[prev in list] [next in list] [prev in thread] [next in thread]
List: wekalist
Subject: [Wekalist] Help: Nifti Loader
From: Leonel Rangel Jimenez <leonel.rangeljime () gmail ! com>
Date: 2020-05-13 21:50:07
Message-ID: CAAxw3po2LWAHQ_5u6tbDsjTZ7HKCNp-0aZq6Jv08RPeHiAU05Q () mail ! gmail ! com
[Download RAW message or body]
[Attachment #2 (multipart/alternative)]
I am new to machine learning and am looking for some assistance in working
with Weka and MRI T1 datasets. I found the Weka Nifti Loader package and
installed it, hoping to be able to load several T1s at once and then
combine three classifiers for the purpose of having a way to automatically
run QC on these files as seen in the following paper:
Alfaro-Almagro F, Jenkinson M, Bangerter NK, et al. Image processing and
Quality Control for the first 10,000 brain imaging datasets from UK
Biobank. NeuroImage. 2018;166:400-424. doi:10.1016/j.neuroimage.2017.10.034
<https://www.sciencedirect.com/science/article/pii/S1053811917308613>
However, the paper has very little documentation on the use of Weka, so
upon trying to load the directory (in which I have ~100 T1s), I got an
error stating that 'no such file or directory exists' despite it being
easily found in my Mac's Finder. So Far, I have only attempted this within
the Weka UI since I have no experience in using the terminal commands for
Weka. I also attempted to work with a single .nii.gz file but got the
OutOfMemory error.
Organization of the Nifti files is also a little confusing given the
package description that 'The directory to be loaded must contain as many
subdirectories as there are classes of MRI data.' Not entirely sure what is
meant by this, so how should the files be organized?
Any suggestions for how to load the files? Or are the number/organization
of files and size the issue here?
If anyone has an example directory to run trials with, I would greatly
appreciate it. Please let me know if I can provide anymore information
regarding this.
[Attachment #5 (text/html)]
<div dir="ltr"><div><div dir="ltr" class="gmail_signature" \
data-smartmail="gmail_signature"><p style="margin:0px 0px \
1em;padding:0px;border:0px;font-variant-numeric:inherit;font-variant-east-asian:inherit;font-stretch:inherit;line-height:inherit;font-family:Arial,"Helvetica \
Neue",Helvetica,sans-serif;font-size:15px;vertical-align:baseline;box-sizing:inherit;clear:both;color:rgb(36,39,41)">I \
am new to machine learning and am looking for some assistance in working with Weka \
and MRI T1 datasets. I found the Weka Nifti Loader package and installed it, hoping \
to be able to load several T1s at once and then combine three classifiers for the \
purpose of having a way to automatically run QC on these files as seen in the \
following paper:</p><p style="margin:0px 0px \
1em;padding:0px;border:0px;font-variant-numeric:inherit;font-variant-east-asian:inherit;font-stretch:inherit;line-height:inherit;font-family:Arial,"Helvetica \
Neue",Helvetica,sans-serif;font-size:15px;vertical-align:baseline;box-sizing:inherit;clear:both;color:rgb(36,39,41)"><a \
href="https://www.sciencedirect.com/science/article/pii/S1053811917308613" \
rel="nofollow noreferrer" \
style="margin:0px;padding:0px;border:0px;font-style:inherit;font-variant:inherit;font- \
weight:inherit;font-stretch:inherit;line-height:inherit;font-family:inherit;vertical-align:baseline;box-sizing:inherit">Alfaro-Almagro \
F, Jenkinson M, Bangerter NK, et al. Image processing and Quality Control for the \
first 10,000 brain imaging datasets from UK Biobank. NeuroImage. 2018;166:400-424. \
doi:10.1016/j.neuroimage.2017.10.034</a></p><p style="margin:0px 0px \
1em;padding:0px;border:0px;font-variant-numeric:inherit;font-variant-east-asian:inherit;font-stretch:inherit;line-height:inherit;font-family:Arial,"Helvetica \
Neue",Helvetica,sans-serif;font-size:15px;vertical-align:baseline;box-sizing:inherit;clear:both;color:rgb(36,39,41)">However, \
the paper has very little documentation on the use of Weka, so upon trying to load \
the directory (in which I have ~100 T1s), I got an error stating that 'no such \
file or directory exists' despite it being easily found in my Mac's Finder. \
So Far, I have only attempted this within the Weka UI since I have no experience in \
using the terminal commands for Weka. I also attempted to work with a single .nii.gz \
file but got the OutOfMemory error.</p><p style="margin:0px 0px \
1em;padding:0px;border:0px;font-variant-numeric:inherit;font-variant-east-asian:inherit;font-stretch:inherit;line-height:inherit;font-family:Arial,"Helvetica \
Neue",Helvetica,sans-serif;font-size:15px;vertical-align:baseline;box-sizing:inherit;clear:both;color:rgb(36,39,41)">Organization \
of the Nifti files is also a little confusing given the package description that \
'The directory to be loaded must contain as many subdirectories as there are \
classes of MRI data.' Not entirely sure what is meant by this, so how should the \
files be organized?</p><p style="margin:0px 0px \
1em;padding:0px;border:0px;font-variant-numeric:inherit;font-variant-east-asian:inherit;font-stretch:inherit;line-height:inherit;font-family:Arial,"Helvetica \
Neue",Helvetica,sans-serif;font-size:15px;vertical-align:baseline;box-sizing:inherit;clear:both;color:rgb(36,39,41)">Any \
suggestions for how to load the files? Or are the number/organization of files and \
size the issue here?</p><p style="margin:0px 0px \
1em;padding:0px;border:0px;font-variant-numeric:inherit;font-variant-east-asian:inherit;font-stretch:inherit;line-height:inherit;font-family:Arial,"Helvetica \
Neue",Helvetica,sans-serif;font-size:15px;vertical-align:baseline;box-sizing:inherit;clear:both;color:rgb(36,39,41)">If \
anyone has an example directory to run trials with, I would greatly appreciate it. \
Please let me know if I can provide anymore information regarding \
this.</p><br><br><br></div></div></div>
_______________________________________________
Wekalist mailing list -- wekalist@list.waikato.ac.nz
Send posts to wekalist@list.waikato.ac.nz
To unsubscribe send an email to wekalist-leave@list.waikato.ac.nz
To subscribe, unsubscribe, etc., visit \
https://list.waikato.ac.nz/postorius/lists/wekalist.list.waikato.ac.nz List \
etiquette: http://www.cs.waikato.ac.nz/~ml/weka/mailinglist_etiquette.html
[prev in list] [next in list] [prev in thread] [next in thread]
Configure |
About |
News |
Add a list |
Sponsored by KoreLogic