Could someone please explain the difference between the export options for fixed landmarks (fiducials) and semiLM patches in 3D Slicer? I’m not familiar with the .mrk.json, .json, .fcsv, and *.fcsv formats or the advantage of using one over the other. I’m planning to import these files into R for GM…

Well as you discovered, that’s one reason not to use excel. In excel save your original fcsv in csv format using save as. Open the csv file in notepad (or a simple text editor) and paste these on top of the file (including the # sign) save and try opening in Slicer now. # Markups fiducial file v…

First off, if you want to read markups into R, we have a few simple convenience functions that you might find useful. GitHub - muratmaga/SlicerMorph_Rexamples: Some functions to import SlicerMorph data into R (look at read.markups.fcsv.R and read.markups.json.R). Another option is to use the log_pa…

Great, thank you! This is exactly what I needed to know.

I’m so grateful for your infinite patience. New problem: I accidentally saved the file after I applied the text to columns function, and now when I try and reload the file into 3D Slicer it won’t read the fiducial coordinates. I tried using the TEXTJOIN function to rejoin the text into a single col…

I certainly have discovered a lot in the last 12 hours, including the sheer panic. I will not be saving those edited files again. Thank you, thank you, thank you! Maybe it’s time to lose the incessant need to meticulously check my data at every step.

[image] anromero: o lose the incessant need to meticulously check my data at every step. You should do that, particularly when you are learning the software and creating a workflow. The thing is you really shouldn’t be editing those fcsv, but just looking at the contents to make yourself fam…

Got it. Wasn’t doing any editing, just wanting to see what was in them in a way that didn’t make my eyes cross. But it’s easy enough to import them and do that in R, I suppose. Thanks again!

It takes just 2-3 commands to read or write control points from/to csv file - see examples here . While this is really easy to do, maybe we should expose csv (not fcsv) import/export of markups control point coordinates somewhere on the GUI.

[image] lassoan: While this is really easy to do, maybe we should expose csv (not fcsv) import/export of markups control point coordinates somewhere on the GUI. I would discourage this, because there is already enough confusion about LPS/RAS and how the format is changed thru times and how co…

I don’t mean it as a save format, strictly as an import/export format. But I fully agree that if we can educate people to move away from csv and use json instead then that’s much better.

By the way, Excel can import json files very nicely as a data source, the same way as it can generate live table views from various other databases (see step-by-step instructions below). So, Excel’s limitation is not that it cannot load JSON files, but in what analysis it can do on them and that you…

Export formats for markups

Support

jamesobutler (James Butler) March 15, 2022, 2:37pm 17

@rsookias See the following post below.

Topic		Replies	Views
Issue saving fiducials Support markups-fiducials , markups	2	485	February 24, 2022
MarkupsLine .fcsv loads as MarkupsFiducials Support markups	44	3316	September 11, 2020
Importing Landmarks from excel file into 3D Slicer Support markups-fiducials , file-import	9	2457	June 7, 2021
How to make proper landmark folder Support segmentation , markups-fiducials	19	1838	October 23, 2020
How to export all my JSON markup files into one table without running a GPA on it Support markups-fiducials	4	133	April 10, 2025

Export formats for markups

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