Freesurfer July 2008

freesurfer@nmr.mgh.harvard.edu

55 participants
74 discussions

mri_volcluster --ERROR: you must specify a pos or neg sign with --fwhm
by PKUNWAR＠nmr.mgh.harvard.edu 26 Aug '09

26 Aug '09

Hi all, I was going through the FSFAST TUTORIAL from wiki( https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial?action=highlight&v…) I got the follwoing error during mri_volcluster, "NOT Adjusting threshold for 1-tailed test ERROR: you must specify a pos or neg sign with --fwhm" I have fwhm.dat file with 4. something vlaue. Command used, [galen:odd-v-0] (nmr-std-env) mri_volcluster --in tal.rfx.osgm/osgm/sig.nii --thmin 2 --fwhmdat tal.rfx.osgm/fwhm.dat --cwpvalthresh 0.1 --mask tal.rfx.osgm/mask.nii --fsaverage --sum tal.rfx.osgm/osgm/cluster.sum --cwsig tal.rfx.osgm/osgm/cwsig.cluster.nii --out tal.rfx.osgm/osgm/sig.cluster.nii --ocn tal.rfx.osgm/osgm/ocn.cluster.nii without --fwhmdat flag, it gave me another error "ERROR: need csd with --cwsig" will appreciate for help thanks pratap ----------------------------------- FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.0.1-20070927 RedHat release: CentOS release 4.4 (Final) Kernel info: Linux 2.6.9-42.0.3.ELsmp x86_64 NMR Center info (/space/freesurfer exists): machine: galen SUBJECTS_DIR: /autofs/space/galen_003/users/carl/Tutorial/buckner_data/FsFastTutorialData/FSFTUTDIR/subjects PWD: /space/galen/3/users/carl/Tutorial/buckner_data/FsFastTutorialData/FSFTUTDIR/fb1-preproc-study/group-analysis-tut/sm-gamma-fwhm5/odd-v-0

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design matrix : inter-run effetcs
by Andersson Frederic 02 Dec '08

02 Dec '08

Hi, Computing individual fMRI analysis (several runs) and looking at the design matrix (X.mat), I saw that only one regressor represents each condition. I was expecting that the number of regressors concerning a condition would be the number of runs (as SPM). There are "inter-run effect" regressors but is this better if I affect a different value for each of run and each condition (see examples below). Other question concerning design matrix : only 3 movement parameters included in the design matrix. Why 3 rather than the 6 computed during movement correction? Concerning inter-run effects and movement parameters, is there any advantage of reducing the number of regressors but having a less ideal model? >>> 1 condition = 1regressor 0 = rest 1=conditionA 2=conditionB Pardagim files : RUN#1 RUN#2 RUN#3 0 0 0 0 0 0 3 0 3 0 3 0 6 0 6 0 6 0 9 0 9 0 9 0 12 0 12 0 12 0 15 1 15 1 15 1 18 1 18 1 18 1 21 1 21 1 21 1 24 1 24 1 24 1 27 1 27 1 27 1 30 0 30 0 30 0 33 0 33 0 33 0 36 0 36 0 36 0 39 0 39 0 39 0 42 2 42 2 42 2 45 2 45 2 45 2 48 2 48 2 48 2 51 2 51 2 51 2 54 2 54 2 54 2 57 0 57 0 57 0 >>> 1 condition = 1regressor / run 0=rest 1=conditionA run#1 2=conditionB run#1 3=conditionA run#2 4=conditionB run#2 5=conditionA run#3 6=conditionB run#3 Pardagim files : RUN#1 RUN#2 RUN#3 0 0 0 0 0 0 3 0 3 0 3 0 6 0 6 0 6 0 9 0 9 0 9 0 12 0 12 0 12 0 15 1 15 3 15 5 18 1 18 3 18 5 21 1 21 3 21 5 24 1 24 3 24 5 27 1 27 3 27 5 30 0 30 0 30 0 33 0 33 0 33 0 36 0 36 0 36 0 39 0 39 0 39 0 42 2 42 4 42 6 45 2 45 4 45 6 48 2 48 4 48 6 51 2 51 4 51 6 54 2 54 4 54 6 57 0 57 0 57 0 Frédéric ANDERSSON.

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Re: [Freesurfer] volumes in wmparc.stats vs. aparc.stats
by bell0368＠umn.edu 08 Oct '08

08 Oct '08

I was wondering how the calculations of the wm volume were performed as well. The six values below are volume values from aseg I believe. I assume mris_wm_volume does more than sub-divide these regions into the wm parcellations, but probably also includes partial volume estimations along the wm/gm surface, is this correct? I basically have the same question for the gm volume values in aparc.stats; do they include partial volume calculations from the gm/pial and gm/white borders? Which binary is used to create these values for gm in aparc.stats... is it mri_segstats (with --pv)? I was assuming it would be an mris (surface) calculation as well. I am asking because if you use tkmedit to view the ?h.surface files and load the aparc+aseg or wmparc segmentation volumes in also, the surfaces and the segmentations don't seem to line up. Is there a way to create a segmentation volume that includes partial-volumed voxels at the gray/white and gray/pial boundries? Thanks for your help. Chris Bell the interior voxels are only included in the volume if they are one of the following in the aseg.mgz: case Left_Cerebral_Cortex: case Right_Cerebral_Cortex: case Left_Cerebral_White_Matter: case Right_Cerebral_White_Matter: case Left_WM_hypointensities: case Right_WM_hypointensities: cheers, Bruce On Tue, 15 Jul 2008, Marin Richardson wrote: OK, so aparc.stats is better for cortical gray matter. I want to look at the parcellated white matter volumes as well - is the only/best option to use the wm volumes from wmparc.stats? Also, when using mris_wm_volume to calculate total white matter, I saw the result defined as the volume within the white matter surface minus non-WM structures? Can you tell me which regions are and are not included? Marin Doug Greve <[EMAIL PROTECTED]> 7/15/2008 12:02 PM >>> It is better to use the aparc as it is derived from surface measurements, which have sub-voxel resolution. The wmparc.stats are generated by counting 1mm^3 voxels. doug Marin Richardson wrote: Hi all, I noticed that the gray volumes for parcellated cortical regions in wmparc.stats are different from those for the same region in aparc.stats (e.g. ctx-lh-middletemporal = 8419 in wmparc.stats, middletemporal = 9466 in lh.aparc.stats). Why are the values different and which one is a better measure to use? Thanks, Marin

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Checking for spikes
by Brittany Cassidy 06 Aug '08

06 Aug '08

Hello all, I was looking for a general way to check for spiking from Freesurfer or the FSFast stream. Any ideas are appreciated. Thanks! -Brittany

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mri_watershed regions appearing round edge, freesurfer 4.0.2
by Ian Malone 05 Aug '08

05 Aug '08

Hi, Has anyone encountered this before? I have a few volumes for which mri_watershed output volumes are fine apart from some non-zero voxels near the edges (which are not connected to the brain). The volumes are in transverse format and the most noticeable effect is some inferior slices (neck, lower jaw) which are not being masked out, though there are also some voxels close to the coronal edges. For both sets of edges there is a one or two voxel thick layer parallel to either the coronal or transverse plane. This is with Freesurfer 4.0.2, T1 images in Analyze format. Thanks for your time, Ian Malone

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Sample size
by Claus Reinsberger 04 Aug '08

04 Aug '08

Hi Freesurfers, could anybody tell, whether there is a way for a proper estimation of a sample size to plan a prospective study (cortical thickness measurements using qdec)? I suppose I can only refer to other publications examining a similiar cohort using freesurfer - is that right? I appreciate your help very much, Claus

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importing vertices and applying path_new_path_from_marked_vertices
by Aaron Shmookler 31 Jul '08

31 Jul '08

Hello, Here's what I did: 1) mris_convert ?h.inflated file.asc 2) extract vertices of interest into file2.asc Here is what I want to do: I want to import the vertices from file2.asc into tksurfer and apply the *path_new_path_from_marked_vertices *function so that I can then create a label. How might I do this? Thanks, Aaron

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3.0.2
by p.s.bjerkan＠studmed.uio.no 31 Jul '08

31 Jul '08

Hi! Need the centos4 x86_64 version of 3.0.2 Can´t find it on the ftp server or on the wiki. Thanks! Petr

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again: qdec error
by Dorit Kliemann 30 Jul '08

30 Jul '08

Dear all, I wanted to open qdec for the first time and experienced an error that was posted some days ago... ( RE: [Freesurfer] qdec ERROR: Rendering vtkXOpenGLRenderWindow ; Juranek, Jenifer ) " ERROR: In /usr/pubsw/packages/vtk/5.0.4/src/VTK/Rendering/vtkXOpenGLRenderWindow.cxx, line 219 vtkXOpenGLRenderWindow (0x49220f0): Could not find a decent visual" In contrast to the previously reported incident, I was finally able to open qdec by just clicking 'ok' on 3 of those exact same error messages. Still - I could not read in any .dat files..... I tried to follow the advice given in the previous threat " In the file /etc/X11/xorg.conf, within the section titled Section "Module", make sure this line exists: Load "glx" You might need to have your administrator perform this change, as it requires root access. You will have to restart your X server after making this change (Ctrl-Bksp)." ..but I don¹t have the referred file in the X11 folder (xorg.conf). FYI, I¹m using the latest Freesurfer version and for a colleague of mine qdec works without having that xorg.conf file..... It is possible that there is any other reason for the qdec error? Thanks, Dorit

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set up of initial data directories
by Stephen Rose 30 Jul '08

30 Jul '08

Hi I am a new freesurfer user so I apologize in advance for the basic questions. If I already have my MPRAGE images in mgz format (i.e I don't need to convert the raw dicom data with mri_convert), what changes to the command line (below) do I need so that the all the correct data directories are initially set up (and not call mri_convert)? recon-all -i <path-to-structural> -s <subjid> When viewing the results of autorecon1 and 2 are all the surfaces and segmentation results shown in raw image space and not Talairach space? Thanks for your help Stephen A/Prof. Stephen Rose Principal Research Fellow Centre for Magnetic Resonance Centre for Clinical Research University of Queensland Brisbane, QLD, 4072 Australia Telephone: +61 7 33466101 Mobile: 0412023958 Fax: +61 7 33653833

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Freesurfer July 2008