Freesurfer

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30076 discussions

difference between ROI and whole surface glmfit regression
by Robert Levy 27 Sep '07

27 Sep '07

Hi, I was wondering what differences there could be between a glmfit regression performed on the whole surface, and the same done in an ROI. I normally see very little difference, (other than the CWP being relative to that space when monte carlo is used for multiple comparisons correction) which is why I am surprised to see a big difference between ROI and whole surface resulting from the commands shown below. The image attached is a medial snapshot of the unrestricted regression resulting from the first command shown below. The second command, ROI-restricted, resulted in no activity in the ROI (no image attached because nothing to show). I thought that maybe the smoothing had different effects in the ROI than in the unrestricted regression, so I also took out the smoothing as a test. The results of this where just an unsmooth appearance of the whole surface version, and still nothing in the ROI version, so it can't be smoothing that causes these clusters to vanish. Thanks in advance for your thoughts or help on this, Rob setenv SUBJECTS_DIR /space/ventzl/1/users/SUBJECTS_DIR cd $SUBJECTS_DIR source /usr/local/freesurfer/nmr-dev-env # 1. showing that the ROI differs from the unrestricted version (nothing in ROI version) mri_glmfit \ --really-use-average7 \ --y DTI_ADI_reg_glmfit/rh.FA.ADI_Com_ASD.fsfast.mgh \ --glmdir DTI_ADI_reg_glmfit/rh.FA.ADI_Com_ASD.fsfast.glmdir \ --fsgd fsgd_and_contrast_files/DTI_ADI_Com_age_ASD.fsgd \ --C fsgd_and_contrast_files/DTI_ADI_age.mat \ --surf average7 rh \ --pca \ --fwhm 4.6 mri_glmfit \ --really-use-average7 \ --y DTI_ADI_reg_glmfit/rh.FA.ADI_Soc_ASD.fsfast.mgh \ --glmdir DTI_ADI_reg_glmfit/ROI/rh.FA.ADI_Soc_ASD.fsfast.glmdir \ --fsgd fsgd_and_contrast_files/DTI_ADI_Soc_age_ASD.fsgd \ --C fsgd_and_contrast_files/DTI_ADI_age.mat \ --label average7/label/dACC_rACC_final-lh.label \ --surf average7 rh \ --pca \ --fwhm 4.6 # 2. taking out smoothing: whole surface version is fuzzier, still nothing in ROI version mri_glmfit \ --really-use-average7 \ --y DTI_ADI_reg_glmfit/rh.FA.ADI_Com_ASD.fsfast.mgh \ --glmdir DTI_ADI_reg_glmfit/rh.FA.ADI_Com_ASD.fsfast.glmdir \ --fsgd fsgd_and_contrast_files/DTI_ADI_Com_age_ASD.fsgd \ --C fsgd_and_contrast_files/DTI_ADI_age.mat \ --surf average7 rh \ --pca mri_glmfit \ --really-use-average7 \ --y DTI_ADI_reg_glmfit/rh.FA.ADI_Soc_ASD.fsfast.mgh \ --glmdir DTI_ADI_reg_glmfit/ROI/rh.FA.ADI_Soc_ASD.fsfast.glmdir \ --fsgd fsgd_and_contrast_files/DTI_ADI_Soc_age_ASD.fsgd \ --C fsgd_and_contrast_files/DTI_ADI_age.mat \ --label average7/label/dACC_rACC_final-lh.label \ --surf average7 rh \ --pca -- Robert P. Levy, B.A. Research Assistant, Manoach Lab Massachusetts General Hospital Charlestown Navy Yard 149 13th St., Room 2611 Charlestown, MA 02129 email: levy(a)nmr.mgh.harvard.edu phone: 617-726-1908 fax: 617-726-4078 http://nmr.mgh.harvard.edu/manoachlab

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Skull Stripping
by Paul Greenberg 27 Sep '07

27 Sep '07

Hello, I've got a data set that has already been skull stripped; how should I run this through the recon_all process? Is there a flag to skip the skullstripping stage? Thanks, Paul -- Paul Greenberg, Ph.D. Radiology Department, University of California, San Diego VA San Diego Healthcare System (116A-13) 3350 La Jolla Village Drive San Diego, CA 92161 Phone: (858) 552-8585 ext. 2903 Fax: (858) 642-3836 pgreenberg(a)ucsd.edu

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question about thalamus labels
by Goldman, Aaron (NIH/NIMH) [C] 27 Sep '07

27 Sep '07

Hi, I was wondering if any of the subcortical labels in freesurfer (I'd assume either thalamus or ventral dc) included lateral and medial geniculate nucleus. Thanks, -Aaron-

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convert mnc->analyze->mgz
by roberto toro 27 Sep '07

27 Sep '07

Hi, I've been having troubles trying to convert from minc volumes into mgz... I'll appreciate any hint first, going directly from mnc to mgz changes the aspect ratio of the volume, so (following someone elses advice) I'm trying to use minc to analyze as intermediate step. I've been using mnc2nii subject.mnc subject.hdr for the conversion, and if I display the volumes (using NeuroLens) the conversion looks fine. but then, when I do mri_convert -it analyze -i subject -o subject.mgz, the volume is shifted to one side (in addition to left/right swapped). If you look at the coronal sections I'm attaching, you see that a piece of ear the right ear is appearing at the left. I don't know if this is a know issue or something particular to my data... but, is it possible to create a mgz volume from raw data? I mean, using the .img part of the analyze file and specifying manually the volume dimension, voxel size, orientation, etc? thanks in advance, roberto

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Problem concerning maximum values from mri_volcluster
by Dan Dillon 26 Sep '07

26 Sep '07

Dear FreeSurfers, I'm getting odd results from mri_volcluster-the max voxel listed for a given cluster often does not appear to actually be the max in that cluster. This most often appears to happen with small clusters and negative significance values. Below is an example made with abs threshold = 3 and minsizevox = 12 (note that I'm plotting the output from mri_volcluster here, not the raw data, so all the depicted voxels have passed the threshold/cluster requirement). The cursor is at the max voxel as listed by mri_volcluster (significance value is -3.31). However, as can be seen in the example, there is a more extreme/significant value just two voxels over (laterally)-the value there is -4.03. Below is a second example from the same analysis. In this case, I have the cursor on a voxel whose significance value is -5.39. The problem is that mri_volcluster does not list a max voxel with such a significant value-the largest (negative) significance value listed is -4.09. When I first saw things like this I was looking at the raw data, and assumed I was seeing highly significant voxels that were not part of a large enough cluster to meet my minimum voxel size requirement. But the plots shown here were outputted by mri_volcluster using those thresholds (12 voxels, thmin = 3), so that can't be the problem. Am I doing something incorrect here and/or mis-reading the results of mri_volcluster? Any thoughts/advice would be appreciated. I have seen a few cases of this, not just the ones I'm showing here. Again, it seems to come up most frequently for smaller clusters and with negative significance values, although that just may be when it's most obvious to me. Here's the command I used to generate the output for the examples: mri_volcluster --in FPP_HiRisk_MC_375/bold/FPP_MCReg_8_23/tal-rfx/Rcue_v_RSF/sig --in_type bfloat --reg FPP_HiRisk_MC_375/bold/FPP_MCReg_8_23/tal-rfx/register.dat --thmin 3 --minsizevox 12 --out Test_FPPHiRisk_MC375_Rc_v_RSF --out_type bfloat Thanks in advance. Dan Dillon Affective Neuroscience Lab Harvard University

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How to read out wmparc
by Juergen Haenggi 26 Sep '07

26 Sep '07

Dear Freesurfer users Is there a similar function like asegstats2table or aparcstats2table in order to read out wmparc.stats? Thanks Best regards Juergen Haenggi ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of 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(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------

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High-resolution limits of FS4
by Morgan Hough 26 Sep '07

26 Sep '07

Hi there, I just wanted to check on the spatial resolution limits of FS4. Is it possible to process a whole-brain, 0.5mm isotropic voxel size volume without downsampling it? Thanks in advance. Cheers, -Morgan

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tkmedit scripting: control window size?
by Graham Wideman 25 Sep '07

25 Sep '07

Folks: In a tcl script for tkmedit, is there a way to control the size of the graphics window? I see functions for all sorts of other aspects of the view, but not this -- maybe I'm missing something? Thanks, Graham

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what ever happened to spatialsmooth-sess
by Sebastian Moeller 25 Sep '07

25 Sep '07

Dear Doug, dear fsfast experts, now that the shinny new FreeSurfer has its first point release I got around playing with its FSFAST version (befor I forget freesurfer- Linux-centos4_x86_64-stable-pub-v4.0.1-full, on 64 bit SUSE 10.1). I looks like a lot was changed under the hood (and improved I am sure) now my old scripts certainly need some help to keep going. My first stumbling block is spatialsmooth-sess, which complaines about a missing "ip" binary, (and rightly so, since ip got folded into fslmaths, I fathom). 1. Please let me know, what the recommended replacement for spatialsmooth-sess is nowadays. 2. And while I am asking, can I truly switch FSFAST default formats by "export FSF_OUTPUT_FORMAT=whatever" before sourcing SetUpFreeSurfer? 3. I would be happy about a link to a newer tutorial/howto fsf to use as a template to "modernize" my scripts thank you very much for the powerful tools as always & ahoi Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 0 15 77 - 1 90 31 41 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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t-value saved values
by Glenn Lawyer 25 Sep '07

25 Sep '07

Hi, I asked about this last week, and had a nice discussion with Doug, but somehow in that we never got the answer to my original question. When FreeSurfer saves t-values (in F.mgh), what is it actually saving? The numbers in the file do not have a t-distribution (even when the source data for the glm is random noise). Is a transform applied to the t-values before the write, as is done with the p-values?

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