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 <gr...@nmr.mgh.harvard.edu > <mailto:gr...@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 > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@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 > > <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> > > > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@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 > > > gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> > > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@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 > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@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 > gr...@nmr.mgh.harvard.edu <mailto:gr...@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 gr...@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
