Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

newbie question event-related
by Sebastian Moeller 28 Aug '06

28 Aug '06

Hi List, hi Doug, for the first time I have now data, that realloy wants event-related analysis (200ms stimulation every 10 seconds). Now, using a TER of 0.2 in the para-file and using "-dt event-related" in mkanalysis-sess.new (3.0.3 pub x86_64 centos4) was the easy part, but what do I have to specify in mkcontast-sess? Especially thi "-ircorr" complex (with -deltarang and -taurange) is daunting. Is it necessary to specify anything here to get a real event-related analysis, or does fs-fast already know enough without these parameters (as I specified delta, tau and even taummax in mkanalysis)? So far any nicorr value I used produced errors on the way... I would be delighted for any pointer of how to properly convinve fs-fast to analyse my data ;). Ahoi & thanks Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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tkmedit crashes/freezes
by Derin Cobia 28 Aug '06

28 Aug '06

I've been experiencing some crashes/freezing using tkmedit lately, and have been able to reproduce it pretty reliably. It occurs when I scroll through the slices of the subject either using the arrows keys or clicking through on the toolbar. It happens when viewing a variety of volumes (brainmask, T1, etc), and from a variety of perspectives (coronal, sagittal, etc); it also happens on different subjects as well. This occurs no matter what workstation I use in the lab (networked environment). My X freezes up as well as the keyboard, but the mouse doesn't. I used to be able to restart my X remotely, but now tkmedit locks up so bad I have to reboot. Any ideas? Dell Precision 670 Workstations CentOS 4.1 (32-bit) -------- freesurfer-Linux-centos4-stable-pub-v3.0.3 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /pkg/brainmap/freesurfer FSFAST_HOME /pkg/brainmap/freesurfer/fsfast SUBJECTS_DIR /disk/k2/freesurfer/neuromorph_v1_flash/ FUNCTIONALS_DIR /pkg/brainmap/freesurfer/sessions MINC_BIN_DIR /pkg/brainmap/freesurfer/mni/bin MINC_LIB_DIR /pkg/brainmap/freesurfer/mni/lib PERL5LIB /pkg/brainmap/freesurfer/mni/lib/perl5/5.8.0 GSL_DIR /pkg/brainmap/freesurfer/lib/gsl QTDIR /usr/lib/qt-3.3 TCLLIBPATH /pkg/brainmap/freesurfer/lib/tcltktixblt/lib FSL_DIR /pkg/brainmap/freesurfer/fsl [derin@fozzy ~]$ which tkmedit /pkg/brainmap/freesurfer/bin//tkmedit cd /disk/k2/freesurfer/neuromorph_v1_flash/ Thanks in advance. -Derin

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nii header info
by Najmeh Khalili M. 28 Aug '06

28 Aug '06

Hello, I was wondering if there is a command that dumps the header information of .nii file. Also, does mri_convert transfer dti acquisition parameters (b-value, directions) from the DICOM to nifti? (Our dti sequence does write its parameters to the DICOM file.) Any pointer's appreciated. cheers, Naj

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questions about group analysis
by Ray Fix 27 Aug '06

27 Aug '06

Hello, I have some questions about doing group analysis. I know these are really basic... but everyone loves easy softballs, right? Question 1. How should I define multiple classes? The tutorial examples show two classes, male and female. If I have patient and controls, in addition to male and female, should I define it : class Patient class Control class Male class Female Variable Age Input subject1 Patient Male 24 Input subject2 Control Female 39 : or do I have to boil it down to one column?? class PatientFemale class PatientMale class ControlFemale class ControlMale Variable Age Input subject1 PatientMale 24 Input subject2 ControlFemale 39 : or should I separate these into different FSGD files? or some other way? Question 2: Best practice for a small study If I have lots of slopes, but not so many samples (<50), is it advisable to make one big FSFD file or make several small FSGD files with all those slopes? Question 3: DOSS versus DODS By staring at Doug Greve's excellent slides http:// surfer.nmr.mgh.harvard.edu/docs/ftp/pub/docs/fsgroupana.pdf I was able to figure out whad doss and dods do the design matrix. Can someone make a simple statement as when to use one instead of the other? Question 4: Multiple Comparison Section 4 of the tutorial gets into multiple comparison. I started to run the sample and realized it will probably take my computer 3 years to finish executing ;) Can someone tell me what problem this is solving for me? What is multiple comparison and where do you run into trouble by not doing it? That's all I can think of for now. Thank you. Ray PS: I did notice there is a broken link in the wiki tutorial. On the page https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ GroupAnalysis there is a link in section 3.0 that points to information about creating contrast vectors. It is broken. I think it should point to: https://surfer.nmr.mgh.harvard.edu/fswiki/ FsTutorial_2fCreateContrastVectors

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visualizing surfaces
by camilo＠nmr.mgh.harvard.edu 25 Aug '06

25 Aug '06

Hi Freesurfer, Is there a way to visualize 3 surfaces at the same time. I am trying to visualize the BEMs in my flash directory. So far, I can only load 2 of them by loading the main surface and the axiliar surface. Thanks, Camilo

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new feature for glmfir/fsgd
by Doug Greve 25 Aug '06

25 Aug '06

I've added a new feature to the FreeSurfer Group Descriptor (FSGD) file which allows you to easily use the volume subcortical structures as covariates in a mri_glmfit analysis. An example is: GroupDescriptorFile 1 Title test Class main VariableFromASeg Left-Hippocampus Variables Age Input subject1 main 20 Input subject2 main 30 Input subject3 main 40 ... The above fsgdf will have two variables: Age and the volume of the left hippocampus. The volume is obtained from stats/aseg.stats. Within the design matrix, the left hippocampal regressor will appear after that of Age (you'll need to know this to set up your contrast matrices). mri_glmfit will fill in the values. mri_glmfit will write an fsgd as part of it's output, and this will include the volumes. This is formally equivalent to something like: GroupDescriptorFile 1 Title test Class main Variables Age Left-Hippocampus Input subject1 main 20 2000 Input subject2 main 30 3000 Input subject3 main 40 4000 ... You can have more than one VariableFromASeg statement. There are mechanisms to use something other than aseg.stats (eg, if you have your own continuous variables such as age, IQ, etc). I wrote and tested this on a flight from new mexico to boston, so I have not tested it out extensively. Let me know if you experience any turbulence. I'll add some docs to the wiki when I have time. doug -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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mris_preproc and thickness
by Sasha Wolosin 25 Aug '06

25 Aug '06

Dear all, Does "--meas thickness" as an input for mris_preproc always specify to use the ?h.thickness file in the surf folder? Is there a way to specify a different thickness file as input for mris_preproc? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. 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 e-mail in error, please immediately notify the sender via telephone or return e-mail.

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Ubuntu linx
by Chacko Cherian 23 Aug '06

23 Aug '06

Hello all, I am using an Ubuntu linux machine to run a few subjects.I ve been having trouble using tksurfer on it but tkmedit seems to be working pretty fine.Could someone please let me know why this problem has occured?Is it something to do with the souce code and the graphics libraries? Thanks in advance Chacko Cherian.

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incompatible vertex number in rh.thickness
by walhovd＠nmr.mgh.harvard.edu 23 Aug '06

23 Aug '06

Hi I just got a a new error message (pasted below this mail) when trying to run a glm I've previously run successfully. It does not get to open/use the rh.thickness file of one of my subjects (MRISreadNewCurvature: incompatible vertex number in file /var/lab-data/barn/recon2//028/surf/rh.thickness). When I delete this particular subject from the fsgd list, the glm runs smoothly, so the error is not in how the glm is set up. The mysterious thing is that I ran glms with this subject in December -05, and none of the files have been changed or saved after this (the rh.thickness file was last saved in September -05). I've tried different versions of Freesurfer, but the same thing happens. I'm grateful for any suggestions on how to solve this problem. Best regards Kristine Error message: nthsubj = 22/28, 028 --------------------------------------- INFO: loading surface /var/lab-data/barn/recon2//028/surf/rh.sphere.reg INFO: Volume /tmp/mritotal_9571/brain_8_dxyz.mnc cannot be found. INFO: Volume /usr/pubsw/packages/mni/current/bin//../share/mni_autoreg/average_3 05_8_dxyz.mnc cannot be found. INFO: The transform was made with average_305.mnc. nvertices = 130773 INFO: loading input thickness as curv Loading surface source data thickness as curv Reading curvature file /var/lab-data/barn/recon2//028/surf/rh.thickness MRISreadNewCurvature: incompatible vertex number in file /var/lab-data/barn/reco n2//028/surf/rh.thickness ERROR: reading curvature ERROR: could not load thickness gdfReadHeader: reading /var/lab-data/barn/recon2//glm_230806/kidsgroups_sex/kids groups_sex.txt INFO: ignoring tag SomeTag WARNING: no variables on 'Variables' line found INFO: gd2mtx_method is doss INFO: Normalized Design Matrix Condition Number is 1 INFO: found 4 elements in group contrast vector 1.000 1.000 -1.000 -1.000; $Id: mris_glm.c,v 1.43 2005/08/17 22:19:35 greve Exp $ Kristine B Walhovd University of Oslo Dept. of Psychology PB 1094 Blindern 0317 Oslo Norway

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inter-rater variation in scan workups?
by Glenn Lawyer 22 Aug '06

22 Aug '06

Hi, We are having a small discussion at our lab regarding inter- and intra-rater reliability numbers for our scan workups. We have a number of lab technicians processing the scans, a situation which I suspect is common to many research groups. I can think of a number of steps in the processing stream where operator input could change surface thickness measures. Yet I can't recall ever seeing inter/intra-rater reliability measures in publications. Nor is it mentioned in the FS documentation, and I don't think it is presented at the FS courses. The people I have asked about it (two different labs) have all said something like "ignore it, nobody does it." How are other people handling this issue? -- -------------------------------------- I'm only in it for the glory. > Glenn Lawyer < > +352 061 967 244 < > Instituttgruppe for psykiatri < > Postboks 1130 Blindern < > 0318 Oslo < < http://folk.uio.no/davidgl > <><><><><><><><><><><><><><><><><:)

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