Freesurfer

freesurfer@nmr.mgh.harvard.edu

5 participants
30076 discussions

Sulcal CSF measure
by Morgan Hough 23 Oct '07

23 Oct '07

Hi there, I was wondering if sulcal CSF differences should be reported given the difficulty in its identification from T1 data? How is sulcal CSF defined by FS? Thanks in advance for your time. Cheers, -Morgan

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model for pair-T test
by Wang, Xin 23 Oct '07

23 Oct '07

Hello, group, Could anybody tell me how to do the pair T test and the repeat measurement F test? I will really appreciate if you can share the steps and GLM of the tests. I am using the old freesurfer group analysis. Thank you, very much, Xin Wang

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activation patterns and par files
by Cameron Ellis 23 Oct '07

23 Oct '07

Hi all, I have run two different group analyses in stable3. All of the analysis parameters between the two are identical except that one uses a paradigm file containing three conditions and the other uses a paradigm file containing five conditions. The first three conditions in the analysis using the five condition paradigm file are identical to those in the three condition paradigm files, meaning the timing and definitions are exactly the same. The five condition paradigm file just contains additional conditions that were not originally defined, as additions to the three condition paradigm files. The problem is that the activation patterns I receive for contrasts using only the first three conditions of the five condition paradigm files are different from the activation patterns of contrasts using the three condition paradigm files. I do not know why this would be. Is there something about not defining all events that would lead to differences of this sort? I have visually inspected all of my paradigm files so I am sure the only diffences between them are the additional 2 conditions in the five condition files. I have attached images of the differences and below are the paths to both analyses as well as the commands run to produce the 5 condition results. The three condition commands were identical except for calling the different analysis. Any help or insight would be much appreciated! Cameron 3condition: /space/troy/3/users/retrievalnewest/Controlssh+smvsnh/bold/retrievalSPMHRF/sphsmooth-rfx/sh+smvsnh 5condition: /space/troy/3/users/retrievalnewest/Controlssh+smvsnh/bold/retrievalSPMHRF_5cond/sphsmooth-rfx/sh+smvsnh mkanalysis-sess.new -analysis retrievalSPMHRF_5cond -TR 2.5 -paradigm paradigmmacro5 -designtype event_related -spmhrf 0 -nconditions 5 -timewindow 25 -prestim 5 -funcstem fmcsm -taumax 30 -polyfit 2 -inorm selxavg-sess -sf sessidall -df sesspar -analysis retrievalSPMHRF_5cond mkcontrast-sess -contrast -sh+smvsnh -analysis retrievalSPMHRF_5cond -ncond 5 -a 1 -a 2 -c 3 func2sph-sess -sf sessidall -df sesspar -analysis retrievalSPMHRF_5cond sphsmooth-sess -smoothsteps 20 -analysis retrievalSPMHRF_5cond -insphdir sph -outsphdir sphsmooth -hemi rh -sf sessidall -df sesspar isxavg-re-sess -analysis retrievalSPMHRF_5cond -contrast sh+smvsnh -group Controlssh+smvsnh -space sph -spacedir sphsmooth -hemi rh -sf sessidcontrolssh+smvsnh -df sesspar

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Create thickness map
by lan lin 22 Oct '07

22 Oct '07

Hello, Is it possible to create a thickness map and use functional image's value to replace thickness value? Thanks, Ines

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intrasubject segmentation variance
by Thomas Doering 22 Oct '07

22 Oct '07

Dear freesurfers, i was running Freesurfer on the same subject on two independent Computers. The first Computer PC1has 2 physical Intel processors with 2 logical each - (dual core) - 1.6GHz with 4Gb Ram and the second PC2 has 2 physical Intel processors with 4 logical - (quad core) - 3 GHz with 8 Gb Ram. After running on these two Computers - i start at the exactly same time - i got a surprising result: My faster Computer PC2 took 41h to run the subject and the slower Computer took 31h. I wonder if somebody have some comment on this, because i have no idea what is wrong ( When i have the Linux System Monitor on, watching the CPU History, it seems that the slower PC hat a more effective occupation/usage than the faster - switching faster between one CPU and the other one...) Another small question: In the final segmentation table, i noticed that there are some small diferences between the results of PC1 and PC2: for ex.: PC1:ctx - rh-caudalmiddle frontal = 5029 5029 PC2:ctx - -"- 5360 5360 , so a diference of ~6%. I guess these are variations due to the algorithm.. Are there some established limits for that diferences? Thanks for help, Thomas

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About tissue probability maps from aseg.mgz
by Burak Ozkalayci 22 Oct '07

22 Oct '07

Dear surfers, I want to ask whether it is possible to have a tissue probability map of the brain according to aseg.mgz. If I am not wrong aseg.mgz is the MAP estimate of a Markov Random Field based segmentation hence we shall get the probability maps for each label or tissue. Is it possible? Best, Burak

2 1

WMparc step command line
by Amy DeLuca 22 Oct '07

22 Oct '07

could someone send me the command line for the last step in recon3 stream. The new version differs from the wiki table and I need to run just that last WMParc step. Thanks Amy

2 1

mgz header dump
by Michael Harms 21 Oct '07

21 Oct '07

I'm sure this is trivial, but I can't find the answer: How do you dump the header contents of an mgz file to the terminal? How about the optional information stored after the image data? thanks, Mike H. -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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Version 4.1 questions
by Kt Labadie 19 Oct '07

19 Oct '07

I have 2 questions related to version 4.1. 1) The ReconAllDevTable on the Martinos Center Freesurfer Wiki is not updated to reflect the new steps in version 4.1. Does anyone have a breakdown of these new steps? I was not sure of the flags for these new steps, or where they fit in (are they part of 2-pial, 2-cp or 3?) Is the wiki going to be updated to reflect this new version? 2) When I load an image in tkmedit (after it has been run all the way through step 3) I get an error message and it won't load the aseg. The aseg is there, I just have to load it manually. Did the following flag change with the new version? brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white - segmentation mri/aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt Thanks. KT LaBadie

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Talairach transformations in tkmedit and tkregister2
by Dr. Claudia Wheeler-Kingshott 17 Oct '07

17 Oct '07

Hi, We have a problem with the Talairach transformations. When we load the talairach.mgz file using tkmedit the axial and coronal orientations are swapped and displaced in the window. The puzzling thing is that if we use tkregister2, the registration is very good. Any idea of why? I found a previous message that had a similar problem but using both the tkmedit and tkregister2. Can we assume that in our case it is all fine, given that tkregister2 seems to be OK? Claudia -- ----------------------------------------- Claudia Wheeler-Kingshott, PhD Senior Lecturer Department of Inflammation Institute of Neurology, UCL Queen Square London WC1N 3BG tel. 0207 8373711 x4301 email: c.wheeler-kingshott(a)ion.ucl.ac.uk

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