NITRC ARTS biomarker Forum: help

RE: DTI Phase Encoding Direction

Jose Raniery — Tue, 17 Feb 2026 14:46:26 GMT

Dear Dr. Arfanakis,
<div> </div>
<div>Thank you very much for your prompt response.</div>
<div>I will check the output using 'vertical' then.</div>
<div> </div>
<div>Best,</div>

RE: DTI Phase Encoding Direction

Konstantinos Arfanakis — Thu, 12 Feb 2026 16:56:40 GMT

<div>Dear Jose,</div>
<div> </div>
<div>The ‘horizontal' and ‘vertical' terminology is exclusive to the TORTOISE software that is used inside ARTS. Based on our experience, the data should be processed with 'vertical'. We recommend that the processed diffusion data is checked to see if the distortions are corrected. We believe that 'horizontal' and 'vertical' correspond to 'row' and 'column' in image space, respectively. </div>
<div> </div>
<div>Regards,</div>
<div>Konstantinos</div>
<div> </div>

DTI Phase Encoding Direction

Jose Raniery — Wed, 11 Feb 2026 18:45:27 GMT

Hello,
I am currently trying to use ARTS with my dataset, and I noticed that the script expects the DTI Phase Encoding Direction to be specified simply as either vertical or horizontal.
This terminology is confusing from an MR neuroimaging perspective, since phase encoding is usually defined either in image space (ROW/COL, i/j axes) or in anatomical space (AP/PA, LR/RL, SI/IS), rather than vertical/horizontal. 
In my dataset, the metadata shows for example "PhaseEncodingAxis": "j" and "InPlanePhaseEncodingDirectionDICOM": "COL". By conventions, this corresponds to the column direction (j axis), which in image space is the column axis, but depending on viewer orientation and world-coordinate mapping, this may appear visually vertical or horizontal.
So how can I set phase encoding safely as vertical or horizontal?
Thank you very much for your time.
Cheers,
Raniery

Issues with installation of ARTs software on mac

Samuel Teshome — Wed, 17 Sep 2025 15:45:54 GMT

Having a lot of trouble installing the ARTs software, I was able to install singularity, homebrew, and virtualbox/vagrant. But I ran into an error when trying to us vagrant to start up the VM (screenshot of the exact error attached).
What I think is happening is that the VM is built for an Intel (x86_64) architecture, but my MacBook Air uses Apple Silicon (ARM architecture). Unfortunately, VirtualBox on Apple Silicon does not support running x86 virtual machines, which triggers the error: 'VBOX_E_Platform_arch_not_supported' . Has anyone else encountered this issue? How did you resolve it or work around it?"

CAT Preprocessing error for T1_n4_reorient

Louisa Wood — Thu, 03 Jul 2025 14:57:38 GMT

This is no longer an issue!

RE: WMH undersegmentation due to T1w-FLAIR registration failure

Arnold Evia Jr. — Thu, 19 Dec 2024 17:30:21 GMT

Hello Jenna,
For participants with poor T1w-FLAIR co-registration, I suggest providing ARTS with a registration matrix from a successful registration. ARTS accepts the registration matrix generated by FSL’s FLIRT.
The following command is how flirt is executed in ARTS. Note that the command is executed in the participant’s folder. The input image must be FLAIR_n4_reorient.nii.gz, and the reference image must be T1_n4_reorient.nii.gz. Both images are generated by ARTS and can be found in the participant’s FLAIR and T1 folders. You can modify the registration options as you want, but I recommend keeping dof as 6 for rigid body registration.
<pre class="western">flirt -in FLAIR/FLAIR_n4_reorient.nii.gz \
 -ref T1/T1_n4_reorient.nii \
 -searchrx -30 30 \
 -searchry -30 30 \
 -searchrz -30 30 \
 -usesqform \
 -coarsesearch 10 \
 -finesearch 5 \
 -dof 6 \
 -omat FLAIR/coreg_to_t1.mat \
 -inweight FLAIR/pre_brain_mask.nii.gz \
 -refweight T1/brain_mask.nii.gz \
 -out T1/FLAIR.nii.gz</pre>
Once you have an acceptable registration, copy the output matrix defined by the -omat option into a new folder called user_input. The user_input folder needs to be in the participant’s folder, at the same level as the QC folder, T1 folder, etc. The filename for the registration matrix must be coreg_to_t1.mat
Then, you can run ARTS on the participant again. ARTS will reprocess the data and use the registration matrix you provided instead of calculating the co-registration.
You can create a registration matrix and then rerun ARTS for each participant one at a time, or you can create the registration matrix for all the problematic participants and then rerun ARTS on all of them in one run. Let me know if anything is unclear in the above process.
-Arnold

WMH undersegmentation due to T1w-FLAIR registration failure

jblujus — Wed, 18 Dec 2024 20:20:30 GMT

Hi,
I hope you are doing well. I have processed approximately 100 datasets through the ARTS toolbox and just finished visual QC of the outputs. All look great except for a small subset, for which the WMH is substantially undersegmented due to registration issues between the T1w and FLAIR images. 
To solve this issue, is there a way to fix the co-registration and feed this into ARTS to regenerate the WMH map? Or would you suggest generating a binary WMH segmentation map via a secondary program (e.g., LST in SPM) and incorporating this map into a rerun of ARTS? 
Thanks in advance, Jenna

RE: Negative ARTS score

Konstantinos Arfanakis — Fri, 06 Sep 2024 13:36:17 GMT

Dear Jenna,
Thank you for your message. It is certainly possible to only have negative ARTS scores if your participants have lower likelihood of arteriolosclerosis. The lower the ARTS score, the lower the likelihood of arteriolosclerosis. In other words, the participant of your study that has the lowest score has lower likelihood of arteriolosclerosis than the participant that has the highest score. As the ARTS score increases so does the likelihood of arteriolosclerosis.
I hope this answers your question.
Feel free to post any other questions you may have.
Konstantinos
 
Originally posted by jblujus:
<blockquote>
Hello,
First, thank you for this great resource! I have implemented the ARTS toolbox in a small sample of older adults (N = 11, age range 60-79, mean age = 69) by feeding in DICOM files for T1, DWI, and FLAIR data. The QC outputs look fine. However, all of the resulting ARTS scores are negative. How would you interpret these scores? Would a negative score indicate the participant is likelier to have no or mild arteriolosclerosis than moderate to severe arteriolosclerosis?
Thank you,
Jenna 
</blockquote>

Negative ARTS score

jblujus — Fri, 06 Sep 2024 0:02:50 GMT

Hello,
First, thank you for this great resource! I have implemented the ARTS toolbox in a small sample of older adults (N = 11, age range 60-79, mean age = 69) by feeding in DICOM files for T1, DWI, and FLAIR data. The QC outputs look fine. However, all of the resulting ARTS scores are negative. How would you interpret these scores? Would a negative score indicate the participant is likelier to have no or mild arteriolosclerosis than moderate to severe arteriolosclerosis?
Thank you,
Jenna

RE: ARTS File Naming Bug

Konstantinos Arfanakis — Mon, 20 May 2024 22:24:36 GMT

Hi Mike,
The new version is now available. You should not have any problems with parentheses any more. Please let us know if you have any other questions.
Konstantinos