Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

Model setup - comparing correlations
by Martin Kavec 18 Mar '10

18 Mar '10

Hi, in my group analysis I found a significant difference in correlation of physiological parameter X and cortical thickness Y1 in an ROI. For each subject and each cortical parcel I also have a average of parameter Y2 and its correlation to X (calculated using GLM in SPSS). Y1 ~ X Y2 ~ X My question is, whether there is any meaningful approach how to test whether for any cortical parcel correlation between Y1 ~ X and Y2 ~ X are statistically different/similar? This kind of resembles me a conjunction analysis in fMRI, but I am not sure how would I test this. Also - and sorry for slight off topic - I think that SPSS should be my friend. Many thanks for suggestions, Martin

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Talairach_MNI
by Kelly Silva 18 Mar '10

18 Mar '10

Hello, I would like to know if the output coordinates from the "mri_surfcluster" command is on the MNI space or on the Talairach. Thanks in advance. Best, Kelly ____________________________________________________________________________________ Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

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q about disc space
by Janani Dhinakaran 17 Mar '10

17 Mar '10

Hello. How much space is required for running one recon-all? If I needed to work on several people's brains, say 4-5, how much memory am I likely to need? Thanks! -- I am the Sun, I know no darkness.

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segmentation using freesurfer
by Xiaoying Tang 17 Mar '10

17 Mar '10

Hi All, Is it possible to get only csf via using freesurfer to do segmentation? Best, Xiaoying

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recon-all failture
by Gabriel Go.Es. 17 Mar '10

17 Mar '10

I was trying to run a recon-all and I recibe an error message, wich you can find attached (recon-all.log), it appears to be a rpoblem with the skull stripping (the watershed) i tryed the flag -nowatershed, but the recon does not work. what can i do??? any help will be so apreciated Best Regards Gabriel ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=127,y=105, z=104, r=9864 iterations GLOBAL CSF_MIN=0, CSF_intensity=9, CSF_MAX=38 , nb = 22419 RIGHT_CER CSF_MIN=0, CSF_intensity=9, CSF_MAX=51 , nb = 1530 LEFT_CER CSF_MIN=0, CSF_intensity=9, CSF_MAX=45 , nb = 1332 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=35 , nb = 9837 LEFT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=37 , nb = 9522 OTHER CSF_MIN=2, CSF_intensity=16, CSF_MAX=47 , nb = 198 mri_watershed Error: GLOBAL region of the brain empty ! Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Mon Mar 15 09:45:02 CET 2010 _________________________________________________________________ Ahora Messenger en tu Blackberry® 8520 con Movistar por 0 €. ¿A qué esperas? http://serviciosmoviles.es.msn.com/messenger/blackberry.aspx

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Mri_aparc2aseg problems
by Alex Fornito 17 Mar '10

17 Mar '10

Hi all, I¹m really stuck on a problem I was hoping to get help with. I¹m having trouble determining the correspondence between ROIs in a surface-based annotation and those in a volume-based annotation generated using mri_aparc2aseg. I have some custom-generated surface annotations and have been using a recently updated binary of mri_aparc2aseg which adds 10,000 to the values of left hemi annotation labels and 20.000 to the right hemi labels in the converted volume, to help distinguish the two hemisphere¹s rois. To check the correspondence between the surface and volume, I chose an roi 10386 from the volume. To check it on the surface I did the following in matlab: [v,l,ct]=read_anntotation('lh.fsavg_500_compact.aparc.annot'); new=zeros(size(v)); new(find(l==ct.table(386,5)))=1; % note the roi index should be 10,000 less that of the volume. F=write_wfile('386.w',new,v); I did this for both the fsaverage surface and a single subject surface, and compared it with the volume representation for the same single subject. The attached pic called vol386 shows the roi in blue, overlaid on the volume parcellation in greyscale. It is located in the left inferior temporal lobe. The attached surf386 pic however, indicates this region is in the retrosplenial cortex for both the single subject (left) and fsaverage (right). Am I missing something here? Have I misunderstood the correspondence between surface and volume rois? Thanks for your help, Alex

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Recon-All Talairach error
by Dave Brohawn 17 Mar '10

17 Mar '10

Hello, I am working on unpacking a subject scanned in Bay 8 on Thursday, 3/11/2010. I entered recon-all -autorecon-all -s FB0011090A and after unpacking for approximately 45 minutes, it reported: Wed Mar 17 12:52:07 EDT 2010 talairach_avi done #-------------------------------------------- #@# Talairach Failure Detection Wed Mar 17 12:52:07 EDT 2010 /autofs/space/seymour_001/users/folate_subjects/FB0011090A/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0176, pval=0.0000 < threshold=0.0050) Linux seymour 2.6.18-128.7.1.el5 #1 SMP Mon Aug 24 08:20:55 EDT 2009 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Wed Mar 17 12:52:07 EDT 2010 Should I run without a talairach check if I manually look and it looks ok? Let me know, and thanks, Dave Brohawn FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4-stable-v4.5.0-20100311 RedHat release: CentOS release 5.3 (Final) Kernel info: Linux 2.6.18-128.7.1.el5 i686 NMR Center info (/space/freesurfer exists): machine: seymour SUBJECTS_DIR: /space/seymour/1/users/folate_subjects/ PWD: /space/seymour/1/users/folate_subjects ssh seymour setenv SUBJECTS_DIR /space/seymour/1/users/folate_subjects/ cd /space/seymour/1/users/folate_subjects

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mri_convert: dicom to mgh
by Chris Adamson 17 Mar '10

17 Mar '10

Hello all, I'm wondering how mri_convert computes the centre of the image (shown as ImgPos in the output of mri_convert). I have two questions: 1. I had a non-mosaic SIEMENS format DICOM volume and ImgPos was copied from (0x0020,0x0032) DS Image Position (Patient), but the X and Y values are negated, why is that? 2. How does mri_convert compute ImgPos for mosaic format SIEMENS DICOM files? Thanks in advance, Chris. -- Dr Christopher Adamson, PhD (Melb.), B Software Engineering (Hons., Monash) Research Officer Developmental and Functional Brain Imaging, Critical Care and Neurosciences Murdoch Childrens Research Institute The Royal Children’s Hospital Flemington Road Parkville Victoria 3052 Australia T 9345 4306 M XXXX XXX XXX E chris.adamson(a)mcri.edu.au www.mcri.edu.au

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a question about wmparc.stats and aseg.stats
by Guang Zeng 16 Mar '10

16 Mar '10

Hi, there, I have a question about wmparc.stats and aseg.stats, In aseg.stats, I read, # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1132816.000000, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 1156812, unitless # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1156812.000000, mm^3 In wmparc.stats, I read # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 206821.000000, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 244540, unitless # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 244540.000000, mm^3 Why the BrainSegVolNotVent and BrainSegVol are so small in wmparc.stats? Those values in wmparc.stats are the sum of what? If I want to get the correct Brain Segmentation Volume Without Ventricles, which value I should use? the one from wmparc.stats or the one from aseg.stats? Thanks! Guang _________________________________________________________________ Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID27925::T:WLMTAGL:ON:…

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using control points versus editing wm.mgz
by Mehul Sampat 16 Mar '10

16 Mar '10

Hi Folks, I understand that control points should be used to fix errors due to bad skull stripping or intensity normalization (are there any other scenarios when one should use control points ?) I followed the instructions on making corrections for issues due to intensity normalization. http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints As I understand, one can fix issues due to intensity normalization either by using control points or editing wm.mgz. I would like to only edit wm.mgz and not use control points. Is this okay ? In your experience, are there situations, where this would be a bad idea ? Thanks Mehul ps: The motivation for this is that I want to use the longitudinal processing stream and I only want to edit the base and not edit the cross-sectional time-points.

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