Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

Password VM FStutorial
by Etienne Abassi 24 Apr '20

24 Apr '20

External Email - Use Caution Dear all, I tried to install the virtual image of Freesurfer you provided on this page: https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67_win It worked well, but I can't find the password for the "Developer" account, and so I can't log into the VM. Could you please provide the password ? I thank you in advance for you time. Best, Etienne -- Etienne Abassi, PhD Student Institut des Sciences Cognitives Marc Jeannerod - CNRS UMR 5229 67, Boulevard Pinel - 69675 BRON (Lyon), France

1 0

Trac-All NaN
by Hua, Jessica 23 Apr '20

23 Apr '20

External Email - Use Caution Hi FreeSurfer, I ran the trac-all -stat command on some of my participants, and I noticed that some of the values that were outputted contained NaN. Why are the values coming out as NaN? fmajor_PP.avg33_mni_bbr.AD_Avg.txt S11018a_LGI S11019a_LGI S11021a_LGI NaN NaN 0.00109668 0.00116704 NaN 0.00110631 0.00118262 NaN 0.00113231 0.00119589 NaN 0.00116401 0.00121558 NaN 0.00117549 0.00123733 NaN 0.00119309 0.00126087 NaN 0.00123177 0.00127355 0.00116328 0.00127236 0.00126695 0.00115413 0.00129993 0.00125837 0.00117334 0.00131861 0.00125611 0.00117423 0.00134501 0.00130347 0.00117161 0.00135121 0.00133526 0.00117097 0.00136288 0.00135801 0.00116546 0.00136839 0.00138131 0.0011961 0.00141117 0.00137605 0.00126803 0.00143167 0.00139927 0.00132198 0.00144947 0.00140814 0.00135481 0.00145095 0.00141403 0.00136342 0.00144231 0.00143846 0.00136409 0.0014307 0.00144842 0.00134806 0.00141466 0.00144669 0.00138324 0.00139904 0.00144974 0.00143263 0.00139749 0.00146505 0.00145596 0.00143352 0.00149473 0.0014523 0.00144366 0.00150771 0.0014622 0.00144891 0.00151567 0.00148269 0.00147786 0.0015513 0.00151399 0.00153047 0.00158431 0.00155476 0.00160898 0.00163524 0.00162621 0.00166298 0.00166918 0.0016651 0.0016538 0.00165915 0.00165803 0.00169534 0.00171513 0.00164646 0.00176355 0.00178509 0.00167836 0.00179073 0.00186456 0.00175883 0.00181997 0.00187805 0.00183493 0.00178465 0.00189962 0.00187421 0.00175515 0.00192235 0.00189781 0.00171387 0.0019091 0.00184765 0.00160073 0.00191175 0.00181558 0.00157862 0.00191679 0.00182829 0.00165907 0.00185513 0.00185947 0.0017003 0.00181572 0.00189271 0.00172307 0.00181154 0.0018763 0.00159418 0.0018311 0.0018657 0.00159179 0.00172958 0.00189407 0.00164795 0.00165341 0.00191997 0.00167435 0.00156794 0.00190814 0.00168963 0.00146072 0.001859 0.00172164 0.00138372 0.00178192 0.00175954 0.00136893 0.00170486 0.0018261 0.0013654 0.00164533 0.0018264 0.00135974 0.00155251 0.00176598 0.00137226 0.00149038 0.00166574 0.00133654 0.00146834 0.00152383 0.00134757 0.00148128 0.00138086 0.00136271 0.00147022 0.00132929 0.00136545 0.00144934 0.00127674 0.00137979 0.00145088 0.00125313 0.00137398 0.00151918 0.00125802 0.00137699 0.00151537 0.00126461 0.00136867 0.00146195 0.00126159 0.00136882 0.00140568 0.0012639 0.00134777 0.00138923 0.00126469 0.00127934 0.00138564 0.00127229 0.00122813 0.00138057 0.00128295 0.00118596 0.00138419 0.00129555 0.00117204 0.0013933 0.00131012 0.00114282 0.0013934 0.00129255 0.00114104 0.00141831 0.0012982 0.00116965 0.00141932 0.00128999 0.00118427 0.00139441 0.00128321 0.00117267 0.0013619 0.00127428 0.00117105 0.00133817 0.00124349 0.00114046 0.00131501 0.00121045 NaN 0.0012865 0.00117847 NaN 0.00126657 0.00114993 NaN 0.00123952 0.00113779 NaN NaN 0.00112863 Jessica --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri

2 1

ROIs to surface overlays / Arithmetic on surface overlays
by Funk, Quentin 23 Apr '20

23 Apr '20

External Email - Use Caution Freesurfer experts, I have a volumetric ROI (integer valued) in MNI space. I'd really like to display them on the fsaverage brain as a surface overlay so that it's clear what regions I'm looking at. Using something like this, I get pretty good results: mri_vol2surf --mov ROI_integers.nii --regheader fsaverage --hemi lh --out left_overlay.mgh --projfrac-max 0.15 .17 .01 but the edges are kind of a mess, see: https://imgur.com/a/53RVGCM Is there any way to smooth these edges while maintaining the "lookup table' nature of the surface overlay? Any kind of interpolation ruins that, so it's a bit hard (you can't see in that image, but there are multiple regions shown). Alternatively, is there any way I can do arithmetic with surfaces? If there were a tool like fslmaths for surface overlays, solving this problem would be relatively straightforward. Thanks for any help you can provide! -quentin funk Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas and among the top 20 hospitals nationwide. Houston Methodist is the only nationally ranked Honor Roll hospital in the state and is designated as a Magnet hospital for excellence in nursing. houstonmethodist.org | twitter.com/MethodistHosp | 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.

2 1

Cortical thickness measure for external analysis.
by Miguel Ángel Rivas Fernández 23 Apr '20

23 Apr '20

External Email - Use Caution Dear Freesurfer experts, We are interested in running external analysis with thickness measurements of two brain regions. Can we use safely the metrics exported or by contrary a previous transformation is required before export the stats of each subject? Thanks for your time. Best regards, -- *Miguel Ángel Rivas Fernández*

2 1

Calculating standard error in Matlab from whole brain analyses
by Graduate Imaging 22 Apr '20

22 Apr '20

External Email - Use Caution Hi FreeSurfer experts, I ran a vertex wise analysis that consisted of six groups with two continuous covariates which yielded a cluster after mri_glm-fit. I've extracted the values from the ocn.dat file. I ran a post hoc analyses in matlab to determine which group is significantly different using the command below: X = load('Group.Xg.dat'); design matrix from freesurfer C = load('C.dat'); post hoc contrast(s) Y = load('Whole.brain.cluster.dat'); values from the ocn.dat file [beta rvar] = fast_glmfit(Y,X) [F pvalues] = fast_fratio(beta,X,rvar,C) This outputs an array of beta values where the first six would be the intercept. How would I calculate the standard error of the intercept for each group? Would it be rvar/(sqroot(n)).

2 4

(no subject)
by Ерохин Александр 22 Apr '20

22 Apr '20

External Email - Use Caution Hello together, The FreeSurfer distribution takes 10G of the disk space in my local installation. It has numerous tools, but it’s not modular, or at lest it’s very hard to tell boundaries between modules. E.g. /bin folder contains around 860 executables all in one place. Is it possible to trim down the distribution provided to minimize the size but keep it functional in terms of computation for recon-all steps? For example trim away all GUI executables and support libraries. As far as I can see, the directories taking most of the space are: 2.2G ./subjects 3.1G ./average 2.5G ./bin 1.3G ./lib But I am not sure what could be removed and what not in order to keep all recon-all steps functional. Many thanks, Aleksandr.

3 4

recon-all.v6.hires (macos) ERROR: cannot find conf2hires
by Tali Weiss 22 Apr '20

22 Apr '20

External Email - Use Caution Dear FreeSurfer Developers, 1. I have mp2rage on 7T (Siemens, MAGNETOM Terra) resolution 1 mm3 , from the forum i see it is recommend to use: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp/ If i correctly it ignore INV1, INV2 and the only input is the UNI. Is it correct? 2. I have macOS Sierra (version 10.13.6) I Copy these files into $FREESURFER_HOME/bin and apply: sudo chown root:wheel <file> sudo chmod 755 <file> ls -l -rwxr-xr-x@ 1 root wheel 22917 Apr 18 10:11 conf2hires.txt -rwxr-xr-x@ 1 root wheel 323951 Apr 18 10:29 recon-all.v6.hires I tried to run recon-all.v6.hires -all -s <foldername> -i <.nii> -conf2hires ERROR: cannot find conf2hires Thank you for your help Tali

3 2

group analysis of large data sets
by Wang, Xin 22 Apr '20

22 Apr '20

Hello, FreeSurfer Group, What is the maximal matrix size for glm_fit process? How to use FreeSurfer for group analyses of more than 2000 subjects, 128 variables, and 128 Classes? Thank you. Xin

4 5

Group analysis in QDEC: FWHM size for thickness and volume
by Steve Petersen 22 Apr '20

22 Apr '20

External Email - Use Caution Dear Freesurfer experts, I have two questions regarding group analysis in QDEC: 1. What is the most appropiate FWHM size when comparing the volume and cortical thickness of two groups? I was thinking in use 5 FWHM for volume and 10 FWHM for thickness, any suggestion? 2. After perform the correction for multiple comparisons, terminal says that it has been found a cluster in the right superior parietal lobule (please, see the attached screenshot). However this cluster do not appear in the fsaveage image. Is there any tutorial that explains how to plot the significant cluster in the fsaverage?. Maybe in freeview? [image: imagen.png] Thanks in advance. Best regards, Steve.

2 1

Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags?
by Billah, Tashrif 22 Apr '20

22 Apr '20

Douglas, A little more elaboration would help. What is "it" and what are "them"? -Tashrif .

2 5

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