Hello freesurfer experts,
I am having difficulties using mris_ca_train and mris_ca_label. I am trying to get third party-software to accept a user-defined parcellation in the form of a .gcs file, which I created from sample data using mris_ca_train. I have reproduced the portion of the workflow that is buggy. When I run the software, it calls mris_ca_train, followed by mris_ca_label and mri_annotation2label. On mri_annotation2label, it produces the following output and writes no label files:
[truffles:mridat] (nmr-stable5.1-env) mri_annotation2label --subject nmr00535_FS --hemi lh --annotation icotest --outdir nmr00535_FS/label/regen subject = nmr00535_FS annotation = icotest hemi = lh outdir = nmr00535_FS/label/regen surface = white
Reading surface /autofs/cluster/neuromind/rlaplant/mridat/nmr00535_FS/surf/lh.white Loading annotations from /autofs/cluster/neuromind/rlaplant/mridat/nmr00535_FS/label/lh.icotest.annot reading colortable from annotation file... colortable with 643 entries read (originally /cluster/neuromind/rlaplant/mridat/nmr00535_FS/label/ico3_regenerated_clut_lh.txt) Seg base 0 *max index = -1*
The annotation at this point is corrupted and cannot be opened in matlab and shows up empty in tksurfer. The annotation I started with as input to mris_ca_train shows up just fine. The commands i used for mris_ca_train and mris_ca_label are as follows:
mris_ca_train -t $TEST_DIR/ico3_clut.txt lh sphere.reg ico3_morph $SUBJECTS $TEST_DIR/lh_test.gcs
mris_ca_label nmr00535_FS lh sphere.reg $TEST_DIR/lh_test.gcs $TEST_DIR/nmr00535_FS/label/lh.icotest.annot
Can anyone point out where my labels are being clobbered?
thanks, R
Hi Roan So /autofs/cluster/neuromind/rlaplant/mridat/nmr00535_FS/label/lh.icotest.annot Looks ok when loaded in tksurfer? Bruce
On Dec 5, 2012, at 4:34 PM, Roan LaPlante rlaplant@nmr.mgh.harvard.edu wrote:
/autofs/cluster/neuromind/rlaplant/mridat/nmr00535_FS/label/lh.icotest.annot
No, it is empty in tksurfer. But lh.ico3_morph.annot shows up fine. Somewhere in mris_ca_train or mris_ca_label something seems to go wrong.
thanks, R
On Wed, Dec 5, 2012 at 8:20 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Roan So
/autofs/cluster/neuromind/rlaplant/mridat/nmr00535_FS/label/lh.icotest.annot Looks ok when loaded in tksurfer? Bruce
On Dec 5, 2012, at 4:34 PM, Roan LaPlante rlaplant@nmr.mgh.harvard.edu wrote:
/autofs/cluster/neuromind/rlaplant/mridat/nmr00535_FS/label/lh.icotest.annot
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
sorry, I don't have the original email anymore. How did you create lh.ico3_morph.annot?
On Wed, 5 Dec 2012, Roan LaPlante wrote:
No, it is empty in tksurfer. But lh.ico3_morph.annot shows up fine. Somewhere in mris_ca_train or mris_ca_label something seems to go wrong.
thanks, R
On Wed, Dec 5, 2012 at 8:20 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Roan So /autofs/cluster/neuromind/rlaplant/mridat/nmr00535_FS/label/lh.icotest.anno t Looks ok when loaded in tksurfer? Bruce
On Dec 5, 2012, at 4:34 PM, Roan LaPlante <rlaplant@nmr.mgh.harvard.edu> wrote: >/autofs/cluster/neuromind/rlaplant/mridat/nmr00535_FS/label/lh.icotest.anno t The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.-- Roan LaPlante Athinoula A. Martinos Center for Biomedical Imaging
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Roan LaPlante