Hi Jeff, I found the problem. The first line looks something like this:
#!ascii label /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_R01BTX_pat9_sess1_recon/label/MedOrbitofrontal_LH_CD_R01BTX_pat9_sess1.label , from subject ontal_LH_CD_R01BTX_pat9_sess1.label vox2ras=TkReg
when mri_vol2roi was originallywritten, it was not expecting such long file names. The "DidntWork" label has a length that is a little too long. The "DidWork" is just short enough. You can just edit the label to remove the pathpart of the .label file (ie,"/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_R01BTX_pat9_sess1_recon/label" . That information is not used at all, so it can actually be anything.
doug
On 05/15/2013 03:01 PM, jwaugh@nmr.mgh.harvard.edu wrote:
Thank you Doug. I really appreciate your help. I've attached two label files from the same subject, one that worked and one that didn't. Both were created using mri_cor2label and used aparc+aseg.mgz. I have viewed the non-working labels using tkmedit and they look good. Again, I appreciate your help - right now a clever idea is held up by this func2roi problem!
- Jeff
Can you put it in a place where I can see it? I tried to look, but I did
not have perms. You can also just email it to me
On 5/14/13 6:26 PM, jwaugh@nmr.mgh.harvard.edu wrote:
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, Jeffit 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 _______________________________________________ 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 greve@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/
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Douglas N Greve