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/transforms/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_average_vol-tmp-2117/orig-WB101_1/.mgh... ERROR: failure writing /study/NCCAM/Data/MRI/processed/structural/freesurfer//average/tmp/make_average_vol-tmp-2117/orig-WB101_1/.mgh /study2/NCCAM/Data/MRI/processed/structural/freesurfer ERROR: mri_convert failed.
Many thanks in advance, Martina
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
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.eduwrote:
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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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.eduwrote:
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/**compliancelinehttp://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.
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Martina Ly