NITRC Robust Brain Extraction (ROBEX) Forum: open-discussion

Cannot handle filename that contains white space

Yann Legrands — Fri, 18 Mar 2022 12:08:08 GMT

Version: 1.2
Platform: windows 10

Steps to reproduce:
.\ROBEX.exe "C:\filename.nii" "C:\res ult.nii"

Step 4 of 9: calculating features...** ERROR (nifti_image_write_hdr_img2): cannot open output file 'C:\temp_res ult.nii\phqghume\1.nii.gz'

Robex will create a temporary folder. If the desired striipped image filename contains white space, e.g. "C:\res ult.nii", the temporary folder would be [b]"C:\temp_res\"[/b], however, the code still looks for a folder named [b]"C:\temp_res ult.nii\"[/b], thus lead to error.

does support other sequence

poorneshwaran — Tue, 20 Apr 2021 13:08:43 GMT

HI,
As of the research paper, robex perform good in t1. will it support for different modalities like t2,dwi?

Error at step 9

Stephen L. — Fri, 28 Feb 2020 13:35:56 GMT

Hello,

I wanted to try your very interesting software for brain extraction on my Windows 10 computer, but I get an error at step 9:

Step 9 of 9: warping back to original space...ExceptionObject caught !

itk::ExceptionObject (01136A6C)
Location: "unknown"
File: ..\..\..\..\..\InsightToolkit-4.4.2\Modules\IO\NIFTI\src\itkNiftiImageIO.cxx
Line: 500
Description: itk::ERROR: NiftiImageIO(1BC3BC38): nifti_image_load failed for file: C:\Giga\myanalysis\mip.nii

It does not look like a big error, simply a IO error. I can confirm the file is accessible, and in fact the whole pipeline works except for this very last step, so I am not sure what is happening here.

Consistently excludes hypothalamus

Brandon Vaughan — Mon, 26 Aug 2019 20:37:48 GMT

I am finding that the ROBEX does a great job at getting a clean extraction except for one thing -- the hypothalamus is almost always cut out of the image. Is there a way to decrease the amount of tissue ROBEX cuts out so that it is likely to capture the hypothalamus?

Unresponsive Robex in Slic3r

Dailen Brown — Fri, 14 Jun 2019 3:05:26 GMT

I'm trying to use the Robex brain extractor in Slic3r, but when I hit apply, nothing seem to happen. I tried to find the ne volume that was created and display it to check if the extraction worked, but every time I do slic3r just closes. I'm pretty new to all this and would appreciate any help.

runROBEX with BSD or OS X (readlink -f issue)

John Muschelli — Mon, 18 Sep 2017 15:32:47 GMT

Having the same problem - is there any resolution on this?

License of ROBEX source code

Stefan Zellmann — Wed, 02 Aug 2017 10:44:03 GMT

Hi,

it says on the webpage that ROBEX uses ITK and maxflow and thus exposes the BSD and Apache 2.0 licenses. On the nitrc download page, under "Specification/Licenses", BSD, GPL, and LGPL are mentioned.

The license file coming with the sources only refers to the licenses of the 3rd party packages from above, and the source code is not annotated with license headers.

I now wonder under which license the actual ROBEX sources (not the 3rd party libs) are distributed. I hope I haven't overlooked something, but I can't find this info anywhere - would be nice if you could tell me.

runROBEX with BSD or OS X (readlink -f issue)

LabNuero CogDevel — Mon, 31 Jul 2017 16:32:58 GMT

OS X (Mac) uses BSD's readlink which does not have the -f option used by runROBEX.sh
[quote]readlink: illegal option -- f[/quote]

I'm getting around this by redefining readlink at the top of the runROBEX.sh file [code]
realreadlink=$(which readlink)
[ -z "$realreadlink" ] && exiterr "the 'readlink' program is not installed on your system. $0 cannot be run!"
if ! readlink -f test >/dev/null 2>/dev/null; then
readlink() {
[ "$1" == "-f" ] && shift # skip to the next thing if we have "-f"
path="$(cd $(dirname "$1");pwd)"
rp=$($realreadlink "$path") # returns empty if not a link
[ -z "$rp" ] && rp="$path"
fullpath="$path/$(basename "$1")"
echo "$fullpath"
}
fi[/code]

ROBEX installation for windows 32-bit

tannaz akbarpour — Sat, 10 Jun 2017 6:47:33 GMT

hello everyone
I tried to install ROBEX win32 version. when running ROBEX.exe , no process is started.
what is the problem?

RE: Using ROBEX for animal MRI brain extraction

Gamal Akabani — Sun, 27 Nov 2016 1:37:10 GMT

Hi,

I am having the same issue. I need to extract the brain of pigs for logitudinal registration.

Thank you,

GA