Freesurfer

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30132 discussions

Freesurfer failure with diseased brains
by H. Reynolds 23 Jul '10

23 Jul '10

Hi, I've been using Freesurfer's 'recon-all' function to process T1 datasets of healthy age-matched, MCI and early-onset Alzheimer's brains. It has been successful with the two healthy controls I've tried, but only half of the MCI and EAD brains work - Freesurfer fails and exits 'with errors'. We think that the reason for this may be due to the severe atrophy going on in the MCI and EAD brains, but are not sure - does anybody have any suggestions for why Freesurfer keeps failing? Thanks, Heather

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segmentation output not in alignment
by Rumana Chowdhury 23 Jul '10

23 Jul '10

Dear all I put a T1w image through the recon-all process and it completed without errors, but the segmentation output (aparc.a2009s+aseg) does not line up with the subjects own brain.mgz or orig.mgz. I have had a similar problem with other T1w images that I've used. Any ideas why this might be and how to correct? Many thanks for your help Rumana --

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recon-all image output
by Michele Placci 23 Jul '10

23 Jul '10

Dear experts, we run this command in a file of MRI 3D .nii : recon-all -force -all -notal-check -i /my_directory_input/my_file.nii -subjid my_directory_output and i get the attached image of output for a single time point, after 40 hours of elaboration. We don't understand why there isn't the right side of the brain. Any suggestions? Thank you all.

3 4

Registration with fsaverage
by Corey Keller 22 Jul '10

22 Jul '10

Hi Freesurfers, I am trying to check the spherical alignment of an individual subject registered to fsaverage via lh.sphere.reg. I am using the following command in tksurfer: tksurfer CL lh sphere and get the error code below. Could someone let me know what I am missing here? Should I be using tkregister2 instead? And if so, what is the correct command to use? Also, it says it can't find the talairach file but talairach.xfm is in the subject's transform folder. Thanks in advance. Best, Corey Resting_State/subjects> tksurfer CL lh sphere surfer: current subjects dir: /media/SW_Preload/Users/Corey/ckeller/Research/Resting_State/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /media/SW_Preload/Users/Corey/ckeller/Research/Resting_State/subjects surfer: Reading header info from /media/SW_Preload/Users/Corey/ckeller/Research/Resting_State/subjects/CL/mri/T1.mgz surfer: vertices=118989, faces=237974 can't find talairach file '/media/SW_Preload/Users/Corey/ckeller/Research/Resting_State/subjects/CL/surf/../mri/orig/COR-.info/../transforms/talairach.xfm' mrisReadTriangleFile(/media/SW_Preload/Users/Corey/ckeller/Research/Resting_State/subjects/CL/surf/lh.orig): surface doesn't match /media/SW_Preload/Users/Corey/ckeller/Research/Resting_State/subjects/CL/surf/lh.sphere No such file or directory mrisReadTriangleFile failed. No such file or directory MRISreadOriginalProperties: could not read surface file /media/SW_Preload/Users/Corey/ckeller/Research/Resting_State/subjects/CL/surf/lh.orig No such file or directory WARNING: No colortable found! surfer: double buffered window surfer: tkoInitWindow(CL) surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... mrisReadTriangleFile(/media/SW_Preload/Users/Corey/ckeller/Research/Resting_State/subjects/CL/surf/lh.white): surface doesn't match /media/SW_Preload/Users/Corey/ckeller/Research/Resting_State/subjects/CL/surf/lh.sphere mrisReadTriangleFile failed.

2 1

strange result in qdec and mri_glmfit
by Joana Braga Pereira 22 Jul '10

22 Jul '10

Dear Freesurfer experts, I've just finished running a qdec analysis of a comparison of cortical thickness between controls and patients with 2 covariates and found a strange result. When i set the threshold at FDR some clusters appear in red which are the corrected results from my analysis. However the rest of the cortex acquires a grey homogeneous colour that seems strange. When i check the thresholds in qdec i found that they were set from 100 to -100... Any ideas why this happened? Afterwards i did the mri_glmfit simulations with these results from qdec and saw that the summary cluster table indicated a single bilateral cluster of more than 70 000 mm size, as if the program considered the homogenous grey colour as a significant result between groups. Any help would be greatly appreciated. Best, Joana

2 1

Creating a label
by liang wang 22 Jul '10

22 Jul '10

Hi, I can create a label file from either ?h.aparc.annot (using mri_annotation2label) or aparc+aseg.mgz (using mri_cor2label). However, I find the two same label are shown different using tksurfer. Specifically, the label created by mri_annotation2label display compact and clear, whereas one obtained by mri_cor2label seemingly includes more tiny, disperse vertices. Does anyone know what's happening? Thanks. Liang -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wanglbit(a)gmail.com

2 1

Segmentation fault during mri_segment
by Diandra Lucia 21 Jul '10

21 Jul '10

Hi again, As we process more cases, we've run into four cases that have had the same problem. Each has segfaulted during mri_segment during autorecon2; here is one example: #@# Mask BFS Mon Jul 19 23:38:35 EDT 2010 /home/pnlstaff/freesurfer/subjects/case2403/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Mon Jul 19 23:38:41 EDT 2010 mri_segment brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (105.0): 105.7 +- 6.1 [80.0 --> 125.0] GM (72.0) : 71.1 +- 8.6 [30.0 --> 96.0] setting bottom of white matter range to 79.6 setting top of gray matter range to 88.2 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 12443 sparsely connected voxels removed... thickening thin strands.... Segmentation fault Linux compute-2-7.local 2.6.9-34.ELsmp #1 SMP Fri Feb 24 16:56:28 EST 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Mon Jul 19 23:40:24 EDT 2010 They all segfaulted at exactly the same place. These were run with freesurfer-Linux-rh9-stable-pub-v4.2.0 (without the new version of the mri_ca_normalize you sent me recently). Please let me know if you need anything else (data, etc) to help troubleshoot this. Thanks, Diandra -- Diandra Lucia Research Assistant Project Coordinator INTRuST Neuroimaging Leadership Core Psychiatry Neuroimaging Lab, BWH 1249 Boylston St., Boston, MA 02115 email: diandra(a)bwh.harvard.edu phone: 617-525-6118 cell: 602-332-7013

2 1

problems with mri_label2vol
by Mario Ortega 21 Jul '10

21 Jul '10

Hi, I am a freesurfer user at Washington University. I am attempting to return aseg+aparc into native space to implement the images into another pipeline. My native space is 256x256x176 1mm^3 voxels. mri_label2vol does not accomplish this to the raw_avg or the 001.mgz in the subjects orig directory. However mri_vol2vol does convert the brainmask into the appropriate space. I used this webpage as reference. http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat attached is a screen capture. Thanks, Mario

2 1

3-Way Anova in Qdec
by Jeff Sadino 21 Jul '10

21 Jul '10

Hello, I would like to be able to do 3-way anova in qdec, freesurfer version 4.3.1 and measure the cortical thickness and volume. Is this possible? I have 3 discrete factors, each with two levels: age group: less/more than 50 HIV: yes/no Alzheimers: yes/no When I try to click on the third discrete factor in the qdec design tab, it deselects one of the others. Does it max out at two? Thank you very much, Jeff Sadino

2 1

mri_glmfit weighted random effects
by Shanqing Cai 21 Jul '10

21 Jul '10

Hi, I have a question about the "weighted random effects" option in the "mri_glmfit" command. Are there any specific references (papers or books etc.) for that approach, i.e., using contrast variance images to weigh the contrast images in a second-level analysis. Also, would it be possible for me to access the source code of that particular module ("mri_glmfit") to see how the algorithm is implemented? The FreeSurfer source that used to be accessible from the ftp server (surfer.nmr.mgh.harvard.edu) is not only there for some reason. Thank you very much! Best regards, Shanqing Cai

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