Hello,
I have an annotation file for fsaverage, which I would like to map it to a particular subject. What would be the best way to do so?
I tried a combination of calls to mris_ca_train and mris_ca_label, but the latter gave me an error.
First I ran
mris_ca_train lh lh.sphere.reg fsaverage/label/<file>.annot fsaverage /tmp/<output>.gcs (where <file> and <output> are some file names)
and that executed without any problems.
Then I ran
mris_ca_label <subject_id> lh lh.sphere.reg /tmp/<output>.gcs ./lh.<newfile>.annot (here <subject_id> is some subjects' name, and <output> and <newfile> are some names)
and I got the error: could not open translation file $FREESURFER_HOME/Simple_surface_labels2002.txt
Maybe there is a simpler way to perform this task? Or maybe an easy way to fix this error? Any help will be much appreciated.
Thank you,
Peter
Hi Peter, mri_surf2surf is what you want to use for this. -Louis
On Mon, 17 Jun 2013, Peter Savadjiev wrote:
Hello,
I have an annotation file for fsaverage, which I would like to map it to a particular subject. What would be the best way to do so?
I tried a combination of calls to mris_ca_train and mris_ca_label, but the latter gave me an error.
First I ran
mris_ca_train lh lh.sphere.reg fsaverage/label/<file>.annot fsaverage /tmp/<output>.gcs (where <file> and <output> are some file names)
and that executed without any problems.
Then I ran
mris_ca_label <subject_id> lh lh.sphere.reg /tmp/<output>.gcs ./lh.<newfile>.annot (here <subject_id> is some subjects' name, and <output> and <newfile> are some names)
and I got the error: could not open translation file $FREESURFER_HOME/Simple_surface_labels2002.txt
Maybe there is a simpler way to perform this task? Or maybe an easy way to fix this error? Any help will be much appreciated.
Thank you,
Peter _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Louis,
When I try mri_surf2surf, I get the error ERROR: could not determine type of Yeo2011_7Networks_N1000.annot
Could it be because this is an annotation file, and not a surface such as ?h.curv, ?h.thickness etc? I guess I need something like "mri_annot2annot", does anything like this exist? I tried using mri_annotation2label, mri_label2label and then mri_label2annot, but that's quite complicated and didn't work.
Thanks, Peter
On 06/17/2013 03:00 PM, Louis Nicholas Vinke wrote:
Hi Peter, mri_surf2surf is what you want to use for this. -Louis
On Mon, 17 Jun 2013, Peter Savadjiev wrote:
Hello,
I have an annotation file for fsaverage, which I would like to map it to a particular subject. What would be the best way to do so?
I tried a combination of calls to mris_ca_train and mris_ca_label, but the latter gave me an error.
First I ran
mris_ca_train lh lh.sphere.reg fsaverage/label/<file>.annot fsaverage /tmp/<output>.gcs (where<file> and<output> are some file names)
and that executed without any problems.
Then I ran
mris_ca_label<subject_id> lh lh.sphere.reg /tmp/<output>.gcs ./lh.<newfile>.annot (here<subject_id> is some subjects' name, and<output> and<newfile> are some names)
and I got the error: could not open translation file $FREESURFER_HOME/Simple_surface_labels2002.txt
Maybe there is a simpler way to perform this task? Or maybe an easy way to fix this error? Any help will be much appreciated.
Thank you,
Peter _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
this is what mri_surf2surf is for. What was your command line? Did you check the help?
On Tue, 18 Jun 2013, Peter Savadjiev wrote:
Hi Louis,
When I try mri_surf2surf, I get the error ERROR: could not determine type of Yeo2011_7Networks_N1000.annot
Could it be because this is an annotation file, and not a surface such as ?h.curv, ?h.thickness etc? I guess I need something like "mri_annot2annot", does anything like this exist? I tried using mri_annotation2label, mri_label2label and then mri_label2annot, but that's quite complicated and didn't work.
Thanks, Peter
On 06/17/2013 03:00 PM, Louis Nicholas Vinke wrote:
Hi Peter, mri_surf2surf is what you want to use for this. -Louis
On Mon, 17 Jun 2013, Peter Savadjiev wrote:
Hello,
I have an annotation file for fsaverage, which I would like to map it to a particular subject. What would be the best way to do so?
I tried a combination of calls to mris_ca_train and mris_ca_label, but the latter gave me an error.
First I ran
mris_ca_train lh lh.sphere.reg fsaverage/label/<file>.annot fsaverage /tmp/<output>.gcs (where<file> and<output> are some file names)
and that executed without any problems.
Then I ran
mris_ca_label<subject_id> lh lh.sphere.reg /tmp/<output>.gcs ./lh.<newfile>.annot (here<subject_id> is some subjects' name, and<output> and<newfile> are some names)
and I got the error: could not open translation file $FREESURFER_HOME/Simple_surface_labels2002.txt
Maybe there is a simpler way to perform this task? Or maybe an easy way to fix this error? Any help will be much appreciated.
Thank you,
Peter _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Bruce,
This is the command line I used: mri_surf2surf --srcsubject fsaverage --srcsurfval Yeo2011_7Networks_N1000.annot --trgsubject case01053 --trgsurfval Yeo2011_7Networks_N1000.annot --hemi lh
and I get the error message: ERROR: could not determine type of Yeo2011_7Networks_N1000.annot
(I thought I may need to specify the full name, lh.Yeo2011_7Networks_N1000.annot, or even the full pathname, but either way I would get the same error)
Any help would be much appreciated, thank you very much!
Peter
On 06/18/2013 02:51 PM, Bruce Fischl wrote:
this is what mri_surf2surf is for. What was your command line? Did you check the help?
On Tue, 18 Jun 2013, Peter Savadjiev wrote:
Hi Louis,
When I try mri_surf2surf, I get the error ERROR: could not determine type of Yeo2011_7Networks_N1000.annot
Could it be because this is an annotation file, and not a surface such as ?h.curv, ?h.thickness etc? I guess I need something like "mri_annot2annot", does anything like this exist? I tried using mri_annotation2label, mri_label2label and then mri_label2annot, but that's quite complicated and didn't work.
Thanks, Peter
On 06/17/2013 03:00 PM, Louis Nicholas Vinke wrote:
Hi Peter, mri_surf2surf is what you want to use for this. -Louis
On Mon, 17 Jun 2013, Peter Savadjiev wrote:
Hello,
I have an annotation file for fsaverage, which I would like to map it to a particular subject. What would be the best way to do so?
I tried a combination of calls to mris_ca_train and mris_ca_label, but the latter gave me an error.
First I ran
mris_ca_train lh lh.sphere.reg fsaverage/label/<file>.annot fsaverage /tmp/<output>.gcs (where<file> and<output> are some file names)
and that executed without any problems.
Then I ran
mris_ca_label<subject_id> lh lh.sphere.reg /tmp/<output>.gcs ./lh.<newfile>.annot (here<subject_id> is some subjects' name, and<output> and<newfile> are some names)
and I got the error: could not open translation file $FREESURFER_HOME/Simple_surface_labels2002.txt
Maybe there is a simpler way to perform this task? Or maybe an easy way to fix this error? Any help will be much appreciated.
Thank you,
Peter _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Oh, I see what my error was: I need to use --sval-annot instead of --srcsurfval.
Thanks!
Peter
On 06/18/2013 02:51 PM, Bruce Fischl wrote:
this is what mri_surf2surf is for. What was your command line? Did you check the help?
On Tue, 18 Jun 2013, Peter Savadjiev wrote:
Hi Louis,
When I try mri_surf2surf, I get the error ERROR: could not determine type of Yeo2011_7Networks_N1000.annot
Could it be because this is an annotation file, and not a surface such as ?h.curv, ?h.thickness etc? I guess I need something like "mri_annot2annot", does anything like this exist? I tried using mri_annotation2label, mri_label2label and then mri_label2annot, but that's quite complicated and didn't work.
Thanks, Peter
On 06/17/2013 03:00 PM, Louis Nicholas Vinke wrote:
Hi Peter, mri_surf2surf is what you want to use for this. -Louis
On Mon, 17 Jun 2013, Peter Savadjiev wrote:
Hello,
I have an annotation file for fsaverage, which I would like to map it to a particular subject. What would be the best way to do so?
I tried a combination of calls to mris_ca_train and mris_ca_label, but the latter gave me an error.
First I ran
mris_ca_train lh lh.sphere.reg fsaverage/label/<file>.annot fsaverage /tmp/<output>.gcs (where<file> and<output> are some file names)
and that executed without any problems.
Then I ran
mris_ca_label<subject_id> lh lh.sphere.reg /tmp/<output>.gcs ./lh.<newfile>.annot (here<subject_id> is some subjects' name, and<output> and<newfile> are some names)
and I got the error: could not open translation file $FREESURFER_HOME/Simple_surface_labels2002.txt
Maybe there is a simpler way to perform this task? Or maybe an easy way to fix this error? Any help will be much appreciated.
Thank you,
Peter _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Louis Nicholas Vinke -
Peter Savadjiev