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 jyw.chen@utoronto.ca wrote:
Great! Thanks!
- Jerry
On Wed, Apr 9, 2008 at 3:50 PM, Doug Greve greve@nmr.mgh.harvard.edu 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
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Centergreve@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
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 <jyw.chen@utoronto.ca mailto:jyw.chen@utoronto.ca> wrote:
Great! Thanks! - Jerry On Wed, Apr 9, 2008 at 3:50 PM, Doug Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@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 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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 greve@nmr.mgh.harvard.edu 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 jyw.chen@utoronto.ca wrote:
Great! Thanks!
- Jerry
On Wed, Apr 9, 2008 at 3:50 PM, Doug Greve greve@nmr.mgh.harvard.edu 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
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Centergreve@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
-- Douglas N. Greve, Ph.D. MGH-NMR Centergreve@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
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 faces 327680 Total area 65020.765625 AvgVtxArea 0.396850 AvgVtxDist 0.717994 StdVtxDist 0.193566
$Id: mri_glmfit.c,v 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 X vbmDesign.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 jyw.chen@utoronto.ca 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 greve@nmr.mgh.harvard.edu 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 < jyw.chen@utoronto.ca> wrote:
Great! Thanks!
- Jerry
On Wed, Apr 9, 2008 at 3:50 PM, Doug Greve greve@nmr.mgh.harvard.edu 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
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Centergreve@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
-- Douglas N. Greve, Ph.D. MGH-NMR Centergreve@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
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 faces 327680 Total area 65020.765625 AvgVtxArea 0.396850 AvgVtxDist 0.717994 StdVtxDist 0.193566
$Id: mri_glmfit.c,v 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 http://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 X vbmDesign.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 <jyw.chen@utoronto.ca mailto:jyw.chen@utoronto.ca> 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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> 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 <jyw.chen@utoronto.ca <mailto:jyw.chen@utoronto.ca>> wrote: Great! Thanks! - Jerry On Wed, Apr 9, 2008 at 3:50 PM, Doug Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@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 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@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 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
That was the problem! Thanks! - Jerry
On Thu, Apr 10, 2008 at 5:55 PM, Doug Greve greve@nmr.mgh.harvard.edu 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 faces 327680 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 X vbmDesign.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 < jyw.chen@utoronto.ca> 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 greve@nmr.mgh.harvard.edu 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 < jyw.chen@utoronto.ca> wrote:
Great! Thanks!
- Jerry
On Wed, Apr 9, 2008 at 3:50 PM, Doug Greve < greve@nmr.mgh.harvard.edu> 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
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Centergreve@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
-- Douglas N. Greve, Ph.D. MGH-NMR Centergreve@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
-- Douglas N. Greve, Ph.D. MGH-NMR Centergreve@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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Doug Greve -
Jerry Yeou-Wei Chen