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.mart...@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 > <fis...@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 >>> >>> >>> >>> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. >> If the e-mail was sent to you in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> > >
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