Freesurfer March 2018

freesurfer@nmr.mgh.harvard.edu

115 participants
161 discussions

Start a nNew thread

trouble shooting: pial surface & wm hypointensities
by Marie Sigmund 07 Mar '18

07 Mar '18

2 2

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

2 1

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

1 1

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.

2 1

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 >

1 0

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 >

1 0

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.

1 0

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

2 3

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.

1 0

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

1 0

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 March 2018