Freesurfer March 2020

freesurfer@nmr.mgh.harvard.edu

111 participants
161 discussions

SPM Volumes on FSAVERAGE surfaces
by Ryne Nichols 20 Mar '20

20 Mar '20

External Email - Use Caution All, I'm having trouble getting good surface projections of SPM results. My SPM results come from SPM normalization -- which should be MNI152 space. I'm confused because fsaverage says it is in MNI305 space. I've tried a few commands, but the two that confuses me the most is: mri_vol2surf --mov SPMT_001.nii --mni152reg --trgsubject fsaverage --hemi lh --out lh_spm.mgh --projfrac-max 0 1 .1 Also the similar command: mri_vol2surf --mov SPMT_001.nii --reg $FREESURFER_HOME/average/mni152.register.dat --trgsubject fsaverage --hemi lh --out lh_spm.mgh --projfrac-max 0 1 .1 both give results in a wildly different place on the brain than they should be -- it flips the SPMT_001.nii in the Y direction. If I do mri_vol2surf --mov SPMT_001.nii --regheader fsaverage --hemi lh --out lh_spm.mgh --projfrac-max 0 1 .1 things are close, but nor exactly how they should be (it seems). Finally, if i use a surface that's in MNI152 space (cvs_avg35_inMNI152) things look the way they should, e.g.: mri_vol2surf --mov SPMT_001.nii --regheader cvs_avg35_inMNI152 --hemi lh --out lh_spm.mgh --projfrac-max 0 1 .1 thank you for any help you may provide! -ryne

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Failed to load Surface lh.white
by Alexander Barnett 20 Mar '20

20 Mar '20

External Email - Use Caution Hello FreeSurfer Developers, I am trying to inspect the white matter gray matter surface to verify its accuracy as described in (http://freesurfer.net/fswiki/FsTutorial/ControlPointsV6.0) When I try to open freeview freeview -v 101/mri/brainmask.mgz \ -f 101/surf/lh.white:edgecolor=yellow I get an error that says it Failed to load Surface 101/surf/lh.white. The brainmask.mgz opens fine. When I looked in the /101/surf/ folder, I see lh.white.H, lh.white.K, lh.white.preaparc, lh.smoothwm, but there is no lh.white file. When I inspect the ReconAll table (https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0) I see that there is no step that creates ?h.white files in V6.0 (note: there is a step that will make lh.white in V5.3). How can I properly assess the white matter gray matter surface in V6.0? 1) FreeSurfer Version: freesurfer-i386-apple-darwin11.4.2-stable6-20170119 2) Operating system : MacOS High Sierra version 10.13.6 3) recon-all.log: see attached ReconAllTableStableV6.0 - Free Surfer Wiki<https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0> This table shows the recon-all steps for the stable, publicly released, version 6.0 of FreeSurfer (available here).. See also the OtherUsefulFlags for other recon-all options. surfer.nmr.mgh.harvard.edu Alex Barnett, PhD Postdoctoral Scholar UC Davis, Center for Neuroscience Dynamic Memory Lab

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mri_glmfit and mri_glmfit-sim
by Varun Chandran 20 Mar '20

20 Mar '20

External Email - Use Caution Dear FS experts, I am looking at the relationship between the cortical thickness and a behaviour measure, while controlling for the effects of age and gender. In this analysis, I am using CT_AT.fsgd, contrast_pos.txt and a contrast_neg.txt. GroupDescriptorFile 1 Title Autistictraits Class AT Variables Age Gender AT Input Con_P001 AT -4.142 -0.428 21 Input Con_P002 AT -8.142 -0.428 31 My separate two contrast files: Contrast_pos.txt 0 0 0 1 Contrast_neg.txt 0 0 0 -1 mri_glmfit --y lh.thickness.AT.10B.mgh --fsgd CT91_4.fsgd doss --C Contrast91_pos.txt --surf fsaverage lh --cortex --glmdir glmdirlhposlat.glmdir mri_glmfit --y lh.thickness.AT.10B.mgh --fsgd CT91_4.fsgd doss --C Contrast91_neg.txt --surf fsaverage lh --cortex --glmdir glmdirlhneglat.glmdir mri_glmfit-sim --glmdir glmdirlhposlat.glmdir --cache 1.3 pos --cwp 0.05 mri_glmfit-sim --glmdir glmdirlhneglat.glmdir --cache 1.3 neg --cwp 0.05 By changing the commands appropriately, I am looking at the right hemisphere too. Can anyone please help me to clarify, if I am applying the command lines correctly? Any sort of help would be very much appreciated. Thanks ! best, Varun Arunachalam Chandran PhD scholar (Neurosciences) *School of Psychology and Clinical Language Sciences, University of Reading, Harry Pitt Building, * *Whiteknights campus, Reading-RG6 7BE,* *Berkshire, United Kingdom.*

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cortical area and volume calculation method
by Ting Li 20 Mar '20

20 Mar '20

External Email - Use Caution Dear Freesurfer Experts, Where I can find any document that explaining how the cortical area and volume were calculated? or Could you give me an introduction about it. Thank you so much! Best regards, Ting

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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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Freesurfer March 2020