Does that run only have 1 time point? On 04/27/2016 06:29 PM, Mcnorgan, Christopher wrote: > > Hi, > > First, thanks to Doug Greve for helping me isolate my previous > problem, which turns out to have resulted from a conflicting fsl > installation. Now that that's resolved, I'm having a problem on a > first-level analysis. > > > In preparation for calling selxavg3-sess, I am running preproc-sess on > an individual and am running into an error where the reported DOF is > 0. The peculiar thing is that these steps work fine with another data > set -- from the same participant at an earlier time point doing the > same task with the same parameters (though the procedure to convert > the DICOM to nii data was not necessarily the same at both time > points; unfortunately the original DICOM files are unavailable to me). > I am able to take the time1 data to the completion of FS-FAST, but the > time2 data halts at this error. > > > A potentially relevant difference between the two data sets is that, > for the functional data that worked, I was able to carry out these > steps on the original f.nii file, whereas problematic data was first > converted to a .mgz file in Slicer to fix an "unsupported slice timing > pattern 5" error (a search in the archives suggested that Slicer would > solve this problem, which seems to be the case). I'm not clear where > this dof value comes from and if anything about the .nii file header > can be manipulated to fix the problem. The fact that the slice timing > pattern was off in the problematic data might be symptomatic of a > generally compromised .nii header (SPM doesn't seem to do anything > with much of this header information, allowing some invalid header > information to go undetected). > > > Thanks > > > Below is the tail end of the preproc-sess output where it reports the > error: > > > $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ > cwd /home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T2_501/bold > cmdline mri_glmfit --table > > /home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T2_501/bold/029/tmpdir.mcdat2extreg.26783/table.dat > --glmdir > > /home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T2_501/bold/029/tmpdir.mcdat2extreg.26783/glm > --osgm --y-out > > /home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T2_501/bold/029/tmpdir.mcdat2extreg.26783/y.out.nii > --pca > sysname Linux > hostname accumbens > machine x86_64 > user chris > FixVertexAreaFlag = 1 > UseMaskWithSmoothing 1 > OneSampleGroupMean 1 > y > > /home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T2_501/bold/029/tmpdir.mcdat2extreg.26783/table.dat > logyflag 0 > usedti 0 > glmdir > > /home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T2_501/bold/029/tmpdir.mcdat2extreg.26783/glm > IllCondOK 0 > ReScaleX 1 > DoFFx 0 > Creating output directory > > /home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T2_501/bold/029/tmpdir.mcdat2extreg.26783/glm > Loading y from > > /home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T2_501/bold/029/tmpdir.mcdat2extreg.26783/table.dat > Found 6 data colums > Found 1 data rows > Saving design matrix to > > /home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T2_501/bold/029/tmpdir.mcdat2extreg.26783/glm/Xg.dat > Normalized matrix condition is 1 > Matrix condition is 1 > search space = 6.000000 > DOF = 0 > ERROR: DOF = 0 > > > > > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center [email protected] 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 [email protected] 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.
