Hi everyone,
I get this error when running surface area analysis in QDEC:
Vinas-iMac:~/Documents/Wanda/Wanda_SFS] vinagoghari% mri_glmfit --y /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh --fsgd /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd dods --glmdir /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled --surf fsaverage lh --label /Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label --C /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Avg-Intercept-area.mat --C /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Diff-Control-Relative-Intercept-area.mat gdfReadHeader: reading /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 40.6327 13.0176 1 IntraCranialVol 1.50352e+06 187456 Class Means of each Continuous Variable 1 GroupControl 38.8261 1480505.5707 2 GroupRelative 42.2308 1523881.3029 INFO: gd2mtx_method is dods Reading source surface /Users/vinagoghari/Documents/Wanda/Wanda_SFS/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/vinagoghari/Documents/Wanda/Wanda_SFS cmdline mri_glmfit --y /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh --fsgd /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd dods --glmdir /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled --surf fsaverage lh --label /Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label --C /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Avg-Intercept-area.mat --C /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Diff-Control-Relative-Intercept-area.mat sysname Darwin hostname Vinas-iMac.local machine x86_64 user vinagoghari FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh logyflag 0 usedti 0 FSGD /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd labelmask /Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label maskinv 0 glmdir /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled Loading y from /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh INFO: gd2mtx_method is dods Saving design matrix to /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/Xg.dat Normalized matrix condition is 400.101 Matrix condition is 1e+08 Found 148151 points in label. Pruning voxels by thr: 0.000000 Found 148025 voxels in mask Saving mask to /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/mask.mgh Reshaping mriglm->mask... search space = 73649.347769 ERROR: dimension mismatch between y and X. y has 3528 inputs, X has 49 rows.
My QDEC table has 49 subjects,2 groups, and 4 variables.
Many thanks, Wanda
Can you send the terminal output that starts with mris_preproc?
On 01/28/2014 02:01 PM, Wanda Truong wrote:
Hi everyone,
I get this error when running surface area analysis in QDEC:
Vinas-iMac:~/Documents/Wanda/Wanda_SFS] vinagoghari% mri_glmfit --y /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh --fsgd /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd dods --glmdir /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled --surf fsaverage lh --label /Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label --C /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Avg-Intercept-area.mat --C /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Diff-Control-Relative-Intercept-area.mat gdfReadHeader: reading /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 40.6327 13.0176 1 IntraCranialVol 1.50352e+06 187456 Class Means of each Continuous Variable 1 GroupControl 38.8261 1480505.5707 2 GroupRelative 42.2308 1523881.3029 INFO: gd2mtx_method is dods Reading source surface /Users/vinagoghari/Documents/Wanda/Wanda_SFS/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/vinagoghari/Documents/Wanda/Wanda_SFS cmdline mri_glmfit --y /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh --fsgd /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd dods --glmdir /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled --surf fsaverage lh --label /Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label --C /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Avg-Intercept-area.mat --C /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Diff-Control-Relative-Intercept-area.mat
sysname Darwin hostname Vinas-iMac.local machine x86_64 user vinagoghari FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh logyflag 0 usedti 0 FSGD /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd labelmask /Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label maskinv 0 glmdir /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled Loading y from /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh INFO: gd2mtx_method is dods Saving design matrix to /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/Xg.dat Normalized matrix condition is 400.101 Matrix condition is 1e+08 Found 148151 points in label. Pruning voxels by thr: 0.000000 Found 148025 voxels in mask Saving mask to /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/mask.mgh Reshaping mriglm->mask... search space = 73649.347769 ERROR: dimension mismatch between y and X. y has 3528 inputs, X has 49 rows.
My QDEC table has 49 subjects,2 groups, and 4 variables.
Many thanks, Wanda
-- Wanda Truong, MSc
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
Attached is the full error message I get, starting from mris_preproc.
Thanks!! Wanda
On 28 January 2014 12:34, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Can you send the terminal output that starts with mris_preproc?
On 01/28/2014 02:01 PM, Wanda Truong wrote:
Hi everyone,
I get this error when running surface area analysis in QDEC:
Vinas-iMac:~/Documents/Wanda/Wanda_SFS] vinagoghari% mri_glmfit --y /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh --fsgd /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd dods --glmdir /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled --surf fsaverage lh --label
/Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label
--C
/Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Avg-Intercept-area.mat
--C
/Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Diff-Control-Relative-Intercept-area.mat
gdfReadHeader: reading /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 40.6327 13.0176 1 IntraCranialVol 1.50352e+06 187456 Class Means of each Continuous Variable 1 GroupControl 38.8261 1480505.5707 2 GroupRelative 42.2308 1523881.3029 INFO: gd2mtx_method is dods Reading source surface /Users/vinagoghari/Documents/Wanda/Wanda_SFS/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/vinagoghari/Documents/Wanda/Wanda_SFS cmdline mri_glmfit --y /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh --fsgd /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd dods --glmdir /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled --surf fsaverage lh --label
/Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label
--C
/Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Avg-Intercept-area.mat
--C
/Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Diff-Control-Relative-Intercept-area.mat
sysname Darwin hostname Vinas-iMac.local machine x86_64 user vinagoghari FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh logyflag 0 usedti 0 FSGD /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd labelmask
/Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label
maskinv 0 glmdir /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled Loading y from /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh INFO: gd2mtx_method is dods Saving design matrix to /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/Xg.dat Normalized matrix condition is 400.101 Matrix condition is 1e+08 Found 148151 points in label. Pruning voxels by thr: 0.000000 Found 148025 voxels in mask Saving mask to /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/mask.mgh Reshaping mriglm->mask... search space = 73649.347769 ERROR: dimension mismatch between y and X. y has 3528 inputs, X has 49 rows.
My QDEC table has 49 subjects,2 groups, and 4 variables.
Many thanks, Wanda
-- Wanda Truong, MSc
Freesurfer mailing list 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 Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
Hi Wanda, I can see that it is failing, I just can't see why it is failing (and cannot replicate it here). Can you try a couple of things. First, make sure that the disk is not filling up. Next, can you try it with, say, half the subjects? Does this always occur or is it just recently?
doug
On 01/28/2014 04:36 PM, Wanda Truong wrote:
Hi Doug,
Attached is the full error message I get, starting from mris_preproc.
Thanks!! Wanda
On 28 January 2014 12:34, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Can you send the terminal output that starts with mris_preproc? On 01/28/2014 02:01 PM, Wanda Truong wrote: > Hi everyone, > > I get this error when running surface area analysis in QDEC: > > Vinas-iMac:~/Documents/Wanda/Wanda_SFS] vinagoghari% mri_glmfit --y > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh > --fsgd > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd > dods --glmdir > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled --surf > fsaverage lh --label > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label > --C > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Avg-Intercept-area.mat > --C > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Diff-Control-Relative-Intercept-area.mat > gdfReadHeader: reading > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd > INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. > Continuous Variable Means (all subjects) > 0 Age 40.6327 13.0176 > 1 IntraCranialVol 1.50352e+06 187456 > Class Means of each Continuous Variable > 1 GroupControl 38.8261 1480505.5707 <tel:1480505.5707> > 2 GroupRelative 42.2308 1523881.3029 > INFO: gd2mtx_method is dods > Reading source surface > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/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/vinagoghari/Documents/Wanda/Wanda_SFS > cmdline mri_glmfit --y > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh > --fsgd > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd > dods --glmdir > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled --surf > fsaverage lh --label > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label > --C > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Avg-Intercept-area.mat > --C > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Diff-Control-Relative-Intercept-area.mat > > sysname Darwin > hostname Vinas-iMac.local > machine x86_64 > user vinagoghari > FixVertexAreaFlag = 1 > UseMaskWithSmoothing 1 > OneSampleGroupMean 0 > y /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh > logyflag 0 > usedti 0 > FSGD /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd > labelmask > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label > maskinv 0 > glmdir /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled > IllCondOK 0 > ReScaleX 1 > DoFFx 0 > Creating output directory > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled > Loading y from > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh > INFO: gd2mtx_method is dods > Saving design matrix to > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/Xg.dat > Normalized matrix condition is 400.101 > Matrix condition is 1e+08 > Found 148151 points in label. > Pruning voxels by thr: 0.000000 > Found 148025 voxels in mask > Saving mask to > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/mask.mgh > Reshaping mriglm->mask... > search space = 73649.347769 > ERROR: dimension mismatch between y and X. > y has 3528 inputs, X has 49 rows. > > My QDEC table has 49 subjects,2 groups, and 4 variables. > > Many thanks, > Wanda > > -- > Wanda Truong, MSc > > > _______________________________________________ > 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 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.-- Wanda Truong, MSc
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
I currently have 40.64 GB of disk space (is this enough)?
I tried just now with half the subjects and it gave me the same error. I was successful in completing a thickness analysis using this same method, the only thing difference this time is that I am trying to do a surface area analysis.
Wanda
On 30 January 2014 13:12, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Hi Wanda, I can see that it is failing, I just can't see why it is failing (and cannot replicate it here). Can you try a couple of things. First, make sure that the disk is not filling up. Next, can you try it with, say, half the subjects? Does this always occur or is it just recently?
doug
On 01/28/2014 04:36 PM, Wanda Truong wrote:
Hi Doug,
Attached is the full error message I get, starting from mris_preproc.
Thanks!! Wanda
On 28 January 2014 12:34, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Can you send the terminal output that starts with mris_preproc? On 01/28/2014 02:01 PM, Wanda Truong wrote: > Hi everyone, > > I get this error when running surface area analysis in QDEC: > > Vinas-iMac:~/Documents/Wanda/Wanda_SFS] vinagoghari% mri_glmfit --y > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh > --fsgd >/Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd
> dods --glmdir > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled --surf > fsaverage lh --label >/Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label
> --C >/Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Avg-Intercept-area.mat
> --C >/Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Diff-Control-Relative-Intercept-area.mat
> gdfReadHeader: reading >/Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd
> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. > Continuous Variable Means (all subjects) > 0 Age 40.6327 13.0176 > 1 IntraCranialVol 1.50352e+06 187456 > Class Means of each Continuous Variable > 1 GroupControl 38.8261 1480505.5707 <tel:1480505.5707> > 2 GroupRelative 42.2308 1523881.3029 > INFO: gd2mtx_method is dods > Reading source surface >/Users/vinagoghari/Documents/Wanda/Wanda_SFS/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/vinagoghari/Documents/Wanda/Wanda_SFS > cmdline mri_glmfit --y > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh > --fsgd >/Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd
> dods --glmdir > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled --surf > fsaverage lh --label >/Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label
> --C >/Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Avg-Intercept-area.mat
> --C >/Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Diff-Control-Relative-Intercept-area.mat
> > sysname Darwin > hostname Vinas-iMac.local > machine x86_64 > user vinagoghari > FixVertexAreaFlag = 1 > UseMaskWithSmoothing 1 > OneSampleGroupMean 0 > y /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh > logyflag 0 > usedti 0 > FSGD /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd > labelmask >/Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label
> maskinv 0 > glmdir /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled > IllCondOK 0 > ReScaleX 1 > DoFFx 0 > Creating output directory > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled > Loading y from > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh > INFO: gd2mtx_method is dods > Saving design matrix to > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/Xg.dat > Normalized matrix condition is 400.101 > Matrix condition is 1e+08 > Found 148151 points in label. > Pruning voxels by thr: 0.000000 > Found 148025 voxels in mask > Saving mask to > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/mask.mgh > Reshaping mriglm->mask... > search space = 73649.347769 > ERROR: dimension mismatch between y and X. > y has 3528 inputs, X has 49 rows. > > My QDEC table has 49 subjects,2 groups, and 4 variables. > > Many thanks, > Wanda > > -- > Wanda Truong, MSc > > > _______________________________________________ > 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 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.-- Wanda Truong, MSc
Freesurfer mailing list 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 Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
That should be enough space. Can you try it with the other half? I'm thinking it might be one subject who is messing things up.
On 01/30/2014 04:04 PM, Wanda Truong wrote:
Hi Doug,
I currently have 40.64 GB of disk space (is this enough)?
I tried just now with half the subjects and it gave me the same error. I was successful in completing a thickness analysis using this same method, the only thing difference this time is that I am trying to do a surface area analysis.
Wanda
On 30 January 2014 13:12, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Wanda, I can see that it is failing, I just can't see why it is failing (and cannot replicate it here). Can you try a couple of things. First, make sure that the disk is not filling up. Next, can you try it with, say, half the subjects? Does this always occur or is it just recently? doug On 01/28/2014 04:36 PM, Wanda Truong wrote: > Hi Doug, > > Attached is the full error message I get, starting from mris_preproc. > > Thanks!! > Wanda > > > > On 28 January 2014 12:34, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > > Can you send the terminal output that starts with mris_preproc? > > On 01/28/2014 02:01 PM, Wanda Truong wrote: > > Hi everyone, > > > > I get this error when running surface area analysis in QDEC: > > > > Vinas-iMac:~/Documents/Wanda/Wanda_SFS] vinagoghari% mri_glmfit --y > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh > > --fsgd > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd > > dods --glmdir > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled --surf > > fsaverage lh --label > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label > > --C > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Avg-Intercept-area.mat > > --C > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Diff-Control-Relative-Intercept-area.mat > > gdfReadHeader: reading > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd > > INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. > > Continuous Variable Means (all subjects) > > 0 Age 40.6327 13.0176 > > 1 IntraCranialVol 1.50352e+06 187456 > > Class Means of each Continuous Variable > > 1 GroupControl 38.8261 1480505.5707 <tel:1480505.5707> <tel:1480505.5707 <tel:1480505.5707>> > > 2 GroupRelative 42.2308 1523881.3029 > > INFO: gd2mtx_method is dods > > Reading source surface > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/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/vinagoghari/Documents/Wanda/Wanda_SFS > > cmdline mri_glmfit --y > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh > > --fsgd > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd > > dods --glmdir > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled --surf > > fsaverage lh --label > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label > > --C > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Avg-Intercept-area.mat > > --C > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Diff-Control-Relative-Intercept-area.mat > > > > sysname Darwin > > hostname Vinas-iMac.local > > machine x86_64 > > user vinagoghari > > FixVertexAreaFlag = 1 > > UseMaskWithSmoothing 1 > > OneSampleGroupMean 0 > > y /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh > > logyflag 0 > > usedti 0 > > FSGD > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd > > labelmask > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label > > maskinv 0 > > glmdir /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled > > IllCondOK 0 > > ReScaleX 1 > > DoFFx 0 > > Creating output directory > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled > > Loading y from > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh > > INFO: gd2mtx_method is dods > > Saving design matrix to > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/Xg.dat > > Normalized matrix condition is 400.101 > > Matrix condition is 1e+08 > > Found 148151 points in label. > > Pruning voxels by thr: 0.000000 > > Found 148025 voxels in mask > > Saving mask to > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/mask.mgh > > Reshaping mriglm->mask... > > search space = 73649.347769 > > ERROR: dimension mismatch between y and X. > > y has 3528 inputs, X has 49 rows. > > > > My QDEC table has 49 subjects,2 groups, and 4 variables. > > > > Many thanks, > > Wanda > > > > -- > > Wanda Truong, MSc > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto: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. > > > > > -- > Wanda Truong, MSc > > > _______________________________________________ > 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 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Wanda Truong, MSc
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
Same thing happens with the other half. I'm wondering what file is used for Y - is it lh.area.fwhm10.fsaverage.mgh? and why does it have an input number that is different from X, which should be the number of subjects?
Thanks, Wanda
On 30 January 2014 14:19, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
That should be enough space. Can you try it with the other half? I'm thinking it might be one subject who is messing things up.
On 01/30/2014 04:04 PM, Wanda Truong wrote:
Hi Doug,
I currently have 40.64 GB of disk space (is this enough)?
I tried just now with half the subjects and it gave me the same error. I was successful in completing a thickness analysis using this same method, the only thing difference this time is that I am trying to do a surface area analysis.
Wanda
On 30 January 2014 13:12, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Wanda, I can see that it is failing, I just can't see why it is failing (and cannot replicate it here). Can you try a couple of things. First, make sure that the disk is not filling up. Next, can you tryit
with, say, half the subjects? Does this always occur or is it just recently? doug On 01/28/2014 04:36 PM, Wanda Truong wrote: > Hi Doug, > > Attached is the full error message I get, starting from mris_preproc. > > Thanks!! > Wanda > > > > On 28 January 2014 12:34, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > > Can you send the terminal output that starts with mris_preproc? > > On 01/28/2014 02:01 PM, Wanda Truong wrote: > > Hi everyone, > > > > I get this error when running surface area analysis in QDEC: > > > > Vinas-iMac:~/Documents/Wanda/Wanda_SFS] vinagoghari% mri_glmfit --y > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh > > --fsgd > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd > > dods --glmdir > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled --surf > > fsaverage lh --label > > >/Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label
> > --C > > >/Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Avg-Intercept-area.mat
> > --C > > >/Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Diff-Control-Relative-Intercept-area.mat
> > gdfReadHeader: reading > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd > > INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. > > Continuous Variable Means (all subjects) > > 0 Age 40.6327 13.0176 > > 1 IntraCranialVol 1.50352e+06 187456 > > Class Means of each Continuous Variable > > 1 GroupControl 38.8261 1480505.5707 <tel:1480505.5707> <tel:1480505.5707 <tel:1480505.5707>> > > 2 GroupRelative 42.2308 1523881.3029 > > INFO: gd2mtx_method is dods > > Reading source surface > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/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/vinagoghari/Documents/Wanda/Wanda_SFS > > cmdline mri_glmfit --y > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh > > --fsgd > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd > > dods --glmdir > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled --surf > > fsaverage lh --label > > >/Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label
> > --C > > >/Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Avg-Intercept-area.mat
> > --C > > >/Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Diff-Control-Relative-Intercept-area.mat
> > > > sysname Darwin > > hostname Vinas-iMac.local > > machine x86_64 > > user vinagoghari > > FixVertexAreaFlag = 1 > > UseMaskWithSmoothing 1 > > OneSampleGroupMean 0 > > y /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh > > logyflag 0 > > usedti 0 > > FSGD >/Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd
> > labelmask > > >/Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label
> > maskinv 0 > > glmdir /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled > > IllCondOK 0 > > ReScaleX 1 > > DoFFx 0 > > Creating output directory > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled > > Loading y from > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh > > INFO: gd2mtx_method is dods > > Saving design matrix to > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/Xg.dat > > Normalized matrix condition is 400.101 > > Matrix condition is 1e+08 > > Found 148151 points in label. > > Pruning voxels by thr: 0.000000 > > Found 148025 voxels in mask > > Saving mask to > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/mask.mgh > > Reshaping mriglm->mask... > > search space = 73649.347769 > > ERROR: dimension mismatch between y and X. > > y has 3528 inputs, X has 49 rows. > > > > My QDEC table has 49 subjects,2 groups, and 4 variables. > > > > Many thanks, > > Wanda > > > > -- > > Wanda Truong, MSc > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto: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. > > > > > -- > Wanda Truong, MSc > > > _______________________________________________ > 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 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Wanda Truong, MSc
Freesurfer mailing list 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 Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I don't know, it is a bit bizarre. Can you run mri_info on both lh.area.fwhm10.fsaverage.mgh and Untitled/y.mgh and send me the results?
On 01/30/2014 05:01 PM, Wanda Truong wrote:
Hi Doug,
Same thing happens with the other half. I'm wondering what file is used for Y - is it lh.area.fwhm10.fsaverage.mgh? and why does it have an input number that is different from X, which should be the number of subjects?
Thanks, Wanda
On 30 January 2014 14:19, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
That should be enough space. Can you try it with the other half? I'm thinking it might be one subject who is messing things up. On 01/30/2014 04:04 PM, Wanda Truong wrote: > Hi Doug, > > I currently have 40.64 GB of disk space (is this enough)? > > I tried just now with half the subjects and it gave me the same error. > I was successful in completing a thickness analysis using this same > method, the only thing difference this time is that I am trying to do > a surface area analysis. > > Wanda > > > On 30 January 2014 13:12, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > Hi Wanda, I can see that it is failing, I just can't see why it is > failing (and cannot replicate it here). Can you try a couple of > things. > First, make sure that the disk is not filling up. Next, can you try it > with, say, half the subjects? Does this always occur or is it just > recently? > > doug > > > On 01/28/2014 04:36 PM, Wanda Truong wrote: > > Hi Doug, > > > > Attached is the full error message I get, starting from > mris_preproc. > > > > Thanks!! > > Wanda > > > > > > > > On 28 January 2014 12:34, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > > > > > Can you send the terminal output that starts with mris_preproc? > > > > On 01/28/2014 02:01 PM, Wanda Truong wrote: > > > Hi everyone, > > > > > > I get this error when running surface area analysis in QDEC: > > > > > > Vinas-iMac:~/Documents/Wanda/Wanda_SFS] vinagoghari% > mri_glmfit --y > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh > > > --fsgd > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd > > > dods --glmdir > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled > --surf > > > fsaverage lh --label > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label > > > --C > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Avg-Intercept-area.mat > > > --C > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Diff-Control-Relative-Intercept-area.mat > > > gdfReadHeader: reading > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd > > > INFO: DeMeanFlag keyword not found, DeMeaning will NOT be > done. > > > Continuous Variable Means (all subjects) > > > 0 Age 40.6327 13.0176 > > > 1 IntraCranialVol 1.50352e+06 187456 > > > Class Means of each Continuous Variable > > > 1 GroupControl 38.8261 1480505.5707 <tel:1480505.5707> <tel:1480505.5707 <tel:1480505.5707>> > <tel:1480505.5707 <tel:1480505.5707> <tel:1480505.5707 <tel:1480505.5707>>> > > > 2 GroupRelative 42.2308 1523881.3029 > > > INFO: gd2mtx_method is dods > > > Reading source surface > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/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/vinagoghari/Documents/Wanda/Wanda_SFS > > > cmdline mri_glmfit --y > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh > > > --fsgd > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd > > > dods --glmdir > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled > --surf > > > fsaverage lh --label > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label > > > --C > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Avg-Intercept-area.mat > > > --C > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Diff-Control-Relative-Intercept-area.mat > > > > > > sysname Darwin > > > hostname Vinas-iMac.local > > > machine x86_64 > > > user vinagoghari > > > FixVertexAreaFlag = 1 > > > UseMaskWithSmoothing 1 > > > OneSampleGroupMean 0 > > > y > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh > > > logyflag 0 > > > usedti 0 > > > FSGD > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd > > > labelmask > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label > > > maskinv 0 > > > glmdir > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled > > > IllCondOK 0 > > > ReScaleX 1 > > > DoFFx 0 > > > Creating output directory > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled > > > Loading y from > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh > > > INFO: gd2mtx_method is dods > > > Saving design matrix to > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/Xg.dat > > > Normalized matrix condition is 400.101 > > > Matrix condition is 1e+08 > > > Found 148151 points in label. > > > Pruning voxels by thr: 0.000000 > > > Found 148025 voxels in mask > > > Saving mask to > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/mask.mgh > > > Reshaping mriglm->mask... > > > search space = 73649.347769 > > > ERROR: dimension mismatch between y and X. > > > y has 3528 inputs, X has 49 rows. > > > > > > My QDEC table has 49 subjects,2 groups, and 4 variables. > > > > > > Many thanks, > > > Wanda > > > > > > -- > > > Wanda Truong, MSc > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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. > > > > > > > > > > -- > > Wanda Truong, MSc > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > -- > Wanda Truong, MSc > > > _______________________________________________ > 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 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Wanda Truong, MSc
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
Here's what I get for mri_info lh.area.fwhm10.fsaverage.mgh:
[Vinas-iMac:~/Documents/Wanda/Wanda_SFS] vinagoghari% mri_info lh.area.fwhm10.fsaverage.mgh Volume information for lh.area.fwhm10.fsaverage.mgh type: MGH dimensions: 163842 x 1 x 1 x 46 voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 163842.000 dof: 0 xstart: -81921.0, xend: 81921.0 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 46 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000
talairach xfm : Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 81921.0000 0.0000 0.0000 1.0000 -0.5000 0.0000 -1.0000 0.0000 0.5000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 81921.0000 -0.0000 -0.0000 -1.0000 0.5000 -0.0000 1.0000 -0.0000 0.5000 0.0000 0.0000 0.0000 1.0000
[Vinas-iMac:~/Documents/Wanda/Wanda_SFS] vinagoghari% mri_info /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh Volume information for /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh type: MGH dimensions: 163842 x 1 x 1 x 1584 voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 163842.000 dof: 0 xstart: -81921.0, xend: 81921.0 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1584 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000
talairach xfm : Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 81921.0000 0.0000 0.0000 1.0000 -0.5000 0.0000 -1.0000 0.0000 0.5000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 81921.0000 -0.0000 -0.0000 -1.0000 0.5000 -0.0000 1.0000 -0.0000 0.5000 0.0000 0.0000 0.0000 1.0000
Thank you! Wanda
On 30 January 2014 15:30, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
I don't know, it is a bit bizarre. Can you run mri_info on both lh.area.fwhm10.fsaverage.mgh and Untitled/y.mgh and send me the results?
On 01/30/2014 05:01 PM, Wanda Truong wrote:
Hi Doug,
Same thing happens with the other half. I'm wondering what file is used for Y - is it lh.area.fwhm10.fsaverage.mgh? and why does it have an input number that is different from X, which should be the number of subjects?
Thanks, Wanda
On 30 January 2014 14:19, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
That should be enough space. Can you try it with the other half? I'm thinking it might be one subject who is messing things up. On 01/30/2014 04:04 PM, Wanda Truong wrote: > Hi Doug, > > I currently have 40.64 GB of disk space (is this enough)? > > I tried just now with half the subjects and it gave me the same error. > I was successful in completing a thickness analysis using this same > method, the only thing difference this time is that I am trying to do > a surface area analysis. > > Wanda > > > On 30 January 2014 13:12, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > Hi Wanda, I can see that it is failing, I just can't see why it is > failing (and cannot replicate it here). Can you try a couple of > things. > First, make sure that the disk is not filling up. Next, can you try it > with, say, half the subjects? Does this always occur or is it just > recently? > > doug > > > On 01/28/2014 04:36 PM, Wanda Truong wrote: > > Hi Doug, > > > > Attached is the full error message I get, starting from > mris_preproc. > > > > Thanks!! > > Wanda > > > > > > > > On 28 January 2014 12:34, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > > > > > Can you send the terminal output that starts with mris_preproc? > > > > On 01/28/2014 02:01 PM, Wanda Truong wrote: > > > Hi everyone, > > > > > > I get this error when running surface area analysis in QDEC: > > > > > > Vinas-iMac:~/Documents/Wanda/Wanda_SFS] vinagoghari% > mri_glmfit --y > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh > > > --fsgd > > > >/Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd
> > > dods --glmdir > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled > --surf > > > fsaverage lh --label > > > > > >/Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label
> > > --C > > > > > >/Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Avg-Intercept-area.mat
> > > --C > > > > > >/Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Diff-Control-Relative-Intercept-area.mat
> > > gdfReadHeader: reading > > > >/Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd
> > > INFO: DeMeanFlag keyword not found, DeMeaning will NOT be > done. > > > Continuous Variable Means (all subjects) > > > 0 Age 40.6327 13.0176 > > > 1 IntraCranialVol 1.50352e+06 187456 > > > Class Means of each Continuous Variable > > > 1 GroupControl 38.8261 1480505.5707 <tel:1480505.5707> <tel:1480505.5707 <tel:1480505.5707>> > <tel:1480505.5707 <tel:1480505.5707> <tel:1480505.5707 <tel:1480505.5707>>> > > > 2 GroupRelative 42.2308 1523881.3029 > > > INFO: gd2mtx_method is dods > > > Reading source surface > > > >/Users/vinagoghari/Documents/Wanda/Wanda_SFS/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/vinagoghari/Documents/Wanda/Wanda_SFS > > > cmdline mri_glmfit --y > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh > > > --fsgd > > > >/Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd
> > > dods --glmdir > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled > --surf > > > fsaverage lh --label > > > > > >/Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label
> > > --C > > > > > >/Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Avg-Intercept-area.mat
> > > --C > > > > > >/Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Diff-Control-Relative-Intercept-area.mat
> > > > > > sysname Darwin > > > hostname Vinas-iMac.local > > > machine x86_64 > > > user vinagoghari > > > FixVertexAreaFlag = 1 > > > UseMaskWithSmoothing 1 > > > OneSampleGroupMean 0 > > > y > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh > > > logyflag 0 > > > usedti 0 > > > FSGD > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd > > > labelmask > > > > > >/Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label
> > > maskinv 0 > > > glmdir > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled > > > IllCondOK 0 > > > ReScaleX 1 > > > DoFFx 0 > > > Creating output directory > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled > > > Loading y from > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh > > > INFO: gd2mtx_method is dods > > > Saving design matrix to > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/Xg.dat > > > Normalized matrix condition is 400.101 > > > Matrix condition is 1e+08 > > > Found 148151 points in label. > > > Pruning voxels by thr: 0.000000 > > > Found 148025 voxels in mask > > > Saving mask to > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/mask.mgh > > > Reshaping mriglm->mask... > > > search space = 73649.347769 > > > ERROR: dimension mismatch between y and X. > > > y has 3528 inputs, X has 49 rows. > > > > > > My QDEC table has 49 subjects,2 groups, and 4variables.
> > > > > > Many thanks, > > > Wanda > > > > > > -- > > > Wanda Truong, MSc > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: > >ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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. > > > > > > > > > > -- > > Wanda Truong, MSc > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > -- > Wanda Truong, MSc > > > _______________________________________________ > 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 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Wanda Truong, MSc
Freesurfer mailing list 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 Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
OK, it is y.mgh that is definitely wrong. Can you send me the result of ls -l y.mgh
On 01/31/2014 02:37 PM, Wanda Truong wrote:
Hi Doug,
Here's what I get for mri_info lh.area.fwhm10.fsaverage.mgh:
[Vinas-iMac:~/Documents/Wanda/Wanda_SFS] vinagoghari% mri_info lh.area.fwhm10.fsaverage.mgh Volume information for lh.area.fwhm10.fsaverage.mgh type: MGH dimensions: 163842 x 1 x 1 x 46 voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 163842.000 dof: 0 xstart: -81921.0, xend: 81921.0 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 46 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000
talairach xfm : Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 81921.0000 0.0000 0.0000 1.0000 -0.5000 0.0000 -1.0000 0.0000 0.5000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 81921.0000 -0.0000 -0.0000 -1.0000 0.5000 -0.0000 1.0000 -0.0000 0.5000 0.0000 0.0000 0.0000 1.0000
[Vinas-iMac:~/Documents/Wanda/Wanda_SFS] vinagoghari% mri_info /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh Volume information for /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh type: MGH dimensions: 163842 x 1 x 1 x 1584 voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 163842.000 dof: 0 xstart: -81921.0, xend: 81921.0 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1584 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000
talairach xfm : Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 81921.0000 0.0000 0.0000 1.0000 -0.5000 0.0000 -1.0000 0.0000 0.5000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 81921.0000 -0.0000 -0.0000 -1.0000 0.5000 -0.0000 1.0000 -0.0000 0.5000 0.0000 0.0000 0.0000 1.0000
Thank you! Wanda
On 30 January 2014 15:30, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I don't know, it is a bit bizarre. Can you run mri_info on both lh.area.fwhm10.fsaverage.mgh and Untitled/y.mgh and send me the results? On 01/30/2014 05:01 PM, Wanda Truong wrote: > Hi Doug, > > Same thing happens with the other half. I'm wondering what file is > used for Y - is it lh.area.fwhm10.fsaverage.mgh? and why does it have > an input number that is different from X, which should be the number > of subjects? > > Thanks, > Wanda > > > On 30 January 2014 14:19, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > > That should be enough space. Can you try it with the other half? I'm > thinking it might be one subject who is messing things up. > > On 01/30/2014 04:04 PM, Wanda Truong wrote: > > Hi Doug, > > > > I currently have 40.64 GB of disk space (is this enough)? > > > > I tried just now with half the subjects and it gave me the same > error. > > I was successful in completing a thickness analysis using this same > > method, the only thing difference this time is that I am trying > to do > > a surface area analysis. > > > > Wanda > > > > > > On 30 January 2014 13:12, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > > > Hi Wanda, I can see that it is failing, I just can't see why > it is > > failing (and cannot replicate it here). Can you try a couple of > > things. > > First, make sure that the disk is not filling up. Next, can > you try it > > with, say, half the subjects? Does this always occur or is > it just > > recently? > > > > doug > > > > > > On 01/28/2014 04:36 PM, Wanda Truong wrote: > > > Hi Doug, > > > > > > Attached is the full error message I get, starting from > > mris_preproc. > > > > > > Thanks!! > > > Wanda > > > > > > > > > > > > On 28 January 2014 12:34, Douglas N Greve > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>> wrote: > > > > > > > > > Can you send the terminal output that starts with > mris_preproc? > > > > > > On 01/28/2014 02:01 PM, Wanda Truong wrote: > > > > Hi everyone, > > > > > > > > I get this error when running surface area analysis > in QDEC: > > > > > > > > Vinas-iMac:~/Documents/Wanda/Wanda_SFS] vinagoghari% > > mri_glmfit --y > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh > > > > --fsgd > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd > > > > dods --glmdir > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled > > --surf > > > > fsaverage lh --label > > > > > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label > > > > --C > > > > > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Avg-Intercept-area.mat > > > > --C > > > > > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Diff-Control-Relative-Intercept-area.mat > > > > gdfReadHeader: reading > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd > > > > INFO: DeMeanFlag keyword not found, DeMeaning will > NOT be > > done. > > > > Continuous Variable Means (all subjects) > > > > 0 Age 40.6327 13.0176 > > > > 1 IntraCranialVol 1.50352e+06 187456 > > > > Class Means of each Continuous Variable > > > > 1 GroupControl 38.8261 1480505.5707 > <tel:1480505.5707> <tel:1480505.5707 <tel:1480505.5707>> > > <tel:1480505.5707 <tel:1480505.5707> <tel:1480505.5707 > <tel:1480505.5707>>> > > > > 2 GroupRelative 42.2308 1523881.3029 > > > > INFO: gd2mtx_method is dods > > > > Reading source surface > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/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/vinagoghari/Documents/Wanda/Wanda_SFS > > > > cmdline mri_glmfit --y > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh > > > > --fsgd > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd > > > > dods --glmdir > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled > > --surf > > > > fsaverage lh --label > > > > > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label > > > > --C > > > > > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Avg-Intercept-area.mat > > > > --C > > > > > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Diff-Control-Relative-Intercept-area.mat > > > > > > > > sysname Darwin > > > > hostname Vinas-iMac.local > > > > machine x86_64 > > > > user vinagoghari > > > > FixVertexAreaFlag = 1 > > > > UseMaskWithSmoothing 1 > > > > OneSampleGroupMean 0 > > > > y > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh > > > > logyflag 0 > > > > usedti 0 > > > > FSGD > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd > > > > labelmask > > > > > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label > > > > maskinv 0 > > > > glmdir > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled > > > > IllCondOK 0 > > > > ReScaleX 1 > > > > DoFFx 0 > > > > Creating output directory > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled > > > > Loading y from > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh > > > > INFO: gd2mtx_method is dods > > > > Saving design matrix to > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/Xg.dat > > > > Normalized matrix condition is 400.101 > > > > Matrix condition is 1e+08 > > > > Found 148151 points in label. > > > > Pruning voxels by thr: 0.000000 > > > > Found 148025 voxels in mask > > > > Saving mask to > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/mask.mgh > > > > Reshaping mriglm->mask... > > > > search space = 73649.347769 > > > > ERROR: dimension mismatch between y and X. > > > > y has 3528 inputs, X has 49 rows. > > > > > > > > My QDEC table has 49 subjects,2 groups, and 4 variables. > > > > > > > > Many thanks, > > > > Wanda > > > > > > > > -- > > > > Wanda Truong, MSc > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> > > > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> > > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> <tel:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>>>> > > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> <tel:617-726-7422 <tel:617-726-7422> > > <tel:617-726-7422 <tel:617-726-7422>>> > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > Outgoing: > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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. > > > > > > > > > > > > > > > -- > > > Wanda Truong, MSc > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > -- > > Wanda Truong, MSc > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > -- > Wanda Truong, MSc > > > _______________________________________________ > 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 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Wanda Truong, MSc
This is what I get: [Vinas-iMac:Wanda_SFS/qdec/Untitled] vinagoghari% ls -l y.mgh -rw-r--r-- 1 vinagoghari staff 1055844047 30 Jan 14:54 y.mgh
On 31 January 2014 12:41, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
OK, it is y.mgh that is definitely wrong. Can you send me the result of ls -l y.mgh
On 01/31/2014 02:37 PM, Wanda Truong wrote:
Hi Doug,
Here's what I get for mri_info lh.area.fwhm10.fsaverage.mgh:
[Vinas-iMac:~/Documents/Wanda/Wanda_SFS] vinagoghari% mri_info lh.area.fwhm10.fsaverage.mgh Volume information for lh.area.fwhm10.fsaverage.mgh type: MGH dimensions: 163842 x 1 x 1 x 46 voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 163842.000 dof: 0 xstart: -81921.0, xend: 81921.0 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 46 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000
talairach xfm : Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 81921.0000 0.0000 0.0000 1.0000 -0.5000 0.0000 -1.0000 0.0000 0.5000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 81921.0000 -0.0000 -0.0000 -1.0000 0.5000 -0.0000 1.0000 -0.0000 0.5000 0.0000 0.0000 0.0000 1.0000
[Vinas-iMac:~/Documents/Wanda/Wanda_SFS] vinagoghari% mri_info /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh Volume information for /Users/vinagoghari/Documents/ Wanda/Wanda_SFS/qdec/Untitled/y.mgh type: MGH dimensions: 163842 x 1 x 1 x 1584 voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 163842.000 dof: 0 xstart: -81921.0, xend: 81921.0 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1584 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000
talairach xfm : Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 81921.0000 0.0000 0.0000 1.0000 -0.5000 0.0000 -1.0000 0.0000 0.5000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 81921.0000 -0.0000 -0.0000 -1.0000 0.5000 -0.0000 1.0000 -0.0000 0.5000 0.0000 0.0000 0.0000 1.0000
Thank you! Wanda
On 30 January 2014 15:30, Douglas N Greve <greve@nmr.mgh.harvard.edumailto: greve@nmr.mgh.harvard.edu> wrote:
I don't know, it is a bit bizarre. Can you run mri_info on both lh.area.fwhm10.fsaverage.mgh and Untitled/y.mgh and send me the results? On 01/30/2014 05:01 PM, Wanda Truong wrote: > Hi Doug, > > Same thing happens with the other half. I'm wondering what file is > used for Y - is it lh.area.fwhm10.fsaverage.mgh? and why does it have > an input number that is different from X, which should be the number > of subjects? > > Thanks, > Wanda > > > On 30 January 2014 14:19, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > > That should be enough space. Can you try it with the other half? I'm > thinking it might be one subject who is messing things up. > > On 01/30/2014 04:04 PM, Wanda Truong wrote: > > Hi Doug, > > > > I currently have 40.64 GB of disk space (is this enough)? > > > > I tried just now with half the subjects and it gave me the same > error. > > I was successful in completing a thickness analysis using this same > > method, the only thing difference this time is that I am trying > to do > > a surface area analysis. > > > > Wanda > > > > > > On 30 January 2014 13:12, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > > > Hi Wanda, I can see that it is failing, I just can't see why > it is > > failing (and cannot replicate it here). Can you try a couple of > > things. > > First, make sure that the disk is not filling up. Next, can > you try it > > with, say, half the subjects? Does this always occur or is > it just > > recently? > > > > doug > > > > > > On 01/28/2014 04:36 PM, Wanda Truong wrote: > > > Hi Doug, > > > > > > Attached is the full error message I get, starting from > > mris_preproc. > > > > > > Thanks!! > > > Wanda > > > > > > > > > > > > On 28 January 2014 12:34, Douglas N Greve > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>> wrote: > > > > > > > > > Can you send the terminal output that starts with > mris_preproc? > > > > > > On 01/28/2014 02:01 PM, Wanda Truong wrote: > > > > Hi everyone, > > > > > > > > I get this error when running surface area analysis > in QDEC: > > > > > > > > Vinas-iMac:~/Documents/Wanda/Wanda_SFS] vinagoghari% > > mri_glmfit --y > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh > > > > --fsgd > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd > > > > dods --glmdir > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled > > --surf > > > > fsaverage lh --label > > > > > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label > > > > --C > > > > > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/ contrasts/lh-Avg-Intercept-area.mat > > > > --C > > > > > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/ contrasts/lh-Diff-Control-Relative-Intercept-area.mat > > > > gdfReadHeader: reading > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd > > > > INFO: DeMeanFlag keyword not found, DeMeaning will > NOT be > > done. > > > > Continuous Variable Means (all subjects) > > > > 0 Age 40.6327 13.0176 > > > > 1 IntraCranialVol 1.50352e+06 187456 > > > > Class Means of each Continuous Variable > > > > 1 GroupControl 38.8261 1480505.5707 > tel:1480505.5707 <tel:1480505.5707 tel:1480505.5707> > > <tel:1480505.5707 tel:1480505.5707 <tel:1480505.5707 > tel:1480505.5707>> > > > > 2 GroupRelative 42.2308 1523881.3029 > > > > INFO: gd2mtx_method is dods > > > > Reading source surface > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/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/vinagoghari/Documents/Wanda/Wanda_SFS > > > > cmdline mri_glmfit --y > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh > > > > --fsgd > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd > > > > dods --glmdir > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled > > --surf > > > > fsaverage lh --label > > > > > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/ label/lh.aparc.label > > > > --C > > > > > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/ contrasts/lh-Avg-Intercept-area.mat > > > > --C > > > > > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/ contrasts/lh-Diff-Control-Relative-Intercept-area.mat > > > > > > > > sysname Darwin > > > > hostname Vinas-iMac.local > > > > machine x86_64 > > > > user vinagoghari > > > > FixVertexAreaFlag = 1 > > > > UseMaskWithSmoothing 1 > > > > OneSampleGroupMean 0 > > > > y > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh > > > > logyflag 0 > > > > usedti 0 > > > > FSGD > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/ qdec.fsgd > > > > labelmask > > > > > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/ label/lh.aparc.label > > > > maskinv 0 > > > > glmdir > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled > > > > IllCondOK 0 > > > > ReScaleX 1 > > > > DoFFx 0 > > > > Creating output directory > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled > > > > Loading y from > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh > > > > INFO: gd2mtx_method is dods > > > > Saving design matrix to > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/Xg.dat > > > > Normalized matrix condition is 400.101 > > > > Matrix condition is 1e+08 > > > > Found 148151 points in label. > > > > Pruning voxels by thr: 0.000000 > > > > Found 148025 voxels in mask > > > > Saving mask to > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/mask.mgh > > > > Reshaping mriglm->mask... > > > > search space = 73649.347769 > > > > ERROR: dimension mismatch between y and X. > > > > y has 3528 inputs, X has 49 rows. > > > > > > > > My QDEC table has 49 subjects,2 groups, and 4 variables. > > > > > > > > Many thanks, > > > > Wanda > > > > > > > > -- > > > > Wanda Truong, MSc > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto: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 > <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu
> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> > > > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> > > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> <tel:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>>>> > > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> <tel:617-726-7422 <tel:617-726-7422> > > <tel:617-726-7422 <tel:617-726-7422>>> > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > FileDrop: https://gate.nmr.mgh.harvard. edu/filedrop2 > > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > http://www.nmr.mgh.harvard. edu/facility/filedrop/index.html > > > > http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > Outgoing: > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto: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. > > > > > > > > > > > > > > > -- > > > Wanda Truong, MSc > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto: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 <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu
> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/ greve/ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > -- > > Wanda Truong, MSc > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto: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 <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 tel:617-724-2358 > Fax: 617-726-7422 tel:617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > -- > Wanda Truong, MSc > > > _______________________________________________ > 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 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Wanda Truong, MSc
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
that looks like the right size. I am stumped. What version of FS are you using? Do you have access to other versions?
On 01/31/2014 02:50 PM, Wanda Truong wrote:
This is what I get: [Vinas-iMac:Wanda_SFS/qdec/Untitled] vinagoghari% ls -l y.mgh -rw-r--r-- 1 vinagoghari staff 1055844047 30 Jan 14:54 y.mgh
On 31 January 2014 12:41, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
OK, it is y.mgh that is definitely wrong. Can you send me the result of ls -l y.mgh On 01/31/2014 02:37 PM, Wanda Truong wrote: Hi Doug, Here's what I get for mri_info lh.area.fwhm10.fsaverage.mgh: [Vinas-iMac:~/Documents/Wanda/Wanda_SFS] vinagoghari% mri_info lh.area.fwhm10.fsaverage.mgh Volume information for lh.area.fwhm10.fsaverage.mgh type: MGH dimensions: 163842 x 1 x 1 x 46 voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 163842.000 dof: 0 xstart: -81921.0, xend: 81921.0 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 46 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000 talairach xfm : Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 0.0000 81921.0000 0.0000 0.0000 1.0000 -0.5000 0.0000 -1.0000 0.0000 0.5000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 0.0000 0.0000 81921.0000 -0.0000 -0.0000 -1.0000 0.5000 -0.0000 1.0000 -0.0000 0.5000 0.0000 0.0000 0.0000 1.0000 [Vinas-iMac:~/Documents/Wanda/Wanda_SFS] vinagoghari% mri_info /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh Volume information for /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh type: MGH dimensions: 163842 x 1 x 1 x 1584 voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 163842.000 dof: 0 xstart: -81921.0, xend: 81921.0 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1584 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000 talairach xfm : Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 0.0000 81921.0000 0.0000 0.0000 1.0000 -0.5000 0.0000 -1.0000 0.0000 0.5000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 0.0000 0.0000 81921.0000 -0.0000 -0.0000 -1.0000 0.5000 -0.0000 1.0000 -0.0000 0.5000 0.0000 0.0000 0.0000 1.0000 Thank you! Wanda On 30 January 2014 15:30, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: I don't know, it is a bit bizarre. Can you run mri_info on both lh.area.fwhm10.fsaverage.mgh and Untitled/y.mgh and send me the results? On 01/30/2014 05:01 PM, Wanda Truong wrote: > Hi Doug, > > Same thing happens with the other half. I'm wondering what file is > used for Y - is it lh.area.fwhm10.fsaverage.mgh? and why does it have > an input number that is different from X, which should be the number > of subjects? > > Thanks, > Wanda > > > On 30 January 2014 14:19, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > > That should be enough space. Can you try it with the other half? I'm > thinking it might be one subject who is messing things up. > > On 01/30/2014 04:04 PM, Wanda Truong wrote: > > Hi Doug, > > > > I currently have 40.64 GB of disk space (is this enough)? > > > > I tried just now with half the subjects and it gave me the same > error. > > I was successful in completing a thickness analysis using this same > > method, the only thing difference this time is that I am trying > to do > > a surface area analysis. > > > > Wanda > > > > > > On 30 January 2014 13:12, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>> wrote: > > > > Hi Wanda, I can see that it is failing, I just can't see why > it is > > failing (and cannot replicate it here). Can you try a couple of > > things. > > First, make sure that the disk is not filling up. Next, can > you try it > > with, say, half the subjects? Does this always occur or is > it just > > recently? > > > > doug > > > > > > On 01/28/2014 04:36 PM, Wanda Truong wrote: > > > Hi Doug, > > > > > > Attached is the full error message I get, starting from > > mris_preproc. > > > > > > Thanks!! > > > Wanda > > > > > > > > > > > > On 28 January 2014 12:34, Douglas N Greve > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> > > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>>> wrote: > > > > > > > > > Can you send the terminal output that starts with > mris_preproc? > > > > > > On 01/28/2014 02:01 PM, Wanda Truong wrote: > > > > Hi everyone, > > > > > > > > I get this error when running surface area analysis > in QDEC: > > > > > > > > Vinas-iMac:~/Documents/Wanda/Wanda_SFS] vinagoghari% > > mri_glmfit --y > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh > > > > --fsgd > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd > > > > dods --glmdir > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled > > --surf > > > > fsaverage lh --label > > > > > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label > > > > --C > > > > > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Avg-Intercept-area.mat > > > > --C > > > > > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Diff-Control-Relative-Intercept-area.mat > > > > gdfReadHeader: reading > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd > > > > INFO: DeMeanFlag keyword not found, DeMeaning will > NOT be > > done. > > > > Continuous Variable Means (all subjects) > > > > 0 Age 40.6327 13.0176 > > > > 1 IntraCranialVol 1.50352e+06 187456 > > > > Class Means of each Continuous Variable > > > > 1 GroupControl 38.8261 1480505.5707 <tel:1480505.5707> > <tel:1480505.5707 <tel:1480505.5707>> <tel:1480505.5707 <tel:1480505.5707> <tel:1480505.5707 <tel:1480505.5707>>> > > <tel:1480505.5707 <tel:1480505.5707> <tel:1480505.5707 <tel:1480505.5707>> <tel:1480505.5707 <tel:1480505.5707> > <tel:1480505.5707 <tel:1480505.5707>>>> > > > > 2 GroupRelative 42.2308 1523881.3029 > > > > INFO: gd2mtx_method is dods > > > > Reading source surface > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/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/vinagoghari/Documents/Wanda/Wanda_SFS > > > > cmdline mri_glmfit --y > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh > > > > --fsgd > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd > > > > dods --glmdir > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled > > --surf > > > > fsaverage lh --label > > > > > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label > > > > --C > > > > > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Avg-Intercept-area.mat > > > > --C > > > > > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Diff-Control-Relative-Intercept-area.mat > > > > > > > > sysname Darwin > > > > hostname Vinas-iMac.local > > > > machine x86_64 > > > > user vinagoghari > > > > FixVertexAreaFlag = 1 > > > > UseMaskWithSmoothing 1 > > > > OneSampleGroupMean 0 > > > > y > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh > > > > logyflag 0 > > > > usedti 0 > > > > FSGD > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd > > > > labelmask > > > > > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label > > > > maskinv 0 > > > > glmdir > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled > > > > IllCondOK 0 > > > > ReScaleX 1 > > > > DoFFx 0 > > > > Creating output directory > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled > > > > Loading y from > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh > > > > INFO: gd2mtx_method is dods > > > > Saving design matrix to > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/Xg.dat > > > > Normalized matrix condition is 400.101 > > > > Matrix condition is 1e+08 > > > > Found 148151 points in label. > > > > Pruning voxels by thr: 0.000000 > > > > Found 148025 voxels in mask > > > > Saving mask to > > > > > > /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/mask.mgh > > > > Reshaping mriglm->mask... > > > > search space = 73649.347769 > > > > ERROR: dimension mismatch between y and X. > > > > y has 3528 inputs, X has 49 rows. > > > > > > > > My QDEC table has 49 subjects,2 groups, and 4 variables. > > > > > > > > Many thanks, > > > > Wanda > > > > > > > > -- > > > > Wanda Truong, MSc > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto: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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>> > > > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>>> > > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>>>> > > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>>> <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>>>> <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>>>> > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > Outgoing: > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto: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. > > > > > > > > > > > > > > > -- > > > Wanda Truong, MSc > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto: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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> > > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > -- > > Wanda Truong, MSc > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto: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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > -- > Wanda Truong, MSc > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto: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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Wanda Truong, MSc -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/-- Wanda Truong, MSc
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Douglas N Greve -
Wanda Truong