Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Re: [Freesurfer] HIPPOCAMPUS AND AMYGDALA SEGMENTATION - Invalid MEX-file
by fsbuild 08 Jan '19

08 Jan '19

External Email - Use Caution Hello Alba, As of Mac OS 10.11, El Capitan, DYLD_LIBRARY_PATH and DYLD_FALLBACK_LIBRARY_PATH are ignored as environment variables at run time.  Same for all subsequent releases: Sierra = 10.12; High Sierra = 10.13; Mojave = 10.14. You could try setting MATLAB_ROOT to the parent directory of the ./lib and ./bin directories in the Matlab distribution which from your paths looks like it might be /Applications/freesurfer/MCRv84/runtime/maci64 - R. On Jan 8, 2019, at 12:58, Alba Castells Sánchez <alba.castells.sanchez(a)gmail.com> wrote:        External Email - Use Caution        Dear Freesurfer experts, We installed today (8 jan 2019) the last version of Freesurfer dev and the corresponding Runtime Matlab R2014b .. We tried segmentHA_T1.sh with bert to check if it worked. We had a couple of errors related to an Invalid Mex-file. We add the log. We doubt if it may be related to the fact that our computer is not updated to OS El Capitan and we are using OS High Sierra. It is something very simple but we hadn’t realized until now or wether is something to the software. Could you help us?Thousand thanks! #--------------------------------------------#@# Hippocampal Subfields processing (T1) left martes,  8 de enero de 2019, 18:25:06 CET------------------------------------------Setting up environment variables---DYLD_LIBRARY_PATH is .:/Applications/freesurfer/MCRv84//runtime/maci64:/Applications/freesurfer/MCRv84//bin/maci64:/Applications/freesurfer/MCRv84//sys/os/maci64:/Applications/freesurfer/lib/gcc/lib:Invalid MEX-file '/tmp/MCR_583345147/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64': dlopen(/tmp/MCR_583345147/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64, 6): Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv  Referenced from: /tmp/MCR_583345147/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64  Expected in: /usr/lib/libstdc++.6.0.9.dylib in /tmp/MCR_583345147/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64Error in kvlClear (line 11)Error in segmentSubjectT1_autoEstimateAlveusML (line 115)MATLAB:invalidMEXFileDarwin MacBook-Air-de-Francesca.local 17.7.0 Darwin Kernel Version 17.7.0: Thu Jun 21 22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64 x86_64T1 hippocampal subfields exited with ERRORS at martes,  8 de enero de 2019, 18:25:19 CETFor more details, see the log file /Applications/freesurfer/subjects/bert/scripts/hippocampal-subfields-T1.log_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

HIPPOCAMPUS AND AMYGDALA SEGMENTATION - Invalid MEX-file
by Alba Castells Sánchez 08 Jan '19

08 Jan '19

External Email - Use Caution Dear Freesurfer experts, We installed today (8 jan 2019) the last version of Freesurfer dev and the corresponding Runtime Matlab R2014b . We tried segmentHA_T1.sh with bert to check if it worked. We had a couple of errors related to an Invalid Mex-file. We add the log. We doubt if it may be related to the fact that our computer is not updated to OS El Capitan and we are using OS High Sierra. It is something very simple but we hadn’t realized until now or wether is something to the software. Could you help us? Thousand thanks! #-------------------------------------------- #@# Hippocampal Subfields processing (T1) left martes, 8 de enero de 2019, 18:25:06 CET ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer/MCRv84//runtime/maci64:/Applications/freesurfer/MCRv84//bin/maci64:/Applications/freesurfer/MCRv84//sys/os/maci64:/Applications/freesurfer/lib/gcc/lib: Invalid MEX-file '/tmp/MCR_583345147/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64': dlopen(/tmp/MCR_583345147/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64, 6): Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv Referenced from: /tmp/MCR_583345147/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64 Expected in: /usr/lib/libstdc++.6.0.9.dylib in /tmp/MCR_583345147/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64 Error in kvlClear (line 11) Error in segmentSubjectT1_autoEstimateAlveusML (line 115) MATLAB:invalidMEXFile Darwin MacBook-Air-de-Francesca.local 17.7.0 Darwin Kernel Version 17.7.0: Thu Jun 21 22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64 x86_64 T1 hippocampal subfields exited with ERRORS at martes, 8 de enero de 2019, 18:25:19 CET For more details, see the log file /Applications/freesurfer/subjects/bert/scripts/hippocampal-subfields-T1.log

1 0

FreeSurfer crashing
by vittal korann 08 Jan '19

08 Jan '19

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to run recon-all on schizophrenia patients and controls. For some reason freesurfer is crashing. I wanted to know the reason for frequent crashing. I'm using Ubuntu 16.04 LTS and freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0. Below I have attached the recon-all.log file for your reference. Kindly help me to sort this out. Thank you Regards *Vittal*

2 1

Re: [Freesurfer] FreeSurfer crashing
by fsbuild 08 Jan '19

08 Jan '19

External Email - Use Caution Hello Vittal, Your output resembles the error from a previous post about running the old Freesurfer 5.3 release on Ubuntu 16, https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2016-May/045393.html You can try running that command listed at the end of your log directly from the terminal to see if it gives more detailed info about the error, $ mri_nu_correct..mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz In that post the user saw a perl error, Can't use 'defined(@array)' (Maybe you should just omit the defined()?) If you get a perl error, then following thru the "next in thread" links, one resolution was to install a pre 5.22 version of perl on the machine, https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2016-May/045402.html Another option is to download and try the Freesurfer 6.0 release (which was not available at the time of that posting in 2016); the 6.0 Freesurfer release can be downloaded from, https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall - R. vittal korann January 8, 2019 at 02:17         External Email - Use Caution        Hello FreeSurfer Developers, I'm attempting to run recon-all on schizophrenia patients and controls. For some reason freesurfer is crashing. I wanted to know the reason for frequent crashing. I'm using Ubuntu 16.04 LTS and freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0. Below I have attached the recon-all.log file for your reference. Kindly help me to sort this out. Thank you Regards Vittal _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

[FSL] Threshold fdt_paths multiple seeds --network
by VA Research 08 Jan '19

08 Jan '19

External Email - Use Caution Hello FSL and Freesurfer Experts, We are trying to find the paths between 5 fMRI ROIs (seeds). We are using the --network option. How do we go about thresholding the fdt_path.nii.gz? Thanks so much, Joe probtrackx2 --network -x ${dtidir}/seeds.txt -l --onewaycondition -c 0.2 -S 2000 --steplength=0.5 -P 5000 \ --fibthresh=0.01 --distthresh=0.0 --sampvox=0.0 --avoid=${dtidir}/not_WM.nii.gz \ --forcedir --opd -s ${dtidir}.bedpostX/merged -m ${dtidir}.bedpostX/nodif_brain_mask.nii.gz \ --dir=${dtidir}/FRONTAL_PARIETAL_TRAX

1 0

T1 hypointensities
by Rockers, Elijah D. 07 Jan '19

07 Jan '19

External Email - Use Caution Hello, Are the WM-hypointensities segmented in the same way as the rest of the subcortical regions? i.e., using the probablistic atlas referenced in the 2002 Fischl et al paper? Thanks, - Eli 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 twitter.com/MethodistHosp and facebook.com/HoustonMethodist. ***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.

1 0

LME
by Tefera, Getaneh B 07 Jan '19

07 Jan '19

Dear Freesurfer experts, I have three groups g0, g1, and g2. I am trying to use LME model with random effects y-int and time from the base line. Based on the LME tutorial and the questions and answers from Freesurfer support list: Y=B1+B2*t+B3*g1+B4*g1*t+B5*g2+B6*g2*t+ ... The slope of g0 : 0 1 0 0 0 0 The slope of g1: 0 1 0 1 0 0 The slope of g2: 0 1 0 0 0 1 The slope difference between g0 and g1: 0 0 0 1 0 0 The slope difference between g0 and g2: 0 0 0 0 0 1 The slope difference between g1 and g2: 0 0 0 -1 0 1 1) Is this contrast matrix correct to observe pairwise slope difference? In the tutorial the contrast matrix C = [zeros(3,3) [1 0 0 0 0; -1 0 1 0 0; 0 0 -1 0 1] zeros(3,6)] 2) Is it necessary to combine contrast matrix of the pair difference the same as the tutorial? If so, my contrast matrix can be C=[0 0 0 1 0 0; 0 0 0 -1 0 1] 3) How can we interpret the result for this contrast matrix? 4) How can I obtain B1, B2, ... ? [sz1,sz2] = lme_plannedSampleSize(Zi,ZiCol,Dhat,phisqhat,effsz,... dr,pw,alpha,gr_pr) 5) For sample size calculation how can I get Dhat ( Estimated random effects covariance matrix) and phisqhat (Estimated intra-subject variability)? With regards Getaneh

2 9

Calculating volume using pial files
by Song, Da-Yea 07 Jan '19

07 Jan '19

External Email - Use Caution Hello, I'm trying to calculate the volume using pial files. Is there a way to convert ?h.pial files into nii formats? Or is there a command to calculate the volume? Thank you so much in advance for your help. Best regards, Da-Yea Song ---------------------------------------------------------------------- Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

3 2

(no subject)
by Larissa Bechtle 07 Jan '19

07 Jan '19

External Email - Use Caution Hi everybody, after finishing my group analysis I am currently trying to run a ROI analysis. However I have some problems/general questions. I am trying to draw a ROI on fsaverage in order to use the mri_label2label command afterwards. I opened Freeview, clicked on "load surface" first and then chose lh.inflated_avg (fsaverage -> surf) which worked fine but I cant choose "New ROI" (in order to crate the ROI). So is it possible to draw a ROI when focussing only on the surface? And if this is the case why cant I? Did I chose the wrong file? I am really thankful for any help!! Larissa

2 2

[PETsurfer] Use of MGX and RBV partial volume correction
by Matthieu Vanhoutte 07 Jan '19

07 Jan '19

External Email - Use Caution Dear Freesurfer's experts, I tried to use PETSurfer to correct partial volume effect on my FDG PET images, testing both Muller-Gartner and RBV corrections. I ran the commands specified in PETSurfer website and used the two following commands for both MGX and RBV corrections respectively: mri_gtmpvc --i PET.nii.gz --reg register.dof6.lta --psf-col 5.51 --psf-row 5.51 --psf-slice 5.9 --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx .01 --o ./gtmpvc.output mri_gtmpvc --i PET.nii.gz --reg register.dof6.lta --psf-col 5.51 --psf-row 5.51 --psf-slice 5.9 --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --rbv --o rbv.output.orig 1) However, I found that cortical output mgx.ctxgm.nii.gz of MGX correction encompass more than just GM and values at the boundaries of mgx.ctxgm.nii.gz seem to me very high or aberrant. 2) Concerning RBV correction, output rbv.nii.gz seems to me following more precisely the GM ribbon. However contrary to what is said in PETSurfer website, rbv.nii.gz seems to be in the anatomical space (not in native PET) at the resolution of gtmseg.mgz. How then map rbv.nii.gz to the anatomical space when mapping the volume to the surface ? 3) What are the advantages/inconveniences of RBV vs GMX ? 4) Would it be beneficial to upsample native PET to the anatomical resolution before launching gtmpvc in order to preserve the high resolution of the anatomical tissues during partial volume correction ? Could you have a look at and give me back your opinion on these questions ? I could send the associated files if needed. Thank you. Best, Matthieu

2 12

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer