Freesurfer

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30132 discussions

Research Specialist Position at the Center for Healthy Minds
by CHM Recruiting 18 Oct '19

18 Oct '19

External Email - Use Caution The Center for Healthy Minds at the University of Wisconsin-Madison is hiring a Research Specialist! To learn more about this excellent job opportunity, please view the attached Position Description. Thank you, Center for Healthy Minds

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Group effect Contrast for 6 groups
by cody samth 18 Oct '19

18 Oct '19

External Email - Use Caution Hi, I'm designing an analysis that will have 6 groups (two factors/three levels). I was wondering if I could get some input regarding my contrast for the group effect. Based on the group effect contrast under the FSGD examples for 3 groups I've written a five line contrast file that compares group 1 against the other 5 groups. 1-1 0 0 0 0 1 0 -1 0 0 0 1 0 0 -1 0 0 1 0 0 0 -1 0 1 0 0 0 0 -1 Which from my understanding should cover the rest of the contrasts such as 2v5 3v6 and etc. Is my understanding of this correct?

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Mri_mask producing only zeros
by Sims, Sara A (Campus) 18 Oct '19

18 Oct '19

External Email - Use Caution Freesurfers, I am trying to use mri_mask using surface overlays. I made a label into a volume and then into a surface with 1s inside the label and 0s outside the label. I want to make a connectivity map surface overlay with values only within my label overlay. However when I run it, it creates a surface overlay with only zeros. There is definitely values within the label surface overlay (I triple checked). Code I used: Mri_mask original_surface_overlay label_mask new_masked_output It doesn’t output any errors. Sara A. Sims

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-multistrip exited with errors troubleshooting
by Mohn, Johannes 18 Oct '19

18 Oct '19

External Email - Use Caution Hi all, I'm trying -multistrip to improve skull stripping for subjects where incomplete skull strip lead to inaccurate pial surfaces. The command I'm running is: recon-all -multistrip -clean-bm -s <subjID> -no-isrunning However, multistrip fails. It exits with errors and no new brainmask.mgz files are created. This is independent of the subject. It fails for all. I attached the recon-all.log for one exemplary subject. In contrast, using -gcut (recon-all -skullstrip -clean-bm -gcut -s <subjID>) works but does not remove the problematic skull fragments in most cases. Independent of whether -multistrip or -gcut are better suited to improve the skull stripping, I would like to understand why -multistrip fails in my case and what can be done to make it work. Best, JJ

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brain mask without CSF ...
by stefano.silvoni＠libero.it 18 Oct '19

18 Oct '19

External Email - Use Caution Dear FreeSurfer Experts, I am running a functional analysis of subcortical structures using FS-FAST (freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c) and I would use a brain mask excluding CSF; would it be possible using some option/flag in 'preproc-sess'? or should I do it manually? maybe using a command like that? mri_binarize --i $sbjdir/mri/aparc.a2009s+aseg.mgz --match 702 703 --o $sbjdir/mri/GM-WM_mask.mgz because I saw in FreeSurferColorLUT.txt the following definitions: 702 GrayMatter-FSL-FAST 205 62 78 0 703 WhiteMatter-FSL-FAST 0 225 0 0 or is there another strategy? thanks in advance best stefano silvoni

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covariate with repeated anova
by miracle ozzoude 18 Oct '19

18 Oct '19

External Email - Use Caution Hello Experts, I would like to include covariates in the freesurfer repeated anova steps https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova. When i tried including 3 covariates, mri_glmfit complained about "martix is ill-conditioned". How do i fix it? Below is an example my fsgd file. I've also attached the matrix design in the email. GroupDescriptorFile 1 Class PsyDis1 Class PsyDis2 Variables TP1vsTP2 Age Llesion Rlesion Input Psy1_Pre.long.Psy1 PsyDis1 1 68 96 61 Input Psy1_6mos.long.Psy1 PsyDis1 -1 68 96 61 Input Psy2_Pre.long.Psy2 PsyDis2 1 39 217 140 Input Psy2_6mos.long.Psy2 PsyDis2 -1 39 217 140 contrast: 0 0 1 0 0 Best, Paul

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Re: [Freesurfer] Download link broken
by Hoopes, Andrew 18 Oct '19

18 Oct '19

Hi Tashrif, sorry, we had a network outage last night, but the link should be fixed now. best, Andrew From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Billah, Tashrif" <tbillah(a)bwh.harvard.edu> Reply-To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Date: Friday, October 18, 2019 at 10:08 AM To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Download link broken Hi FreeSurfer team, The following link appears broken since 10/17 evening. https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Lin… Can you look into it? Best, Tashrif ------------------------------------------------------------- Tashrif Billah, MS Research Engineer Brigham and Women's Hospital Harvard Medical School tbillah(a)bwh.harvard.edu<mailto:tbillah@bwh.harvard.edu> http://pnl.bwh.harvard.edu/tashrif-billah-m-s/

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Download link broken
by Billah, Tashrif 18 Oct '19

18 Oct '19

Hi FreeSurfer team, The following link appears broken since 10/17 evening. https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Lin… Can you look into it? Best, Tashrif ------------------------------------------------------------- Tashrif Billah, MS<https://www.linkedin.com/in/tashrif-billah/> Research Engineer Brigham and Women's Hospital Harvard Medical School tbillah(a)bwh.harvard.edu<mailto:tbillah@bwh.harvard.edu> http://pnl.bwh.harvard.edu/tashrif-billah-m-s/

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QDEC cluster output
by Lara Foland-Ross 18 Oct '19

18 Oct '19

External Email - Use Caution Hi Freesurfer experts, I’m running a simple qdec analysis to examine group differences in surface measures between a patient and control group, controlling for age and TBV. I noticed that when I run Monte Carlo Simulations (threshold=1.3, sign=abs), I get the following output in my terminal window: ~~~~~~~~~~~~ # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs Annot 1 7.365 125481 2114.03 -34.4 4.1 1.6 0.01660 0.01500 0.01820 4933 insula 2 3.851 73048 1830.45 -8.4 30.1 29.4 0.03440 0.03210 0.03670 3210 superiorfrontal 3 -3.248 128137 4923.73 -8.1 -64.0 5.8 0.00010 0.00000 0.00020 7680 lingual Simulation complete. ~~~~~~~~~~~~ However, when I click on “Find clusters and go to max”, the output in my terminal window changes to be as follows: ~~~~~~~~~~~~ Generating cluster stats using min threshold of 1.3... Found 3 clusters Contrast: 'lh-Diff-Control-Klinefelter-Intercept-volume', 20fwhm, DOF: 35 ClusterNo Max VtxMax Size(mm2) TalX TalY TalZ NVtxs Annotation --------- --- ------ --------- ---- ---- ---- ----- ---------- 1 -4.0000 33 4923.73 -12.0 -67.1 34.7 7680 precuneus 2 1.7799 9 2114.03 -26.3 23.8 -6.0 4933 lateralorbitofrontal 3 1.4634 21 1830.45 -6.6 33.8 49.8 3210 superiorfrontal ~~~~~~~~~~~~ Lastly, I see that the x/y/z coordinates of the peak coordinates listed above are on the very edge of the corrected cluster. Yet, visual inspection of the peaks from uncorrected significance maps suggest that the peaks it is quite far from the “hottest” parts of the uncorrected significance maps. My questions are: 1. Why are these values different, and what values should I report? 2. Are the peaks listed above the center of gravity? Or highest p value of the cluster? Curious as to why the heatmap values are so different from the values above. Many thanks, Lara

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Re: [Freesurfer] ERROR gtmseg
by Marina Fernández 18 Oct '19

18 Oct '19

External Email - Use Caution Dear Douglas, Did you get the subjects? I hope I loaded them correctly. Best regards, Marina.

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