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Today's Topics:
1. Re: Questions about correction over 2 hemispheres and MCC
(Reem Jan)
2. More than two time-points in longitudinal base = Memory
allocation error? (Liz Bowman)
3. Re: Talairach registration (Mojdeh Zamyadi)
4. Subcortical segmentations (Jordan Pierce)
----------------------------------------------------------------------
Message: 1
Date: Sun, 22 Jul 2012 21:12:44 +0000
From: Reem Jan <r.jan@auckland.ac.nz>
Subject: Re: [Freesurfer] Questions about correction over 2
hemispheres and MCC
To: "Watson, Christopher" <Christopher.Watson@childrens.harvard.edu>
Cc: Freesurfer Mailinglist <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<3375B664D4A0834FB7D0C15D590A9EF11825DBC1@FMHS-MBX1.fmhs.auckland.ac.nz>
Content-Type: text/plain; charset="iso-8859-1"
Hi Bruce, J?rgen and Chris
Thank you for elaborating further. I've gone with a Bonferroni correction as I had a limited number of tests (a-priori hypothesis). But just out of interest Chris, you mentioned you found correlations between subcortical structures, do you have a reference I could look at? The tool that J?rgen suggested requires we enter a correlation coefficient, so I wondered if I could use published values or whether I'd need to calculate my own (if so, could you please recommend a way of doing that in Freesurfer or FSL?)
Many thanks in advance
Kind regards
Reem
-----Original Message-----
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of J?rgen H?nggi
Sent: Sunday, 22 July 2012 7:47 p.m.
To: Watson, Christopher
Cc: Freesurfer Mailinglist
Subject: Re: [Freesurfer] Questions about correction over 2 hemispheres and MCC
Hi Chris
Yes there are such tools. Bonferroni oder Sidak test that take into account the correlated measures. Here you can find these tools
http://www.quantitativeskills.com/sisa/calculations/bonfer.htm
Cheers
J?rgen
On [DATE], "Watson, Christopher" <[ADDRESS]> wrote:
> What about, for example, the correlations I've seen in a cohort of subjects.
>
> In 158 subjects aged 10-19 (both controls and patients), the
> correlation between L & R thalamus is 0.91, and the correlations
> between L & R of caudate, putamen, pallidum, hippocampus, and amygdala were all 0.75 or higher.
>
> I would think that a Bonferroni correction would be incredibly
> conservative and, in my opinion, just plain wrong because true
> significant diff's would be missed. Is there any principled way of
> dealing with multiple tests that are correlated?
>
> Thanks,
> Chris
> ________________________________________
> From: Bruce Fischl [fischl@nmr.mgh.harvard.edu]
> Sent: Saturday, July 21, 2012 12:01 PM
> To: Watson, Christopher
> Cc: Douglas N Greve; freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Questions about correction over 2
> hemispheres and MCC
>
> Hi Chris,
>
> bonferroni will be overly conservative in that case, but we rarely
> really know the true covariance structure of the data, so we would
> rather err on the side of being conservative.
>
> cheers
> Bruce
> On Fri, 20 Jul 2012, Watson, Christopher
> wrote:
>
>> Hi Doug et al,
>>
>> The 2nd question is something I've wondered about. Doesn't a
>> Bonferroni correction assume that the measures are independent?
>> If so, I think in the case of subcortical structures, it is incorrect
>> to use this method, as e.g. the putamen and pallidal volumes are not
>> independent of one another.
>> If not, and it is acceptable to use when there are dependencies
>> between measures, how do you calculate the FWE? It wouldn't be equal
>> to alpha/n, unless I am misunderstanding something.
>>
>> Thanks,
>> Chris
>> ________________________________________
>> From: freesurfer-bounces@nmr.mgh.harvard.edu
>> [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
>> [greve@nmr.mgh.harvard.edu]
>> Sent: Friday, July 20, 2012 2:38 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Questions about correction over 2
>> hemispheres and MCC
>>
>> Hi Reem, it looks like you've done everything correctly (sorry for
>> the null result). As for your second, question, I don't think there
>> is a way other than Bonferroni. You can try FDR, but it makes the
>> interpretation a little messy.
>> doug
>>
>> On 07/19/2012 07:59 PM, Reem Jan wrote:
>>>
>>> Hi Doug
>>>
>>> I hope it?s okay that I double check I?m doing the correction over 2
>>> hemispheres correctly and ask a question regarding correction for
>>> multiple comparisons. I will briefly describe what I have done:
>>>
>>> I have 2 groups of subjects ? Drug addicts (n= 17) and controls (n=20).
>>>
>>> 1.I ran a surface thickness study:
>>>
>>> ?For the ?mri_glmfit? command, I used DOSS and specified a contrast
>>> of
>>> +1 -1 0 (Controls > MA)
>>>
>>> ?I ran a pre-cached simulation with the following command:
>>> mri_glmfit-sim --glmdir lh.group_age.glmdir --cache 4 pos
>>>
>>> ?This simulation should only have corrected for the left hemisphere
>>> as I understand it. My cluster summary text file showed me that a
>>> cluster survived in the insula. I interpreted this as ?controls had
>>> higher grey matter thickness in this cluster located in the insula
>>> than drug addicts?. However, this was only corrected over the left
>>> hemisphere (when I ran the same simulation in the right hemisphere,
>>> nothing survived multiple comparison correction).
>>>
>>> ?I now wanted to correct the lh results for 2 hemispheres. From the
>>> help menu of ?mri_glmfit-sim?, I understood you can do this in 2
>>> ways, are both of these correct and give the same result?
>>>
>>> a.mri_glmfit-sim --glmdir lh.group_age.glmdir --cache 4 pos --2
>>> spaces --no-sim csdbase
>>>
>>> b.mri_glmfit-sim --glmdir lh.group_age.glmdir --cache 4 pos
>>> --cwpvalthresh 0.025
>>>
>>> ?No clusters survived the Bonferroni correction over both hemispheres.
>>> So I assume I can no longer report this result?
>>>
>>> 2.I ran a subcortical volume study:
>>>
>>> ?I used SPSS to perform the statistical analysis on each of 14
>>> subcortical structures (left and right). Is there a good way to
>>> correct for multiple comparisons, apart from Bonferroni, which would
>>> be very conservative?
>>>
>>> Many thanks for your advice.
>>>
>>> Kind regards
>>>
>>> Reem
>>>
>>> *Reem Jan***
>>>
>>> BPharm (Hons), RegPharmNZ
>>>
>>> PhD Student / Pharmacist
>>>
>>> School of Pharmacy, Faculty of Medical & Health Sciences, The
>>> University of Auckland, Private Bag 92019, Auckland, New Zealand.
>>>
>>> Ph: +64 9 373 7599 ext 81138. DDI: +64 9 923 1138
>>>
>>> F: +64 9 367 7192
>>>
>>> *From:*freesurfer-bounces@nmr.mgh.harvard.edu
>>> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] *On Behalf Of
>>> *Douglas Greve
>>> *Sent:* Friday, 20 July 2012 11:52 a.m.
>>> *To:* freesurfer@nmr.mgh.harvard.edu
>>> *Subject:* Re: [Freesurfer] slice-by-slice predictors
>>>
>>> Sorry, not possible.
>>>
>>> On 7/19/12 6:56 PM, Caspar M. Schwiedrzik wrote:
>>>
>>> Hi!
>>> Is it possible to have slice-by-slice predictors in Freesurfer, and
>>> if so, how?
>>> Thanks,
>>> Caspar
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> greve@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>
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----------------------------------------------------------------------------
J?rgen H?nggi, Ph.D.
Division Neuropsychology
Institute of Psychology
University of Zurich
Binzmuehlestrasse 14, PO Box 25
8050 Zurich, Switzerland
0041 44 635 73 97 (phone office)
0041 76 445 86 84 (phone mobile)
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------------------------------
Message: 2
Date: Mon, 23 Jul 2012 10:21:33 +1000
From: Liz Bowman <ea_bowman@hotmail.com>
Subject: [Freesurfer] More than two time-points in longitudinal base =
Memory allocation error?
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <SNT135-W17F702D9DC415BB91613828CDD0@phx.gbl>
Content-Type: text/plain; charset="iso-8859-1"
Hello,
I have several patients scans taken over multiple time points (up to nine time points in some patients). I thought I might be able to use these to create a base template for longitudinal processing, however the process fails and exits with errors if I try to create a base with more than two time points from a patient.
This is a sample of the error log of the most recent attempt, with three timepoints:
Resolution: 1 S( 128 128 128 ) T( 128 128 128 ) Iteration(f): 1 -- diff. to prev. transform: 0.876663 Iteration(f): 2 -- diff. to prev. transform: 0.0148738 Iteration(f): 3 -- diff. to prev. transform: 0.00156813 < 0.01 :-)
Resolution: 0 S( 256 256 256 ) T( 256 256 256 ) Iteration(f): 1 -- diff. to prev. transform: 0.263086 Iteration(f): 2mri_robust_template(1035) malloc: *** mmap(size=262144) failed (error code=12)*** error: can't allocate region*** set a breakpoint in malloc_error_break to debugMRIalloc(256, 256, 256): could not allocate 262144 bytes for 68th slice
Cannot allocate memoryDarwin 550D-UOM88670.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
recon-all -s KSx3 exited with ERRORS at Mon Jul 23 10:15:13 EST 2012
For more details, see the log file /Applications/freesurfer/subjects/KSx3/scripts/recon-all.logTo report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
I would be grateful for any advice.
Regards,
EA Bowman
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Message: 3
Date: Mon, 23 Jul 2012 09:43:24 -0400
From: Mojdeh Zamyadi <mojdehzm@gmail.com>
Subject: Re: [Freesurfer] Talairach registration
To: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Cc: freesurfer@nmr.mgh.harvard.edu
Message-ID: <500D54FC.7070903@gmail.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
thanks Bruce :)
-Mojdeh
On 07/20/2012 04:27 PM, Bruce Fischl wrote:
> Hi Mojdeh
>
> it's really hard to say how much you should correct. In general we
> don't do that much. A couple of control points or a few voxels added
> to the wm.mgz can have a big effect if you are experienced. Mostly
> just see if the ?h.white and pial surface are visually accurate, and
> if not see if some small intervention might fix them.
>
> cheers
> Bruce
>
>
>
> On Fri, 20 Jul 2012, Mojdeh Zamyadi wrote:
>
>> Hi Bruce,
>>
>> Thank's for the reply! I'm not concerned about hippocampal volume for
>> now, mostly needing cortical thickness for my project! Yes, I am
>> using v5.1. So in case of cortical thickness I shouldn't worry too
>> much about Talairach registration? could you please tell me what are
>> the main things I should check and pay attention to for cortical
>> thickness? I'm following the troubleshooting page
>> (http://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction)
>> and I see some discrepancies in the pial/WM surfaces but again I am
>> not sure how much I should correct!
>>
>> Thanks again,
>> -Mojdeh
>>
>> On 07/20/2012 04:15 PM, Bruce Fischl wrote:
>>> Hi Mojdeh
>>>
>>> it won't affect any individual thickness measures, *but* will affect
>>> the estimated total intracranial volume (eTIV). We don't typically
>>> use eTIV for thickness correction, but do for things like
>>> hippocampal volume. Are you using version 5.1? If so, that's the
>>> problem. Nick has a fix for this that he can direct you about, or
>>> you can wait for 5.2 and rerun the Talairach registration then.
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>> On Fri, 20 Jul 2012, Mojdeh Zamyadi wrote:
>>>
>>>> Hi all,
>>>>
>>>> Sorry for re-posting this but it seems it didn't get through!
>>>>
>>>> I've just started to do cortical thickness analysis on some
>>>> subjects and
>>>> I'm noticing some miss-registrations, more specifically the Talairach
>>>> image is smaller than the target image no matter what subject I
>>>> look at!
>>>> I just wanted to make sure if this is something normal and to what
>>>> extend it's going to effect the individual cortical thickness
>>>> calculations. I guess I'm not sure how the Talairach transformation is
>>>> used in further steps of the cortical thickness calculation.
>>>>
>>>> I tried to attach example coronal, sagittal and horizontal slices
>>>> of one
>>>> of my subjects but apparently it was too big for the mailing list.
>>>> Pleas
>>>> let me know if there is a way to attach images here.
>>>>
>>>> I greatly appreciate your advice.
>>>>
>>>> Thanks,
>>>> Mojdeh Zamyadi, MSc
>>>> Clinical Research Project Assistant
>>>> The Hospital for Sick Children
>>>> 555 University Avenue
>>>> Toronto, ON, M5G 1X8
>>>> _______________________________________________
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
>>>>
>>>
>>>
>>> The information in this e-mail is intended only for the person to
>>> whom it is
>>> addressed. If you believe this e-mail was sent to you in error and
>>> the e-mail
>>> contains patient information, please contact the Partners Compliance
>>> HelpLine at
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>>
>>
>>
------------------------------
Message: 4
Date: Mon, 23 Jul 2012 08:34:59 -0700 (PDT)
From: Jordan Pierce <jepierce87@yahoo.com>
Subject: [Freesurfer] Subcortical segmentations
To: Freesurfer Support <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<1343057699.64865.YahooMailNeo@web113005.mail.gq1.yahoo.com>
Content-Type: text/plain; charset="iso-8859-1"
Hi,
I have a question about subcortical segmentations: there are a lot of places across subjects where the thalamus label seems to include white matter (images attached), am I right to think that this needs to corrected and is there any reason the program might do this so often?
Thanks,
?
Jordan Pierce
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