Hello freesurfer experts, I am trying to normalize my continuous variables in my fsgd file. Is this the correct term to add to my fsgd file in order for mri_glmfit to normalize it?
GroupDescriptorFile 1 Title PCS Class group1 Class group2 Normalize 1 Variables Age Education Scoreone Scoretwo Input 053 group1 47 18 3.4 5.6 Input 054 group2 50 16 5.3 2.8
Thank you, Paul
No, that flag does not exist, but it is a good idea! You'll have to normalize them by hand.
On 7/24/16 1:33 PM, miracle ozzoude wrote:
Hello freesurfer experts, I am trying to normalize my continuous variables in my fsgd file. Is this the correct term to add to my fsgd file in order for mri_glmfit to normalize it?
GroupDescriptorFile 1 Title PCS Class group1 Class group2 Normalize 1 Variables Age Education Scoreone Scoretwo Input 053 group1 47 18 3.4 5.6 Input 054 group2 50 16 5.3 2.8
Thank you, Paul
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Actually, I checked the code and found that I had already put a flag in there to do this (I'm so clever). Add
ReScaleFlag 1
in addition to
DeMeanFlag 1
On 7/25/16 11:22 AM, Douglas Greve wrote:
No, that flag does not exist, but it is a good idea! You'll have to normalize them by hand.
On 7/24/16 1:33 PM, miracle ozzoude wrote:
Hello freesurfer experts, I am trying to normalize my continuous variables in my fsgd file. Is this the correct term to add to my fsgd file in order for mri_glmfit to normalize it?
GroupDescriptorFile 1 Title PCS Class group1 Class group2 Normalize 1 Variables Age Education Scoreone Scoretwo Input 053 group1 47 18 3.4 5.6 Input 054 group2 50 16 5.3 2.8
Thank you, Paul
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello Doug, The ReScaleFlag 1 command did not work. Only the demean command. Paul
On Mon, Jul 25, 2016 at 6:17 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Actually, I checked the code and found that I had already put a flag in there to do this (I'm so clever). Add
ReScaleFlag 1
in addition to
DeMeanFlag 1
On 7/25/16 11:22 AM, Douglas Greve wrote:
No, that flag does not exist, but it is a good idea! You'll have to normalize them by hand.
On 7/24/16 1:33 PM, miracle ozzoude wrote:
Hello freesurfer experts, I am trying to normalize my continuous variables in my fsgd file. Is this the correct term to add to my fsgd file in order for mri_glmfit to normalize it?
GroupDescriptorFile 1 Title PCS Class group1 Class group2 Normalize 1 Variables Age Education Scoreone Scoretwo Input 053 group1 47 18 3.4 5.6 Input 054 group2 50 16 5.3 2.8
Thank you, Paul
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
what do you mean it did not work? can you be more specific?
On 07/26/2016 12:21 PM, miracle ozzoude wrote:
Hello Doug, The ReScaleFlag 1 command did not work. Only the demean command. Paul
On Mon, Jul 25, 2016 at 6:17 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Actually, I checked the code and found that I had already put a flag in there to do this (I'm so clever). Add ReScaleFlag 1 in addition to DeMeanFlag 1 On 7/25/16 11:22 AM, Douglas Greve wrote:No, that flag does not exist, but it is a good idea! You'll have to normalize them by hand. On 7/24/16 1:33 PM, miracle ozzoude wrote:Hello freesurfer experts, I am trying to normalize my continuous variables in my fsgd file. Is this the correct term to add to my fsgd file in order for mri_glmfit to normalize it? GroupDescriptorFile 1 Title PCS Class group1 Class group2 Normalize 1 Variables Age Education Scoreone Scoretwo Input 053 group1 47 18 3.4 5.6 Input 054 group2 50 16 5.3 2.8 Thank you, Paul _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I added normalizing and demeaning code like you suggested in my fsgd file and perform the GLM analysis (mri_glmfit). However, my covariates were only demeaned (DeMeanFlag 1) but they were not normalized (ReScaleFlag 1). Hence I received this error from freesurfer. I have attached my fsgd files and contrast matrix INFO: demeaning continuous variables Continuous Variable Means (all subjects) 0 Age 39.9375 17.3312 1 Education 15.5625 1.99902 2 Firstscore 1.03375 0.341785 3 Secondscore 1.03906 0.370678 4 Thirdscore 1.13844 0.4768 5 Averagescore 1.07375 0.364046 Class Means of each Continuous Variable 1 Group1 35.6316 15.0526 1.0342 1.2111 1.4289 1.2305 2 Group2 46.2308 16.3077 1.0331 0.7877 0.7138 0.8446 INFO: gd2mtx_method is dods Reading source surface /Users/ctartaglia/Desktop/improvervsdeclinermri/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470
$Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ cwd /Users/ctartaglia/Desktop/improvervsdeclinermri cmdline mri_glmfit --y lh.NeuroTrackerscore.thickness.10B.mgh --fsgd NeuroTrackerscore.fsgd dods --C new.firstmatrix.mtx --C new.secondmatrix.mtx --C new.thirdmatrix.mtx --C new.fourthmatrix.mtx --C new.fifthmatrix.mtx --C new.sixthmatrix.mtx --C new.seventhmatrix.mtx --C new.eightmatrix.mtx --C new.ninethmatrix.mtx --C new.tenthmatrix.mtx --surf fsaverage lh --cortex --glmdir lh.NeuroTrackerscore.glmdir sysname Darwin hostname twh-ct-lab4-imac.uhn.ca machine x86_64 user ctartaglia FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Users/ctartaglia/Desktop/improvervsdeclinermri/lh.NeuroTrackerscore.thickness.10B.mgh logyflag 0 usedti 0 FSGD NeuroTrackerscore.fsgd labelmask /Users/ctartaglia/Desktop/improvervsdeclinermri/fsaverage/label/lh.cortex.label maskinv 0 glmdir lh.NeuroTrackerscore.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory lh.NeuroTrackerscore.glmdir Loading y from /Users/ctartaglia/Desktop/improvervsdeclinermri/lh.NeuroTrackerscore.thickness.10B.mgh INFO: gd2mtx_method is dods Saving design matrix to lh.NeuroTrackerscore.glmdir/Xg.dat Normalized matrix condition is 115605 Design matrix ------------------ 1.000 0.000 -0.729 0.000 -0.026 0.000 1.889 0.000 1.535 0.000 1.428 0.000 1.729 0.000; 1.000 0.000 0.425 0.000 0.474 0.000 -0.568 0.000 -0.866 0.000 -0.501 0.000 -0.716 0.000; 1.000 0.000 0.194 0.000 0.974 0.000 -0.715 0.000 -1.001 0.000 -0.438 0.000 -0.771 0.000; 1.000 0.000 -0.960 0.000 -1.027 0.000 -0.568 0.000 -0.408 0.000 -0.354 0.000 -0.496 0.000; 1.000 0.000 -0.440 0.000 -1.027 0.000 0.075 0.000 -0.246 0.000 -0.124 0.000 -0.139 0.000; 1.000 0.000 -0.440 0.000 1.474 0.000 -0.188 0.000 0.132 0.000 -0.208 0.000 -0.111 0.000; 1.000 0.000 0.079 0.000 0.474 0.000 -0.480 0.000 -0.165 0.000 -0.124 0.000 -0.276 0.000; 1.000 0.000 -0.902 0.000 -0.527 0.000 -0.100 0.000 0.429 0.000 0.044 0.000 0.108 0.000; 1.000 0.000 1.291 0.000 0.474 0.000 -0.188 0.000 -0.246 0.000 -0.040 0.000 0.108 0.000; 1.000 0.000 -0.440 0.000 1.474 0.000 -0.480 0.000 -0.569 0.000 -0.900 0.000 -0.743 0.000; 1.000 0.000 0.598 0.000 0.474 0.000 -0.773 0.000 -0.408 0.000 0.317 0.000 -0.249 0.000; 1.000 0.000 -0.844 0.000 0.474 0.000 1.597 0.000 1.535 0.000 0.736 0.000 1.317 0.000; 1.000 0.000 -0.787 0.000 0.474 0.000 1.363 0.000 0.024 0.000 0.422 0.000 0.603 0.000; 1.000 0.000 -0.960 0.000 -1.027 0.000 1.480 0.000 1.265 0.000 1.428 0.000 1.509 0.000; 1.000 0.000 -1.075 0.000 -1.527 0.000 -0.100 0.000 -0.327 0.000 -0.270 0.000 -0.276 0.000; 1.000 0.000 0.887 0.000 0.474 0.000 -0.276 0.000 0.887 0.000 0.527 0.000 0.438 0.000; 1.000 0.000 0.483 0.000 0.474 0.000 0.544 0.000 0.240 0.000 0.149 0.000 0.301 0.000; 1.000 0.000 2.445 0.000 -1.527 0.000 -1.241 0.000 -0.246 0.000 -0.585 0.000 -0.743 0.000; 1.000 0.000 1.175 0.000 -1.027 0.000 -1.270 0.000 -1.568 0.000 -1.508 0.000 -1.595 0.000; 0.000 1.000 0.000 0.217 0.000 0.847 0.000 0.254 0.000 0.411 0.000 0.474 0.000 0.427; 0.000 1.000 0.000 -1.513 0.000 -0.654 0.000 0.254 0.000 0.141 0.000 -0.239 0.000 0.015; 0.000 1.000 0.000 0.102 0.000 -0.154 0.000 -1.764 0.000 -1.181 0.000 -0.763 0.000 -1.276; 0.000 1.000 0.000 -1.340 0.000 -0.154 0.000 1.600 0.000 1.166 0.000 1.062 0.000 1.361; 0.000 1.000 0.000 -1.687 0.000 0.346 0.000 1.366 0.000 1.274 0.000 0.999 0.000 1.306; 0.000 1.000 0.000 0.275 0.000 0.847 0.000 -0.828 0.000 -0.264 0.000 -0.239 0.000 -0.452; 0.000 1.000 0.000 -0.186 0.000 0.847 0.000 0.869 0.000 0.276 0.000 0.328 0.000 0.509; 0.000 1.000 0.000 0.737 0.000 -0.154 0.000 -0.623 0.000 -0.506 0.000 -0.239 0.000 -0.480; 0.000 1.000 0.000 -0.013 0.000 1.347 0.000 -0.623 0.000 0.006 0.000 -0.008 0.000 -0.205; 0.000 1.000 0.000 1.025 0.000 -1.655 0.000 -0.331 0.000 -0.641 0.000 -0.532 0.000 -0.562; 0.000 1.000 0.000 0.160 0.000 -0.154 0.000 1.600 0.000 0.654 0.000 0.369 0.000 0.894; 0.000 1.000 0.000 1.833 0.000 -2.155 0.000 -1.852 0.000 -1.828 0.000 -1.287 0.000 -1.771; 0.000 1.000 0.000 0.391 0.000 0.847 0.000 0.079 0.000 0.492 0.000 0.076 0.000 0.235; -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 115605 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit --y lh.NeuroTrackerscore.thickness.10B.mgh --fsgd NeuroTrackerscore.fsgd dods --C new.firstmatrix.mtx --C new.secondmatrix.mtx --C new.thirdmatrix.mtx --C new.fourthmatrix.mtx --C new.fifthmatrix.mtx --C new.sixthmatrix.mtx --C new.seventhmatrix.mtx --C new.eightmatrix.mtx --C new.ninethmatrix.mtx --C new.tenthmatrix.mtx --surf fsaverage lh --cortex --glmdir lh.NeuroTrackerscore.glmdir 2. The FSGD file (if using one) 3. And the design matrix above
On Tue, Jul 26, 2016 at 12:23 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
what do you mean it did not work? can you be more specific?
On 07/26/2016 12:21 PM, miracle ozzoude wrote:
Hello Doug, The ReScaleFlag 1 command did not work. Only the demean command. Paul
On Mon, Jul 25, 2016 at 6:17 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Actually, I checked the code and found that I had already put a flag in there to do this (I'm so clever). Add ReScaleFlag 1 in addition to DeMeanFlag 1 On 7/25/16 11:22 AM, Douglas Greve wrote:No, that flag does not exist, but it is a good idea! You'll have to normalize them by hand. On 7/24/16 1:33 PM, miracle ozzoude wrote:Hello freesurfer experts, I am trying to normalize my continuous variables in my fsgd file. Is this the correct term to add to my fsgd file in order for mri_glmfit to normalize it? GroupDescriptorFile 1 Title PCS Class group1 Class group2 Normalize 1 Variables Age Education Scoreone Scoretwo Input 053 group1 47 18 3.4 5.6 Input 054 group2 50 16 5.3 2.8 Thank you, Paul _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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miracle ozzoude