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GUI spontaneously aborts and no response when try to restart

April 19, 2021, 8:56 pm
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[color=#000000]Hello. [/color]

Thank you for the great program, 

I used AES-SDM before, now started to use SDM-PSI. 
It worked good but all of sudden when I am trying to change working directory, the program aborted and dose not start again. 
I got very recent version, don't think number of raw/column is the problem. 
It happened in sever computers... 

The program turned spontaneously, I don't have any error related message or something. 

Could you be able to help for this problem? 

Thank you so much. 
Sang Soo. 
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Issues with MRIcron on SDM (Mac)

April 20, 2021, 9:08 am
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Dear expert users, 

I have launched SDM for the first time on a Mac using OSx, but it seems that SDM can't see the MRIcron software file (.app): it always shows the red X near to the bar that specifies the directory file, even if I try to select another executable file (please see the image attached) included on the contents folder of MRIcron program. However, MRIcron works normally when I open it separately. 
Has anyone already faced this problem? 

Thanks to you all, 
greetings, 
Giulia.
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RE: Egger test for publication bias

April 21, 2021, 8:10 am
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Dear Anna

SDM conducts a meta-regression of standard error across imputations and then applies Rubin's rules (see "metabias" at https://cran.r-project.org/web/packages/metansue/metansue.pdf)

With best wishes,

Joaquim
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t_thr t values and where to find them

April 22, 2021, 12:45 pm
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Hello, 

I have two questions re the t_thr column: 

[b]1. [/b]I'm filling out the sdm table and am struggling filling out the t_thr column. It seems that very few papers (at least the ones that I'm looking at) report the t value they used to threshold their statistical maps. I have noted the various p value the studies used to threshold, and entered these values into the converter on the sdm website (https://www.sdmproject.com/utilities/?show=Statistics). However, the results I get seem odd: e.g. One-sample p to t converter: p = 0.001, n=20, t= .[b]-[/b]3.5794

Is this correct? All the examples I see on the website are around 3.1. Is the p value input supposed to be thresholded or unthresholded? 

[b]2.[/b] Is it worth the hassle of finding the individual t value for each study, or is it better to allow the automatic conservative sdm approach, p=.0001? If this is better, or necessary in some cases where I cannot get the t value, what do I input into the sdm table? 

Best wishes, 
Molly
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Meta-regression parameters problems

April 26, 2021, 8:12 pm
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Dear experts,

I want to conduct meta-regression to examine whether age and sex have an effect on the main results. And I use Linear Model button on the SDM-PSI V6.21 GUI.
Here I have a problem: If I want to examine the effect of age, should I set age as 1 and sex as 0? Or just set age as 1 (Age=mi_lm age,0+1+0+0+0,50,,5)?

Thanks very much.

Xiaoying
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The issue of the number of references included

April 26, 2021, 10:14 pm
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Dear experts,

I did not find an answer in the tutorial which did not tell the minimum number of literatures required to be included in a meta-analysis using SDM software.So, I'd like to ask the experts about this.

Thanks very much

you lantao
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When should I apply multiple corrections? (e.g. bonferroni correction)

April 26, 2021, 10:32 pm
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Dear expert users,
Recently I performed separate meta-analyses for the different groups through SDM (version 5.15). To avoid multiple comparisons, I ensured that each dataset was not reused in a meta-analysis. Sometimes the literature appears in several groups, as there are several different data sets available in one study.    

I would like to know if I made multiple comparisons and if I need to take multiple corrections.

P.s. Most of the articles I referenced used the default thresholds, but one article chose a corrected threshold of Z>5(Wilson,2018).

Thank you so much,
Susie Yu.
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Extent threshold changing from input to output

April 27, 2021, 6:57 am
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Hello, 

I set the extent threshold to 10 voxels when thresholding but when the analysis is complete, and webpage of results + images created, this threshold seems to change: On the results webpage, it states: "Extent threshold: cluster size ≥ 1 voxels" and Blobs of ≥ 1 voxels"; And the images are automatically labelled: "MyTest1_z_uncorrected_p_0.00500_1.nii.gz", i.e. with a 1 rather than a 10.

Anyone else experiencing this? Is this a bug? Or is the parameter of 10 contiguous voxels applied despite appearances? 

Best, 
Molly
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SDM bug: not opening on 2 separate devices

April 29, 2021, 3:49 am
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Hi, 

The SDM software is not opening at all. I've tried on two separate devices, Mac and Windows, and the same issue occurs: I open the app, it appears to load for a second or so, but cancels without warning and does not open. I've deleted and re-downloaded the software on both devices, but the same issue occurs. It has been working fine for months up until yesterday. Perhaps the is a bug. 

Best, 
Molly
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RE: I can't open it.....

May 3, 2021, 4:35 am
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Dear all,

for all of you having a similar issue (gui not starting), could you please check this other thread?

https://www.nitrc.org/forum/forum.php?thread_id=12372&forum_id=3982

hope this helps!

Anton
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Are separate independent meta-analyses multiple comparisons？Is multi-correction necessary?

May 3, 2021, 8:04 am
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We performed separate meta-analyses for the different groups. We ensured that each dataset was not reused in a meta-analysis to avoid multiple comparisons.
If a literature appears in several groups, it is because several different data sets are available in that study for analysis in different groups.
In addition, we referenced several articles using similar research methods, mostly without multiple corrections, and one of them reported in the main text only those results that survived at a more conservative threshold (Z-score ≥ 5.0)(Robin Paul Wilson,2018).

I would like to know if several analyses in this case are multiple comparisons. Is it necessary to take multiple corrections (e.g. Bonferroni correction)? Thank you in advance for your answer.

P.s. SDM software (SDM, version 5.15, http://www.sdmproject.com, formerly "Signed Differential Mapping") was used for the meta-analyses.
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Preprocessing original T-maps

May 4, 2021, 2:20 am
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Dear experts,

I just ran preprocessing with 8 original t-maps (fMRT). However, the peaks calculated with SDM do not always correspond to those reported in the respective papers. May the reason for that be that in the papers they sometimes use cluster-corrected thresholds?

So what can I do, if these peaks do not correspond (actually, for the deactivations, they never correspond): insert a t-threshold other than the one automatically created by SDM? Or use peak coordinates instead? 

Thank you very much for a quick response.
Nicola
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multimodal conjunction analysis issue - links to older SDM versions?

May 10, 2021, 5:18 am
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Hello, 

I understand (via reading old entries on this forum) that the Multimodal analysis for conjunction analyses is not working in the Windows or Mac V6.21. Apparently it can work on Linux, but I'm not familiar with that system. Apparently, the multimodal method used to work just fine on older versions of SDM, but these are not available to download from what I can see on the SDM website. I downloaded the older V6.11 for Windows from the website, but there seems to be still an issue with this version: when selecting a an input folder, the "*_p.nii.gz" files do not appear. Others had the same issue on here but they seem unsolved. 

Does anyone know how to go about performing a conjunction analysis? E.g. if someone has links to download older versions of SDM with which it still worked. 

Thanks, 
Molly
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Permutation number

May 16, 2021, 11:24 am
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Dear Dr. Radua,

I found two permutation settings in SDM-PSI:[list][*]one is in mean-analysis, the default is: 50;[*]another is in FWE correction, the default is: 1000.[/list]Could you please explain a bit more what these two permutation options mean, and if there are any references for the default number?

Thanks!
John
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RE: How to input t value when F value was reported from two way ANOVA

May 17, 2021, 1:25 am
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Dear Hongru 
Hello, I'm facing the same problem as you. I wonder whether your type of the neuroimaging is fmri . And after I  clicked in the Preprocessing button, I don't konw which kind of correlation template to choose. When you completed the SDM table editor, what kind of data did you input?

Looking forward to your reply
Lageny
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Opening results webpage

May 17, 2021, 4:35 am
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To whom it may concern,

I am conducting a meta-analysis on gray matter volume from VBM studies. After thresholding the results, the webpage which shows the results does not automatically open as anticipated. I have tried running the software a few times but it still will not direct me to a webpage. Is there anyway I can fix this?
Also, the brain image on the MRICRON is an empty template every time, does anyone know how I can fix this too?
Furthermore, the FWE correction keeps terminating at the "getting null distribution" phase and states: "std::bad_alloc' what(): std::bad_alloc"- is there anyway of fixing this?
Thank you in advance,
Alexis.
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RE: SDMPsi v6.21 software - error with windows, Family-wise error correction (FWE)

May 17, 2021, 6:14 am
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Hi there, 
I am currently having the same issue and wondering whether you figured out how to solve the problem?
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RE: FWE Troubleshooting

May 17, 2021, 6:27 am
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Hi there,
I am currently having the same issue and wondering whether you figured out how to solve the problem?
Thanks,
Alexis.
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FWE correction failure

May 18, 2021, 10:00 am
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Dear experts,
I have tried many times to execute the FWE correction, but it shows the same repeated message: "terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc" (see image attached).
Does anyone know how to fix this?
Thanks,
Alexis.
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Could we use the same threshold in GingerALE software

May 20, 2021, 8:51 am
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Hello everyone,
I wonder whether the widely used threshold of AES-SDM (anisotropy = 1, full width at half maximum =20 mm, number of randomisations = 50, cluster extent = 10 voxels, uncorrected p < 0.005, peak height threshold = 1)  could be applied in GingerALE? In another word, could we use p<0.005 (uncorrected) and the min volunme = 80mm3 in GingerALE? Are these two thresholds the same?
And there are one more question, are the threshlod (p<0.005,uncorrected) in AES-SDM the same as the threshold (P<0.0025, uncorrected) in SDM-PSI?
I would be grateful if you could reply.
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