Freesurfer January 2019

freesurfer@nmr.mgh.harvard.edu

119 participants
167 discussions

Programs samples two surface parcellation into volumetric segmentation
by Yerong Li 09 Jan '19

09 Jan '19

External Email - Use Caution Dear Freesurfer experts: In notice "mris_sample_parc" samples a volumetric parcellation onto a surface, I am trying to find a program that samples "annot" files to volumetric parcellations. I need to know the connection between labels in [lh.aparc.annot, rh.aparc.annot] and labels in [aparc+aseg.mgz]. I am expecting a program with two inputs [lh.aparc.annot, rh.aparc.annot] and output [aparc+aseg.mgz] ** Basically I have fibers from tracking algorithms and I am reconstructing connectivity matrices on the surface parcellation, that's why I need the subcortical segmentation file aparc+aseg.mgz. Yerong

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On relationship between aparc+aseg.mgz and ?h.aparc.annot
by Yerong Li 09 Jan '19

09 Jan '19

External Email - Use Caution Dear Freesurfer experts: I am on ROI analysis tutorial: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROIV6.0 And I am trying to understand the relationship between: /label/?h.aparc.annot and /mri/aparc+aseg.mgz /label/?h.aparc.a2009s.annot and /mri/aparc.a2009s+aseg.mgz I understand /label/?h.aparc.annot corresponds to "Desikan-Killiany atlas" and its labels have 35 different labels (except unknown 0), while in several cases you mentioned that "/mri/aparc+aseg.mgz" corresponds to "Desikan-Killiany atlas", which I DO NOT understand. "/mri/aparc+aseg.mgz" to me are subcortical segmentations while "/label/?h.aparc.annot" are cortical(surface) parcellations. "Desikan-Killiany atlas" should mean "cortical (surface) parcellations". That's why I do not understand why "/mri/aparc+aseg.mgz" corresponds to "Desikan-Killiany atlas"? Could anyone help me understand this? Yerong

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Re: [Freesurfer] (no subject)
by Emil H.J. Nijhuis 09 Jan '19

09 Jan '19

External Email - Use Caution Dear Ruopeng, I tried the UpdateFreeview <https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview?action=fullsearch&…> procedure below, however I received the error message: >> This application failed to start because it could not find or load the Qt platform plugin "xcb" in "". Reinstalling the application may fix this problem. Abort << Any advice on how to solve this problem? With best regards, Emil Date: Mon, 7 Jan 2019 17:52:39 +0100 > From: "Larissa Bechtle" <Larissa.Bechtle(a)web.de> > Subject: Re: [Freesurfer] (no subject) > To: "Freesurfer support list" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > > <trinity-2a602680-bd3f-4cdb-be33-806428c61a78-1546879959319@msvc-mesg-web003 > > > > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Hi Ruopeng, > > Thank you very much for your quick answer and advice. So I am going to > update freeview! > Thanks! > Larissa > > Gesendet mit der WEB.DE Mail App > > Am 07.01.19 um 17:35 schrieb Ruopeng Wang > > > Hi Larissa, > > > > The latest development version of freeview supports drawing labels on > > surface. You can take a look here on how to update freeview: > > > > https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview > > > > In the latest version, you can draw paths on surface and use custom fill > > to create/edit labels, just like in tksurfer. > > > > Best, > > Ruopeng > > > > On 1/7/19 11:22 AM, Larissa Bechtle wrote: > > > 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 > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > End of Freesurfer Digest, Vol 179, Issue 11 > ******************************************* >

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mris_pmake version issue
by Raij, Tommi A. 08 Jan '19

08 Jan '19

Dear FreeSurfers, I am trying to update an mris_pmake command line that works with the pub v5.3.0 version with a new command line that works with pub v6.0.0 version. The purpose is to compute the distance between two vertex points on the pial surface using the cvs_avg35_inMNI152 brain. We are using CentOS (6.6 on the workstation running FS v5.3.0 and 7.4 on the workstation running FS v6.6.0) outside Martinos Center. nmr-std-env setenv SUBJECTS_DIR /usr/pubsw/packages/freesurfer/subjects setenv SUBJECT cvs_avg35_inMNI152 Old command line (gives a reasonable result on v5.3.0): mris_pmake --subject cvs_avg35_inMNI152_temp --hemi lh --surface0 pial --curv0 sulc --curv1 sulc --mpmOverlay euclidean --mpmProg pathFind --mpmArgs startVertex:121981,endVertex:132633 Start->End vertices [ 121981->132633 ] Total path cost [ 29.668283 ] If I try to run this on v6.0.0, I receive the error: mris_pmake: unrecognized option '--surface0' I first tried removing --surface0 option, but then the error becomes mris_pmake: unrecognized option '--curv0' I then tried removing the --curv0 and eventually --curv 1 options as well, but these gave more similar errors (unrecognized option) or core dumped. Looking at older posts on the FreeSurfer list, I tried removing all three --surface0 --curv0 --curv 1 options, but this gives a clearly incorrect result where the startVertex and endVertex values are apparently not read from the command line: Start->End vertices [ 0->0 ] Total path cost [ 0.000000 ] I tried renaming --surface0 to --surface and --curv0 to --curv, as it seems that some of the options have been renamed, and to some degree this worked as there were no more 'unrecognized option' errors. However, the result is still Start->End vertices [ 0->0 ] Total path cost [ 0.000000 ] Any suggestions would be greatly appreciated. Btw the command line documentation (mris_pmake --help) does not seem to be quite match the version distributed with FS v6.0.0, at least when it comes to the option names for surface and curve, and if there are separate definitions for 0 and 1. Thank you! Best regards, Tommi Raij

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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

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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

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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*

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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

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[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

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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.

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Freesurfer January 2019