I think you have a typo on this line:
current_sphere_=standard_mesh_atlases/resample_fsaverage/fs_LR-deformed_to-fsaverage.${h}.sphere.164k_fs_LR.surf.gii
Peace,
Matt.
From: Nicola Toschi <[email protected]<mailto:[email protected]>>
Date: Friday, October 27, 2017 at 8:16 AM
To: "[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>, Matt
Glasser <[email protected]<mailto:[email protected]>>
Subject: Fwd: Mapping Myeling maps to fsaverage space - again....
Hi Matt,
I am sorry for writing directly (I am copying the list though).
I have been trying to post this message for a couple of days now, but it's not
showing up. Any idea what I am doing wrong?
Thanks!
Nicola
-------- Forwarded Message --------
Subject: Mapping Myeling maps to fsaverage space - again....
Date: Fri, 27 Oct 2017 13:07:51 +0200
From: Nicola Toschi <[email protected]><mailto:[email protected]>
To: hcp-users
<[email protected]><mailto:[email protected]>
Hello list,
I am sorry to revive an old questions (nad one that you have written a
wiki for), but I keep not being able to get my script to resample native
myelin maps to fsaverage to work (please see below for test script on 1
subject).
I'd be most grateful if anyone could take a look and let me knof if
anything jumps out. The error message i keep getting is only in step 5,
and it is
"ERROR: input metric has different number of nodes than input sphere"
Thank you very much in advance!
nicola
______________________________________________________________________________
base=/run/media/nicola/Seagate_Backup_Plus
sub=100307
for h in L R
do
#step 1
echo "Step 1" ${h}
sphere_in=${sub}/MNINonLinear/Native/${sub}.${h}.sphere.MSMAll.native.surf.gii
sphere_project_to=${base}/standard_mesh_atlases/fsaverage.${h}_LR.spherical_std.164k_fs_LR.surf.gii
sphere_unproject_from=${base}/standard_mesh_atlases/resample_fsaverage/fs_LR-deformed_to-fsaverage.${h}.sphere.164k_fs_LR.surf.gii
sphere_out=${sub}.L.sphere.fsaverage.native.surf.gii
wb_command -surface-sphere-project-unproject ${sphere_in}
${sphere_project_to} ${sphere_unproject_from} ${sphere_out}
#step 2
echo "step 2" ${h}
surface_in=${sub}/T1w/Native/${sub}.${h}.midthickness.native.surf.gii
current_sphere=${sphere_out}
new_sphere=standard_mesh_atlases/resample_fsaverage/fsaverage_std_sphere.${h}.164k_fsavg_${h}.surf.gii
surface_out=${sub}/T1w/${sub}.${h}.midthickness.164k_fs_${h}.surf.gii
surface_out2_uselater=${surface_out}
wb_command -surface-resample ${surface_in} ${current_sphere}
${new_sphere} BARYCENTRIC ${surface_out}
#step 3
echo "step 3" ${h}
surface_in=${sub}/T1w/Native/${sub}.${h}.midthickness.native.surf.gii
current_sphere=${sub}/MNINonLinear/Native/${sub}.${h}.sphere.MSMAll.native.surf.gii
new_sphere=${base}/standard_mesh_atlases/fsaverage.${h}_LR.spherical_std.164k_fs_LR.surf.gii
surface_out=${sub}/T1w/${sub}.${h}.midthickness_MSMALL.164k_fs_LR.surf.gii
surface_out3_uselater=${surface_out}
wb_command -surface-resample ${surface_in} ${current_sphere}
${new_sphere} BARYCENTRIC ${surface_out}
done
echo "step 4"
cifti_in=${sub}/MNINonLinear/${sub}.MyelinMap_BC_MSMAll.164k_fs_LR.dscalar.nii
metric_out_left=${sub}/T1w/${sub}.MyelinMap_BC_MSMAll.164k_fs_LR_L.func.gii
metric_out_right=${sub}/T1w/${sub}.MyelinMap_BC_MSMAll.164k_fs_LR_R.func.gii
wb_command -cifti-separate ${cifti_in} COLUMN -metric CORTEX_LEFT
${metric_out_left} -metric CORTEX_RIGHT ${metric_out_right}
for h in L R
do
echo "step 5" ${h}
#metric_in=${sub}/MNINonLinear/${sub}.MyelinMap_BC_MSMAll.164k_fs_LR.dscalar.nii
metric_in=${sub}/T1w/${sub}.MyelinMap_BC_MSMAll.164k_fs_LR_${h}.func.gii
current_sphere_=standard_mesh_atlases/resample_fsaverage/fs_LR-deformed_to-fsaverage.${h}.sphere.164k_fs_LR.surf.gii
new_sphere=standard_mesh_atlases/resample_fsaverage/fsaverage_std_sphere.${h}.164k_fsavg_${h}.surf.gii
metric_out=${sub}/T1w/${sub}.MyelinMap.${h}.164k_fsavg_6.func.gii
current_area=${surface_out3_uselater}
new_area=${surface_out2_uselater}
echo "NEW AREA is "${new_area}
wb_command -metric-resample ${metric_in} \
${current_sphere} \
${new_sphere} \
ADAP_BARY_AREA \
${metric_out} \
-area-surfs \
${current_area} \
${new_area}
done
______________________________________________________________________________
nicola@janus:/run/media/nicola/Seagate_Backup_Plus> bash map.sh
Step 1 L
step 2 L
step 3 L
Step 1 R
step 2 R
step 3 R
step 4
step 5 L
NEW AREA is 100307/T1w/100307.R.midthickness.164k_fs_R.surf.gii
While running:
/usr/local/workbench/bin_rh_linux64/../exe_rh_linux64/wb_command
-metric-resample
100307/T1w/100307.MyelinMap_BC_MSMAll.164k_fs_LR_L.func.gii
100307/MNINonLinear/Native/100307.R.sphere.MSMAll.native.surf.gii
standard_mesh_atlases/resample_fsaverage/fsaverage_std_sphere.L.164k_fsavg_L.surf.gii
ADAP_BARY_AREA 100307/T1w/100307.MyelinMap.L.164k_fsavg_6.func.gii
-area-surfs 100307/T1w/100307.R.midthickness_MSMALL.164k_fs_LR.surf.gii
100307/T1w/100307.R.midthickness.164k_fs_R.surf.gii
ERROR: input metric has different number of nodes than input sphere
step 5 R
NEW AREA is 100307/T1w/100307.R.midthickness.164k_fs_R.surf.gii
While running:
/usr/local/workbench/bin_rh_linux64/../exe_rh_linux64/wb_command
-metric-resample
100307/T1w/100307.MyelinMap_BC_MSMAll.164k_fs_LR_R.func.gii
100307/MNINonLinear/Native/100307.R.sphere.MSMAll.native.surf.gii
standard_mesh_atlases/resample_fsaverage/fsaverage_std_sphere.R.164k_fsavg_R.surf.gii
ADAP_BARY_AREA 100307/T1w/100307.MyelinMap.R.164k_fsavg_6.func.gii
-area-surfs 100307/T1w/100307.R.midthickness_MSMALL.164k_fs_LR.surf.gii
100307/T1w/100307.R.midthickness.164k_fs_R.surf.gii
ERROR: input metric has different number of nodes than input sphere
nicola@janus:/run/media/nicola/Seagate_Backup_Plus>
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