Error uploading dataset

I tried the TRPV1 dataset, and it worked fine on my machine, but when I want to upload my own data, I got an error message: “Relative paths are not specified in images, so data input must be a single file!” .
Here’s my .star file looks like:

_rlnMicrographName #1 
_rlnDefocusU #2 
_rlnDefocusV #3 
_rlnDefocusAngle #4
DOT1_0001_SumCorr.mrc 21439.410156 21022.109375 8.920000
DOT1_0002_SumCorr.mrc 20407.679688 20132.439453 1.930000

and my mrc files are in the same directory of the star file.
Can anyone give me some advice?

Don’t know why it’s not recognizing the paths, but if you want a quick workaround in the meantime, just use:

relion_preprocess --operate_on --operate_out out_stack

which will generate a stack with all your particles and a star file referencing it (although for some reason relion always adds an extra “mrcs” to the stack name). This is what I have been doing with no problems so far.


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Hi Huanyu,

Looks like your star file is missing _rlnImageName. That field is what we use to read star files and know both where the corresponding mrc file for a given particle is, and also the index into that mrc file (_rlnImageName has a format like <image_idx>@<mrc_file>).

Oliver’s suggestions seems like a good way to generate a new star file that contains the necessary fields.


Hi Oliver,

I have a related question. After the normal pre-processing procedures in relion, all particles are grouped per microscope image. Since I have hundreds, I just want to sweep them into one file and work with that.

Can you elaborate on the relion_preprocess method? I can’t get it to locate the correct input file (which you labeled I want it to locate a from the particle extraction.

The error:
MetaDataTable::read: File does not exists

Other thing I tried: Sweeping mrcs together can also be done with imod’s ‘newstack’, but then I don’t have a correct .star file obviously, because it refers to the initial filenames.

I would be very happy with a smart workaround.



Hi Gideon, if you have a in your relion dir, the following command should work:

relion_preprocess --operate_on --operate_out particles_for_cryosparc

This should generate two files -, and particles_for_cryosparc.mrcs.mrcs (which you should rename to particles_for_cryosparc.mrcs).

The error you give indicates that relion can’t find your file - are you sure it is in the same dir where you are running relion_preprocess, or if not are you giving the appropriate relative path (e.g. Particles/


I indeed triple checked the relative path before (folder/subfolder/, but it seems I still did something wrong there. I have copied the into the relion folder and now it works.

Thank you!