Freesurfer July 2010

freesurfer@nmr.mgh.harvard.edu

101 participants
140 discussions

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

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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

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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

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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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A question on mis-classified cortical gray matter
by caoaize 21 Jul '10

21 Jul '10

Hello FreeSurfer Experts, I met a problem on cortex gray matter segmentation. In my case, a small part of gray matter is lost, i.e. they are classifed as CSF but not gray matter. I attached a picture here, where the problem area is highlighted by blue circle. Does someone have experience on how to check and improve cortex area segmentation? Can I manually editing? Any feedback will be very appreciated. Aize _________________________________________________________________ MSN十年回馈，每位用户可免费获得价值25元的卡巴斯基反病毒软件2010激活码，快来领取！ http://kaba.msn.com.cn/?k=1

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Creating aparc.a2009s+aseg.mgz for the averaged data
by liang wang 19 Jul '10

19 Jul '10

Hi, When I use make_average_subject to generate an average data, I can't find aparc.a2009s+aseg.mgz within the new average/mri. To get common parcellation to all subjects, I need to create this file. I understand that " mri_aparc2aseg --s average --a2009s " enable to perform what I want. However, when running this command, a error message shows up "ERROR: cannot find /drive3/Stammer/Thickness/average/mri/ribbon.mgz". As displayed by this message, I did not find the ribbon.mgz file. I don't konw how to figure out this problem. Any suggestions? By the way, my make_average_surface file is updated by Nick's new one. And it does not include ribbon.mgz before updating. 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

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2009 Destrieux Parcellation on pre 4.5 recons
by Michael Waskom 19 Jul '10

19 Jul '10

Hi Experts, Is there any reason one should not generate the 2009 Destriuex parcellation for brains that were recon-ned with earlier versions of Freesurfer? (ie using recon-all with -cortparc2 and -parcstats2 while in the 4.5 environment) Thanks! Cheers, Mike

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Grey matter discrepancy between mris_anatomical_stats and sum of lh/rh.aparc.stats
by Matthew Ku 19 Jul '10

19 Jul '10

Dear Freesurfer Experts, When in the process of analyzing grey matter volumes, I have found that the totals from the summing of the lh.aparc.stats and rh.aparc.stats do not match with the total grey matter volume found from the mris_anatmoical_stats command. Does anyone know which value is more accurate in terms of grey matter volume? Thanks, _________________________________________ Matthew Ku University of Pennsylvania School of Engineering Class of 2013 (845) 596-3840 mattku(a)seas.upenn.edu

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ROI with mri_label2vol
by Arslan, Ali 19 Jul '10

19 Jul '10

Hi, I'm trying to create a ROI of V1 from the labels (for each hemisphere) I defined. I was able to create an volume with the command below mri_label2vol --label $SUBJ/label/lh.v1.ali.label --label $SUBJ/label/rh.v1.ali.label --temp $SUBJ/mri/T1.mgz --reg $SUBJ/stats/register.dat --fillthresh 0.5 --o $SUBJ/ROI/test_v1_T_000.bshort What I want are these 1) This command gives me an ROI which includes the gray matter but I want a smoother ROI which also has some nearby white matter voxels so that I make sure ROI doesn't leave any V1 voxel out for my functional analysis later on. I looked at the --proj flag for this but couldn't find any explanation about it. Would it help me about this? Where can I find more information about it? Would changing --labvoxvol make sense? 2) The resulting ROI is not binary and I would like to make it so (actually left and right hemispheres are in different densities, e.g. one seems lighter and the other one is darker in my viewer). Can I output the volume as binary from mri_label2vol or should I convert it later on (and how)? Best, Ali

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fsaverage label into MNI mask
by Esther Walton 19 Jul '10

19 Jul '10

Hi, I want to turn a fsaverage-label (lh.DLPFC.label) into a mask (nifti) in MNI space and used these two commands: 1) To turn the label into a volume (within $SUBJECTS_DIR): mri_label2vol --label lh.DLPFC.label --subject fsaverage --temp ./fsaverage/mri/brainmask.mgz --o left_DLPFC_july19b.nii.gz --identity 2) To turn the DLPFC nifti into MNI space: mri_vol2vol --mov left_DLPFC_july19b.nii.gz --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --o left_DLPFC_MNI_july19b.nii.gz --interp nearest --reg $FREESURFER_HOME/average/mni152.register.dat However, even though the final output file is in MNI, the ROI doesn't align with the MNI152 brain. Could it be that the FSL and the FS MNI152 brain are not the same and therefore the registration file is not the right one to use? Thanks for your help, Esther _________________________________________________________________ The New Busy think 9 to 5 is a cute idea. Combine multiple calendars with Hotmail. http://www.windowslive.com/campaign/thenewbusy?tile=multicalendar&ocid=PID2…

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Freesurfer July 2010