Freesurfer March 2010

freesurfer@nmr.mgh.harvard.edu

101 participants
153 discussions

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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fixing bad tal registrations
by Garth Coombs 16 Mar '10

16 Mar '10

Hi, I recently ran into a problem with some of my tal registrations during the recon-all process (see below message to Martino's Tech). In order to fix the problem, it was suggested that we run bbregister outside of the recon-all stream and then feed that registration into the subsequent recon stages. Does this make sense, and how would I go about doing this? I'm not sure what the --mov file should be, or if there is a way to specify fstal as the reference structural. Thanks for your help! -Garth Hi Doug & FreeSurfers, I recently re-ran a large number of recons and have been checking to make sure they all ran correctly, and I have come up with a couple of questions about the talairach transform/recon checking. For some of my recons, the green line outlining the white matter on the individual brain extends slightly further than the cortex surface of the fstal brain. While it looks relatively well aligned (e.g. ventricles, brain stem), the fstal brain looks slightly too small for the subject's brain. Additionally, the green outline tends to extend into the skull of fstal in the sagittal plane. An example is: setenv SUBJECTS_DIR /autofs/space/brownie_003/users/gcoombs/ SUBJECTS_DIR/ tkregister2 --mgz --fstal --surf orig --s amac_anat or tkregister2 --mgz --fstal --surf orig --s amra_anat In order to fix these talairach transforms, it seems like the best option would be to scale the brain; however, we will be doing a cortical thickness analysis on this group, and we do not want to scale the brain if it will somehow affect the outcomes. Is this something we should worry about? Another question we have is about general recon quality control: when checking that the recons ran smoothly, what should we look for? I look to make sure that the pial and white matter surface lines don't include dura or any other matter and that they follow the structures correctly, skull stripping, and intensity normalization, but is there anything else that is particularly important? Any advice would be greatly appreciated! Thanks, Garth

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DTI Analysis
by Ryan 16 Mar '10

16 Mar '10

Hello all, I'm doing a volumetric group analysis of DTI data and am now stuck. I ran mri_preproc, mri_info, and mri_glmfit to create sig.mgh. I run the following command and load sig.mgh as an overlay: tkmedit fsaverage brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white I'm wondering if this is the correct usage for the sig.mgh file, and if someone could point me in the right direction for what steps are next? Thank you. -Ryan

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Correction at the cluster level in Freesurfer
by Olivier Colliot 16 Mar '10

16 Mar '10

Hi Freesurfers, I was wondering if there exists a procedure in Freesurfer to have corrections for multiple comparisons at the cluster level (as in SPM for example). Many thanks Olivier

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optseq2 installation
by Florence POMARES 16 Mar '10

16 Mar '10

Forget the previous message, we can run it now. Thank you for your response De : Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Date : 15 mars 2010 18:51:19 HNEC À : Florence POMARES <florence.borgetto(a)univ-st-etienne.fr> Cc : freesurfer(a)nmr.mgh.harvard.edu Objet : Rép : [Freesurfer] optseq installation what do you mean it is not recognized? To make it executable, you need to run chmod a+x optseq2 to run it, either put it into your PATH, or cd to where it is located and run ./optseq2 the "./" is necessary if it is not in the PATH doug Florence POMARES wrote: Dear Doug, Thank you for your answer. We run it from shell (a comand window of X11 because we are connected to the server by the way of a MacIntosh) but it isn't recognized. How can we make it executable ? We just upload optseq2 on the Linux server... Le 12 mars 10 à 20:30, Florence POMARES a écrit : Début du message réexpédié : *De : *Douglas N Greve <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu >> *Date : *12 mars 2010 20:09:57 HNEC *À : *Florence POMARES <florence.borgetto(a)univ-st-etienne.fr <mailto:florence.borgetto@univ-st-etienne.fr >> *Cc : *freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu > *Objet : **Rép : [Freesurfer] optseq installation* Did you make it executable? They are run from the shell, not matlab. doug Florence POMARES wrote: Dear Optseq Developpers, Few years ago we used to design our paradigm with optseq. We would like to use it again but we can't install it. We went on the web site : http://surfer.nmr.mgh.harvard.edu/optseq/ we download the linux version 2 we upload it to the our old linux server with matlab optseq and optseq2 aren't recognize as command. we also tried to install the cywin version on a PCwindows with cygwin and matlab. but when we execute the optseq2.exe it says that it doesn't find the input point of _isnand in the library of the dynmic links cywin1.ddl we don't know what to do. would you please help us ? thank you

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Freesurfer March 2010