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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