Yes, the labels are in the subjects' label directories; putting the full path to the labels solved the problem. Thank you,
Prapti
-----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Thursday, 12 February 2009 8:39 AM To: Prapti Gautam Cc: Nick Schmansky; Freesurfer Mailing List Subject: Re: [Freesurfer] mri_label2label error
Are the labels in the subjects' 'label' directories? If not, then this is usually fixed by putting the full path to the labels. Can you double
check that that failed?
Prapti Gautam wrote:
Hi there,
I'm trying to copy the dlpfc label I've made using mri_label2label ,
but
keep getting the following error. I've tried putting in paths in the command line, but haven't been able to rectify the problem. I was wondering if this might be a permission issue with the freesurfer folders. Any help will be greatly appreciated.
I've pasted the error output below:
$ mri_label2label --srclabel lh.dlpfc.annot.label --srcsubject 40052_practice --trgsubject 40686_before --trglabel lh.dlpfc.annot.label --regmethod surface --hemi lh
srclabel = lh.dlpfc.annot.label srcsubject = 40052_practice trgsubject = 40686_before trglabel = lh.dlpfc.annot.label regmethod = surface
srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0
SUBJECTS_DIR is /media/storage2/proc/freesurfer/40_w2/40_w2_fs4/before/ FREESURFER_HOME is /usr/local/freesurfer_4.0.1 Loading source label. No such file or directory mri_label2label: could not open label file lh.dlpfc.annot.label Illegal seek ERROR reading lh.dlpfc.annot.label
Thanks,
Prapti
-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Friday, 6 February 2009 3:47 PM To: Prapti Gautam Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] creating label for dlpfc
Prapti,
You can use mri_label2label to do that, something like:
mri_label2label --srclabel rh.your_dlpfc.label \ --srcsubject subject_you_drew_label_on \ --trgsubject the_other_subject \ --trglabel rh.your_dlpfc.label \ --regmethod surface \ --hemi rh
so you draw the label on one subject (saved as rh.your_dlpfc.label in this example), and you would do this mri_label2label command for each subject that doesnt have a label. this assumes you've run freesurfer recon-all -all for each subject already, so that each has the
sphere.reg
file (which is how it does the label mapping).
see also mri_label2label --help.
Nick
On Fri, 2009-02-06 at 15:14 +1100, Prapti Gautam wrote:
Dear all,
I am trying to measure the volume of the dorsolateral prefrontal cortex in a large group of subjects. I have created a new label that only includes the dlpfc for a subject but realised that the same
label
file cannot be used on another subject. Has anyone created a customised ROI for dlpfc to use in a group of large subjects or can point me in the right direction ? The only other option I know is to individually create a label file for each subject which would be very time consuming.
Thanking you in advance,
Prapti
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