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
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