Re: [Freesurfer] correction for multiple comparisons

[Marie Schneider]

Thanks very much for your help and your advice.

Are there any publications which describe the principles of the Monte Carlo
simulation when used for correction of multiple comparisons?

-Marie




2012/6/12 Douglas N Greve 

> yes, though I would probably do it outside of qdec as it can take a while
> (hours or days)
>
>
> On 06/12/2012 08:03 AM, Marie Schneider wrote:
>
>> Thank you very much for your answer.
>>
>> Are 10 000 iterations also used when I am running a Monte Carlo
>> simulation in qdec?
>>
>> Thanks, Marie
>>
>> 2012/6/9 Douglas N Greve > gr...@nmr.mgh.harvard.**edu >>
>>
>>
>>they are two different correction schemes. If they gave the same
>>answer,
>>then it would not make sense to have both. the monte carlo tries to
>>compute the probability of a cluster of the given size under the null
>>hypothesis. FDR controls for the number of false positives relative to
>>the total number of positives under the assumption that if any 5% of
>>your positives are false, then you would not change your conclusion.
>>
>>For monte carlo, we generally use 1 iterations. If you are
>>using the
>>whole hemisphere, then you can used the cached tables. See the
>>"command-line" tutorial.
>>
>>doug
>>
>>On 06/08/2012 08:03 AM, Marie Schneider wrote:
>>> Dear FreeSurfer experts,
>>>
>>> I have some questions about corrections for multiple comparisons in
>>> FreeSurfer. I have two samples, one consisting of two groups and one
>>> consisting of three groups.
>>>
>>> I do the comparison with the sample of two groups in qdec.
>>Correcting
>>> for multiple comparisons, I get a significant result using FDR,
>>but no
>>> significant result using Monte Carlo simulation. How can that be?
>>>
>>> I analyze the sample with the three groups by mri_glmfit. In your
>>> tutorial, I only found how to correct for multiple comparisons with
>>> the Monte Carlo simulation using the command line, but not how to
>>> correct with FDR using the command line. Is there a possibility
>>to do
>>> this? If not, how many iterations are usual to use within the Monte
>>> Carlo simulation?
>>>
>>> Any help is appreciated.
>>>
>>> Thank you very much,
>>>
>>> Marie
>>>
>>>
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>>> >
>>
>>> 
>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer
>>
>>--
>>Douglas N. Greve, Ph.D.
>>MGH-NMR Center
>>gr...@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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>>
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> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: 
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Re: [Freesurfer] Building FreeSurfer with OpenMP enabled

[Akio Yamamoto]

Hi Nick,

I confirmed that the program run in multi-thread mode by adding the 
"-openmp" flag. Thank you so much for your help.

May I ask a few more questions?

(1) Again, I find minor difference between the two results obtained by 
running in single-thread and multi-thread mode (say, numthreads is 4 or 8).
Is it also possible to ignore this minor difference?  Or, this means the 
program does not function correctly?

(2) Is there any special reason why we can use more than one thread only 
in 'mri_ca_register'?
At this point in time, I would like to speed up 'mri_em_register' as 
well (and some others programs too, in the future).
Any comment or suggestion?

Best regards,
Akio

(2012/06/13 2:05), Nick Schmansky wrote:
> Akio,
>
> the results of our dev tree will be different from the stable branch (as
> we are continually incorporating improvements in the dev tree which
> eventually make their way into the public stable release).  The new
> OpenMP code will also change the results, but we have found not
> significant differences.
>
> To enable usage of more than one thread (currently just in
> mri_ca_register), you must add the flag -openmp  to the
> recon-all command line (where numthreads is, say, 8, to use 8 cores).
>
> Nick
>
> On Tue, 2012-06-12 at 18:25 +0900, Akio Yamamoto wrote:
>> Hi all,
>>
>> I'm attempting to build FreeSurfer with OpenMP enabled.
>>
>> After checking out a copy of the main dev trunk from the CVS repository,
>> I did the configuration with "--enable-openmp" option and run 'make'.
>> Compilation successfully finished and all of 'make check' tests passed.
>>
>> Now I have two questions.
>>
>> (1) Although 'recon-all' finished without error, the results are
>> slightly different from those obtained by the binary distribution
>> (stable v5.1.0). I also find that the message format in a log file
>> (recon-all.log) is not the same as that of the stable version, so I
>> wonder if the source code in the main dev trunk is modified/updated from
>> the stable version...
>> Is it okay to ignore the slight difference of the results?
>>
>> (2) Despite the openmp option being enabled, it looks like the program
>> runs as a single-thread mode. I actually find the message "NUMBER OF
>> OPENMP THREADS = 1" in a log file.
>> Do I need to specify some option when running 'recon-all' script?
>>
>>
>> Any suggestion and/or help would be appreciated.
>>
>> Best,
>> Akio Yamamoto
>>
>>
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>>
>>
>
>
>
> The information in this e-mail is intended only for the person to whom it is
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Re: [Freesurfer] Building FreeSurfer with OpenMP enabled

[Bruce Fischl]

Hi Akio

we are going to work our way through the time-intensive binaries and 
parallelize them, but it will take us time to get to them.

cheers
Bruce
On Thu, 14 Jun 
2012, Akio Yamamoto wrote:

> Hi Nick,
>
> I confirmed that the program run in multi-thread mode by adding the
> "-openmp" flag. Thank you so much for your help.
>
> May I ask a few more questions?
>
> (1) Again, I find minor difference between the two results obtained by
> running in single-thread and multi-thread mode (say, numthreads is 4 or 8).
> Is it also possible to ignore this minor difference?  Or, this means the
> program does not function correctly?
>
> (2) Is there any special reason why we can use more than one thread only
> in 'mri_ca_register'?
> At this point in time, I would like to speed up 'mri_em_register' as
> well (and some others programs too, in the future).
> Any comment or suggestion?
>
> Best regards,
> Akio
>
> (2012/06/13 2:05), Nick Schmansky wrote:
>> Akio,
>>
>> the results of our dev tree will be different from the stable branch (as
>> we are continually incorporating improvements in the dev tree which
>> eventually make their way into the public stable release).  The new
>> OpenMP code will also change the results, but we have found not
>> significant differences.
>>
>> To enable usage of more than one thread (currently just in
>> mri_ca_register), you must add the flag -openmp  to the
>> recon-all command line (where numthreads is, say, 8, to use 8 cores).
>>
>> Nick
>>
>> On Tue, 2012-06-12 at 18:25 +0900, Akio Yamamoto wrote:
>>> Hi all,
>>>
>>> I'm attempting to build FreeSurfer with OpenMP enabled.
>>>
>>> After checking out a copy of the main dev trunk from the CVS repository,
>>> I did the configuration with "--enable-openmp" option and run 'make'.
>>> Compilation successfully finished and all of 'make check' tests passed.
>>>
>>> Now I have two questions.
>>>
>>> (1) Although 'recon-all' finished without error, the results are
>>> slightly different from those obtained by the binary distribution
>>> (stable v5.1.0). I also find that the message format in a log file
>>> (recon-all.log) is not the same as that of the stable version, so I
>>> wonder if the source code in the main dev trunk is modified/updated from
>>> the stable version...
>>> Is it okay to ignore the slight difference of the results?
>>>
>>> (2) Despite the openmp option being enabled, it looks like the program
>>> runs as a single-thread mode. I actually find the message "NUMBER OF
>>> OPENMP THREADS = 1" in a log file.
>>> Do I need to specify some option when running 'recon-all' script?
>>>
>>>
>>> Any suggestion and/or help would be appreciated.
>>>
>>> Best,
>>> Akio Yamamoto
>>>
>>>
>>> ___
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>>> 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
>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>> error
>> but does not contain patient information, please contact the sender and 
>> properly
>> dispose of the e-mail.
>
>
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[Freesurfer] suggestions for bandpass filters?

[Caspar M. Schwiedrzik]

Dear all,
I would like to apply a bandpass filter both to my fMRI data as well as to
regressors in my GLM. I was wondering whether anyone has suggestions for
particular filter types and filter orders?
I find this seldomly reported in fMRI papers.
I was thinking in using Matlab's filtfilt.
Any suggestions would be appreciated.
Thanks,
Caspar
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Re: [Freesurfer] Building FreeSurfer with OpenMP enabled

[Nick Schmansky]

Aiko,

Per question (1), there will always be slight differences due to the
nature of our algorithms, but the thing to do to convince yourself that
the differences are not significant is to conduct a group analysis
(following the procedures we describe in our tutorials) comparing say
4threads to 8threads.  You shouldnt find statistically different results
in thickness or structure volumes.  Let us know if you do and where.

Nick

> Hi Nick,
>
> I confirmed that the program run in multi-thread mode by adding the
> "-openmp" flag. Thank you so much for your help.
>
> May I ask a few more questions?
>
> (1) Again, I find minor difference between the two results obtained by
> running in single-thread and multi-thread mode (say, numthreads is 4 or
> 8).
> Is it also possible to ignore this minor difference?  Or, this means the
> program does not function correctly?
>
> (2) Is there any special reason why we can use more than one thread only
> in 'mri_ca_register'?
> At this point in time, I would like to speed up 'mri_em_register' as
> well (and some others programs too, in the future).
> Any comment or suggestion?
>
> Best regards,
> Akio
>
> (2012/06/13 2:05), Nick Schmansky wrote:
>> Akio,
>>
>> the results of our dev tree will be different from the stable branch (as
>> we are continually incorporating improvements in the dev tree which
>> eventually make their way into the public stable release).  The new
>> OpenMP code will also change the results, but we have found not
>> significant differences.
>>
>> To enable usage of more than one thread (currently just in
>> mri_ca_register), you must add the flag -openmp  to the
>> recon-all command line (where numthreads is, say, 8, to use 8 cores).
>>
>> Nick
>>
>> On Tue, 2012-06-12 at 18:25 +0900, Akio Yamamoto wrote:
>>> Hi all,
>>>
>>> I'm attempting to build FreeSurfer with OpenMP enabled.
>>>
>>> After checking out a copy of the main dev trunk from the CVS
>>> repository,
>>> I did the configuration with "--enable-openmp" option and run 'make'.
>>> Compilation successfully finished and all of 'make check' tests passed.
>>>
>>> Now I have two questions.
>>>
>>> (1) Although 'recon-all' finished without error, the results are
>>> slightly different from those obtained by the binary distribution
>>> (stable v5.1.0). I also find that the message format in a log file
>>> (recon-all.log) is not the same as that of the stable version, so I
>>> wonder if the source code in the main dev trunk is modified/updated
>>> from
>>> the stable version...
>>> Is it okay to ignore the slight difference of the results?
>>>
>>> (2) Despite the openmp option being enabled, it looks like the program
>>> runs as a single-thread mode. I actually find the message "NUMBER OF
>>> OPENMP THREADS = 1" in a log file.
>>> Do I need to specify some option when running 'recon-all' script?
>>>
>>>
>>> Any suggestion and/or help would be appreciated.
>>>
>>> Best,
>>> Akio Yamamoto
>>>
>>>
>>> ___
>>> 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
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>
>
>
>

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[Freesurfer] QDEC Analysis of only one group

[Dhinakaran Chinappen]

Dear Freesurfer Experts,

For one of our studies, I have used QDEC to analyze the relationship
between cortical thickness and a series of variables.

I wanted to double check to see if it is okie to have a qdec table which
only includes the diseased population and the covariates (such as FSIQ).

After multiple comparison correction, a few clusters were obtained, where
the correlation between thickness and the covariate differs from zero.

Please let me know if QDEC should only be used for comparison between
groups or if it okie to study only one cohort and subsequently analyze the
trend of a variable with cortical thickness.

Best,
Dhinakaran.
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Re: [Freesurfer] QDEC Analysis of only one group

[Douglas N Greve]

It is okay to study a single cohort with covariates.
doug

On 06/14/2012 11:54 AM, Dhinakaran Chinappen wrote:
> Dear Freesurfer Experts,
>
> For one of our studies, I have used QDEC to analyze the relationship 
> between cortical thickness and a series of variables.
>
> I wanted to double check to see if it is okie to have a qdec table 
> which only includes the diseased population and the covariates (such 
> as FSIQ).
>
> After multiple comparison correction, a few clusters were obtained, 
> where the correlation between thickness and the covariate differs from 
> zero.
>
> Please let me know if QDEC should only be used for comparison between 
> groups or if it okie to study only one cohort and subsequently analyze 
> the trend of a variable with cortical thickness.
>
> Best,
> Dhinakaran.
>
>
>
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@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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Re: [Freesurfer] QDEC Analysis of only one group

[Dhinakaran Chinappen]

Thank you Prof. Greve. Hope all is well on your side.

On Thu, Jun 14, 2012 at 8:03 PM, Douglas N Greve
wrote:

> It is okay to study a single cohort with covariates.
> doug
>
> On 06/14/2012 11:54 AM, Dhinakaran Chinappen wrote:
> > Dear Freesurfer Experts,
> >
> > For one of our studies, I have used QDEC to analyze the relationship
> > between cortical thickness and a series of variables.
> >
> > I wanted to double check to see if it is okie to have a qdec table
> > which only includes the diseased population and the covariates (such
> > as FSIQ).
> >
> > After multiple comparison correction, a few clusters were obtained,
> > where the correlation between thickness and the covariate differs from
> > zero.
> >
> > Please let me know if QDEC should only be used for comparison between
> > groups or if it okie to study only one cohort and subsequently analyze
> > the trend of a variable with cortical thickness.
> >
> > Best,
> > Dhinakaran.
> >
> >
> >
> > ___
> > 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
> gr...@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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> is
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> e-mail
> contains patient information, please contact the Partners Compliance
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Re: [Freesurfer] matrix error

[Douglas N Greve]

In matlab
Xsss = sqrt(sum(X.^2));
Xn = X ./ repmat(Xsss,[ntptot 1]);
Then look at the condition of Xn


On 06/12/2012 06:12 PM, mdkrue...@uwalumni.com wrote:
> due to their similarity is it not possible to run this analysis? also 
> how did you adjust for the scale presented here?
>
> On Tue, Jun 12, 2012 at 5:06 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> When I adjusted for the scale, the matrix is still ill-conditioned. It
> looks like some of the columns are very similar to each other.
> doug
>
> On 06/12/2012 05:15 PM, mdkrue...@uwalumni.com
>  wrote:
> > Hello-
> >
> > I am trying to analyze the cortical thickness between two groups of
> > subjects Cl1 and CL2. When i run the GLM i receive the error:
> >
> > matrix is ill-conditioned or badly scaled, condno = 1e+08
> >
> > I am under the impression the error could be due to the
> > non-uniformity in the range/scale of the regressors.
> >
> > here is my information:
> >
> > contrast is 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
> >
> >
> > 1)  mri_glmfit --y lh.PvNPeverything.10.mgh --fsgd
> PvNPeverything.fsgd
> > dods --C PvNP_everything.mtx --surf UNM_ALLGOOD lh --cortex --glmdir
> > lh.PvNPeverything.glmdir
> >
> > 2) (sample of my fsgd) - there are no columns with all 0's in them
> > GroupDescriptorFile 1
> > Title Methedone Comparison
> > Class Cl1
> > Class Cl2
> > Variables
> 
> WAISIQtrait_anxietyalcohol_yearheroin_yearcocaine_yearcannabis_yearmeth_yearamphetamines_yearmeth_amphet_yearhallucinogens_year
> >
> >
> 
> inhalants_yearmethodne_yearopiates_yearpills_yearopitates_pills_yearother_year
> > total_years
> > InputM87160505Cl18633103911011180066049
> > InputM87161888Cl110959007220032
> > InputM87107477Cl1893412091309961001910057
> > InputM87199897Cl1117440230100915015360
> > InputM87146570Cl19442260380637
> > InputM87189755Cl59110.52150331.50036
> > InputM87169696Cl186222011140025
> > InputM87187366Cl110651280270020275
> > InputM87178857Cl211748044805570400.080.08042.08
> > InputM87165923Cl2103405201500011023
> > InputM87110556Cl213460401150020
> > InputM87183811Cl29743150830026
> >
> > 3) design matrix
> >
> > 1 0   86  0   33  0   10  0   3
>   0   9   0   11  0   0   0   1  
> 0   1   0
> > 1 0   8   0   0   0   0   0   6
>   0   6   0   0   0   49  0
> > 1 0   109 0   59  0   0   0   0
>   0   7   0   22  0   0   0   0  
> 0   0   0
> > 0 0   0   0   0   0   0   0   0
>   0   0   0   0   0   32  0
> > 1 0   89  0   34  0   12  0   0
>   0   9   0   13  0   0   0   9  
> 0   9   0
> > 6 0   10  0   0   0   1   0   9
>   0   10  0   0   0   57  0
> > 1 0   89  0   40  0   15  0   5
>   0   2   0   30  0   10  0   0  
> 0
> > 100   2   0   0   0   0   0   0
>   0   0   0   0   0   0   0   59  
>0
> > 1 0   77  0   44  0   0   0   0
>   0   3   0   0   0   0   0   0  
> 0   0   0
> > 0 0   0   0   0   0   0   0   0
>   0   0   0   0   0   3   0
> > 1 0   91  0   22  0   6   0   0
>   0   3   0   0   0   0   0   0  
> 0   0   0
> > 0 0   0   0   0   0   0   0   0
>   0   0   0   0   0   8   0
> > 1 0   103 0   29  0   20  0   3
>   0   11  0   27  0   0   0   11  
>0
> > 110   5   0   0   0   0   0   0
>   0   1   0   1   0   0   0   78  
>0
> > 1 0   117 0   44  0   0   0   23
>  0   0   0   10  0   0   0   0
>   0   0
> > 0 0   0   0   0   9   0   15  0
>   0   0   15  0   3   0   60  0
> > 1 0   94  0   42  0   26  0   0
>   0   3   0  

Re: [Freesurfer] correction for multiple comparisons

[Douglas N Greve]

Here are a couple
Hayasaka 2003 Neuroimage
Hagler 2006 Neuroimage
The Hagler reg is specifically for surfaces
doug


On 06/14/2012 03:13 AM, Marie Schneider wrote:
> Thanks very much for your help and your advice.
>
> Are there any publications which describe the principles of the Monte 
> Carlo simulation when used for correction of multiple comparisons?
>
> -Marie
>
>
>
>
> 2012/6/12 Douglas N Greve  >
>
> yes, though I would probably do it outside of qdec as it can take
> a while (hours or days)
>
>
> On 06/12/2012 08:03 AM, Marie Schneider wrote:
>
> Thank you very much for your answer.
>
> Are 10 000 iterations also used when I am running a Monte
> Carlo simulation in qdec?
>
> Thanks, Marie
>
> 2012/6/9 Douglas N Greve  
>  >>
>
>
>they are two different correction schemes. If they gave the
> same
>answer,
>then it would not make sense to have both. the monte carlo
> tries to
>compute the probability of a cluster of the given size
> under the null
>hypothesis. FDR controls for the number of false positives
> relative to
>the total number of positives under the assumption that if
> any 5% of
>your positives are false, then you would not change your
> conclusion.
>
>For monte carlo, we generally use 1 iterations. If you are
>using the
>whole hemisphere, then you can used the cached tables. See the
>"command-line" tutorial.
>
>doug
>
>On 06/08/2012 08:03 AM, Marie Schneider wrote:
> > Dear FreeSurfer experts,
> >
> > I have some questions about corrections for multiple
> comparisons in
> > FreeSurfer. I have two samples, one consisting of two groups
> and one
> > consisting of three groups.
> >
> > I do the comparison with the sample of two groups in qdec.
>Correcting
> > for multiple comparisons, I get a significant result using FDR,
>but no
> > significant result using Monte Carlo simulation. How can
> that be?
> >
> > I analyze the sample with the three groups by mri_glmfit. In
> your
> > tutorial, I only found how to correct for multiple
> comparisons with
> > the Monte Carlo simulation using the command line, but not
> how to
> > correct with FDR using the command line. Is there a possibility
>to do
> > this? If not, how many iterations are usual to use within
> the Monte
> > Carlo simulation?
> >
> > Any help is appreciated.
> >
> > Thank you very much,
> >
> > Marie
> >
> >
> > ___
> > 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
> gr...@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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>  >
>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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>
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> person to
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>the e-mail
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>Compliance HelpLine at
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>you in error
>but does not cont

[Freesurfer] task-related functional connectivity analyses freesurfer 5.1.0

[Maya Rosen]

Dear Freesurfers,

I'm really glad to see the (relatively) new functional connectivity
commands. It seems to be working really well.

Has anyone tried to do task-related functional connectivity? I would like
to compare functional connectivity with the hippocampus during two
different conditions of my task, but I haven't found any documentation on
how to do this or even if it is possible with the current commands. I'm
thinking of trying to use a tpexclude file and excluding all time points
except Condition A and running functional connectivity on just those time
points. And then making a separate tpexclude file that excludes all of the
time points except those in Condition B and running functional connectivity
on that (both with hippocampal seeds). This would give me maps for each
condition. Is there a standard statistical test to compare one map to
another? This seems to be a work-around, so I'm curious if anyone has a
better solution to do task-related functional connectivity in Freesurfer 5.

Please let me know if you've done this or know how to!

Thanks!

Maya
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[Freesurfer] Scripting with fs 5.1 vs 5.0

[Nicole Senecal]

Hi all,

I'm having trouble getting anything through on 5.1 using scripts, although
I can run recon-all at the commandline. I'm running freesurfer on a remote
cluster, not locally. Specifics of the cluster itself aside, with 5, I
could run:

*vbbatch -c *
*"PATH=$PATH:/usr/local/freesurfer_64bit_5; export PATH; *
*FREESURFER_HOME=/usr/local/freesurfer_64bit_5; export FREESURFER_HOME; *
*SUBJECTS_DIR=/jet/kable/CorticalThickness/Subjects; export SUBJECTS_DIR;**
*
*recon-all -i SW419_Day1.mgz -subject SW419Day1_fullrecon -all" -d1 -r*

With 5.1, I have to specify MINC_BIN_DIR within this command (get an error
if I don't, saying that it's not defined) and I still get stuck in the
talairach transform, with:
mritotal -verbose -debug -clobber -modeldir /../share/mni_autoreg -protocol
icbm transforms/tmp.talairach.22637/src.mnc transforms/talairach.auto.xfm
mritotal: Command not found.

Clearly mritotal is working if recon-all at the commandline works. Do I
need to specify more environmental variables somewhere for 5.1? I've tried
specifying MINC_BIN_DIR, MINC_LIB_DIR, and MNI_DIR in the command as well,
with no luck.

My bash profile includes:
PATH=$PATH:/usr/local/freesurfer5-1/bin
FREESURFER_HOME=/usr/local/freesurfer5-1
SUBJECTS_DIR=/jet/kable/CorticalThickness/Subjects
MINC_BIN_DIR=/usr/local/freesurfer5-1/mni/bin
MINC_LIB_DIR=/usr/local/freesurfer5-1/mni/lib
PERL5LIB=/usr/local/freesurfer5-1/mni/lib/perl5/5.8.5
MNI_DIR=/usr/local/freesurfer5-1/mni
FSFAST_HOME=/usr/local/freesurfer5-1/fsfast
FSF_OUTPUT_FORMAT=nii

And on startup I see:
 freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer5-1
FSFAST_HOME   /usr/local/freesurfer5-1/fsfast
FSF_OUTPUT_FORMAT nii
SUBJECTS_DIR  /jet/kable/CorticalThickness/Subjects
MNI_DIR   /usr/local/freesurfer5-1/mni
FSL_DIR   /usr/local/fsl

thanks,
Nicole


-- 
Nicole Senecal
Neuroscience Graduate Group
Kable Lab
3720 Walnut St., Room C37
Philadelphia, PA  19104
Lab phone:  215-746-4371
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[Freesurfer] 1 Group (2 Levels) 2 Covariates

[Jeff Sadino]

Hello,

I want to do an analysis with 1 Group (Control and HIV) with two covariates
(Age and ICV).  Qdec only lets me choose one covariate.  So instead I
choose two nuisance variables.  No matter how many different permutations I
run on this, I can not get it to duplicate my SAS results, and the Qdec
results look suspiciously wrong.  Also, when I do it manually with the
mri_glmfit command, I still can not duplicate the SAS results.  I have
tried both demeaning and not demeaning.  This should be pretty straight
forward?  Am I missing something obvious?  How would one do a 1 Group (2
levels) 2 Covariate analysis in QDEC?

Thank you,
Jeff
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