Athena,

What name did you give the average subject? If one wasnt specified when make_average_subject was run, then the name 'average' is used as the default. Enter that name (average) into the 'Common space subject' text box and press enter.

You also probably want to inspect your average subject just to make sure that it looks ok. That is:

tksurfer average rh inflated tksurfer average lh inflated

Also, because you are using your own average subject, to conduct a group analysis, you will need to sample your subject data to that average subject. To do that, for each subject, run:

recon-all -s subjid -qcache -target average

Nick

On Wed, 2009-09-16 at 11:18 -0400, Drosos, Athena wrote:

Hello all,

I am trying to create an average subject from our pediatric brains and run group analyses with qdec.

After I ran the make_average_subject command, the terminal exited with no errors.

I then open qdec, load our data table, select our common-space subject, select our variables, and hit analyze. An error message pops up that reads: Couldn't find file: /Users/athenadrosos/CRPS/CTgroup_analysis/fsaverage/surf/rh.curv

When I look in this directory all ?h.curv, ?h.pial, ?h.sulc, ?h.thickness, ?h.sphere are shown as shortcuts. Are these files supposed to be created, where should they be, how can I fix this?

The qdec display opens with a gray inflated brain, and the only options on the left side of the gui are to select inflated, pial or white.

The end of the terminal window has errors that read:

Writing to /Users/athenadrosos/CRPS/CTgroup_analysis/qdec/rh.avgpermissions/contrasts.s ig.mgh reading group avg surface area 907 cm^2 from file ERROR: could not find volume /Users/athenadrosos/CRPS/CTgroup_analysis/fsaverage/surf/../mri/orig. Does it exist? Reading in average area /Users/athenadrosos/CRPS/CTgroup_analysis/fsaverage/surf/rh.white.avg.area.m gh reading group avg surface area 1131 cm^2 from file ERROR: could not find volume /Users/athenadrosos/CRPS/CTgroup_analysis/fsaverage/surf/../mri/orig. Does it exist? Reading in average area /Users/athenadrosos/CRPS/CTgroup_analysis/fsaverage/surf/rh.pial.avg.area.mg h reading group avg surface area 907 cm^2 from file ERROR: could not find volume /Users/athenadrosos/CRPS/CTgroup_analysis/fsaverage/surf/../mri/orig. Does it exist? Couldn't find file /Users/athenadrosos/CRPS/CTgroup_analysis/fsaverage/surf/rh.curv

============================================================ Completed loading of analyzed data.

How can I point to the correct /mri/orig. And where should it be? Is it created by the make_average_subject script?

Thank you so much for any help on this matter.

Athena

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer