Freesurfer November 2011

freesurfer@nmr.mgh.harvard.edu

110 participants
165 discussions

Number of maximal permutations / pooled variance estimates
by Jürgen Hänggi 30 Nov '11

30 Nov '11

Dear FS experts I have a question regarding the number of maximal permutations. I compare a single patient versus a group of six control subjects. Intuitively, I guess that only six different permutations are possible. However, when running 100 permutations in FS with mri_glmfit-sim, I get different results for each permutations as confirmed in the CSD file. So, I am not sure any longer whether the permutations are built by permuting the subjects or anything else. The other question is how mri_glmfit estimates the variance. Because I have only one subject in the patient group, there is not variance in that group and therefore I guess mri_glmfit used pooled (across both groups) estimates of variance, isn't it? Any comment is highly appreciated Thanks in advance Best regards Jürgen ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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bugs fix
by Knut J Bjuland 30 Nov '11

30 Nov '11

Which of the files in ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86… should be download and added to Freesurfer 5.1 to fix bug? Knut J

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bbregister - measure of consistency
by Joana Braga Pereira 30 Nov '11

30 Nov '11

Dear Doug and Freesurfers, I have a structural MRI and DTI set of images that i've corregistered (individually) using bbregister. My mincost files show a value that varies between 0.1 and 0.2 for all subjects. I read the paper by Grieve et al., 2009 Neuroimage and was wondering whether it is correct to explain in the current paper that i'm writting that the values of my mincost files are the result of calculating AAD, which is a measure of registration consistency. I was planning on presenting the above values as a proof that bbregister performed an accurate registration between my MRI and DTI images. Is this correct? Many thanks for your help! Joana

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Re: [Freesurfer] Brain Volume measures
by Douglas N Greve 30 Nov '11

30 Nov '11

That is basically correct. mri_segstats uses the same functions internally that mris_volume and mris_wm_volume use. doug Alexopoulos, Dimitrios wrote: > Just for clarification, the surface-based cortical GM volumes in the 'aseg.stats' file are calculated using: > mris_volume hem.pial AND mris_volume hem.white > For each hemisphere, determine the total volume inside the pial surface and subtract > the total volume inside the white surface. > > Cortical WM volumes in the 'aseg.stats' are determined using" > mris_wm_volume subject hem > > Is this correct? > > Jim > > > > ________________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve(a)nmr.mgh.harvard.edu] > Sent: Wednesday, November 30, 2011 11:46 AM > To: Jeff Sadino > Cc: andrei.sherstyuk; skogachi(a)gmail.com; freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Brain Volume measures > > Hi Jeff, the total cortical gray matter is based on the volume between > the white and pial surfaces. The other structures you mention below are > based on the automatic volume segmentation. > doug > > Jeff Sadino wrote: > >> Hello, >> >> Thank you Bruce and Doug for your answers to my previous question >> about a bad talairach.lta file. I am now grabbing volumes using >> fs5.0.0 and would like to ask for clarification. On the Morphometry >> Stats page >> at http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats, it says >> that the cortex is based on the pial surface. I am wondering what >> this includes. I loaded up the pial surface in tkmedit along with >> aseg.mgz. It looks like the following regions are completely outside >> the pial surface: cerebellum, 4th ventricle, Brain-Stem, optic chiasm. >> Is it correct that these regions are excluded? And then it looks >> like the hippocampus, amygdala, and inferior-lateral-ventricle are >> only halfway outside the pial surface. Is that correct? If it is, >> then is there a recommended way to exclude the hippocampus, amygdala, >> and inferior-lateral-ventricle regions in the cortical gray matter? >> Do these regions get properly accounted for in the subcortical gray >> calculation? >> >> And then for the white matter, the webpage says that it is based on >> the white surface. Looking at the white surface (lh.white), all of >> the subcortical gray matter and ventricles are enclosed in the >> surface. Can someone explain how the subcortical gray gets excluded? >> >> Finally, for the SubCortGray reported in aseg.stats file, does that >> exclude the following areas: >> Left-Lateral-Ventricle >> Left-Inf-Lat-Vent >> 3rd-Ventricle >> 4th-Ventricle >> CSF >> Left-vessel >> Right-Lateral-Ventricle >> Right-Inf-Lat-Vent >> Right-vessel >> 5th-Ventricle >> Left-Cerebellum-White-Matter >> Right-Cerebellum-White-Matter >> WM-hypointensities >> >> What about the brain stem? Why is the cerebellum Gray Matter >> included? I ask because the only way I can get close to the >> SubCortGray by using the aseg file is by excluding those regions. >> >> Once again, thank you for your invaluable help! >> Jeff Sadino >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. > > > The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email. > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Surface Area from mri_surfcluster versus mri_segstats
by MCLAREN, Donald 30 Nov '11

30 Nov '11

I've noticed that if I run mri_surfcluster to produce a label file, then merge the labels into a single label using mri_mergelabels, then mri_segstats with the slabel option with the fsaverage subject; I get different surface areas from mri_surfcluster (summed all the cluster areas) and mri_segstats (1 area). Is there something wrong with my implementation of these three commands or is it expected that the two methods would produce different values? Best Regards, Donald McLaren ================= D.G. McLaren, Ph.D. Postdoctoral Research Fellow, GRECC, Bedford VA Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email.

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Freesurfer projecting vector results for segmented cortical regions
by Weisinger, Brian (NIH/NIMH) [F] 30 Nov '11

30 Nov '11

hello we are trying to project a vector of results for segmented cortical regions (i.e., ... "lh_middletemporal_thickness" 0.000757119 "rh_middletemporal_thickness" 8.06E-05 "lh_parahippocampal_thickness" -0.000510407 "rh_parahippocampal_thickness" 0.000625997 "lh_pericalcarine_thickness" 0.000499749 "rh_pericalcarine_thickness" 0.000903678 "lh_superiortemporal_thickness" 0.001732855 "rh_superiortemporal_thickness" 0.000184256 "lh_temporalpole_thickness" 0.001075362 "rh_temporalpole_thickness" -0.000381165 "lh_transversetemporal_thickness" 0.000558122 "rh_transversetemporal_thickness" 6.65E-05 ...) however, we are unsure of how to do this. so, our question is— what is the sequence of steps we need to take to visualize our results on the segmented 3D template in tksurfer. Thanks for your help, Brian Weisinger

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Surface X, Y, Z to Tailarach or Volume Index
by Frank Leone 30 Nov '11

30 Nov '11

Dear all, I wrote my own function to show the 3D surfaces in Matlab, works splendidly. I now however want to be able to point out Tailarach/MNI coordinates on the 3D surface. I however only have the x, y, z format that is saved in the asc files, which is just where a certex is located in space, with no relation to the original brain whatsoever. The only thing I can retrieve is the vertex index (because that's in the asc file). How can convert the 3D X, Y, Z values (the same values you get in the console if you click on a point on the surface in tksurfer) to either Vertex RAS/Talairach or Volume index? I read the information on conversions between surface Talairach and Volume Index, that works, but this case is different: I am actually referring to the 3D locations of the vertices. Hopefully someone can help me, thanks a lot in advance, best, Frank

2 1

cortical thickness values in a specified gyrus...
by Gonzalo Rojas Costa 30 Nov '11

30 Nov '11

Hi: In rh.aparc.a2009s.stats file, appears the average cortical thickness (ThickAvg) value for frontal middle gyrus (G_front_middle): how can I get the values of the cortical thickness in that gyrus (for example), not the average value ?... Sincerely, Gonzalo Rojas Costa

3 2

persistent bvecs error
by Alexander Lebedev 30 Nov '11

30 Nov '11

Dear Freesurfer users and developers, I decided to run Tracula with our DTI data and eventually got bvecs error. I tried different solutions without any results: added decimals after zeros, shortened all decimal points to 3, modified my locale - nothing helped. I'm providing you my trac-all log, original (with shortened and long decimal points: MMADI_C* ) and output bvecs- and bvals-, parameter file and my locale as well. [Workstation: CentOS 5.6 x86_64] Any advises and suggestions are very welcome... Thank you beforehand. --- Best Regards, Alex Lebedev Stavanger University Hospital, Norway P.S.: And one short question... I was just thinking that it might make sense to perform some of the preprocessing steps in FSL (considering that FS and FSL share these algorithms and the preprocessing for TBSS ran perfectly), but I didn't find any solution on this. Is there such an opportunity? *** LOCALE: LANG=en_US.UTF-8 LC_CTYPE="en_US" LC_NUMERIC="en_US" LC_TIME="en_US" LC_COLLATE="en_US" LC_MONETARY="en_US" LC_MESSAGES="en_US" LC_PAPER="en_US" LC_NAME="en_US" LC_ADDRESS="en_US" LC_TELEPHONE="en_US" LC_MEASUREMENT="en_US" LC_IDENTIFICATION="en_US" LC_ALL=en_US

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Re: [Freesurfer] FSGD file with two set of regressors adding up to 1
by Douglas N Greve 30 Nov '11

30 Nov '11

Hi Orjan, it looks like there are some errors in your design. The "Variables" function is only for continuous variables (covariates) such as Age. Sex and diagnosis are discrete variables and they should be coded as part of the class (eg, if you only wanted to add sex, then you'd have 4 classes Q1-Q4 for males and the same for females). doug Ørjan Bergmann wrote: > Dear Dr. Greve, > > I have been working with FreeSurfer for a while now, amongst others in > collaboration with my colleague Dr. Lars-Morten Rimol here in Oslo. We > have contected you on issues relating to FreeSurfer before, and hope > you have some insights as to how to deal with a particular problem > we've come across. > > We have a set of subjects divided into four groups, depending on how > they score on a particular test; the first group are those scoring in > the lower 25% (i.e. Q1), those scoring from 25-50% (Q2), etc. Each of > these groups additionally belong to one of 3 diagnostic groups; Scz, > BD and NOS. > > We have formulated this as a FSGD file: > Class Q1 > Class Q2 > Class Q3 > Class Q4 > Variables Age Sex Scz BD NOS > > We are interested in seeing if, when correcting for the age, sex and > diagnosis, there are differences between the groups. E.g. a contrast > vector would be [1 -1 0 0 0 0 0 0 0]. > > The problem is of course that the resulting design matrix resulting > from this FSGD file becomes singular since its first 4 colums and its > 3 columns each add up to 1. Clearly this design matrix is singular. > > In the context of FSGD-files, do you know of any other way to solve > this problem? > > --- > Mvh > Ørjan Bergmann, PhD > Post. Doc. > TOP-prosjektet > Universitetet i Oslo > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Freesurfer November 2011