--
You received this message because you are subscribed to the Google Groups "neurosynth" group.
To unsubscribe from this group and stop receiving emails from it, send an email to neurosynthlis...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.
To unsubscribe from this group and stop receiving emails from it, send an email to neurosy...@googlegroups.com.
To unsubscribe from this group and stop receiving emails from it, send an email to neurosynthlis...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/neurosynthlist/dca83108-ffea-4aeb-9f0a-a1cb9f1a257e%40googlegroups.com.
To unsubscribe from this group and stop receiving emails from it, send an email to neurosy...@googlegroups.com.
Can you post your code snippet. That will be helpful.
Hello I am doing something similar custom analysis, can you help me set FDR threshold 0.05 for meta analysis. I am not sure where should I specify that threshold.--
On Saturday, 8 November 2014 15:02:21 UTC-5, Tal Yarkoni wrote:Hi Vanessa,The default FDR threshold changed to 0.01 a long time ago. The main reason for that is that I suspect that the chi-square p values are (slightly) anti-conservative relative to a full-blown permutation analysis (which is not feasible to run given the scale of the dataset and number of terms). So I lowered it to a level where that shouldn't be an issue.Re: your discrepant analyses, that's harder to say. One easy way to determine if the meta-analysis code is working properly for you is to run an analysis on some "big" features that are on the website and compare them (e.g., memory, language, emotion, etc.). If you're using the latest dataset with default parameters, the local images should be identical to what's on the website. If they are, and you still get an empty image now whereas you didn't before, then most likely the earlier result was noise. If you were running with the wonky ~3,800-feature dataset produced by the parsing error, those results would definitely not be trustworthy (sorry!). If that's not the issue, then I'm not sure; nothing else should have changed...TalOn Sat, Nov 8, 2014 at 1:51 PM, vanessa sochat <vso...@stanford.edu> wrote:Hi Tal,--Were there changes when you updated the neurosynth methods? I noticed that the default threshold for meta analysis is now 0.01 (that's not actually an issue) - the problem I'm running into is that when I do a meta analysis with the same sets of IDS I had before, same threshold of 0.05, the entire image map is white (0 and -0 values). I'm not really sure what is going on - it's definitely put me at a stop in my analyses for this weekend. Do you have any ideas?I am doing:ma = meta.MetaAnalysis(ns.db,members,q=float(fdr))ma.save_results(outdir, prefix=outprefix, image_list=image_list)Best,Vanessa--
You received this message because you are subscribed to the Google Groups "neurosynth" group.
To unsubscribe from this group and stop receiving emails from it, send an email to neurosy...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.
You received this message because you are subscribed to the Google Groups "neurosynth" group.
To unsubscribe from this group and stop receiving emails from it, send an email to neurosynthlist+unsubscribe@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/neurosynthlist/dca83108-ffea-4aeb-9f0a-a1cb9f1a257e%40googlegroups.com.
--
You received this message because you are subscribed to the Google Groups "neurosynth" group.
To unsubscribe from this group and stop receiving emails from it, send an email to neurosynthlist+unsubscribe@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/neurosynthlist/CAPVJSddYemcN4fKB07rN9gaF2T8iDnfcZ_XkLVWAidZNqQtBvw%40mail.gmail.com.
Hello,Thanks for your reply.My code snippet:import neurosynth as nsfrom neurosynth.base.dataset import Datasetfrom neurosynth.analysis import metadataset = Dataset('/data0/research/neurosynth/neurosynth-data/database.txt')dataset.add_features('/data0/research/neurosynth/neurosynth-data/features.txt')idfile = open('/data0/research/neurosynth/neurosynth-data/Ids.txt',"r") ## I gave list of pubmed IDs in IDs fileids=idfile.readlines()
ma = meta.MetaAnalysis(dataset, ids, q(float(0.05)))
## I want to set FDR threshold of 0.05 for my meta analysis I used above code for that but it gave me a result which have p values=0 for all the data points.So I am not sure whether I am doing it right or not. Hope you could help me. Thanks in advance for your help.
On Wed, May 6, 2020 at 1:06 AM Sudhakar <rs...@iiita.ac.in> wrote:
Can you post your code snippet. That will be helpful.
On Wed, 6 May 2020, 07:20 priyanka gorijala, <priyanka...@gmail.com> wrote:
To unsubscribe from this group and stop receiving emails from it, send an email to neurosynthlis...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/neurosynthlist/dca83108-ffea-4aeb-9f0a-a1cb9f1a257e%40googlegroups.com.
--
You received this message because you are subscribed to the Google Groups "neurosynth" group.
To unsubscribe from this group and stop receiving emails from it, send an email to neurosynthlis...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/neurosynthlist/CAPVJSddYemcN4fKB07rN9gaF2T8iDnfcZ_XkLVWAidZNqQtBvw%40mail.gmail.com.
--
You received this message because you are subscribed to the Google Groups "neurosynth" group.
To unsubscribe from this group and stop receiving emails from it, send an email to neurosynthlis...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/neurosynthlist/CAFPSfNc-KoqZ67a%3D_uVbN1MwMyURw9zcGtiNKTkWzZ%2BZ9r8okw%40mail.gmail.com.
To unsubscribe from this group and stop receiving emails from it, send an email to neurosy...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/neurosynthlist/dca83108-ffea-4aeb-9f0a-a1cb9f1a257e%40googlegroups.com.
--
You received this message because you are subscribed to the Google Groups "neurosynth" group.
To unsubscribe from this group and stop receiving emails from it, send an email to neurosy...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/neurosynthlist/CAPVJSddYemcN4fKB07rN9gaF2T8iDnfcZ_XkLVWAidZNqQtBvw%40mail.gmail.com.
--
You received this message because you are subscribed to the Google Groups "neurosynth" group.
To unsubscribe from this group and stop receiving emails from it, send an email to neurosy...@googlegroups.com.
To unsubscribe from this group and stop receiving emails from it, send an email to neurosynthlis...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/neurosynthlist/c2f222e8-b590-41e9-8005-da54058258aa%40googlegroups.com.