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edickie / ciftify

The tools of the Human Connectome Project (HCP) adapted for working with non-HCP datasets
https://edickie.github.io/ciftify/
MIT License
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Trouble with cifitfy_subject_fmri #144

Open martahedl opened 3 years ago

martahedl commented 3 years ago

Hi! Lately, I've been experiencing problems when running ciftify_subject_fmri. It seems like the subcortical structures are no longer recognized; I'm getting the following warnings/erros:

WARNING: volume label file has empty definition of 'ACCUMBENS_LEFT',

for 15 subcortical/cerebellar structures. It seems like these types of errors/warnings have co-occured with updating FreeSurfer to 7.1.0, but I don't know whether there is an association between the two. Any help would be appreciated!

Thanks in advance, Marlene.

martahedl commented 3 years ago

To add to my post above, I'd like to add that I've been running the following command

ciftify_subject_fmri --surf-reg MSMSulc --ciftify-work-dir ${HCP_DIR} --already-in-MNI --OutputSurfDiagnostics ${CLEANED_FUNC_STANDARD} ${SUBJECT_ID}-${SESSION_ID} rest

I should also mention that running ciftify_recon_all still finishes without error.

Thanks again, Marlene.

marcelzwiers commented 2 years ago

I am also seeing that warning (using FS 6), but I also get an error afterwards:

[..]
WARNING: volume label file has empty definition of 'THALAMUS_RIGHT', skipping

cmd: wb_command -cifti-resample /data/marzwi/46603245.dccn-l029.dccn.nl/tmpp86_9pzg/temp_subject_dilate.dtseries.nii COLUMN /data/marzwi/46603245.dccn-l029.dccn.nl/tmpp86_9pzg/temp_template.dlabel.nii COLUMN ADAP_BARY_AREA CUBIC /data/marzwi/46603245.dccn-l029.dccn.nl/tmpp86_9pzg/temp_atlas.dtseries.nii -volume-predilate 10 
 Failed with returncode 255

While running:
/opt/hcp-workbench/1.3.2/bin_rh_linux64/../exe_rh_linux64/wb_command -cifti-resample /data/marzwi/46603245.dccn-l029.dccn.nl/tmpp86_9pzg/temp_subject_dilate.dtseries.nii COLUMN /data/marzwi/46603245.dccn-l029.dccn.nl/tmpp86_9pzg/temp_template.dlabel.nii COLUMN ADAP_BARY_AREA CUBIC /data/marzwi/46603245.dccn-l029.dccn.nl/tmpp86_9pzg/temp_atlas.dtseries.nii -volume-predilate 10

ERROR: AccumbensLeft volume model missing from input cifti
marcelzwiers commented 2 years ago

Could it have to do with the workbench version? I also tried v1.5.0, which gave the same error as above (v1.3.2), but v1.1.1 produced a different error:

WARNING: Failed to parse caret volume extension: CaretVolumeExtension encountered an unexpected element: MetaData, line number: 4 column number: 13

cmd: wb_command -cifti-create-dense-timeseries /data/marzwi/46603245.dccn-l029.dccn.nl/tmp99y7e5n7/temp_subject.dtseries.nii -volume /project/3015089.01/deep-brain_EPI/bids_GE_bold2bold_flatw/derivatives/ciftify/003/MNINonLinear/Results/cmrr2p0isomb3me2TR2095/cmrr2p0isomb3me2TR2095.nii.gz /data/marzwi/46603245.dccn-l029.dccn.nl/tmp99y7e5n7/ROIs.nii.gz 
 Failed with returncode 255

While running:
/opt/hcp-workbench/1.1.1/bin_rh_linux64/../exe_rh_linux64/wb_command -cifti-create-dense-timeseries /data/marzwi/46603245.dccn-l029.dccn.nl/tmp99y7e5n7/temp_subject.dtseries.nii -volume /project/3015089.01/deep-brain_EPI/bids_GE_bold2bold_flatw/derivatives/ciftify/003/MNINonLinear/Results/cmrr2p0isomb3me2TR2095/cmrr2p0isomb3me2TR2095.nii.gz /data/marzwi/46603245.dccn-l029.dccn.nl/tmp99y7e5n7/ROIs.nii.gz

ERROR: parcel volume is not of type label
marcelzwiers commented 2 years ago

I am totally stuck, any help would be really appreciated :-)