Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

Freesurfer FAQ
by Pedro Paulo Oliveira Jr 02 Nov '07

02 Nov '07

Hi, I started the Wiki Page on FreeSurfer FAQ: http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions_2fFAQ Any corrections and suggestions are welcome! I think we can avoid some questions to the list if we increase the FAQ. Regards Pedro Paulo Oliveira Jr.

2 1

Volume of sub-cortical structures
by Dan Dillon 01 Nov '07

01 Nov '07

Dear FreeSurfers, Hopefully a very easy question . . . I want to compare the volume of subcortical structures in two groups of subjects. All I need to do that is the volume information contained in aseg.stats, right? Just want to double-check before I get started. Thanks! Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 495-1889 E-mail: dillon(a)wjh.harvard.edu

3 2

topology defect
by Michael Harms 01 Nov '07

01 Nov '07

Hello, We have a case where -autorecon2 completed successfully, yet the right surface appears to have a topological defect. We discovered this because we got the following message upon trying to run 'mris_volume' on the pial surface: --- mris_volume: surface rh.pial has an incorrect topology (eno=1) --- Here is the output of mris_euler_number on that surface: --- euler # = v-e+f = 2g-2: 133519 - 400551 + 267033 = 1 --> 1 holes F =2V-4: 267033 != 267038-4 (1) 2E=3F: 801102 != 801099 (3) total defect index = 4 --- Below I've appended the final lines from the log file of the Fix Topology stage (FS v3.0.5). I've also attached two jpgs of the likely problem -- note the small black spot on the inflated surface, and the break of the orig and white surfaces in the medial temporal region of the tkmedit snapshot. (There is a small break in the pial surface as well, but it is hard to see in the jpg). Should we just try running the Topology Fixer again? What should we try in order to get a correct topology for this surface? thanks, Mike H. ------------------------ CORRECTING DEFECT 35 (vertices=61, convex hull=108) After retessellation of defect 35, euler #=-4 (133456,400244,266784) : difference with theory (-2) = 2 CORRECTING DEFECT 36 (vertices=86, convex hull=119) After retessellation of defect 36, euler #=-2 (133489,400394,266903) : difference with theory (-1) = 1 CORRECTING DEFECT 37 (vertices=9, convex hull=34) After retessellation of defect 37, euler #=-1 (133494,400421,266926) : difference with theory (0) = 1 CORRECTING DEFECT 38 (vertices=136, convex hull=61) After retessellation of defect 38, euler #=0 (133507,400486,266979) : difference with theory (1) = 1 CORRECTING DEFECT 39 (vertices=32, convex hull=74) After retessellation of defect 39, euler #=1 (133519,400551,267033) : difference with theory (2) = 1 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.04-->6.15) (max @ vno 133750 --> 134053) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.22 (0.04-->6.15) (max @ vno 133750 --> 134053) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 120 mutations (34.1%), 232 crossovers (65.9%), 195 vertices were eliminated building final representation... 3035 vertices and 0 faces have been removed from triangulation after topology correction, eno=1 (nv=133519, nf=267033, ne=400551, g=0) writing corrected surface to /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/011228_12436/surf/rh.orig... edge (34451<-->132983) has one single face 264775 ! edge (34451<-->132972) has one single face 264857 ! edge (132972<-->34451) has one single face 264857 ! edge (132972<-->132983) has one single face 264959 ! edge (132983<-->34451) has one single face 264775 ! edge (132983<-->132972) has one single face 264959 ! 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 59.9 minutes reading input surface /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/011228_12436/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... edge 34451 <--> 133998 has 1 face(s)! (264775) 133827 34451 133998 !!! edge 34451 <--> 133986 has 1 face(s)! (264857) 133909 133986 34451 !!! edge 133986 <--> 133998 has 1 face(s)! (264959) 133986 133992 133998 !!! 3 defective edges removing intersecting faces 000: 269 intersecting 001: 48 intersecting 002: 24 intersecting 003: 20 intersecting 004: 24 intersecting 005: 14 intersecting 006: 3 intersecting /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/011228_12436/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.02 hours removing intersecting faces 000: 202 intersecting 001: 43 intersecting 002: 20 intersecting expanding nbhd size to 2 003: 20 intersecting 004: 18 intersecting 005: 12 intersecting 006: 3 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated

1 0

Qdec covariates
by Alexander Fornito 31 Oct '07

31 Oct '07

Hi all, If i run a model in qdec that inludes 1 discrete and 1 continuous factor, does the output for the group contrast covary for the continuous variable? For example, if I want to compare two groups, and include group as my discrete factor and age as a continuous factor, will the output for the group contrast (Does the average thickness differ between grp1 and grp2?) covary for age? I've notice that running it without continuous factors leads to different results, so I just wanted to confirm this is the case. Also, just wanted to check that group contrasts are run as level_1 - level_2, so that positive values (i.e., red-yellow) indicate level_1 > level_2. Thanks for your help, Alex

3 2

white matter problem
by Matt Colvin 30 Oct '07

30 Oct '07

Dear Freesurfer gurus, Hello, my name is Matt Colvin, with the Conte Center at Washington University in St. Louis. I came across a problem with a particular brain where the wm and pial lines cut out a chunk of white and grey matter. I have not come across a problem quite like this one so I was wondering if anybody had a suggestion as to how to fix it? I believe it is in the insula of the left hemi of this brain, though I am not certain (the region gets labeled as "unknown" in the parcellation). I have attached two screen caps which show the problem area. Thanks for any help anyone could offer. --Matt Colvin

2 1

old Mac ver.
by Kirk, Gregory 29 Oct '07

29 Oct '07

Hi, I have a radiologist that wants to do some freesurfer work, visualizing subcortical parcelations and orig and T1 volumes. The volume processing was done with freesurfer-v3.0. Can I install the current freesurfer-Darwin-tiger-stable-pub-v4.0.1-full.dmg and have it correctly visualize the volumetric parcellation data generated with 3.0 or do I need to get the PowerPC 3.0 version from you ( if possible ). thanks Greg.

2 1

freesurfer help
by Seth Elkin-Frankston 29 Oct '07

29 Oct '07

Hello, I'm running v.4.0.1 on CentOS 5. When attempting to run autorecon1 I receive the error below. Any help is appreciated. Thanks Seth Elkin-Frankston ---- Iteration 1 Mon Oct 29 09:47:59 EDT 2007 nu_correct -clobber ./tmp.mri_nu_correct.mni.8422/nu0.mnc ./tmp.mri_nu_correct.mni.8422/nu1.mnc [NeuroBio@lr8to10-dhcp-131-112.bumc.bu.edu:/usr/local/freesurfer/subjects/Bo bFS/mri/] [2007-10-29 09:47:59] running: /usr/local/freesurfer//mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /usr/tmp/nu_correct_8477/ ./tmp.mri_nu_correct.mni.8422/nu0.mnc ./tmp.mri_nu_correct.mni.8422/nu1.imp /usr/local/freesurfer//mni/bin/volume_stats: error while loading shared libraries: libstdc++.so.5: cannot open shared object file: No such file or directory nu_estimate_np_and_em: crashed while running volume_stats (termination status=32512) nu_correct: crashed while running nu_estimate_np_and_em (termination status=32512) ERROR: nu_correct Linux lr8to10-dhcp-131-112.bumc.bu.edu 2.6.18-8.1.15.el5 #1 SMP Mon Oct 22 08:32:04 EDT 2007 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Mon Oct 29 09:47:59 EDT 2007

3 2

FSfast tutorial
by McLean John (NHS Greater Glasgow & Clyde) 29 Oct '07

29 Oct '07

Hi, I am trying to work through the FSfast tutorial. When i enter the following command: tkmedit-sess -s mgh-101.1 -a sm-gamma-fwhm5 -c odd-v-0 -aparc+aseg i get the following error: INFO: Found session in: ./mgh-101.1 grep: ./mgh-101.1/session.info: No such file or directory INFO: Found session in: ./mgh-101.1 grep: ./mgh-101.1/session.info: No such file or directory -------------------------------------------------------------- tkmedit-sess logfile is /usr/local/freesurfer/fsfast/tutorialdata/fsfast-tutorial/fb1-analysis-study/log/tkmedit-sess.log -------------------------------------------------------------- setenv SUBJECTS_DIR /usr/local/freesurfer/subjects/buckner_data/tutorial_subjs ERROR: sm-gamma-fwhm5 does not exist. Try running mkanalysis-sess Does anyone have any thoughts on this? Is FS looking for a file i dont have? I have set $FSFTUTDIR correctly and i am working in fb1-analysis-study as instructed in the tutorial. Best wishes ********************************************************************** This message may contain confidential and privileged information. If you are not the intended recipient please accept our apologies. Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Please inform us that this message has gone astray before deleting it. Thank you for your co-operation. NHSmail is used daily by over 100,000 staff in the NHS. Over a million messages are sent every day by the system. To find out why more and more NHS personnel are switching to this NHS Connecting for Health system please visit www.connectingforhealth.nhs.uk/nhsmail **********************************************************************

1 0

summary-sess of FA values
by Robert Levy 27 Oct '07

27 Oct '07

Hi, Is there any way to get something like the output of roisummary-sess, but for ROI-constrained FA values instead of BOLD? What I'm actually want to use this for, is to get FA values at a single vertex for each subject in the group, so I can plot a regression line against a behavioral measure. Thanks, Rob http://nmr.mgh.harvard.edu/~levy

2 1

mris_preproc error for mc sim...
by Cameron Ellis 26 Oct '07

26 Oct '07

Hi, In anattempt to prepare to run a monte carlo cluster threshold simulation with a group of subjects in stable3, I run into the following error using mris_preproc: [troy:retrievalnewest] (nmr-stable3-env) mris_preproc --fsgd SM2_glm_MC_controls.fsgd --target allsubavg --hemi lh --sf sessidallsh+smvsnh --a retrievalS PMHRF_5cond_40TW --c sh+smvsnh.mat --out SM2_glm_MC_controls_sh+smvsnh.mgh ERROR: cannot find /autofs/space/troy_003/users/retrievalnewest/SM0C1/bold/retrievalSPMHRF_5cond_40TW//space/troy/3/users/retrievalnewest/MC_contrasts/single.mat/ces.bhdr I do not know why fsfast is looking for this file here or how to indicate where it is. Am I running in the wrong env? When I try dev I get this error: [troy:retrievalnewest] (nmr-std-env) mris_preproc --fsgd SM2_glm_MC_controls.fsgd --target allsubavg --hemi lh --sf sessidcontrolssh+smvsnh --a retrievalSPMHRF_5cond_40TW --c sh+smvsnh.mat --out SM2_glm_MC_controls_sh+smvsnh.mgh if: Expression Syntax. Any suggestions? Cameron

2 4

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