Description:
I am trying to extract from dtseries the info from the freesurfer parcellation (e.g. hippocampus ROIs e.g. 17 and 53). From the documentation we should be able to specific the roi
file (e.g. images/segmentation/freesurfer/mri/aparc+aseg_bold.nii.gz
or aparc+aseg_t1.nii.gz
) that we want to use in the input list file. However, I am getting 2 errors with either input file.
Call:
qunex_container fc_extract_roi_timeseries \
--container='/gpfs/gibbs/pi/n3/software/Singularity/qunex_suite-1.0.3.sif' \
--flist='/gpfs/gibbs/pi/n3/Studies/bihyper/processing/scripts/lists/gbc_pb15172_test.list' \
--roiinfo='/gpfs/gibbs/pi/n3/Studies/bihyper/analysis/seeds/bihyper_hippocampus_CAB-NP_freesurfer.names' \
--targetf="/gpfs/gibbs/pi/n3/Studies/bihyper/analysis/seeds/extract_hippocampus/" \
--options="roimethod:mean|savegroup:long|saveind:none|eventdata=mean"
Logs:
No logs created.
Output errors:
- when using
aparc+aseg_t1.nii.gz
→ command worked but outputs for left and right hippocampus are exactly the same.
- Location of output:
/gpfs/gibbs/pi/n3/Studies/bihyper/analysis/seeds/extract_hippocampus/extracted_hippocampus_CAB-NP_freesurfer.txt
- Exemple for 1 session:
roi V1_f1_max
CAB-NP-LeftHippocampus 0.019139
CAB-NP-RightHippocampus 0.016607
FS-LHipp 0.024058
FS-RHipp 0.024058
- when using
aparc+aseg_bold.nii.gz
Processing session pb13736 ... reading image file(s) ... 1 frames read, done.
... creating ROI mask
Matlab Error! Processing Failed!
reshape: SIZE is not divisible by the product of known dimensions (= 91282)
Goal is to run this extraction and also run fc_compute_seedmap
with this names file.
Thanks for your help!
Clara