Hi, Hopefully this is something simple. When I try to check the talairach transform for my subjects I type:
tkregister2 --mgz --s SM1C2_autoreconall --fstal --surf orig
and then I get this error:
subject = SM1C2_autoreconall Reading lh surface orig MRISread(/space/troy/3/users/retrievalnewest/SM1C2_autoreconall/surf/lh.orig): could not open file No such file or directory /usr/local/freesurfer/stable/bin/tkregister2.bin: could not read surface orig No such file or directory
orig.mgz is in the mri folder. why is it looking for lh.orig? Without the surf tag, tkregister loads the transform fine but I do not get the green surface outlines to assist with the registration. A more detailed transcription of the error is pasted below if needed. Thanks, Cameron
[troy:SM1C2_autoreconall] (nmr-std-env) cd .. [troy:retrievalnewest] (nmr-std-env) pwd /autofs/space/troy_003/users/retrievalnewest [troy:retrievalnewest] (nmr-std-env) tkregister2 --mgz --s SM1C2_autoreconall --fstal --surf orig
surfname set to orig INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.49.2.4 2006/03/27 21:48:16 greve Exp $ Diagnostic Level -1
%Mon Jan 8 14:55:02 2007>>> /usr/local/freesurfer/dev/mni/bin/minctracc -clobber -debug /tmp/mritotal_2618/src_8_dxyz.mnc /usr/local/freesurfer/dev/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc transforms/talairach.auto.xfm -transformation /tmp/mritotal_2618/src_8tmp2c.xfm -lsq9 -xcorr -model_mask /usr/local/freesurfer/dev/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc -center -2.114464 54.148323 -58.055290 -step 4 4 4 -tol 0.004 -simplex 2
talairach.xfm --------------------- 0.790 -0.163 0.022 8.207; 0.189 0.845 -0.535 -58.555; 0.093 0.573 0.939 13.334; 0.000 0.000 0.000 1.000; INFO: loading target /space/troy/3/users/retrievalnewest/SM1C2_autoreconall/mri/orig.mgz INFO: changing target type to float Ttarg: -------------------- -1.000 -0.000 0.000 125.117; 0.000 -0.000 1.000 -84.596; -0.000 -1.000 0.000 84.914; 0.000 0.000 0.000 1.000; INFO: loading movable /usr/local/freesurfer/stable/average/mni305.cor.mgz INFO: changing move type to float Tmov: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 0.790 -0.163 0.022 8.207; 0.189 0.845 -0.535 -58.555; 0.093 0.573 0.939 13.334; 0.000 0.000 0.000 1.000; subject = SM1C2_autoreconall Reading lh surface orig MRISread(/space/troy/3/users/retrievalnewest/SM1C2_autoreconall/surf/lh.orig): could not open file No such file or directory /usr/local/freesurfer/stable/bin/tkregister2.bin: could not read surface orig No such file or directory
Does the lh.orig surface exist for that subject?
Cameron Ellis wrote:
Hi, Hopefully this is something simple. When I try to check the talairach transform for my subjects I type:
tkregister2 --mgz --s SM1C2_autoreconall --fstal --surf orig
and then I get this error:
subject = SM1C2_autoreconall Reading lh surface orig MRISread(/space/troy/3/users/retrievalnewest/SM1C2_autoreconall/surf/lh.orig): could not open file No such file or directory /usr/local/freesurfer/stable/bin/tkregister2.bin: could not read surface orig No such file or directory
orig.mgz is in the mri folder. why is it looking for lh.orig? Without the surf tag, tkregister loads the transform fine but I do not get the green surface outlines to assist with the registration. A more detailed transcription of the error is pasted below if needed. Thanks, Cameron
[troy:SM1C2_autoreconall] (nmr-std-env) cd .. [troy:retrievalnewest] (nmr-std-env) pwd /autofs/space/troy_003/users/retrievalnewest [troy:retrievalnewest] (nmr-std-env) tkregister2 --mgz --s SM1C2_autoreconall --fstal --surf orig
surfname set to orig INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.49.2.4 2006/03/27 21:48:16 greve Exp $ Diagnostic Level -1
%Mon Jan 8 14:55:02 2007>>> /usr/local/freesurfer/dev/mni/bin/minctracc -clobber -debug /tmp/mritotal_2618/src_8_dxyz.mnc /usr/local/freesurfer/dev/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc transforms/talairach.auto.xfm -transformation /tmp/mritotal_2618/src_8tmp2c.xfm -lsq9 -xcorr -model_mask /usr/local/freesurfer/dev/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc -center -2.114464 54.148323 -58.055290 -step 4 4 4 -tol 0.004 -simplex 2
talairach.xfm --------------------- 0.790 -0.163 0.022 8.207; 0.189 0.845 -0.535 -58.555; 0.093 0.573 0.939 13.334; 0.000 0.000 0.000 1.000; INFO: loading target /space/troy/3/users/retrievalnewest/SM1C2_autoreconall/mri/orig.mgz INFO: changing target type to float Ttarg: -------------------- -1.000 -0.000 0.000 125.117; 0.000 -0.000 1.000 -84.596; -0.000 -1.000 0.000 84.914; 0.000 0.000 0.000 1.000; INFO: loading movable /usr/local/freesurfer/stable/average/mni305.cor.mgz INFO: changing move type to float Tmov: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 0.790 -0.163 0.022 8.207; 0.189 0.845 -0.535 -58.555; 0.093 0.573 0.939 13.334; 0.000 0.000 0.000 1.000; subject = SM1C2_autoreconall Reading lh surface orig MRISread(/space/troy/3/users/retrievalnewest/SM1C2_autoreconall/surf/lh.orig): could not open file No such file or directory /usr/local/freesurfer/stable/bin/tkregister2.bin: could not read surface orig No such file or directory
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Cameron,
If a bad talairach alignment prevents the creation of the surfaces (the files in the subjects surf directory), then just exclude the '--surf orig' flag from the tkregister2 cmd line. Use the 'Compare' button to switch between the template (the blurry image) and your subject. It is a lot more work to do the alignment this way, versus having the subject surface overlap the template, but you can still get the job done.
Nick
On Mon, 2007-01-08 at 16:33 -0500, Cameron Ellis wrote:
Hi, Hopefully this is something simple. When I try to check the talairach transform for my subjects I type:
tkregister2 --mgz --s SM1C2_autoreconall --fstal --surf orig
and then I get this error:
subject = SM1C2_autoreconall Reading lh surface orig MRISread(/space/troy/3/users/retrievalnewest/SM1C2_autoreconall/surf/lh.orig): could not open file No such file or directory /usr/local/freesurfer/stable/bin/tkregister2.bin: could not read surface orig No such file or directory
orig.mgz is in the mri folder. why is it looking for lh.orig? Without the surf tag, tkregister loads the transform fine but I do not get the green surface outlines to assist with the registration. A more detailed transcription of the error is pasted below if needed. Thanks, Cameron
[troy:SM1C2_autoreconall] (nmr-std-env) cd .. [troy:retrievalnewest] (nmr-std-env) pwd /autofs/space/troy_003/users/retrievalnewest [troy:retrievalnewest] (nmr-std-env) tkregister2 --mgz --s SM1C2_autoreconall --fstal --surf orig
surfname set to orig INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.49.2.4 2006/03/27 21:48:16 greve Exp $ Diagnostic Level -1
%Mon Jan 8 14:55:02 2007>>> /usr/local/freesurfer/dev/mni/bin/minctracc -clobber -debug /tmp/mritotal_2618/src_8_dxyz.mnc /usr/local/freesurfer/dev/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc transforms/talairach.auto.xfm -transformation /tmp/mritotal_2618/src_8tmp2c.xfm -lsq9 -xcorr -model_mask /usr/local/freesurfer/dev/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc -center -2.114464 54.148323 -58.055290 -step 4 4 4 -tol 0.004 -simplex 2
talairach.xfm --------------------- 0.790 -0.163 0.022 8.207; 0.189 0.845 -0.535 -58.555; 0.093 0.573 0.939 13.334; 0.000 0.000 0.000 1.000; INFO: loading target /space/troy/3/users/retrievalnewest/SM1C2_autoreconall/mri/orig.mgz INFO: changing target type to float Ttarg: -------------------- -1.000 -0.000 0.000 125.117; 0.000 -0.000 1.000 -84.596; -0.000 -1.000 0.000 84.914; 0.000 0.000 0.000 1.000; INFO: loading movable /usr/local/freesurfer/stable/average/mni305.cor.mgz INFO: changing move type to float Tmov: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 0.790 -0.163 0.022 8.207; 0.189 0.845 -0.535 -58.555; 0.093 0.573 0.939 13.334; 0.000 0.000 0.000 1.000; subject = SM1C2_autoreconall Reading lh surface orig MRISread(/space/troy/3/users/retrievalnewest/SM1C2_autoreconall/surf/lh.orig): could not open file No such file or directory /usr/local/freesurfer/stable/bin/tkregister2.bin: could not read surface orig No such file or directory
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello all,
I have just completed a group analysis of cortical thickness, including running the full Monte Carlo simulation to obtain cluster-wise multiple comparison corrections. Now I would like to know, for the clusters I'm interested in, how best to go about doing a statistical power analysis for an upcoming grant application, based on the completed analysis. Is there some easy way to extract the thickness for all individual subjects for a specified cluster, either for all vertices within the cluster, for the mean of all vertices within the cluster, or even for the peak vertex (maximum group difference), so that I can compute group mean and standard deviations for a measure of effect size?
Thanks,
Don
I guess the easiest way is to save the output cluster number (--ocn option to mri_surfcluster), then create a segmentation lookup table (like FreeSurferColorLUT.txt), one row for each of your clusters. Then run mri_segstats, passing the ocn as the --seg, your new color table as --ctab, the mri_glmfit --y input as --in, and use the --avgwf output of mri_segstats. The output in this case will be an average thickness (or whatever --y was) for each subject for each cluster. I have not tried this before, so let me know if this works.
doug
Don.Rojas@uchsc.edu wrote:
Hello all,
I have just completed a group analysis of cortical thickness, including running the full Monte Carlo simulation to obtain cluster-wise multiple comparison corrections. Now I would like to know, for the clusters I'm interested in, how best to go about doing a statistical power analysis for an upcoming grant application, based on the completed analysis. Is there some easy way to extract the thickness for all individual subjects for a specified cluster, either for all vertices within the cluster, for the mean of all vertices within the cluster, or even for the peak vertex (maximum group difference), so that I can compute group mean and standard deviations for a measure of effect size?
Thanks,
Don
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Cameron Ellis -
Don.Rojas＠UCHSC.edu -
Doug Greve -
Nick Schmansky