Freesurfer November 2012

freesurfer@nmr.mgh.harvard.edu

105 participants
177 discussions

Interpretation of voxel values in TRACULA "path.pd" images
by Jon Clayden 21 Dec '12

21 Dec '12

Dear all, I understand that the various "path.pd" image files that are created by TRACULA represent a posterior distribution over the corresponding tract location, but I was wondering if someone could explain to me exactly what the values in these images mean. I assume that they are not probabilities as such, since they have values ranging up to several hundreds. Thanks in advance, Jon

3 10

tracula - posterior density just one-dimensional curve
by Andi Heckel 20 Dec '12

20 Dec '12

Dear Tracula team, I have noticed in a multisubject tracula analysis, that the posterior density in many if not all paths in the path.pd.nii.gz file is just a bright one-dimensional curve, rather than a true distribution. The path.map.nii.gz is empty. This is true for both flirt and bbreg registered versions in many subjects. Trac-all finished wiithout errors. So did Recon-all. Could it actually be a memory (RAM) problem ? We are running tracula on a cluster with only 2.5 GB per core. thx for any help and kind regards, andi

3 4

Fwd: tracula problem:poor forceps major tract
by bryon mueller 20 Dec '12

20 Dec '12

After processing dozens of subjects through tracula I have found some subjects with tracts that are one voxel along the entire tract, for example the forceps major. After reviewing the data I believe the bvecs files are pointing the correct direction, I believe the registration between the T1/freesurfer segmentation and DTI is reasonably good (registration was performed with bbr), at least the anat_brain_mask-vent.bbr and dtifit_FA are reasonable and cortex.bbr and lowb_brain seem reasonably well registered. The brain extraction does look poor in that a large chunk of posterior skull remains in the anat_brain_mask-vent.bbr image but the as the registrations, segmentations and parcellations look OK I believe this isn't the cause of my problems. I do see one issue: the registration between the dtifit_FA.bbr and fmajor_PP_avg33_mni_bbr_logprior_0 images. Sections of the logprior volume are entirely in the lateral ventricles of the DTI data. Please see attached jpg. This subject large lateral ventricles and I am wondering if such subjects can be run successfully in tracula. Much thanks for any suggestions.

2 2

recon-all: too many levels of symbolic links
by Linda Zhang 20 Dec '12

20 Dec '12

Dear all, I've been running recon-all on my dataset, but all of them are exiting with the same error. The command line is: recon-all -subjid ncpoCCW -autorecon2 -autorecon3 The error reads: #@# Ex-vivo Entorhinal Cortex Label lh Sat Aug 25 11:54:33 HKT 2012 INFO: lh.EC_average subject does not exist in SUBJECTS_DIR INFO: Creating symlink to lh.EC_average subject... cd /home/virtualuser/freesurfer/subjects; ln -s /home/virtualuser/freesurfer/subjects/lh.EC_average; cd - mris_spherical_average -erode 1 -orig white -t 0.4 -o ncpoCCW label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject ncpoCCW. processing subject lh.EC_average... MRISread(/home/virtualuser/freesurfer/subjects/lh.EC_average/surf/lh.sphere.reg): could not open file eroding label 1 times before writing thresholding label stat at 0.400 before writing Too many levels of symbolic links mris_spherical_average: could not read surface file /home/virtualuser/freesurfer/subjects/lh.EC_average/surf/lh.sphere.reg Too many levels of symbolic links Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux recon-all -s ncpoCCW exited with ERRORS at Sat Aug 25 11:54:37 HKT 2012 What should I do? Thanks! Cheers, Linda

2 10

selxavg3 error : NaN in Xtmp.mat file
by Sid Kundu 07 Dec '12

07 Dec '12

Hi Doug, I created a new first level analysis along with new contrasts and event numbers for a group of subjects I had previously done analyses on. All but one of the subjects finished selxavg3 without error, but one subject gave the following error: Saving X matrix to /home/sidkundu/freesurfer/sessions/Heading-TTP/LMV2010_N19_Heading-TTP/bold/TTP-analysis-3/Xtmp.mat Error using svd Input to SVD must not contain NaN or Inf. Error in cond (line 39) s = svd(A); Error in fast_selxavg3 (line 248) XCond = cond(XtX); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n I looked at the generated Xtmp.mat file and it shows the design matrix X has all zeros in 2 columns, resulting in NaNs in the same columns for Xn, and corresponding NaNs in XtX. I'm wondering what would cause this or why it would only occur for only one subject. _________________________________ Sid Kundu Biomedical Engineering Boston University

3 6

long_mris_slopes error
by Alexandru Hanganu 07 Dec '12

07 Dec '12

Dear Freesurfer Experts, While performing the long_mris_slopes cmd, we receive an error: ------------------------------------------- SUBJECT pls_pd_base00 Running Within-Subject GLM Writing ./tmp-pls_pd_base00_lh_thickness_Rx7HLs/X-long.mat ... mri_glmfit --y /Applications/freesurfer/subjects/pls_pd_base00/surf/lh.long.thickness-stack.mgh --X ./tmp-pls_pd_base00_lh_thickness_Rx7HLs/X-long.mat --allow-zero-dof --no-contrasts-ok --surf pls_pd_base00 lh --label /Applications/freesurfer/subjects/pls_pd_base00/label/lh.long.cortex.label --glmdir ./tmp-pls_pd_base00_lh_thickness_Rx7HLs/glm Traceback (most recent call last): File "/Applications/freesurfer/bin/long_mris_slopes", line 732, in <module> run_cmd(cmd,'mri_glmfit did not work?') File "/Applications/freesurfer/bin/long_mris_slopes", line 422, in run_cmd retcode = subprocess.call(args) File "/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/subprocess.py", line 443, in call return Popen(*popenargs, **kwargs).wait() File "/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/subprocess.py", line 593, in __init__ errread, errwrite) File "/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/subprocess.py", line 1079, in _execute_child raise child_exception OSError: [Errno 8] Exec format error ------------------------------------------- we changed the mris_calc and mri_glmfit files with the new ones (8.2MB / 15.8MB). Can you please help with this ? Thank you in advance, Sincerely, Alex.

4 29

(no subject)
by Hugh Pemberton 04 Dec '12

04 Dec '12

Hi, I have just received this error after a recon-all subjid- ___ all : ERROR: _FindFacePath: could not find path! /home/hughp/freesurfer/subjects/B______________/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated cp ../surf/lh.orig_corrected ../surf/lh.orig Linux naoshi-WS 3.2.0-32-generic #51-Ubuntu SMP Wed Sep 26 21:33:09 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s B______________ exited with ERRORS at Thu Nov 15 11:40:44 EST 2012 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Many thanks in advance, Best, Hugh

2 7

Re: [Freesurfer] functional ROI analysis
by Douglas Greve 04 Dec '12

04 Dec '12

Hi Susan, ok, I see what you are doing now. Let's do it this way: 1. First transfer your label to the volume: mri_label2vol --temp example_func.nii --reg anat2exf.register.dat --proj 0 1 .1 --hemi lh --label lh.your.label --o yourlabel.func.nii 2. Then run segstats: mri_segstats --i cope2.nii --seg yourlabel.func.nii --mask zstat1.nii --maskthresh 2 --masksign abs --o sum.dat The cope and the zstat are now volumes. doug On 11/26/12 8:26 PM, Susan Alice McLaughlin wrote: > Hi Doug, > > Thanks for the quick answer. Sorry to be dense, but does this need > somewhere to include registration matrix, anat2exf.register.dat, to > register to the subject's surface? > > And at this point in the analysis, the feat folder does not include > copes and zstats separated out by hemisphere, although there are > zstat[#].surf.lh.w and .rh.w files in the main feat folder. > > Again, sorry for my limited understanding of file structure. > > Susan > > > On Mon, 26 Nov 2012, Douglas N Greve wrote: > >> Hi Susan, you can't use func2roi-sess. You'll have to put together some >> commands, but it should not be too hard, something like >> >> mri_segstats --i lh.cope2.nii --slabel subjectname lh your.label --mask >> lh.zstat1.nii --maskthresh 2 --masksign abs --o sum.dat >> >> where zstat1 is your all/nothing contrast sampled onto the surface and >> cope2 is some other contrast sampled on the surface. >> You can do this for each subject, then run asegstats2table giving it >> paths to all of your sum.dat files >> >> doug >> >> >> >> >> On 11/26/2012 07:01 PM, Susan Alice McLaughlin wrote: >>> Hi, >>> >>> I am hoping do a surface-based functional ROI analysis on >>> subject-specific ROIs that are both defined structurally and are >>> masked by an all/nothing functional contrast. func2roi-sess seems >>> perfect for this except that my data are not in an FS-FAST >>> data/analysis structure, but are instead pre-processed and >>> preliminarily analyzed using FSL and mapped to the surface using >>> reg-feat2anat. >>> >>> Is there any way to pass my original analysis into func2roi-sess? I >>> tried using: >>> >>> func2roi-sess -roidef LH_ant_STG_soundthresh2 -analysis >>> 1012_Run4_featFULLrev.feat/stats/zstat4.nii.gz -anatlabel lh_ant_STG >>> -maskcontrast 1012_Run4_featFULLrev/stats/zstat16.nii.gz >>> -maskthreshold 2 -s 1012 -d >>> >>> but get "ERROR: cannot find any sessions." >>> >>> Or is there another tool more appropriate for what I am trying to >>> do? I am looking at mri_segstats, but my hand-drawn ROIs (drawn on >>> fsaverage in tksurfer and morphed to each subject using >>> label_2_label) are in .label format and are on the surface. >>> >>> Thanks in advance for and advice or suggestions. >>> >>> Susan McLaughlin >>> Doctoral Candidate >>> SPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex) >>> Dept. of Speech and Hearing Sciences >>> University of Washington >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to >> whom it is >> addressed. If you believe this e-mail was sent to you in error and >> the e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to >> you in error >> but does not contain patient information, please contact the sender >> and properly >> dispose of the e-mail. >> >> > > Susan McLaughlin > Doctoral Candidate > SPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex) > Dept. of Speech and Hearing Sciences > University of Washington > >

3 2

flipping surface data
by kelsi 04 Dec '12

04 Dec '12

Hi Freesurfers, Is there a tool to flip the orientation of surface data to the opposite hemisphere? We are working with stroke patients, and I would like to do analysis of the contralesional hemisphere of all the patients. However, this requires putting them on the same hemisphere for ttests, etc. I saw an earlier thread online about a program for flipping in the works, I was just wondering if this is now possible? Thank you! Kelsi

3 3

question on invoking partial volume calculations in freesurfer 4.3
by John Drozd 30 Nov '12

30 Nov '12

Hello, My freesurfer version is freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0 I noticed that the aparc+aseg.mgz label map is resampled to 1mm x 1mm x 1mm voxels, eventhough the .mgz grayscale mri image file remains as per the original voxel size and is not 1x1x1. mri_convert .nii to .mgz translates the grayscale image down the y direction in the horizontal plane transverse/axial slices. I noticed that the aseg.stats files list the number of voxels and the volume, and these numbers match because the voxel size is 1 x 1 x 1. My question is whether freesurfer 4.3 can be invoked to perform partial volume error corrections, and if so how do you invoke this feature? My interests lie in segmentations of the lateral ventricles including their posterior and inferior horns. thank you, john

2 2

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 November 2012