I found the fix. My subject list in my fsgd file had an extra forward slash (i.e. WB101_1/). After deleting that forward slash, make_average_volume is now running normally. I also deleted the forward slash from freesurfer/ for the SUBJECTS env variable for consistency's sake. 

On Sun, Feb 12, 2012 at 5:24 PM, Martina Ly <ly.martina@gmail.com> wrote:
Thanks for your reply Bruce. I used:

export SUBJECTS_DIR=/study/NCCAM/Data/MRI/processed/structural/freesurfer/

make_average_subject --out average --fsgd mnp_ltm_v2.fsgd

On Sun, Feb 12, 2012 at 5:16 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
can you give us the command line you used? And what the SUBJECTS env variable was (if you used it)?


On Sun, 12 Feb 2012, Martina Ly wrote:

Dear freesurfers, I am coming across an error in the beginning of
make_average_volume of make_average_subject where mri_convert fails.
make_average_surface finished without a problem so hopefully that part will
not need to be re-run. I've check permissions, cpu space, paths but couldn't
find anything... Any help/suggestions would greatly appreciated. Below is
the error message:

INFO: Applying transformation from file/study/NCCAM/Data/MRI/processed/structural/freesurfer//WB101_1//mri/transfo
rms/talairach.xfm...
---------------------------------
INFO: Transform Matrix (linear_ras_to_ras)
 1.156   0.062   0.028  -2.110;
-0.102   1.113   0.318  -31.524;
-0.029  -0.322   1.218   4.598;
 0.000   0.000   0.000   1.000;
INFO: Transform dst volume info is not used (valid flag = 0).
INFO: assumes that the dst volume given is the same as the dst for the
transform
mghWrite(/study/NCCAM/Data/MRI/processed/structural/freesurfer//average/tmp
/make_average_vol-tmp-2117/orig-WB101_1/.mgh, -1): could not open file
---------------------------------
Applying LTAtransformInterp (resample_type 1)
writing to/study/NCCAM/Data/MRI/processed/structural/freesurfer//average/tmp/make_ave
rage_vol-tmp-2117/orig-WB101_1/.mgh...
ERROR: failure writing/study/NCCAM/Data/MRI/processed/structural/freesurfer//average/tmp/make_ave
rage_vol-tmp-2117/orig-WB101_1/.mgh
/study2/NCCAM/Data/MRI/processed/structural/freesurfer
ERROR: mri_convert failed.

Many thanks in advance,
Martina





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