bert -hippocampal-subfields-T1 Then, to gather volumes from our analysed subjects, we have run this script quantifyHippocampalSubfields.sh <T1>-<analysisID> <output_file> <OPTIONAL_subject_directory> In particular, this is how it looks in our terminal: -bash-4.2$ quantifyHippocampalSubfields.sh T1 hippo_demo.txt /rds/general/project/amyloidpet/live/freesurfer Gathering results from subjects in: /rds/general/project/amyloidpet/live/freesurfer Using the suffix name: T1 And writing them to: hippo_demo.txt However, we are not able to find the output anywhere. Could you help us figuring out what could be the reason why can’t find it? I have attached the recon-all.log for one of our analysed subjects. Many thanks for your help. Kind regards, Flavia

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mri hippocampal subfields:output file
by Loreto, Flavia 18 Mar '20

18 Mar '20

External Email - Use Caution Dear FreeSurfer experts, Version: FreeSurfer 6.0 Platform: Bash remotely through High Performance Computing (HPC) on a MacOS Mojave We have run hippocampal subfields segmentation analyses and we are now having problems exporting the volumetric outputs. We have run Iglesias’ ‘obsolete’ script to obtain hippocampal volumes, as our system does not support the dev version of Freesurfer. recon-all -all -s bert -hippocampal-subfields-T1 Then, to gather volumes from our analysed subjects, we have run this script quantifyHippocampalSubfields.sh <T1>-<analysisID> <output_file> <OPTIONAL_subject_directory> In particular, this is how it looks in our terminal: -bash-4.2$ quantifyHippocampalSubfields.sh T1 hippo_demo.txt /rds/general/project/amyloidpet/live/freesurfer Gathering results from subjects in: /rds/general/project/amyloidpet/live/freesurfer Using the suffix name: T1 And writing them to: hippo_demo.txt However, we are not able to find the output anywhere. Could you help us figuring out what could be the reason why can’t find it? I have attached the recon-all.log for one of our analysed subjects. Many thanks for your help. Kind regards, Flavia

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longitudinal FreeSurfer help
by Swati Rane 17 Mar '20

17 Mar '20

External Email - Use Caution Dear FreeSurfer experts, I simply do not understand the LME setup for longitudinal analyses. Here is what I have: 3 groups each with variable longitudinal data (in terms of umber of time points and interval between timepoints). I am interested in detecting if the rates of longitudinal atrophy in each of the 3 groups and whether it is significantly different between the 3 groups. 1. My Qdec file contains: fsid, fsid_base, time, age, group, gender 2. I read in the relevant files with (output of surf2surf, lh.cortex, lh.sphere) 3. I read the Qdec file removed the first column, obtained the subject IDs, keep numerical data and get a sorted ‘M’ matrix 4. X=[intercept time grp1 time*grp1 grp2 time*grp2 grp3 time*grp3 age@timepoint1 gender] 5. After that, should I use voxel wise mass-univariate model or spatiotemporal mass-univariate model lme_mass_fit_vw or lme_mass_fit_EMinit? 6. After that I don’t understand the subsequent steps. Can you help me understand? Any help is appreciated. Thanks! Swati

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overlay threshold in freeview
by Rachele Sanfelici 17 Mar '20

17 Mar '20

External Email - Use Caution Dear Freesurfer experts, I created .mgh files from a dimensionality reduction analyses (similar to parcels from a known parcellation). These matrices have low values near to 0. When I overlay each of the .mgh file in freeview, it gets automatically thresholded with what seemed to me the median or mean of all the vertices' values (i.e., when looking at the "configure overlay" option)--however, this is not the case. Thus, I wanted to ask how the threshold is precisely set, so that I can automate and incorporate it in other scripts for binarizing my matrices. Thanks a lot in advance for your help, Rachele

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Re: [Freesurfer] cent OS8 and Freesurfer 5.3 {Disarmed}
by fsbuild 16 Mar '20

16 Mar '20

External Email - Use Caution Hello Suzanne, I have not tried running Freesurfer version 5 on CentOS8, but it would not surprise me if it is not entirely compatible with the newer versions of the system libraries on CentOS8. The Freesurfer version 7 beta release just came out this February (https://surfer.nmr.mgh.harvard.edu/fswiki/dev7beta1) and development is working on getting the full release out (with subsequent 7.X point releases to follow).  So I think the expectation going forward is for users to eventually migrate from freesurfer 6 to 7.  But I don’t know of any planned updates or changes to rev 5 (which is essentially 2 releases old now). If you want to maintain OS compatibility for older freesurfer releases, then one option is to use a VM or a container to keep and run older versions of CentOS.   I think CentOS6 is going to be end of life'd this coming November, but you should be able to download virtual disk images of the last release of CentOS 7, 6, 5, etc. for quite some time from osboxes.org and other sites. - R. On Mar 16, 2020, at 19:36, Suzanne Baker <slbaker(a)lbl.gov> wrote:        External Email - Use Caution        are there any plans to make Freesurfer 5.3 compatible with Linux cent os8?_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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