RE: [Freesurfer] mri_watershed - BEM surfaces problem
matlab's reducepatch Date: Thu, 10 Apr 2008 10:39:37 -0700 From: [EMAIL PROTECTED] To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_watershed - BEM surfaces problem P.S. Also, I was wondering if there is a utility to reduce the number of vertices of a given surface (i.e. to make a less precise triangulation) at will. I thought I may use the pial left and right halves greatly reduced (from about 140k vertices to 10k or less) for the brain surface instead of the mri_watershed output. _ Use video conversation to talk face-to-face with Windows Live Messenger. http://www.windowslive.com/messenger/connect_your_way.html?ocid=TXT_TAGLM_WL_Refresh_messenger_video_042008___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Interactions for continuous variables
That was the problem!
Thanks!
- Jerry
On Thu, Apr 10, 2008 at 5:55 PM, Doug Greve [EMAIL PROTECTED]
wrote:
I think the problem is that the last line is a blank line. Remove that
and retry.
doug
Jerry Yeou-Wei Chen wrote:
I am getting the following error when I run mri_glmfit with my custom
design matrix:
WARNING: matlab elment type is 940126218, which is not a matrix.
could not allocate 822685706 x 805908489 matrix
Cannot allocate memory
unsupported matlab format -849662976 (unknown)
Cannot allocate memory
Below is the full output, and I have attached my custom design matrix
(orig is my original matrix, the other is formatted like Xg.dat)
Thanks,
- Jerry
-
Full output:
-
*% mri_glmfit --y rh.vbmDesign.thickness.10.mgh --X vbmDesign.mat --glmdir
rh.vbmDesign.glmdir --surf fsaverage rh --C N_FvsM.mat
Reading source surface
/scratch/freesurfer/subjects/adina/descic39_allSubjects_readyForStats/fsaverage/surf/rh.white
reading group avg surface area 822 cm^2 from file
Reading in average area
/scratch/freesurfer/subjects/adina/descic39_allSubjects_readyForStats/fsaverage/surf/rh.white.avg.area.mgh
Number of vertices 163842
Number of faces327680
Total area 65020.765625
AvgVtxArea 0.396850
AvgVtxDist 0.717994
StdVtxDist 0.193566
$Id: mri_glmfit.c,v MailScanner has detected a possible fraud attempt from
1.138.2.1 claiming to be MailScanner has detected a possible fraud
attempt from 1.138.2.1 claiming to be MailScanner warning: numerical
links are often malicious: 1.138.2.1 http://1.138.2.1 2007/09/12
15:38:19 nicks Exp $
cwd
/scratch/freesurfer/subjects/adina/descic39_allSubjects_readyForStats/oldStats_vbmDesign
cmdline mri_glmfit --y rh.vbmDesign.thickness.10.mgh --X vbmDesign.mat
--glmdir rh.vbmDesign.glmdir --surf fsaverage rh --C N_FvsM.mat
sysname Linux
hostname kdavis8-efef.uhnres.utoronto.ca
machine i686
user jerryc
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y
/scratch/freesurfer/subjects/adina/descic39_allSubjects_readyForStats/oldStats_vbmDesign/rh.vbmDesign.thickness.10.mgh
logyflag 0
XvbmDesign.mat
usedti 0
glmdir rh.vbmDesign.glmdir
DoFFx 0
Creating output directory rh.vbmDesign.glmdir
Loading y from
/scratch/freesurfer/subjects/adina/descic39_allSubjects_readyForStats/oldStats_vbmDesign/rh.vbmDesign.thickness.10.mgh
MatrixReadTxT: could not scan value [36][1]
WARNING: matlab elment type is 940126218, which is not a matrix.
could not allocate 822685706 x 805908489 matrix
Cannot allocate memory
unsupported matlab format -849662976 (unknown)
Cannot allocate memory
*
On Thu, Apr 10, 2008 at 11:02 AM, Jerry Yeou-Wei Chen
[EMAIL PROTECTED] wrote:
Thanks for the clarification, Doug.
The Wiki page for mri_glmfit says to Specify the design matrix in
matlab4 format.
- Jerry
On Wed, Apr 9, 2008 at 5:19 PM, Doug Greve [EMAIL PROTECTED]
wrote:
From mri_glmflit --help :
--X design matrix file
Explicitly specify the design matrix. Can be in simple text or in
matlab4
format. If matlab4, you can save a matrix with
save('X.mat','X','-v4');
It does not need/expect any extension.
doug
Jerry Yeou-Wei Chen wrote:
Regarding custom design matrices, does the --X flag require a design
matrix in matlab format? If so, can I simply create it in a text editor
and
name it with the suffix .mat?
Also, if I use the --X to specify a design matrix, am I still supposed
to specify the fsgd file?
Thanks,
- Jerry
On Wed, Apr 9, 2008 at 4:58 PM, Jerry Yeou-Wei Chen
[EMAIL PROTECTED] wrote:
Great! Thanks!
- Jerry
On Wed, Apr 9, 2008 at 3:50 PM, Doug Greve
[EMAIL PROTECTED] wrote:
You can pass custom design and contrast matrices to mri_glmfit, so
you can pass the same matrices to mri_glmfit that you would use with
spm.
Alternatively, you can set up an fsgd file with a 3rd continuous
variable
that is the produce of the first two.
doug
Jerry Yeou-Wei Chen wrote:
Hello,
I would like to know how to examine an interaction between
continuous variables.
In SPM, my understanding is that a new interaction regressor,
comprised of the product of the two continuous variables of interest,
can be
coded and entered into the model.
Would this be appropriate for CTA group analysis in FreeSurfer? Is
there any difference if I use the old command line method or the QDEC
GUI?
Thanks,
- Jerry
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[Freesurfer] tksurfer buttons grayed out
We're taking a look at using FreeSurfer for our lab's analysis of cortical thickness...just ran a fully automated recon-all on one of our lab's brains that generated no error messages and looks good in the Inspection of Freesurfer Output exercise from your tutorial. However, I noticed while moving through this exercise that the curvature file button, pial surface button, and the thickness map button are grayed out (not available for use) in the tksurfer toolbox. If this means there was some subtle error in the output - any ideas where to begin troubleshooting? Perhaps automatic topology defect correction? Not sure how obvious the topology defects you refer to would be on inspection; there were no holes or handles that I could see in the inflated surface, though ours was more lumpy than the tutorial's...Some dura was left in and was designated cortex, lying outside of the pial surface generated. Could this be the issue? If so, would the solution be an adjustment of the watershed parameters fix it, or is that really intended for large over-inclusions of skull? Thanks - Jennifer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tksurfer buttons grayed out
Hi Jennifer, did you try loading them with file-... (curvature for thickness and surface configuration for pial). You can also ctrl-right click on either one to bring up the appropriate file menu. We don't load them by default I don't think. Bruce On Fri, 11 Apr 2008 [EMAIL PROTECTED] wrote: We're taking a look at using FreeSurfer for our lab's analysis of cortical thickness...just ran a fully automated recon-all on one of our lab's brains that generated no error messages and looks good in the Inspection of Freesurfer Output exercise from your tutorial. However, I noticed while moving through this exercise that the curvature file button, pial surface button, and the thickness map button are grayed out (not available for use) in the tksurfer toolbox. If this means there was some subtle error in the output - any ideas where to begin troubleshooting? Perhaps automatic topology defect correction? Not sure how obvious the topology defects you refer to would be on inspection; there were no holes or handles that I could see in the inflated surface, though ours was more lumpy than the tutorial's...Some dura was left in and was designated cortex, lying outside of the pial surface generated. Could this be the issue? If so, would the solution be an adjustment of the watershed parameters fix it, or is that really intended for large over-inclusions of skull? Thanks - Jennifer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] converting a region defined by a surface to a label file
Hello, We have some white matter surfaces created using non-FS software in which we have subsequently cut-out via hand contouring specific gyri and sulci of interest (e.g., cingulate). I would like to be able to use these extracted surfaces to create a label file in FS corresponding to the matching surface region within FS. Is there a way to accomplish this using existing Freesurfer binary or matlab functions? More specifically, we can define these extracted surfaces in the native scan space, and get them into a vtk format (which should be readable by mris_convert). Do you have any suggestions for the easiest way to then translate the region defined by this surface into a corresponding region on the FS white matter surface? Ideally, since our in-house surface defines an enclosed set of vertices, the ensuing label file in FS would represent an enclosed set of vertices as well. thanks for your suggestions, 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: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
