Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

failure to start tksurfer
by Lars M. Rimol 19 Nov '15

19 Nov '15

Hi, I'm unable to initiate tksurfer. Can anyone tell me why this happens? [10:57 lmr@dmed4870 lmr] > tksurfer fsaverage lh inflated subject is fsaverage hemi is lh surface is inflated surfer: current subjects dir: /home/lmr/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/lmr checking for nofix files in 'inflated' Reading image info (/home/lmr/subjects/fsaverage) Reading /home/lmr/subjects/fsaverage/mri/orig.mgz surfer: Reading header info from /home/lmr/subjects/fsaverage/mri/orig.mgz surfer: vertices=163842, faces=327680 surfer: single buffered window surfer: tkoInitWindow(fsaverage) Received X error! Error code : 2 Request code : 154 Minor code : 3 Error text : 'BadValue (integer parameter out of range for operation)' Can't create a context! surfer: failed, trying double buffered window Received X error! Error code : 2 Request code : 154 Minor code : 3 Error text : 'BadValue (integer parameter out of range for operation)' Can't create a context! surfer: failed, no suitable display found sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway

1 0

Re: [Freesurfer] freesurfer vs ITK build from sources on ubuntu(LUCID)
by Nedialko I. Krouchev 18 Nov '15

18 Nov '15

To follow up on my previous message: the FS build is not facilitated by the scarcity and incompleteness of build instructions. For example ITK, PETSC (and possibly other packages) which are not even mentioned explicitly as FS prerequisites (!) need to be installed at a (version-matching!) dev-level (in ubuntu this can be done through the package-mgmt system), and the corresponding directories skillfully linked to the FS build configure options. This - paired with the scarcity of binaries for the various unix platforms hardly contributes for expanding the circle of FS users, unless the users in question are accomplished unix gurus familiar with all the inner workings of a modern code maintenance. Please contact me offline for further details and exchange.

1 0

recon-all script order
by Lauren Bystrom 18 Nov '15

18 Nov '15

Hello all, I am trying to run freesurfer on a set of subjects that have tumors in their brain. To get around the tumor, I only want to run freesurfer on one of the hemispheres. When I use hemi -?h, freesurfer exits once it hits the other hemisphere. This is a problem because it doesn't go back to finish the rest of recon-all for the hemisphere I want. Is there a way to change the order of files created with the recon-all script so all of the volumetric, and all of the wm, and all of broadmann's area, etc. is completed for one hemisphere before being run for the other? Thanks! Lauren Bystrom

2 2

FreeSurfer question
by Tsapanou, Angeliki 18 Nov '15

18 Nov '15

Hello, I am dealing with a problem on FreeSurfer a couple of days now. I want to fix the scull strip and I run the following commands: cd /users/Angeliki/studyname export SUBJECTS_DIR=studyname/subjid/session/T1/ recon-all -skullstrip -wsthresh 20 -clean-bm -no-wsgcaatlas -subjid FreeSurfer Then, the command works and the part of the cerebellum that I don't need turns brown. I close it and I save the script with: gedit ~/FreeSurfer/Angeliki/run_reconalls_aut1.sh And type at the script for echo: recon-all -autorecon2 -autorecon3 -subjid FreeSurfer Finally, I submit it to the cluster with the command: ~/FreeSurfer/Angeliki/run_reconalls_aut1.sh The problem is that even though it runs properly (and I tried to add some control points and they work), the brown part of the cerebellum does not disappear, but remains there. Is there something I have to change? Thank you, Best, Angeliki Tsapanou

2 3

gender as nuisance factor
by Tesse, Marcello 18 Nov '15

18 Nov '15

Dear FreeSurfer experts, > > > I a PhD student at King's college London. > > I am running cortical thickness analysis with QDEC. > > I would like to investigate some cortical thickness differences > between 2 groups, > > using as nuisance factors 'age' and 'gender'. > > > No problem at all with age. But the gender as dicotomic variable is > > listed on fixed factor in qdec, in design window. > > My question is: > > how can I run the analysis using 'gender' as nuisance factor?? > > > > thank you very much > > MARCELLO

2 2

selxavg3-sess error empty conditions in paradigm file
by Danielle Miller 18 Nov '15

18 Nov '15

Hello Freesurfer Experts, I am reposting this as this has not come up on the mail archive thread. I keep running into the following error (see below) when selxavg3-sess gets to my third subject. I am assuming this is because this subject does not have all of the conditions modeled (that is, this particular subject does not have any incorrect responses). Is there a way to model an empty condition to get around this? I want a general contrast of Incorrect > Correct, but some subjects do not make any errors and therefore would not have this condition in their paradigm files. Any advice would be greatly appreciated. #@# CC_003_recon ############################### /Volumes/VA_Imaging/Projects/dmiller/COGCON/FSFAST/CC_003_recon ------------------------- $Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $ /Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m /Applications/freesurfer/fsfast/toolbox/fast_ldanaflac.m /Applications/freesurfer-5.3/matlab/MRIread.m ------------------------- outtop = /Volumes/VA_Imaging/Projects/dmiller/COGCON/FSFAST Extension format = nii.gz INFO: key PerSession unrecognized, line 6, skipping INFO: key ApplySubCortMask unrecognized, line 12, skipping 1 Correct-v-Incorrect.mat 2 Incorrect-v-base.mat nruns = 4 autostimdur = outanadir = /Volumes/VA_Imaging/Projects/dmiller/COGCON/FSFAST/CC_003_recon/Bold1/correct.sm15.mni305 Found 57600/537168 (10.7) voxels in mask Creating Design Matrix ... creation time = 0.008 sec DoMCFit = 1 ntptot = 740, nX = 27, DOF = 713 Saving X matrix to /Volumes/VA_Imaging/Projects/dmiller/COGCON/FSFAST/CC_003_recon/Bold1/correct.sm15.mni305/Xtmp.mat ??? Error using ==> svd Input to SVD must not contain NaN or Inf. Error in ==> cond at 39 s = svd(A); Error in ==> fast_selxavg3 at 254 XCond = cond(XtX); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n Thanks, Danielle -- Ph.D. Program in Behavioral Neuroscience Boston University School of Medicine L-815 72 E. Concord St Boston, MA 02118 VA Boston Healthcare System Jamaica Plain Memory Disorders Research Center 150 South Huntington Ave D11-103 Boston, MA 02130 OFFICE:(857) 364-2130

2 1

Multimodality analysis in FreeSurfer
by Silas 18 Nov '15

18 Nov '15

Dear Freesurfer team, I've scanned a group of subjects and gained structural and myelination data. Then, I've used mris_preproc to map the data onto the surface of fsaverage (and concatenating the data). I would like to investigate the correlation between cortical thickness and myelination by mapping this correlation onto the fsaverage (an one sample group mean analysis) - is this possible? Do you have an existing guide approaching this problem? Thank you! Best, Silas

2 3

Obtaining MNI-305 Coordinates for Destrieux ROIs
by Riley North 18 Nov '15

18 Nov '15

Hello, I was following the conversation (recreated below) about converting the Destrieux ROI labels to MNI-305 coordinates and was wondering if all issues were resolved but not posted to the list. I attempted the same commands as were recommended in the original conversation: *mri_annotation2label --subject fsaverage --hemi lh --annotation aparc.a2009s * followed by *mri_surfcluster --in fsaverage/surf/rh.thickness --clabel my_label.label --sum sum.my_label --centroid --thmin 0 --hemi lh --subject fsaverage --nofixmni * *(where my_label is a given Destrieux ROI)* The 'sum' files returned by the second command all show the same MNI x-y-z coordinates as one another: [-29.4 -22.0 17.4] for lh ROIs and [29.8 -20.7 18.0] for rh ROIs. The original poster also said he observed that the x-y-z coordinates were the same for all of the ROIs for a given hemisphere. Like the original poster, I'm trying to get a single x-y-z MNI305-space coordinate triplet for each Destrieux ROI for use in network display software. Is there a modification to the above command that will return what I'm looking for? The original conversation (italicized) is posted below in chronological order: *Post #1: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42598.html <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42598.html>* *Hi Freesurfer Experts, For the purpose of defining nodes in a graph theory analysis, I would like to generate a list of X Y Z coordinates in MNI space for all the labels in the Destrieux atlas. I came across a previous post with the following steps:* *Step 1: mri_annotation2label --subject fsaverage --hemi lh --annotation aparc.a2009s --outdir /Users/ElijahMak Step 2: mri_surfcluster --in /Applications/freesurfer/subjects/fsaverage/surf/lh.thickness --clabel lh.G_and_S_frontomargin.label --sum sum.lh.G_and_S_frontomargin --centroid --thmin 0 --hemi lh --subject fsaverage Everything went smoothly, but I would like to check my steps with you before I proceed to generate the coordinates individually for each ROI per hemisphere. The output from #2 is sum.lh.G_and_S_frontomargin. When I load it, I see dhcp-172-17-218-173:~ ElijahMak$ cat sum.lh.G_and_S_frontomargin # Cluster Growing Summary (mri_surfcluster) # $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $ # $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ # CreationTime 2015/08/10-12:29:31-GMT # cmdline mri_surfcluster --in /Applications/freesurfer/subjects/fsaverage/surf/lh.thickness --clabel lh.G_and_S_frontomargin.label --sum sum.lh.G_and_S_frontomargin --centroid --thmin 0 --hemi lh --subject fsaverage # cwd /Users/ElijahMak # sysname Darwin # hostname dhcp-172-17-218-173.eduroam.wireless.private.cam.ac.uk <http://dhcp-172-17-218-173.eduroam.wireless.private.cam.ac.uk/> # machine x86_64 # FixVertexAreaFlag 1 # FixSurfClusterArea 1 # # Input /Applications/freesurfer/subjects/fsaverage/surf/lh.thickness # Frame Number 0 # srcsubj fsaverage # hemi lh # surface white # SUBJECTS_DIR /Applications/freesurfer/subjects # SearchSpace_mm2 65416.6 # SearchSpace_vtx 932 # Bonferroni 0 # Minimum Threshold 0 # Maximum Threshold infinity # Threshold Sign abs # AdjustThreshWhenOneTail 1 # Area Threshold 0 mm^2 # clabelfile lh.G_and_S_frontomargin.label # clabelinv 0 # Overall max 3.33248 at vertex 83949 # Overall min 0 at vertex 0 # NClusters 1 # Total Cortical Surface Area 65416.6 (mm^2) # FixMNI = 1 # # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ NVtxs 1 3.332 83949 82219.39 -29.4 -22.0 17.4 163842 Are those TalX TalY TalZ the values I'm looking for? Many thanks for your time. Best Wishes, Elijah* *Reply to Post #1: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42656.html <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42656.html>* *Those are more-or-less talairach coords, not MNI. If you add --nofixmni, the results will be reported in mni305 coords. - Douglas N Greve* *Post #2: **https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42693.html <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42693.html>* *Hi Douglas, Thanks for the help! However, when I tried the --nofixmni flag, all the ROIs appeared to have identical MNI coordinates. I have pasted the output from 3 ROIS in the LH.* *# ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ NVtxs 1 3.332 83949 82219.39 -29.4 -22.0 17.4 163842 1 3.533 117158 82219.39 -29.4 -22.0 17.4 163842 1 3.170 83424 82219.39 -29.4 -22.0 17.4 163842 The same thing happens to the ROIs on the RH (XYZ: 29.8 29.8 18.0). Best Wishes, * *Elijah * Thanks, Riley

1 0

direction for restart in the middle
by Krieger, Donald N. 18 Nov '15

18 Nov '15

I have run freesurfer 6Beta on the scan with very large CSF spaces With flags: -bigventricles and -notal-check . I used the latter flag per suggestions in the log as the first run failed on a talaraich check. This second run appears to be hung as it has not written anything new into the recon-all.log file for 7 hours. I would like to restart this at a reasonable point rather than at the beginning. Can you recognize where it is and what is are suggested restart flags? Here are the files which have appeared in the mri directory. aseg.auto.mgz aseg.presurf.mgz brainmask.mgz error.log mri_nu_correct.mni.log.bak nu_noneck.mgz orig_nu.log segment.dat talairach.log transforms wm.mgz aseg.auto_noCCseg.label_intensities.txt brain.finalsurfs.mgz brain.mgz filled.mgz norm.mgz orig orig_nu.mgz T1.mgz talairach_with_skull_2.log v.mgz wm.seg.mgz aseg.auto_noCCseg.mgz brainmask.auto.mgz ctrl_pts.mgz mri_nu_correct.mni.log nu.mgz orig.mgz rawavg.mgz talairach.label_intensities.txt talairach_with_skull.log wm.asegedit.mgz Here are the last 50 lines or so of the log file: ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2 ion: 3.10.73-1.el6.elrepo.x86_64 CompilerName: GCC CompilerVersion: 40400 ...skipping... mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 201 lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.767.2.2 2015/07/06 21:59:21 greve Exp $ before topology correction, eno=-510 (nv=99342, nf=199704, ne=299556, g=256) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations marking ambiguous vertices... 111330 ambiguous faces found in tessellation segmenting defects... 38 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 13 into 0 -merging segment 23 into 0 -merging segment 29 into 0 -merging segment 32 into 0 -merging segment 36 into 0 -merging segment 16 into 12 -merging segment 15 into 14 31 defects to be corrected 0 vertices coincident reading input surface /oasis/scratch/comet/donkri/temp_project/subjects/201/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2710 (-4.6355) -vertex loglikelihood: -8.2866 (-4.1433) -normal dot loglikelihood: -3.4816 (-3.4816) -quad curv loglikelihood: -6.0138 (-3.0069) Total Loglikelihood : -27.0531 CORRECTING DEFECT 0 (vertices=53053, convex hull=8873) Thanks for your direction on this. - Don

2 2

Hippocampal Subfields 6.0 with 5.3 recons
by O'Shea,Andrew 18 Nov '15

18 Nov '15

Hello all, I was wondering if anyone with knowledge of the new hippocampal subfield segmentation that is going to be released with version 6.0 could answer a quick question. We have previously processed subjects in v5.3 and would like to use the new hippocampal seg algorithm. How "standalone" is the new process? Does the new process use any inputs from the recon-all stream which have changed in the upcoming version? Thanks! -Andrew

2 1

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