I have checked the label file directly - it is of comparable size with others, and has the same structure. I've rerun the mri_cor2label command and regenerated the labels for all subjects. Most confusing, func2roi works for some subjects in this cohort and not others. In contrast, the whole cohort has been used with parallel labels with no problem.
If there is "something wrong with [my] label", what things could it be? Has anyone else seen this particular error message?
Thanks, Jeff
it looks like ther is something wrong with that label On 05/14/2013 04:34 PM, jwaugh@nmr.mgh.harvard.edu wrote:
Hello Freesurfers, I would appreciate any advice or help you can provide.
I am using the following command, run under Stable 3 (to keep the current analysis comparable to prior papers):
func2roi-sess -roidef MedOrbitofrontal_LH_t6_0_sm5_0thresh -analysis newROIs_tap_lh_long_CD_R01BTX_pat9_sess1_sm5 -maskcontrast newROIs_tap_lh_long_CD_R01BTX_pat9_sess1_sm5_contrast -labelfile /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_R01BTX_pat9_sess1_recon/label/MedOrbitofrontal_LH_CD_R01BTX_pat9_sess1.label -maskthresh 6.0 -masktail pos -maskmap t -s CD_R01BTX_pat9_sess1 -df sessdirfile
The error message is as follows (it outputs exactly like this, apparently intermingled with another output): ras2vox src (tkreg) Qsrc ------------- -0.320 -0.000 -0.000 32.000; -0.000 -0.00mri_vol2roi: could not scan # of lines from /autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_R01BTX_pat9_sess1_recon/label/MedOrbitofrontal_LH_CD_R01BTX_pat9_sess1.label No such file or directory 0 -0.320 32.000; 0.000 0.200 0.000 15.000; 0.000 0.000 0.000 1.000;
I have never seen this error before - any suggestions why I'm getting it? This same command structure ran perfectly on separate ROIs over the last few days. I confirmed that the corresponding .label files are structured identically to those for other ROIs that worked.
Just in case it's helpful, this is the command that I used to generate the .label files: mri_cor2label --c /cluster/ablood/1/${experimental_directory}/${recons_directory}/${identifier}_recon/mri/aparc+aseg.mgz --id 1014 --l /cluster/ablood/1/${experimental_directory}/${recons_directory}/${identifier}_recon/label/MedOrbitofrontal_LH_${identifier}.label.
Thank you! Jeff
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