Freesurfer

freesurfer@nmr.mgh.harvard.edu

5 participants
30076 discussions

Tenure track position in Biomedical Imaging Science at Harvard (fwd)
by Bruce Fischl 21 Nov '16

21 Nov '16

FYI ---------- Forwarded message ---------- Date: Mon, 21 Nov 2016 10:45:52 -0500 From: Hanspeter Pfister <pfister(a)g.harvard.edu> To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>, Bruce Rosen <bruce(a)nmr.mgh.harvard.edu> Subject: Tenure track position in Biomedical Imaging Science at Harvard Hi Bruce and Bruce, I hope all is well. I would appreciate if you could distribute the following job ad for a tenure track position in biomedical imaging science at Harvard. Best wishes, - Hanspeter

1 0

Error w/ recon-all
by James Wilks 21 Nov '16

21 Nov '16

Hello FreeSurfer Developers, I’m trying to run recon-all on a cluster of images, however I keep getting an error each time. Here’s the output and command line: [jawilks@tykwer subjects]$ recon-all -subjid run_02 -all Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /export/home/jawilks/freesurfer/subjects Actual FREESURFER_HOME /export/home/jawilks/Applications/freesurfer -rw-rw-r-- 1 jawilks jawilks 60144 Nov 18 18:46 /export/home/jawilks/freesurfer/subjects/run_02/scripts/recon-all.log Linux tykwer.engin.umich.edu 2.6.18-416.el5 #1 SMP Wed Oct 26 12:04:18 EDT 2016 x86_64 x86_64 x86_64 GNU/Linux mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_convert) mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_convert) mri_convert: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_convert) mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_convert) mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_convert) mri_convert: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_convert) tkregister2_cmdl: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by tkregister2_cmdl) tkregister2_cmdl: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by tkregister2_cmdl) tkregister2_cmdl: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by tkregister2_cmdl) mri_make_uchar: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_make_uchar) mri_make_uchar: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_make_uchar) mri_make_uchar: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_make_uchar) mri_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_normalize) mri_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_normalize) mri_normalize: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_normalize) mri_watershed: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_watershed) mri_watershed: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_watershed) mri_watershed: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_watershed) mri_gcut: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_gcut) mri_gcut: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_gcut) mri_gcut: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_gcut) mri_segment: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_segment) mri_segment: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_segment) mri_segment: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_segment) mri_label2label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_label2label) mri_label2label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_label2label) mri_label2label: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_label2label) mri_em_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_em_register) mri_em_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_em_register) mri_em_register: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_em_register) mri_ca_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_ca_normalize) mri_ca_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_ca_normalize) mri_ca_normalize: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_ca_normalize) mri_ca_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_ca_register) mri_ca_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_ca_register) mri_ca_register: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_ca_register) mri_ca_label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_ca_label) mri_ca_label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_ca_label) mri_ca_label: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_ca_label) mri_pretess: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_pretess) mri_pretess: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_pretess) mri_pretess: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_pretess) mri_fill: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_fill) mri_fill: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_fill) mri_fill: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_fill) mri_tessellate: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_tessellate) mri_tessellate: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_tessellate) mri_tessellate: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_tessellate) mri_concatenate_lta: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_concatenate_lta) mri_concatenate_lta: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_concatenate_lta) mri_concatenate_lta: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_concatenate_lta) mri_normalize_tp2: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_normalize_tp2) mri_normalize_tp2: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_normalize_tp2) mri_normalize_tp2: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_normalize_tp2) mris_smooth: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_smooth) mris_smooth: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_smooth) mris_smooth: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_smooth) mris_inflate: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_inflate) mris_inflate: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_inflate) mris_inflate: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_inflate) mris_curvature: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_curvature) mris_curvature: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_curvature) mris_curvature: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_curvature) mris_sphere: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_sphere) mris_sphere: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_sphere) mris_sphere: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_sphere) mris_fix_topology: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_fix_topology) mris_fix_topology: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_fix_topology) mris_fix_topology: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_fix_topology) mris_topo_fixer: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_topo_fixer) mris_topo_fixer: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_topo_fixer) mris_topo_fixer: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_topo_fixer) mris_ca_label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_ca_label) mris_ca_label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_ca_label) mris_ca_label: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_ca_label) mris_euler_number: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_euler_number) mris_euler_number: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_euler_number) mris_euler_number: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_euler_number) mris_make_surfaces: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_make_surfaces) mris_make_surfaces: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_make_surfaces) mris_make_surfaces: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_make_surfaces) mris_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_register) mris_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_register) mris_register: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_register) mris_volmask: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_volmask) mris_volmask: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_volmask) mris_volmask: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_volmask) mris_anatomical_stats: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_anatomical_stats) mris_anatomical_stats: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_anatomical_stats) mris_anatomical_stats: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_anatomical_stats) mrisp_paint: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mrisp_paint) mrisp_paint: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mrisp_paint) mrisp_paint: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mrisp_paint) mris_curvature_stats: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_curvature_stats) mris_curvature_stats: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_curvature_stats) mris_curvature_stats: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_curvature_stats) mris_calc: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_calc) mris_calc: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_calc) mris_calc: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_calc) mri_robust_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_robust_register) mri_robust_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_robust_register) mri_robust_register: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_robust_register) mri_robust_template: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_robust_template) mri_robust_template: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_robust_template) mri_robust_template: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_robust_template) mri_and: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_and) mri_and: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_and) mri_and: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_and) mri_or: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_or) mri_or: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_or) mri_or: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_or) mri_fuse_segmentations: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_fuse_segmentations) mri_fuse_segmentations: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_fuse_segmentations) mri_fuse_segmentations: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_fuse_segmentations) mri_segstats: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_segstats) mri_segstats: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_segstats) mri_segstats: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_segstats) ERROR: it appears that recon-all is already running for run_02 based on the presence of /export/home/jawilks/freesurfer/subjects/run_02/scripts/IsRunning.lh+rh. It could also be that recon-all was running at one point but died in an unexpected way. If it is the case that there is a process running, you can kill it and start over or just let it run. If the process has died, you should type: rm /export/home/jawilks/freesurfer/subjects/run_02/scripts/IsRunning.lh+rh and re-run. Or you can add -no-isrunning to the recon-all command-line. The contents of this file are: ---------------------------------------------------------- ------------------------------ SUBJECT run_02 HEMI lh rh DATE Fri Nov 18 18:45:09 EST 2016 USER jawilks HOST tykwer.engin.umich.edu PROCESSID 21465 PROCESSOR x86_64 OS Linux Linux tykwer.engin.umich.edu 2.6.18-416.el5 #1 SMP Wed Oct 26 12:04:18 EDT 2016 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ ---------------------------------------------------------- Thank you in advance, James Wilks

1 0

grayscale display turns red in freeview
by Emmanuel Nwosu 21 Nov '16

21 Nov '16

Hi Am having a bit of a problem that may be easy to resolve. I want to view an LGI two-group comparison I did in mri glm-fit with freeview. Each time I load the overlay (cache.th13.abs.sig.cluster.mgh). The grayscale inflated surface turns red like what is in picture-1 Please have anyone an idea why this is happening and what I can do to change it back to grayscale like picture 2 Thanks for your help Emmanuel

2 8

Problem checking out sources
by Marmaduke Woodman 21 Nov '16

21 Nov '16

hi I followed the instructions for checking out the sources, by logging in first and then trying to checkout ~/src/fs$ cvs -d :pserver:anonymous@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot co -P -r stable5 dev cvs server: cannot find module `dev' - ignored cvs [checkout aborted]: cannot expand modules alas I am a CVS n00b and have no idea what this means.. am I missing something obvious? Thanks, Marmaduke

2 1

Importance of Symbolic Links?
by Jeffrey Crawford 21 Nov '16

21 Nov '16

Hello everyone! I have been fiddling with Version 6 and I have been encountering some difficulty copying Freesurfer folders onto my usb, because my usb cannot write "symbolic links". There are four of them produced by Freesurfer: lh.white.H , lh.white.K, rh.white.H, and rh.white.K. My question is whether these links are important to qdec or other Freesurfer analysis programs, such that me copying files that don't contain them will result in errors down the line? Also, I recognize that I could reformat my usb to UDF and be able to copy symbolic links. I tried this, but I found out that my Freesurfer is running on a very old version of Fedora that doesn't support UDF. So, until I get around to reinstalling Linux on this older computer, I am stuck with my limitations.

2 2

quality control of tracula tractography
by Knut J Bjuland 21 Nov '16

21 Nov '16

Hi, We have done tracula tractography on 180 subjects, and most of the isosurfaces look a lot noisier than the example on the Tracula wiki (see fminor in attached figure). Is there any way to gauge the noisiness of a reconstructed path? And can that information be used for quality control? For instance, here (https://neuro.ebioscience.amc.nl/portal/web/nsg/tracula) they do not accept a noisy fminor (not unlike ours). Another source of information on outliers is the log files that are produced when running -trac-all -stat (based on the shape of the tract). It doesn't seem to flag tracts that are (almost) completely missing (see attached figure, which was not flagged in lh.cab_PP.avg33_mni_bbr.log). Do they fall under the minimum threshold and are therefore not evaluated? Is it recommended to automatically exclude the subjects that are flagged as outliers here? Thank you! Knut Jørgen Bjuland, PHD Sørlandet sykehus

1 0

tracula: thresholding in pathstats.byvoxel
by Knut J Bjuland 21 Nov '16

21 Nov '16

Hi, We have two subjects, one with a lhcab that looks ~OK (somewhat noisy) and one with a lhcab that is almost completely missing (please see attached figures). And yet, looking at their respective pathstats.byvoxel.txt (under dpath/lh.cab_PP_avg33_mni_bbr) we find that both have data for this tract and that the subject with a seemingly missing tract (70) has more observations. Is this a thresholding issue? The default threshold in Freeview when viewing these files is 20% of the 99th percentile of the posterior probability distribution for the path, so how does that affect the data in pathstats.byvoxel and pathstats.overall; are they also thresholded? # subjectname 17 # pathwayname lh.cab # # pathway start x y z AD RD MD FA AD_Avg RD_Avg MD_Avg FA_Avg 56 35 27 0.000890712 0.000603441 0.000699198 0.315126 0.00105762 0.000596839 0.000750432 0.362276 56 36 26 0.00107635 0.000545558 0.000722489 0.41169 0.00104539 0.000615595 0.000758858 0.335287 56 37 26 0.00106187 0.000590571 0.000747672 0.372333 0.00105743 0.000602726 0.000754296 0.354483 56 38 25 0.00102202 0.000600078 0.000740726 0.368605 0.00100576 0.000632157 0.000756689 0.313797 56 39 25 0.00119029 0.000522558 0.000745135 0.485075 0.00107733 0.000611676 0.00076689 0.358958 56 39 24 0.000901928 0.000700433 0.000767598 0.204508 0.0010547 0.000622021 0.000766243 0.338646 56 40 24 0.000983715 0.000610012 0.00073458 0.333454 0.00105292 0.000634273 0.00077382 0.330426 56 41 23 0.00109975 0.000657692 0.000805043 0.318553 0.00115473 0.000602686 0.000786698 0.395328 57 42 23 0.00119796 0.000512441 0.000740946 0.50737 0.00119982 0.00058122 0.000787428 0.43539 57 43 22 0.00108816 0.000588772 0.000755234 0.368538 0.00120245 0.000589771 0.000793995 0.417918 57 44 22 0.00145913 0.000457154 0.000791146 0.628211 0.00131065 0.000556036 0.00080757 0.48867 57 45 21 0.00142093 0.000463346 0.000782542 0.617307 0.0013404 0.000544065 0.000809509 0.514237 57 46 21 0.00142182 0.000445771 0.000771122 0.632204 0.00139366 0.000547482 0.000829538 0.525517 57 47 20 0.000968663 0.000475497 0.000639886 0.434747 0.001285 0.000583274 0.000817181 0.448241 58 48 19 0.00121939 0.000531887 0.000761053 0.482488 0.00133092 0.000590401 0.000837236 0.462653 58 49 19 0.00159589 0.000576742 0.000916457 0.569308 0.00136598 0.000635182 0.000878787 0.437028 58 50 19 0.00164139 0.000624262 0.000963304 0.549971 0.00138664 0.000658869 0.000901467 0.426815 58 50 18 0.00157653 0.000942457 0.00115382 0.332295 0.00137177 0.000715268 0.000934107 0.385317 58 51 18 0.00118225 0.000642473 0.0008224 0.36823 0.00118518 0.000684428 0.000851342 0.330996 58 52 18 0.00109238 0.000519084 0.000710181 0.435882 0.00107605 0.000632073 0.000780059 0.324378 58 53 18 0.00129725 0.000623659 0.000848189 0.430382 0.00108778 0.000647922 0.000794535 0.315793 # pathway end # subjectname 70 # pathwayname lh.cab # # pathway start x y z AD RD MD FA AD_Avg RD_Avg MD_Avg FA_Avg 53 32 26 0.00117731 0.000928949 0.00101174 0.143923 0.00116391 0.00090839 0.000993563 0.153213 53 33 26 0.0010364 0.000859843 0.000918695 0.128905 0.00103869 0.000848443 0.000911856 0.138848 53 33 25 0.00105938 0.000877392 0.000938055 0.127225 0.00105752 0.000865256 0.000929355 0.135088 54 34 25 0.000944648 0.000719044 0.000794246 0.162868 0.000957389 0.000725472 0.000802768 0.16744 54 35 25 0.000972687 0.000738523 0.000816578 0.208351 0.000986717 0.000739063 0.000821629 0.213113 54 36 24 0.00101603 0.000621378 0.000752929 0.305637 0.0010253 0.000631396 0.000762693 0.302995 54 37 24 0.00113992 0.000642822 0.000808521 0.369124 0.0011217 0.000646204 0.000804698 0.353409 55 38 23 0.000890718 0.000584601 0.00068664 0.265622 0.000916719 0.000590972 0.000699556 0.273432 55 39 23 0.0013084 0.000657441 0.000874427 0.41632 0.00129438 0.000656492 0.000869102 0.409684 55 40 22 0.000897226 0.000549981 0.000665729 0.294657 0.000926128 0.000565056 0.000685412 0.294239 56 41 22 0.00129446 0.000643583 0.000860544 0.416518 0.00128053 0.000641873 0.000854761 0.410811 56 42 21 0.00095897 0.000527739 0.000671483 0.356436 0.000986408 0.00054246 0.000690451 0.355442 56 43 21 0.00126047 0.000576778 0.000804674 0.460586 0.00120436 0.000578402 0.000787051 0.4315 57 44 21 0.00141709 0.000815438 0.00101599 0.333322 0.00136115 0.000786714 0.000978188 0.330026 57 45 20 0.00107155 0.000547688 0.000722309 0.398732 0.0010439 0.000565023 0.000724638 0.366345 57 46 19 0.00106184 0.000688623 0.000813027 0.276355 0.00106565 0.000721324 0.000836098 0.250311 58 46 18 0.00138626 0.00111282 0.00120397 0.13344 0.00133896 0.00105932 0.00115254 0.147013 58 46 17 0.00190569 0.00154603 0.00166592 0.127639 0.0017048 0.00136742 0.0014799 0.141036 58 47 17 0.00182424 0.00136918 0.00152086 0.176476 0.00170912 0.00128364 0.00142549 0.178103 58 48 17 0.00179186 0.00155183 0.00163184 0.121897 0.0016827 0.00141198 0.00150224 0.137642 58 49 17 0.00173965 0.00152012 0.00159329 0.0828833 0.00156972 0.00134741 0.00142152 0.101404 58 50 17 0.00146827 0.00123617 0.00131354 0.105179 0.0013648 0.00113875 0.00121408 0.115824 59 51 17 0.000939683 0.000730799 0.000800427 0.151144 0.000913724 0.000729779 0.000791094 0.140851 59 52 17 0.000973182 0.000776841 0.000842288 0.136551 0.000937145 0.000762049 0.00082041 0.130533 59 53 17 0.000974158 0.000799803 0.000857921 0.120722 0.000938325 0.000778099 0.000831516 0.119775 59 54 17 0.00100004 0.000821513 0.000881023 0.135361 0.000956475 0.000793336 0.000847705 0.130042 # pathway end Thank you! sincerely yours, Knut Jørgen Bjuland, PhD Sørlandet sykehus [cid:BD078F74-6DFE-4119-A9F0-74B08B4DE0AF][cid:C07C98A4-AE40-4782-BD2A-9432409D7FCB]

1 0

Fwd:
by Emmanuel Nwosu 21 Nov '16

21 Nov '16

1 0

Hippocampal segmentation
by Rowa Aljondi 20 Nov '16

20 Nov '16

Hello Freesurfer Developers, I'm willing to use the new released version from Freesurfer (6.7.0) to measure the hippocampal volumes. Is that able to provide me the volumes of the anterior (hippocampal head) and posterior (hippocampal tail) parts of the Hippocampus and segmented these parts separately? Thanks, Rowa -- Rowa Aljondi PhD Candidate Faculty of Medicine, Dentistry and Health Sciences The University of Melbourne M: +61 416565756

1 0

fsaverage_sym LR-flipchecks
by James Roe 20 Nov '16

20 Nov '16

? Hi Freesurfer experts I have an ultimate goal of performing direct LH v RH comparisons using the fsaverage_sym template, so these pre-analysis steps are aiming to assess the symmetry of the template. I have performed a first-level fMRI analysis on a subject and am using this to compare the output with the exact same analysis performed on the same subject with LR-flipped data (anatomical, BOLD runs and B0 maps). I then ran recon-all on this flipped subject (treating flipped subject as new subject). Attached is a screenshot showing the different analysis outputs. In the top left image, analyses have been performed and smoothed on fsaverage_sym (RH shows LH flipped anat and BOLD data). As you can see, agreement is generally high, but there are also marked differences, most notably in postcentral/precentral regions. The bottom left shows this output resampled onto the individual surface (for comparison purposes for the next analysis). The top right image shows the output when analyses were performed on the individual surfaces of the original and flipped subject. Here, agreement seems much higher, also in postcentral/precentral regions (although still not symmetrical). The bottom right image shows this output resampled onto fsaverage_sym, and agreement remains very high. So it seems that performing the analysis on fsaverage_sym itself may be affecting the expected symmetry of the output. Originally I aimed to perform a comparison of the vectors of B-values in order to prove symmetry, although I am not sure whether this is a viable option anymore. Do you have any advice as to how I could proceed with this? Finally, it appears that also in the fsaverage_sym template the L/R vertices do not correspond to one another. So will it be possible to flip the analysis values and template in order to perform LH v RH comparisons at the group level? System: Linux CentOS 6 x86_64 (64b) stable v5.3.0 Thank you for your time James

3 7

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