Freesurfer

freesurfer@nmr.mgh.harvard.edu

4 participants
30090 discussions

sub cortical analysis
by John Anderson 24 Aug '17

24 Aug '17

Hi Dr Greve, I am using pet surfer to analyze suv images. I followed all the steps in wiki, I used the option mgx then I fed the images mgx.{ctxgm,subctxgm,gm} into surface based analysis for left and right hemispheres. I want to inquire about the sub cortical analysis. 1. I assume the analysis for sub cortical gray matter (i.e. using the images subctxgm) is volumetric. Correct? 2. Are the following steps correct for sub cortical gray matter analysis mri_vol2vol --mov subctxgm.nii.gz --reg reg.dat --tal --talres 2 --talxfm talairach.xfm --nearest --no-save-reg --o subctxgm.tal2mm.nii.gz mri_mask subctxgm.tal2mm.nii.gz $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz subctxgm.tal2mm_subc.nii.gz & Concatenate all subjects together using mri_concat smooth using mri_fwhm (what is the recommended smoothing for suv)? Then Group analysis: mri_glmfit --y all.suvr.tal2mm.subc.sm10.nii --fsgd fsgd.dat --C contrast.mtx --glmdir dir mri_glmfit-sim --glmdir dir --grf 1.3 pos --cwpvalthresh 0.0166 for "mri_glmfit-sim" in subcortical structure is the flag grf correct or cache? Thanks in advance! John

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QA tools for FS vs 6.0
by Antonietta Pepe 24 Aug '17

24 Aug '17

Dear FreeSurfer list, is any of you aware of a new version of the QA (quality assessment) tools < [ https://surfer.nmr.mgh.harvard.edu/fswiki/QATools | https://surfer.nmr.mgh.harvard.edu/fswiki/QATools ] > working for FS vs 6.0? Should I expect a new release in the near feature? Kind regards, Antonietta ANTONIETTA PEPE IMN, Institut des Maladies Neurodégénératives, UMR 5293 Equipe 5 : GIN, Groupe d’Imagerie Neurofonctionnelle, CEA - CNRS - Université de Bordeaux Université de Bordeaux 146 rue Léo Saignat - CS 61292 - Case 28 33 076 Bordeaux cedex [ http://www.imn-bordeaux.org/ | http://www.imn-bordeaux.org/ ]

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mri_coreg
by John Anderson 24 Aug '17

24 Aug '17

Dear Dr Greve, Kindly, I wanted to know why "mri_coreg" apples smoothing during registration. e.g. mri_coreg --s subject --mov template.nii.gz --reg template.reg.lta Are there any effects on the accuracy of smoothing if I turn off this default feature (specifically in pet surfer pipeline). mri_coreg --s subject --mov template.nii.gz --reg template.reg.lta --no-smooth Thank you for any clarification John

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Xlib: extension "GLX" missing on display "0.0" when running freeview
by fengmei fan 24 Aug '17

24 Aug '17

HI, I installed Freesurfer 6 in CentOS 6.5, when runing freeview, errors occurred: Xlib: extension "GLX" missing on display "0.0" Xlib: extension "GLX" missing on display "0.0" What's wrong? And how to settle this problem? Best, Fengmei Fan Assistant professor, Beijing Huilongguan Hospital, Beijing Huilongguan Medical College of Peking University

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Qdec keyboard input error
by 김현우 24 Aug '17

24 Aug '17

I'm studying freesurfer especially, QDEC to execute group analysis. In QDEC, I can type in Subjects and Design tap. But I can't type in Display tap like threshold p. I've seen several question like me but no one give solution. Here's my environment. OS : CentOS 7.0 Freesurfer : stable 6.0 QDEC : 1.5 Show me how to solve this problem. Thank you. ============================================= Hyunwoo Kim Graduate school of Yonsei University Biosignal Processing Laboratory #201 Sanhakgwan, 1 Yonseidaegil, Heungup, Wonju, Gangwon, 220-710, Republic of Korea Tel. +82-33-760-2809

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Re: [Freesurfer] Hard failure via XNAT pipeline (Freesurfer 6)
by Rockers, Elijah D. 23 Aug '17

23 Aug '17

We'll try to process it on a blade server tongiht... if it succeeds we can edit any incorrect results as needed. The image is from a separate site, it has OK resolution (1x1x1.5) but has an enormous amount of gibbs ringing compared to our on-site images, which is probably causing the issue... Thanks, Eli Date: Wed, 23 Aug 2017 11:54:06 -0400 From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Hard failure via XNAT pipeline (Freesurfer 6) To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <54B7B7A7-CDC3-46F1-8E1B-098142FD3DB2(a)nmr.mgh.harvard.edu<mailto:54B7B7A7-CDC3-46F1-8E1B-098142FD3DB2@nmr.mgh.harvard.edu>> Content-Type: text/plain; charset="us-ascii" That defect is so big you probably ran out of memory. > On Aug 23, 2017, at 11:21 AM, Rockers, Elijah D. <edrockers(a)houstonmethodist.org<mailto:edrockers@houstonmethodist.org>> wrote: > > We encountered a hard failure, below is the tail of the log. We are currently running Freesurfer 6 again locally to see if it succeeds on a desktop machine (this is the first time encountering a hard failure on the XNAT server). Any suggestions? > > -merging segment 180 into 178 > 160 defects to be corrected > 0 vertices coincident > reading input surface /data/build/nnac/20170818_114535/alamode_MRI08162017/20170818114538/alamode_MRI08162017/surf/lh.qsphere.nofix... > reading brain volume from brain... > reading wm segmentation from wm... > Computing Initial Surface Statistics > -face loglikelihood: -8.7982 (-4.3991) > -vertex loglikelihood: -6.2982 (-3.1491) > -normal dot loglikelihood: -3.5611 (-3.5611) > -quad curv loglikelihood: -6.1931 (-3.0965) > Total Loglikelihood : -24.8505 > > CORRECTING DEFECT 0 (vertices=40706, convex hull=11265, v0=89) > XL defect detected... > Segmentation fault (core dumped) > Linux hhvrixnatp01 2.6.32-431.el6.x86_64 #1 SMP Sun Nov 10 22:19:54 EST 2013 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s alamode_MRI08162017 exited with ERRORS at Mon Aug 21 19:27:09 CDT 2017 > > To report a problem, see https://urldefense.proofpoint.com/v2/url?u=http-3A__surfer.nmr.mgh.harvard.… > > Houston Methodist. Leading Medicine. > > Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas for patient care. Houston Methodist is nationally ranked in 8 specialties and is designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at https://urldefense.proofpoint.com/v2/url?u=http-3A__twitter.com_MethodistHo… and https://urldefense.proofpoint.com/v2/url?u=http-3A__facebook.com_HoustonMet… . > > ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you. > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e… -------------- next part -------------- An HTML attachment was scrubbed... URL: https://urldefense.proofpoint.com/v2/url?u=http-3A__mail.nmr.mgh.harvard.ed… ------------------------------

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recon-all error
by Cara Bohon 23 Aug '17

23 Aug '17

I have a couple of subjects "exited with ERRORS" after running almost 48 hours (when my others all took about 13-15 hours on the same server). Both exited during Fix Topology lh. The only time "error" appears is in this line: IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 4 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = -0.0 tol 0.000010 - which prior messages to this list suggest is not meaningful or problematic. I am brand new to Freesurfer, so I'm not quite sure where to start in troubleshooting. The orig.mgz file looks fine to me, but maybe I'm missing something. Any other tips for things to check? I'm attaching a recon-all.log file in case that is helpful. I am running Freesurfer 5.3.0 on Linux. Thanks for any tips on addressing the error! -Cara

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Longitudinal stream for cross-sectional analysis?
by K 23 Aug '17

23 Aug '17

Good morning Martin et al., We are analyzing cortex and subcortical volumes for 2 groups with (mostly) 2 scans per participant. We want to report longitudinal findings as well as cross-sectional group differences at each of the 2 time points. For the time point 1 and time point 2 analyses, does it make sense to use the longitudinal stream-processed data, or is it better to use the cross-sectional stream for each time point independently? For example: Comparing the brain stem volumes for individual participants using longitudinal vs cross-sectional data for time point 1, we notice some differences (cross-sectional volumes tend to be 95-98% as large, varying), and group differences are more pronounced when using the longitudinal data (i.e., some structures did not show significant group differences in volumes using cross-sectional data, but did show significant differences using longitudinal). I know you have written about reduced variability and better precision with the longitudinal stream, but we weren't sure if this also applied to using it only at one time point to report cross-sectional findings. Appreciate your guidance! K Additional keywords: longitudinally, cross-sectionally, single time point, benefits, advantages, drawbacks, cortical thickness, surface area, volumetric

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Longitudinal freesurfer
by neuroimage analyst 23 Aug '17

23 Aug '17

Hi, We are currently doing longitudinal FreeSurfer analysis on subjects some of whom are scanned over a period of 6 years. There were 2 groups. One was the control group and the other was mTBI group. The hypothesis was the control group would have a fairly stable cortical and sub-cortical volume (<1% change over time) while mTBI group would have a decreasing volume. Both the groups are relatively young (most participants between 22-30 years old). Unfortunately, we only have 7 controls that were scanned for over 3 years. What we have observed is there is no pattern in change in volume neither for controls nor for mTBI; with volume increasing from baseline to year1 and then decreasing and then for some increasing again. The delineation looks ok to us. There are a lot of subjects ~120 and hence manual delineation on every subject is not practical. The question is what is the expected measurement variance due to the longitudinal algorithm for healthy controls over time in both cortical and subcortical volumes? Since the effect that we were expecting to see is around 4% in mTBI participants and the delineation too looks okay then what is the best procedure to correct these? OR should we use cross-sectional data for our analysis? We have used longitudinal freesurfer v6 on a centos. I look forward to your thoughts. Thanks Regards Virendra

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Longitudinal spatiotemporal LME vs. V-LME
by Ann-Kathrin Rogge 23 Aug '17

23 Aug '17

Dear freesurfer experts, I have a mixed 2x2 design with group (approx. 18 subjects per group) and timepoint (t0, t1) as factors. I analyzed the thickness data with the longitudinal stream and the spatiotemporal LME as a random intercept model, age as covariate. However, the model does not converge perfectly, although I varied the size of the homogenous covariance regions between 1-2 (parameter k, Bernal-Rusiel et al., 2013). In addition, when I apply a voxelwise-LME, more clusters survive the FDR correction. It seems that the V-LME is more sensitive than the SP-LME in my case (clusters at an uncorrected threshold are more or less the same). I would love to understand why. Could anyone explain this to me? And would it be statistically valid to apply the V-LME to my data? Best, Ann-Kathrin -- *Ann-Kathrin Rogge, Dipl.-Psych.* www.bpn.uni-hamburg.de

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