Freesurfer July 2010

freesurfer@nmr.mgh.harvard.edu

101 participants
140 discussions

different rotation matrix from same DICOM
by Xu, Jun 15 Jul '10

15 Jul '10

Hi, I found out something that I do not understand when I was trying to create rotation matrix from scratch. I have used two methods and hope they will give me the same results. 1st method---form matrix from cross product as described in http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_p… for example: -0.9994 0 0.0343 0.0153 -0.8953 0.4451 0.0307 0.4454 0.8948 I use formed rotation matrix * D (voxel size) --- I got exactly same affine matrix (1:3) as the one in nifti header. However, I tried another method since I would like to use normal vector if there is no row and col vector directly available in DICOM header. 2nd method --- form matrix from vox2ras_rsolveAA.m I got the matrix has the wrong signs although the numbers are exactly same. It cannot be simply apply some (making sensed) unity matrix for the correction (I have already correct normal vector for the sake of the requirement in 1st method ---- reverse the sign for the first 2 row in normal vector, if I do not correct it, the matrix is still not same). For example: 0.9994 -0.0000 0.0343 -0.0153 -0.8953 0.4451 -0.0307 0.4454 0.8948 I was wondering if you would know the reason for it. Thanks, Jun

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Re: [Freesurfer] iPhone app
by Bruce Fischl 14 Jul '10

14 Jul '10

Hi All, I wanted to draw your attention to a new iPhone app that uses FreeSurfer segmentations written by Pedro Paulo de Magalhães Oliveira Junior. You can get it at; http://itunes.apple.com/WebObjects/MZStore.woa/wa/viewSoftware?id=381072423… I think surfaces are coming in future versions, and PPJ (ccd) welcomes comments and suggestions. cheers, Bruce

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selxavg-sess with number of conditions error
by Gabriel A. Tobon 14 Jul '10

14 Jul '10

Hello, I have event related data with 69 different conditions, and every condition does not appear in every run. This causes selxavg-sess to throw an error. Part of the relevant debug output is below. Why does every condition need to appear in every run? Thank you, Gabe echo "$sess " | & tee -a $LF echo /mindhive/nklab/projects/eightcat-cluster/gtobon_analysis/8cat-ev2-final/data/kan_ecev_207ab tee -a /mindhive/nklab/projects/eightcat-cluster/gtobon_analysis/8cat-ev2-final/analysis/log/selxavg3-sess-bold-mc_analyze-100714181048.log /mindhive/nklab/projects/eightcat-cluster/gtobon_analysis/8cat-ev2-final/data/kan_ecev_207ab date | & tee -a $LF date tee -a /mindhive/nklab/projects/eightcat-cluster/gtobon_analysis/8cat-ev2-final/analysis/log/selxavg3-sess-bold-mc_analyze-100714181048.log Wed Jul 14 18:10:48 EDT 2010 if ( ! -d $sess ) then if ( ! -d /mindhive/nklab/projects/eightcat-cluster/gtobon_analysis/8cat-ev2-final/data/kan_ecev_207ab ) then set funcdir = $sess/$fsd set funcdir = /mindhive/nklab/projects/eightcat-cluster/gtobon_analysis/8cat-ev2-final/data/kan_ecev_207ab/bold set anadir = $sess/$fsd/$analysisname set anadir = /mindhive/nklab/projects/eightcat-cluster/gtobon_analysis/8cat-ev2-final/data/kan_ecev_207ab/bold/mc_analyze if ( $#OutParent == 0 ) then if ( 0 == 0 ) then set anadir = $sess/$fsd/$analysisname set anadir = /mindhive/nklab/projects/eightcat-cluster/gtobon_analysis/8cat-ev2-final/data/kan_ecev_207ab/bold/mc_analyze else else echo anadir = $anadir | tee -a $LF echo anadir = /mindhive/nklab/projects/eightcat-cluster/gtobon_analysis/8cat-ev2-final/data/kan_ecev_207ab/bold/mc_analyze tee -a /mindhive/nklab/projects/eightcat-cluster/gtobon_analysis/8cat-ev2-final/analysis/log/selxavg3-sess-bold-mc_analyze-100714181048.log anadir = /mindhive/nklab/projects/eightcat-cluster/gtobon_analysis/8cat-ev2-final/data/kan_ecev_207ab/bold/mc_analyze if ( -e $anadir && $DoGLMFit ) then if ( -e /mindhive/nklab/projects/eightcat-cluster/gtobon_analysis/8cat-ev2-final/data/kan_ecev_207ab/bold/mc_analyze && 1 ) then echo "analysis $analysis alread exists for $sessbase" | tee -a $LF echo analysis mc_analyze alread exists for kan_ecev_207ab tee -a /mindhive/nklab/projects/eightcat-cluster/gtobon_analysis/8cat-ev2-final/analysis/log/selxavg3-sess-bold-mc_analyze-100714181048.log analysis mc_analyze alread exists for kan_ecev_207ab if ( $Skip == 0 && $Overwrite == 0 && ! $monly && ! $perrun && ! $jkrun ) then if ( 0 == 0 && 0 == 0 && ! 0 && ! 0 && ! 0 ) then echo "ERROR: analysis $analysis already exists. You must " | tee -a $LF echo ERROR: analysis mc_analyze already exists. You must tee -a /mindhive/nklab/projects/eightcat-cluster/gtobon_analysis/8cat-ev2-final/analysis/log/selxavg3-sess-bold-mc_analyze-100714181048.log ERROR: analysis mc_analyze already exists. You must echo " specify whether to -skip or -overwrite" | tee -a $LF echo specify whether to -skip or -overwrite tee -a /mindhive/nklab/projects/eightcat-cluster/gtobon_analysis/8cat-ev2-final/analysis/log/selxavg3-sess-bold-mc_analyze-100714181048.log specify whether to -skip or -overwrite exit 1 ; exit 1

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creating binary masks for any given structure in aseg.mgz or aparc+aseg.mgz
by Mehul Sampat 14 Jul '10

14 Jul '10

Hi Folks, I would like to create binary masks for any given structure in aseg.mgz and aparc+aseg.mgz. I would then also like to map the masks back to native space. I think, I should use mri_binarize followed by mri_convert as shown in the two examples below: Example 1: a. mri_binarize --i mri/aseg.mgz --match 10 --o deep-gm-rois/lh-thalamus.mgz b. mri_convert -rl mri/orig/001.mgz -rt nearest deep-gm-rois/lh-thalamus.mgz deep-gm-rois/lh-thalamus.nii Example 2: a. mri_binarize --i mri/aparc+aseg.mgz --match 1022 --o ctx-gm-rois/lh-postcentral.mgz b. mri_convert -rl mri/orig/001.mgz -rt nearest ctx-gm-rois/lh-postcentral.mgz ctx-gm-rois/lh-postcentral.nii Ques 1: Is the best approach for this task ? I noticed in the FAQ that mri_vol2vol is recommended for conversion from freesurfer space to anantomical space. Ques 2: Is it better to use mri_vol2vol than mri_convert with the reslice option ? Thanks Mehul

2 3

Parallel processing
by Brendan Robert Ansell 14 Jul '10

14 Jul '10

Hi FreeSurfer users, is it possible to run FreeSurfer on parallel processors? We would like to run mri_glmfit-sim in parallel to reduce the run time. Have you any experience running FreeSurfer in parallel, or would it be relatively easy to reconfigure? Any thoughts would be greatly appreciated. Thanks in advance, Brendan Ansell Melbourne University

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fieldsign-?h
by dave ma 14 Jul '10

14 Jul '10

Dear FS, after running retinotopy analysis over different subjects i d like now to compare the impact of the activation among the different areas among the subjects. The information to analyse is to find in ..user/bold/retinotopy/fieldsign, the file structure used by Freesurfer. My question is after loading the different fieldsign-?h files and reading them in matlab i got vectors of different length which is the number of the vertices containings values -1,0,1...so far so good, now i wanted to konw how to register those vertices so i can have a common base for a comparison between the different files of the different subjects. I hope someone could help Cheers Dave _________________________________________________________________ http://redirect.gimas.net/?n=M1007xHM2 Räumen Sie Ihr Postfach auf - ganz einfach mit Hotmail!

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Creating table of segmentation volumes
by liang wang 13 Jul '10

13 Jul '10

Hi, I was starting to create a table of segmentation volumes corresponding to several given label (--segno 255 i.e., CC_Anterior). However, I found the volume values for a same strucutre were different between the two files *aseg.stats and wmparc.stats*. For example, for CC_Anterior, one subject was 745 mm^3 in the aseg.stats, but 729 mm^3 in the wmparc.stats. I am not sure why they are different and which file should be selected to represent the volumes. I am appreciated for any suggestions. Best, 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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recon-all -all finished without error but didn't produce aseg.mgz files
by aekairys＠umich.edu 13 Jul '10

13 Jul '10

Hi all, I just ran recon-all -s (subject) -all for several subjects and it looked like they ran successfully, however when I went to check the data in tkmedit, I realized there were no aseg.mgz as wel as other vital files. The subject did not produce an error log. Any one else ever have this happen? Best, Anson K. University of Michigan

3 4

volume of temporal lobe, frontal lobe, etc...
by Gonzalo Rojas 13 Jul '10

13 Jul '10

Hi: How can I automatically compute, the volume of each brain lobe (temporal lobe, occipital lobe, etc) ?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica Las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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Displaying significant difference with a threshold of cluster size
by liang wang 13 Jul '10

13 Jul '10

Hi, Using mri_glmfit, I found significant between-group difference in cortical thickness in some regions. However, there are a lot regions with very small vertices surviving the given threshold. What I need to do is displaying large clusters (e.g. having 20 vertices at least) assumed as "true" difference. I don't know how to make it by a selected threshold of cluster size . Any suggestions would be appreciated. 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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Freesurfer July 2010