Hello all,
Here's an error that i got while running group analysis on a couple of subjects...i checked the rh.orig file and the rh.sphere.reg and i could open both using tksurfer.
Reading /ud/chacko/freesurfer/subjects/AD_norm_cor25all111/AD_norm_group_analysis/subj1/surf/rh.sphere.reg mrisReadTriangleFile(/ud/chacko/freesurfer/subjects/AD_norm_cor25all111/AD_norm_group_analysis/subj1/surf/rh.orig): surface doesn't match /ud/chacko/freesurfer/subjects/AD_norm_cor25all111/AD_norm_group_analysis/subj1/surf/rh.sphere.reg
No such file or directory mrisReadTriangleFile failed.
No such file or directory MRISreadOriginalProperties: could not read surface file orig No such file or directory mris_make_average_surface: could not read orig file for rh.
No such file or directory
Thanks in advance
Chacko.
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Hello all, I also noticed that the program searches for the talairach transform in the wrong directory??could someone tell me why..
THanks
Chacko.
#@# processing subject 8/25 subj13... Reading /ud/chacko/freesurfer/subjects/AD_norm_cor25all111/AD_norm_group_analysis/subj13/surf/rh.sphere.reg Talairach transform /ud/chacko/freesurfer/subjects/AD_norm_cor25all111/maketemp/AD/subj13/mri/transforms/talairach.xfm does not exist ... Loading tal xfm file /ud/chacko/freesurfer/subjects/AD_norm_cor25all111/AD_norm_group_analysis/subj13/mri/transforms/talairach.xfm Read /ud/chacko/freesurfer/subjects/AD_norm_cor25all111/AD_norm_group_analysis/subj13/mri/T1.mgz Surface area: 802.9 cm^2 Applying linear transform Talairach transform /ud/chacko/freesurfer/subjects/AD_norm_cor25all111/maketemp/AD/subj13/mri/transforms/talairach.xfm does not exist ... Loading tal xfm file /ud/chacko/freesurfer/subjects/AD_norm_cor25all111/AD_norm_group_analysis/subj13/mri/transforms/talairach.xfm
--- Chacko Cherian chacko_cherian@yahoo.com wrote:
Hello all,
Here's an error that i got while running group analysis on a couple of subjects...i checked the rh.orig file and the rh.sphere.reg and i could open both using tksurfer.
Reading
/ud/chacko/freesurfer/subjects/AD_norm_cor25all111/AD_norm_group_analysis/subj1/surf/rh.sphere.reg
mrisReadTriangleFile(/ud/chacko/freesurfer/subjects/AD_norm_cor25all111/AD_norm_group_analysis/subj1/surf/rh.orig):
surface doesn't match
/ud/chacko/freesurfer/subjects/AD_norm_cor25all111/AD_norm_group_analysis/subj1/surf/rh.sphere.reg
No such file or directory mrisReadTriangleFile failed.
No such file or directory MRISreadOriginalProperties: could not read surface file orig No such file or directory mris_make_average_surface: could not read orig file for rh.
No such file or directory
Thanks in advance
Chacko.
____________________________________________________________________________________
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When you first run the recon, it stores the full path of the talairach file in the mgh file, then tries to read that path. If you move the recons, then the path will be wrong. But it eventually finds the right one.
Chacko Cherian wrote:
Hello all, I also noticed that the program searches for the talairach transform in the wrong directory??could someone tell me why..
THanks
Chacko.
#@# processing subject 8/25 subj13... Reading /ud/chacko/freesurfer/subjects/AD_norm_cor25all111/AD_norm_group_analysis/subj13/surf/rh.sphere.reg Talairach transform /ud/chacko/freesurfer/subjects/AD_norm_cor25all111/maketemp/AD/subj13/mri/transforms/talairach.xfm does not exist ... Loading tal xfm file /ud/chacko/freesurfer/subjects/AD_norm_cor25all111/AD_norm_group_analysis/subj13/mri/transforms/talairach.xfm Read /ud/chacko/freesurfer/subjects/AD_norm_cor25all111/AD_norm_group_analysis/subj13/mri/T1.mgz Surface area: 802.9 cm^2 Applying linear transform Talairach transform /ud/chacko/freesurfer/subjects/AD_norm_cor25all111/maketemp/AD/subj13/mri/transforms/talairach.xfm does not exist ... Loading tal xfm file /ud/chacko/freesurfer/subjects/AD_norm_cor25all111/AD_norm_group_analysis/subj13/mri/transforms/talairach.xfm
--- Chacko Cherian chacko_cherian@yahoo.com wrote:
Hello all,
Here's an error that i got while running group analysis on a couple of subjects...i checked the rh.orig file and the rh.sphere.reg and i could open both using tksurfer.
Reading
/ud/chacko/freesurfer/subjects/AD_norm_cor25all111/AD_norm_group_analysis/subj1/surf/rh.sphere.reg
mrisReadTriangleFile(/ud/chacko/freesurfer/subjects/AD_norm_cor25all111/AD_norm_group_analysis/subj1/surf/rh.orig):
surface doesn't match
/ud/chacko/freesurfer/subjects/AD_norm_cor25all111/AD_norm_group_analysis/subj1/surf/rh.sphere.reg
No such file or directory mrisReadTriangleFile failed.
No such file or directory MRISreadOriginalProperties: could not read surface file orig No such file or directory mris_make_average_surface: could not read orig file for rh.
No such file or directory
Thanks in advance
Chacko.
Finding fabulous fares is fun. Let Yahoo! FareChase search your favorite travel sites to find flight and hotel bargains. http://farechase.yahoo.com/promo-generic-14795097 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
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Chacko,
The absolute path of the tal .xfm file is stored in the mgz file. If the data is moved, then the code, when it doesnt find the .xfm file in the absolute path, will perform a relative search, which was successful, as shown in the log. The log message could be improved in this respect.
Nick
On Thu, 2007-01-25 at 11:31 -0800, Chacko Cherian wrote:
Hello all, I also noticed that the program searches for the talairach transform in the wrong directory??could someone tell me why..
THanks
Chacko.
#@# processing subject 8/25 subj13... Reading /ud/chacko/freesurfer/subjects/AD_norm_cor25all111/AD_norm_group_analysis/subj13/surf/rh.sphere.reg Talairach transform /ud/chacko/freesurfer/subjects/AD_norm_cor25all111/maketemp/AD/subj13/mri/transforms/talairach.xfm does not exist ... Loading tal xfm file /ud/chacko/freesurfer/subjects/AD_norm_cor25all111/AD_norm_group_analysis/subj13/mri/transforms/talairach.xfm Read /ud/chacko/freesurfer/subjects/AD_norm_cor25all111/AD_norm_group_analysis/subj13/mri/T1.mgz Surface area: 802.9 cm^2 Applying linear transform Talairach transform /ud/chacko/freesurfer/subjects/AD_norm_cor25all111/maketemp/AD/subj13/mri/transforms/talairach.xfm does not exist ... Loading tal xfm file /ud/chacko/freesurfer/subjects/AD_norm_cor25all111/AD_norm_group_analysis/subj13/mri/transforms/talairach.xfm
--- Chacko Cherian chacko_cherian@yahoo.com wrote:
Hello all,
Here's an error that i got while running group analysis on a couple of subjects...i checked the rh.orig file and the rh.sphere.reg and i could open both using tksurfer.
Reading
/ud/chacko/freesurfer/subjects/AD_norm_cor25all111/AD_norm_group_analysis/subj1/surf/rh.sphere.reg
mrisReadTriangleFile(/ud/chacko/freesurfer/subjects/AD_norm_cor25all111/AD_norm_group_analysis/subj1/surf/rh.orig):
surface doesn't match
/ud/chacko/freesurfer/subjects/AD_norm_cor25all111/AD_norm_group_analysis/subj1/surf/rh.sphere.reg
No such file or directory mrisReadTriangleFile failed.
No such file or directory MRISreadOriginalProperties: could not read surface file orig No such file or directory mris_make_average_surface: could not read orig file for rh.
No such file or directory
Thanks in advance
Chacko.
Finding fabulous fares is fun. Let Yahoo! FareChase search your favorite travel sites to find flight and hotel bargains. http://farechase.yahoo.com/promo-generic-14795097 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
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It looks like the sphere.reg is out of synch with the orig. Check their data, sphere.reg should be newer.
Chacko Cherian wrote:
Hello all,
Here's an error that i got while running group analysis on a couple of subjects...i checked the rh.orig file and the rh.sphere.reg and i could open both using tksurfer.
Reading /ud/chacko/freesurfer/subjects/AD_norm_cor25all111/AD_norm_group_analysis/subj1/surf/rh.sphere.reg mrisReadTriangleFile(/ud/chacko/freesurfer/subjects/AD_norm_cor25all111/AD_norm_group_analysis/subj1/surf/rh.orig): surface doesn't match /ud/chacko/freesurfer/subjects/AD_norm_cor25all111/AD_norm_group_analysis/subj1/surf/rh.sphere.reg
No such file or directory mrisReadTriangleFile failed.
No such file or directory MRISreadOriginalProperties: could not read surface file orig No such file or directory mris_make_average_surface: could not read orig file for rh.
No such file or directory
Thanks in advance
Chacko.
Finding fabulous fares is fun. Let Yahoo! FareChase search your favorite travel sites to find flight and hotel bargains. http://farechase.yahoo.com/promo-generic-14795097 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Chacko Cherian -
Doug Greve -
Nick Schmansky