Freesurfer

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30089 discussions

Compatibility of subcortical and cortical segmentations between Version 5.3 and 6.0
by Nils Opel 07 Mar '18

07 Mar '18

Hi Freesurfer Developers, i am currently collecting structural imaging data from several large cohorts that have been processed using different freesurfer versions (5.3 and 6.0). I would be interested on your experiences regarding compatibility between both versions for subcortical and cortical segmentations. More specifically: would it be appropriate to include subcortical and cortical measures derived from both freesurfer versions (5.3 and 6.0) in the same analysis? Thanks a lot in advance and best regards, Nils

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freeview. crash with undefined symbol: _ZN6QMutex12lockInternalEv when I choose colormap lookup table
by Knut J Bjuland 07 Mar '18

07 Mar '18

Dear Freesurfer export, When I chose colormap to lookup table with bert/mri/aseg.mgz freeview crash with the following message. [New Thread 0x7fffce7f4700 (LWP 78012)] /usr/local/freesurfer60/bin/freeview.bin: symbol lookup error: /usr/local/freesurfer60/bin/freeview.bin: undefined symbol: _ZN6QMutex12lockInternalEv [Thread 0x7fffce7f4700 (LWP 78012) exited] [Thread 0x7fffe219d700 (LWP 77903) exited] [Inferior 1 (process 77899) exited with code 0177] Missing separate debuginfos, use: dnf debuginfo-install libXcursor-1.1.15-1.fc27.x86_64 libcrypt-nss-2.26-26.fc27.x86_64 libgcc-7.3.1-5.fc27.x86_64 libgomp-7.3.1-5.fc27.x86_64 libstdc++-7.3.1-5.fc27.x86_64 pcre-8.41-6.fc27.x86_64 sssd-client-1.16.0-8.fc27.x86_64 Whatcan I do to walkaround this error. I also did ldd /usr/local/freesurfer/bin/freeview.bin ldd /usr/local/freesurfer/bin/freeview.bin linux-vdso.so.1 (0x00007ffe435fe000) libQtScriptTools.so.4 => /usr/local/freesurfer/lib/qt/lib/libQtScriptTools.so.4 (0x00007f5d6dbc9000) libQtScript.so.4 => /usr/local/freesurfer/lib/qt/lib/libQtScript.so.4 (0x00007f5d6d7aa000) libQtOpenGL.so.4 => /usr/local/freesurfer/lib/qt/lib/libQtOpenGL.so.4 (0x00007f5d6d58c000) libQtGui.so.4 => /usr/local/freesurfer/lib/qt/lib/libQtGui.so.4 (0x00007f5d6c7da000) libQtCore.so.4 => /usr/local/freesurfer/lib/qt/lib/libQtCore.so.4 (0x00007f5d6c3d5000) libGL.so.1 => /lib64/libGL.so.1 (0x00007f5d6c149000) libXext.so.6 => /lib64/libXext.so.6 (0x00007f5d6bf37000) libvtkverdict.so.5.6 => /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6 (0x00007f5d6de8d000) libvtkGraphics.so.5.6 => /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkGraphics.so.5.6 (0x00007f5d6b6cd000) libfreetype.so.6 => /lib64/libfreetype.so.6 (0x00007f5d6b418000) libvtkmetaio.so.5.6 => /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkmetaio.so.5.6 (0x00007f5d6b290000) libvtkpng.so.5.6 => /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkpng.so.5.6 (0x00007f5d6b16c000) libvtkzlib.so.5.6 => /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkzlib.so.5.6 (0x00007f5d6b058000) libvtksqlite.so.5.6 => /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtksqlite.so.5.6 (0x00007f5d6aeb3000) libvtkImaging.so.5.6 => /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkImaging.so.5.6 (0x00007f5d6aa2e000) libvtkFiltering.so.5.6 => /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkFiltering.so.5.6 (0x00007f5d6a59c000) libvtkCommon.so.5.6 => /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkCommon.so.5.6 (0x00007f5d6a1a7000) libvtksys.so.5.6 => /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtksys.so.5.6 (0x00007f5d6a067000) libvtkGenericFiltering.so.5.6 => /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkGenericFiltering.so.5.6 (0x00007f5d69f2b000) libvtkexoIIc.so.5.6 => /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkexoIIc.so.5.6 (0x00007f5d69de6000) libvtkNetCDF.so.5.6 => /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkNetCDF.so.5.6 (0x00007f5d69cac000) libvtkVolumeRendering.so.5.6 => /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkVolumeRendering.so.5.6 (0x00007f5d695fb000) libvtkRendering.so.5.6 => /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkRendering.so.5.6 (0x00007f5d68fe8000) libvtkftgl.so.5.6 => /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkftgl.so.5.6 (0x00007f5d68edd000) libvtkWidgets.so.5.6 => /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkWidgets.so.5.6 (0x00007f5d68be5000) libvtkHybrid.so.5.6 => /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkHybrid.so.5.6 (0x00007f5d687fd000) libvtkIO.so.5.6 => /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkIO.so.5.6 (0x00007f5d681c8000) libvtkDICOMParser.so.5.6 => /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkDICOMParser.so.5.6 (0x00007f5d680ab000) libX11.so.6 => /lib64/libX11.so.6 (0x00007f5d67d6d000) librt.so.1 => /lib64/librt.so.1 (0x00007f5d67b65000) libz.so.1 => /lib64/libz.so.1 (0x00007f5d6794e000) libcrypt.so.1 => /lib64/libcrypt.so.1 (0x00007f5d67718000) libdl.so.2 => /lib64/libdl.so.2 (0x00007f5d67514000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f5d672f5000) libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007f5d66f6e000) libm.so.6 => /lib64/libm.so.6 (0x00007f5d66c19000) libgomp.so.1 => /lib64/libgomp.so.1 (0x00007f5d669ea000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f5d667d3000) libc.so.6 => /lib64/libc.so.6 (0x00007f5d663f0000) libXrender.so.1 => /lib64/libXrender.so.1 (0x00007f5d661e6000) libfontconfig.so.1 => /lib64/libfontconfig.so.1 (0x00007f5d65fa1000) libgthread-2.0.so.0 => /lib64/libgthread-2.0.so.0 (0x00007f5d65d9f000) libglib-2.0.so.0 => /lib64/libglib-2.0.so.0 (0x00007f5d65a8b000) libpng12.so.0 => /lib64/libpng12.so.0 (0x00007f5d65865000) libSM.so.6 => /lib64/libSM.so.6 (0x00007f5d6565d000) libICE.so.6 => /lib64/libICE.so.6 (0x00007f5d65441000) libGLX.so.0 => /lib64/libGLX.so.0 (0x00007f5d6520f000) libGLdispatch.so.0 => /lib64/libGLdispatch.so.0 (0x00007f5d64f59000) libbz2.so.1 => /lib64/libbz2.so.1 (0x00007f5d64d48000) libpng16.so.16 => /lib64/libpng16.so.16 (0x00007f5d64b15000) libXt.so.6 => /lib64/libXt.so.6 (0x00007f5d648ad000) libXss.so.1 => /lib64/libXss.so.1 (0x00007f5d646a9000) libXft.so.2 => /lib64/libXft.so.2 (0x00007f5d64492000) libjpeg.so.62 => /lib64/libjpeg.so.62 (0x00007f5d6422a000) libxcb.so.1 => /lib64/libxcb.so.1 (0x00007f5d64002000) libfreebl3.so => /lib64/libfreebl3.so (0x00007f5d63dff000) /lib64/ld-linux-x86-64.so.2 (0x00007f5d6dddc000) libexpat.so.1 => /lib64/libexpat.so.1 (0x00007f5d63bcd000) libpcre.so.1 => /lib64/libpcre.so.1 (0x00007f5d6395a000) libuuid.so.1 => /lib64/libuuid.so.1 (0x00007f5d63755000) libXau.so.6 => /lib64/libXau.so.6 (0x00007f5d63551000) Best regards Knut Jørgen

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Clarification on Interpreting results cont'
by Avideh Gharehgazlou 06 Mar '18

06 Mar '18

Hi, Thank you so much for the clarification, so values listed under “CWP” column in "mc-z.abs.th13.sig.cluster.summary" file are my corrected p-values to be reported? (in this case having run monte carlo for multiple comparison correction) CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. AVIS DE CONFIDENTIALITÉ : Ce message électronique, ainsi que tout fichier qui y est joint, est reserve à l'usage exclusif du destinataire visé et peut contenir des renseignements confidentiels et privilégiés. Toute lecture, utilisation, divulgation ou distribution non autorisée est interdite. Si vous n'êtes pas le destinataire visé, veuillez en aviser l'expéditeur par retour de courriel et détruire toutes les copies du message original.

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Re: [Freesurfer] Clarification on interpreting results
by Douglas N. Greve 06 Mar '18

06 Mar '18

On 03/06/2018 12:03 PM, Douglas N. Greve wrote: > > > On 03/06/2018 10:14 AM, Avideh Gharehgazlou wrote: >> Hi, >> >> I have a 2 questions regarding properly interpreting results from >> QDEC. Will you please clarify the following for me? >> >> 1. What is the difference between stats table generated after >> correcting for multiple comparisons (i.e. monte carlo), vs the stats >> table generated after clicking "find clusters and go to max"? Results >> from which stats table should be reported? After searching on the >> web, I am still unclear about what exactly "find clusters and go to >> max" button does... and whether these are corrected results or not? > That button just finds clusters an will move the cursor to the maximum > value inside the cluster. There is no correction for multiple > comparisons with the "find clusters and go to max" button. >> >> 2. My understanding is that "CWP" column in stats table represents >> p-values of each cluster. However, when I manually convert values in >> the "max" column (which I assume are freesurfer p-values reported in >> -log(10)), I get different p-values than what are listed in "CWP" >> column for each cluster. Again, my question is whether I should >> report "CWP" values as my p-values or convert manually myself and >> report those? > The max is the maximum uncorrected vertex-wise significance in the > cluster and is unrelated to the clusterwise p-value (CWP). >> >> I would really appreciate your help! >> >> Thanks so much, >> >> Avi >> >> >> CONFIDENTIALITY NOTICE: This e-mail message, including any >> attachments, is for the sole use of the intended recipient(s) and may >> contain confidential and privileged information. Any unauthorized >> review, use, disclosure or distribution is prohibited. If you are not >> the intended recipient, please contact the sender by reply e-mail and >> destroy all copies of the original message. >> >> AVIS DE CONFIDENTIALITÉ : Ce message électronique, ainsi que tout >> fichier qui y est joint, est reserve à l'usage exclusif du >> destinataire visé et peut contenir des renseignements confidentiels >> et privilégiés. Toute lecture, utilisation, divulgation ou >> distribution non autorisée est interdite. Si vous n'êtes pas le >> destinataire visé, veuillez en aviser l'expéditeur par retour de >> courriel et détruire toutes les copies du message original. >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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Re: [Freesurfer] Demeaning covariates correctly?
by Douglas N. Greve 06 Mar '18

06 Mar '18

Yes, you have done everything correctly. QDEC takes your table.dat file and creates an FSGD file. It is possible to specify in the FSGD file whether to do demeaning or not by including a keyword. It does not find that keyword and so does not do demeaning. But you've already done demeaning so it does not matter. > > > On 03/06/2018 09:54 AM, Avideh Gharehgazlou wrote: >> >> Hi experts, >> >> >> I'm using QDEC to look at between group differences in LGI. According >> to a previous post I demeaned my covariates (age and surface area) >> inputted in my qdec.table.dat file by subtracting each value (i.e. >> each age) by the mean of all participant's ages and dividing it by >> the standard deviation of all participant's ages. When I upload >> qdec.table.dat file onto QDEC, it states the following: >> >> >> MeanSTD >> >> Age -01 >> >> Surface area 01 >> >> >> Assuming that I did demean covariates appropriately, I proceeded with >> stats analysis. However, when I click "analyze" on QDEC, the >> following messages appear in the command window which concerned me if >> I have correctly demeaned for my covariate variables or not: >> >> >> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. >> >> Continuous Variable Means (all subjects) >> >> 0 Age -3.88583e-08 0.997616 >> >> 1 SA 2.47776e-08 0.997616 >> >> Class Means of each Continuous Variable >> >> 1 diagnosisTD0.02160.1167 >> >> 2 diagnosisADHD-0.0528-0.2850 >> >> Again, at the end of the analysis: >> >> >> INFO: NOT demeaning continuous variables >> >> Continuous Variable Means (all subjects) >> >> 0 Age -2.75051e-08 0.997616 >> >> 1 SA 1.94509e-07 0.997616 >> >> Class Means of each Continuous Variable >> >> 1 diagnosisTD 0.02160.1167 >> >> 2 diagnosisADHD-0.0528-0.2850 >> >> >> Will you please tell me if I have correctly demeaned my covariates or >> not? If not, will you please tell me how I Can do this? >> >> >> Thanks so much, >> >> >> Avi >> >> >> >> >> CONFIDENTIALITY NOTICE: This e-mail message, including any >> attachments, is for the sole use of the intended recipient(s) and may >> contain confidential and privileged information. Any unauthorized >> review, use, disclosure or distribution is prohibited. If you are not >> the intended recipient, please contact the sender by reply e-mail and >> destroy all copies of the original message. >> >> AVIS DE CONFIDENTIALITÉ : Ce message électronique, ainsi que tout >> fichier qui y est joint, est reserve à l'usage exclusif du >> destinataire visé et peut contenir des renseignements confidentiels >> et privilégiés. Toute lecture, utilisation, divulgation ou >> distribution non autorisée est interdite. Si vous n'êtes pas le >> destinataire visé, veuillez en aviser l'expéditeur par retour de >> courriel et détruire toutes les copies du message original. >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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Clarification on interpreting results
by Avideh Gharehgazlou 06 Mar '18

06 Mar '18

Hi, I have a 2 questions regarding properly interpreting results from QDEC. Will you please clarify the following for me? 1. What is the difference between stats table generated after correcting for multiple comparisons (i.e. monte carlo), vs the stats table generated after clicking "find clusters and go to max"? Results from which stats table should be reported? After searching on the web, I am still unclear about what exactly "find clusters and go to max" button does... and whether these are corrected results or not? 2. My understanding is that "CWP" column in stats table represents p-values of each cluster. However, when I manually convert values in the "max" column (which I assume are freesurfer p-values reported in -log(10)), I get different p-values than what are listed in "CWP" column for each cluster. Again, my question is whether I should report "CWP" values as my p-values or convert manually myself and report those? I would really appreciate your help! Thanks so much, Avi CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. AVIS DE CONFIDENTIALITÉ : Ce message électronique, ainsi que tout fichier qui y est joint, est reserve à l'usage exclusif du destinataire visé et peut contenir des renseignements confidentiels et privilégiés. Toute lecture, utilisation, divulgation ou distribution non autorisée est interdite. Si vous n'êtes pas le destinataire visé, veuillez en aviser l'expéditeur par retour de courriel et détruire toutes les copies du message original.

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freeview for FS-FAST results
by stdp82＠virgilio.it 06 Mar '18

06 Mar '18

Hi list, is it possible to avoid the clusters < 5 voxels using freeview for FS-FAST results (mni.305) obtained after running mri_glmfit-sim --glmdir my-glm.wls --grf? Thanks Kind regards Stefano

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Demeaning covariates correctly?
by Avideh Gharehgazlou 06 Mar '18

06 Mar '18

Hi experts, I'm using QDEC to look at between group differences in LGI. According to a previous post I demeaned my covariates (age and surface area) inputted in my qdec.table.dat file by subtracting each value (i.e. each age) by the mean of all participant's ages and dividing it by the standard deviation of all participant's ages. When I upload qdec.table.dat file onto QDEC, it states the following: Mean STD Age -0 1 Surface area 0 1 Assuming that I did demean covariates appropriately, I proceeded with stats analysis. However, when I click "analyze" on QDEC, the following messages appear in the command window which concerned me if I have correctly demeaned for my covariate variables or not: INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age -3.88583e-08 0.997616 1 SA 2.47776e-08 0.997616 Class Means of each Continuous Variable 1 diagnosisTD 0.0216 0.1167 2 diagnosisADHD -0.0528 -0.2850 Again, at the end of the analysis: INFO: NOT demeaning continuous variables Continuous Variable Means (all subjects) 0 Age -2.75051e-08 0.997616 1 SA 1.94509e-07 0.997616 Class Means of each Continuous Variable 1 diagnosisTD 0.0216 0.1167 2 diagnosisADHD -0.0528 -0.2850 Will you please tell me if I have correctly demeaned my covariates or not? If not, will you please tell me how I Can do this? Thanks so much, Avi CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. AVIS DE CONFIDENTIALITÉ : Ce message électronique, ainsi que tout fichier qui y est joint, est reserve à l'usage exclusif du destinataire visé et peut contenir des renseignements confidentiels et privilégiés. Toute lecture, utilisation, divulgation ou distribution non autorisée est interdite. Si vous n'êtes pas le destinataire visé, veuillez en aviser l'expéditeur par retour de courriel et détruire toutes les copies du message original.

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Fwd: Question-optseq2
by Mora Alvarez, Maria 06 Mar '18

06 Mar '18

Hi, I’m interested in using optseq2 to optimize my experiment, but I wonder if the software was programmed for optimizing experiments such as the Attention network test, where some cues are presented before the stimuli (See below) [cid:D6F85C6A-6306-43C5-801E-54C09C00A93D] Ref. Fan et al Neuroimage 2005 Thank you very much and warm regards, Maria Mora

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Re: [Freesurfer] analysing scans other than brain
by Antonin Skoch 06 Mar '18

06 Mar '18

Dear Matyas, this (not brain-specific) R package will be maybe more suitable for your purpose: http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12035/full https://cran.r-project.org/web/packages/geomorph/index.html I generally would recommend to rather look for packages used in community of anthropologists or evolutional biologists. Antonin Hi Matyas we have online tutorials on our wiki and data you can download. Not sure how easy it will be though - a lot of what we do is brain specific Bruce On Mon, 5 Mar 2018, Matyas Varga wrote: Dear Bruce, Thank you for your quick reply. I think that whatever software I am going to use, it will require some coding as most similar software are brain specific. I use Matlab on a regular basis, and am happy to learn c in order to complete this project. My ultimate aim is to create a software or adapt an existing one for use on feet, for podiatrist and researchers. I was wondering if you could give me some suggestions as to where to start this using Free Surfer? Thank you. Best Regards Matyas Varga School of Health Sciences Research University of Brighton Aldro Building, 49 Darley Road Eastbourne, BN20 7UR -----Original Message----- From: freesurfer-boun...(a)nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: 05 March 2018 17:05 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] analysing scans other than brain Hi Matyas it is possible, but will be a fair amount of work, probably including some c coding since many of our tools are brain-specific cheers Bruce On Mon, 5 Mar 2018, Matyas Varga wrote: Dear Free Surfer, I was wondering if it was possible to analyse (surface-based morphometry and SPM) NOT brain scans. I am doing my PhD looking at how the shape of children’s feet change as they get older (2-7 years old). I will use a 3D scanner which will provide me with a mesh of triangles of the foot and I am considering to create average age group foot shapes and compare them using surface based morphometry and SPM. I will obviously have to create my own foot ”atlas”. I was wondering if this was possible in Free Surfer? Please let me know if it is possible or if you have any suggestions if it is not. Thank you. Best Regards Matyas Varga PhD student School of Health Sciences Research University of Brighton Aldro Building, 49 Darley Road Eastbourne, BN20 7UR Tel: 01273 644189 ___________________________________________________________ This email has been scanned by MessageLabs' Email Security System on behalf of the University of Brighton. For more information see: https://staff.brighton.ac.uk/is/computing/Pages/Email/spam.aspx ___________________________________________________________ This email has been scanned by MessageLabs' Email Security System on behalf of the University of Brighton. For more information see: https://staff.brighton.ac.uk/is/computing/Pages/Email/spam.aspx ___________________________________________________________ This email has been scanned by MessageLabs' Email Security System on behalf of the University of Brighton. For more information see: https://staff.brighton.ac.uk/is/computing/Pages/Email/spam.aspx _______________________________________________ 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

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