date:20110310

[Freesurfer] effect size for cortical thickness changes

2011-03-10 Thread Ritobrato Datta

Hello All,

Are there reports of studies of cortical thickness changes using freesurfer 
which report effect sizes for the ROIs of interest ie how much of a change in 
millimeters was observed as opposed to p-values reported.

Please let me know.

Thanks a lot

Ri
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Re: [Freesurfer] extracting thickness values from group level map

2011-03-10 Thread Douglas Greve


You're almost there, Beth. When you run mri_surfcluster, specify the 
--ocn output. This will create a 'segmentation' with each value being 
the number of the cluster. Then use mri_segstats specifying the ocn as 
the segmentation and the cluster number you want as the segid. Also 
specify and output 'waveform' file with --avgwf. This will output a text 
file with the values you want.
doug

On 3/10/11 8:43 PM, Beth Mormino wrote:
> Hi Surfers!
>
> I have done a group level analysis relating a variable to thickness
> values.  I have a sig.mgh file that shows the relationship between the
> variable and thickness at each vertex.  Now I would like to threshold
> the sig.mgh file (at values of 3 and above), and then extract an
> average thickness value across this entire mask for all my subjects.
> I have been able to convert the sig.mgh to an annotation using
> mri_surfcluster, but this file contains multiple clusters when all I'd
> like is 1 mask.  Once I get to this step, I assume there is a way to
> then extract thickness values using the thickness.mgh file originally
> fed into mri_glmfit, but can't seem to get this to work with
> mri_segstats.  My solution has been moving the annotation back into
> each subject's space with mri_surf2surf, but this seems like a very
> round-about way of completing this analysis.
>
> Thanks in advance!
> Beth
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>
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[Freesurfer] extracting thickness values from group level map

2011-03-10 Thread Beth Mormino

Hi Surfers!

I have done a group level analysis relating a variable to thickness
values.  I have a sig.mgh file that shows the relationship between the
variable and thickness at each vertex.  Now I would like to threshold
the sig.mgh file (at values of 3 and above), and then extract an
average thickness value across this entire mask for all my subjects.
I have been able to convert the sig.mgh to an annotation using
mri_surfcluster, but this file contains multiple clusters when all I'd
like is 1 mask.  Once I get to this step, I assume there is a way to
then extract thickness values using the thickness.mgh file originally
fed into mri_glmfit, but can't seem to get this to work with
mri_segstats.  My solution has been moving the annotation back into
each subject's space with mri_surf2surf, but this seems like a very
round-about way of completing this analysis.

Thanks in advance!
Beth
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Re: [Freesurfer] Newbie - Group analysis on a single session with multiple runs.

2011-03-10 Thread Douglas N Greve

That is a fine thing to do, I just don't have dedicated code to do it 
(ie, you can't run isxconcat-sess on them). But if you want to do it on 
your own, it will work fine.

doug

Shay Ohayon wrote:
> Hi Doug,
>
> Yes. I am using FSFAST for the analysis, and I do have all conditions
> in each run.
> Can you elaborate more why the higher level analysis is going to be tricky?
> What is wrong with loading the beta regressors from each run and
> building the contrast by averaging same beta regressors from different
> runs?
>
> -- Shay
>
>
> On Thu, Mar 10, 2011 at 2:02 PM, Douglas N Greve
>  wrote:
>   
>> Are you using FSFAST? It does not load all the data into memory, only one at
>> a time. It does make sense to do an individual run analysis (assuming you
>> have all conditions in each one). You can run selxavg3-sess with the
>> -per-run option. The higher level analysis is going to be a little bit
>> tricker.
>>
>>
>> doug
>>
>> Shay Ohayon wrote:
>> 
>>> Hi All,
>>>
>>> We are trying to speed things up in our functional analysis pipeline,
>>> and I wanted to consult with the experts here about the following
>>> suggestion...
>>>
>>> At the moment, we typically collect multiple runs per subject (say,
>>> 10-20).
>>> We usually then run pre-processing on each run, and then do
>>> first-order analysis on all available runs.
>>> This step is obviously a bottleneck because all runs need to be loaded
>>> to memory and the analysis takes a long time.
>>>
>>> As an alternative, we were thinking about doing 1st order analysis on
>>> each individual run, and then combine
>>> them somehow using 2nd order group analysis.
>>>
>>> My silly questions are:
>>> 1. Does this workflow make sense?
>>> 2. How should we go about and do this?
>>> My initial thought was to use mri_glmfit, and to build a 4D volume
>>> that will contain the beta's of interest from each individual 1st
>>> order analysis.
>>>
>>> Thanks,
>>>
>>> -- Shay
>>> ___
>>> 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
>>
>>
>>
>> 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.
>>
>>
>> 
>
>
>   

-- 
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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[Freesurfer] Reconchecker error

2011-03-10 Thread Shashwath Meda

Hi all - I am trying to run the reconchecker program to get some QA done on
my data and I get the below error. Any help on this would be greatly
appreciated!

Also are there any other QA programs that would enable me to easily
visualize the outputs at various stages of Freesurfer recon-all?



**
Running recon_checker on:
Thu Mar 10 17:17:23 EST 2011
Checking Last Version Used:
/usr/analysis/bin/freesurfer/bin/recon-all
Checking ALL Versions Used:
/home/virtualuser/apps/freesurfer/bin/recon-all,
/usr/analysis/bin/freesurfer/bin/recon-all,
---
checking output files ...
Running command:
/autofs/space/tensor_017/users/jpacheco/QAtools/data_checker/recon_all_output_file_checker
-subjid Dykens_2250_3_1_freesurfer
---
/autofs/space/tensor_017/users/jpacheco/QAtools/data_checker/recon_all_output_file_checker:
Command not found.
/autofs/space/tensor_017/users/jpacheco/QAtools/data_checker/recon_all_output_file_checker:
Command not found.
---
checking step order ...
Running command:
/autofs/space/tensor_017/users/jpacheco/QAtools/data_checker/recon_all_status_log_checker
-subjid Dykens_2250_3_1_freesurfer
---
/autofs/space/tensor_017/users/jpacheco/QAtools/data_checker/recon_all_status_log_checker:
Command not found.
/autofs/space/tensor_017/users/jpacheco/QAtools/data_checker/recon_all_status_log_checker:
Command not found.
---
*making snapshots ...*
*Running command:
/autofs/space/tensor_017/users/jpacheco/QAtools/data_checker/jlp_snapshots3.csh
-subjid Dykens_2250_3_1_freesurfer -o QA.html*
*---*
*/autofs/space/tensor_017/users/jpacheco/QAtools/data_checker/jlp_snapshots3.csh:
Command not found.*
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Re: [Freesurfer] Newbie - Group analysis on a single session with multiple runs.

2011-03-10 Thread Shay Ohayon

Hi Doug,

Yes. I am using FSFAST for the analysis, and I do have all conditions
in each run.
Can you elaborate more why the higher level analysis is going to be tricky?
What is wrong with loading the beta regressors from each run and
building the contrast by averaging same beta regressors from different
runs?

-- Shay


On Thu, Mar 10, 2011 at 2:02 PM, Douglas N Greve
 wrote:
> Are you using FSFAST? It does not load all the data into memory, only one at
> a time. It does make sense to do an individual run analysis (assuming you
> have all conditions in each one). You can run selxavg3-sess with the
> -per-run option. The higher level analysis is going to be a little bit
> tricker.
>
>
> doug
>
> Shay Ohayon wrote:
>>
>> Hi All,
>>
>> We are trying to speed things up in our functional analysis pipeline,
>> and I wanted to consult with the experts here about the following
>> suggestion...
>>
>> At the moment, we typically collect multiple runs per subject (say,
>> 10-20).
>> We usually then run pre-processing on each run, and then do
>> first-order analysis on all available runs.
>> This step is obviously a bottleneck because all runs need to be loaded
>> to memory and the analysis takes a long time.
>>
>> As an alternative, we were thinking about doing 1st order analysis on
>> each individual run, and then combine
>> them somehow using 2nd order group analysis.
>>
>> My silly questions are:
>> 1. Does this workflow make sense?
>> 2. How should we go about and do this?
>> My initial thought was to use mri_glmfit, and to build a 4D volume
>> that will contain the beta's of interest from each individual 1st
>> order analysis.
>>
>> Thanks,
>>
>> -- Shay
>> ___
>> 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
>
>
>
> 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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Re: [Freesurfer] Newbie - Group analysis on a single session with multiple runs.

2011-03-10 Thread Douglas N Greve

Are you using FSFAST? It does not load all the data into memory, only 
one at a time. It does make sense to do an individual run analysis 
(assuming you have all conditions in each one). You can run 
selxavg3-sess with the -per-run option. The higher level analysis is 
going to be a little bit tricker.

doug

Shay Ohayon wrote:
> Hi All,
>
> We are trying to speed things up in our functional analysis pipeline,
> and I wanted to consult with the experts here about the following
> suggestion...
>
> At the moment, we typically collect multiple runs per subject (say, 10-20).
> We usually then run pre-processing on each run, and then do
> first-order analysis on all available runs.
> This step is obviously a bottleneck because all runs need to be loaded
> to memory and the analysis takes a long time.
>
> As an alternative, we were thinking about doing 1st order analysis on
> each individual run, and then combine
> them somehow using 2nd order group analysis.
>
> My silly questions are:
> 1. Does this workflow make sense?
> 2. How should we go about and do this?
> My initial thought was to use mri_glmfit, and to build a 4D volume
> that will contain the beta's of interest from each individual 1st
> order analysis.
>
> Thanks,
>
> -- Shay
> ___
> 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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[Freesurfer] Newbie - Group analysis on a single session with multiple runs.

2011-03-10 Thread Shay Ohayon

Hi All,

We are trying to speed things up in our functional analysis pipeline,
and I wanted to consult with the experts here about the following
suggestion...

At the moment, we typically collect multiple runs per subject (say, 10-20).
We usually then run pre-processing on each run, and then do
first-order analysis on all available runs.
This step is obviously a bottleneck because all runs need to be loaded
to memory and the analysis takes a long time.

As an alternative, we were thinking about doing 1st order analysis on
each individual run, and then combine
them somehow using 2nd order group analysis.

My silly questions are:
1. Does this workflow make sense?
2. How should we go about and do this?
My initial thought was to use mri_glmfit, and to build a 4D volume
that will contain the beta's of interest from each individual 1st
order analysis.

Thanks,

-- Shay
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Re: [Freesurfer] Small voxel size

2011-03-10 Thread Bruce Fischl


not sure. They will be less accurate I would think
On Thu, 10 Mar 2011, 
Tricia Merkley wrote:



OK, thanks so much for letting me know.  Any idea how it might affect cortical 
thickness or subcortical volume results (over-estimation/under-estimation)?

We do try to use the same image acquisition parameters for all subjects in a 
given study of course, but this was an unusual case...

Thanks,
Tricia

--- On Thu, 3/10/11, Bruce Fischl  wrote:

From: Bruce Fischl 
Subject: Re: [Freesurfer] Small voxel size
To: "Tricia Merkley" 
Cc: "freesurfer@nmr.mgh.harvard.edu" 
Date: Thursday, March 10, 2011, 6:37 AM

Hi Tricia,

I don't think you can use that subject. It will only have 39% of the SNR
of the others. Sorry :<

Bruce
On Wed, 9 Mar 2011, Tricia Merkley wrote:


The native resolution of the other subjects is (1,1,1)mm voxel size and 
(256,256,160) voxels, whereas this subject is (0.7,0.7,0.8) mm voxel size and 
(288,288,165) voxels.  Sorry that wasn't clear in my previous email.  I'd 
appreciate any insight that anyone might be able to share.

Thanks,
Tricia

--- On Wed, 3/9/11, Bruce Fischl  wrote:

From: Bruce Fischl 
Subject: Re: [Freesurfer] Small voxel size
To: "Tricia Merkley" 
Cc: "freesurfer@nmr.mgh.harvard.edu" 
Date: Wednesday, March 9, 2011, 5:01 PM

What is the resolution of your other subjects?



On Mar 9, 2011, at 5:21 PM, Tricia Merkley  wrote:

Hello,

One of our subjects was scanned with (0.7,0.7,0.8) mm voxel size, although all 
other acquisition parameters were the same as the other subjects.  I'm 
wondering to what extent this might affect the results of the subcortical 
segmentation, cortical thickness measurements, etc., as compared to 1mm cubic 
voxels.  When would it be appropriate to use the '-cm' flag for mri_convert?

Thanks,
Tricia Merkley



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Re: [Freesurfer] Small voxel size

2011-03-10 Thread Tricia Merkley

OK, thanks so much for letting me know.  Any idea how it might affect cortical 
thickness or subcortical volume results (over-estimation/under-estimation)?

We do try to use the same image acquisition parameters for all subjects in a 
given study of course, but this was an unusual case...

Thanks,
Tricia

--- On Thu, 3/10/11, Bruce Fischl  wrote:

From: Bruce Fischl 
Subject: Re: [Freesurfer] Small voxel size
To: "Tricia Merkley" 
Cc: "freesurfer@nmr.mgh.harvard.edu" 
Date: Thursday, March 10, 2011, 6:37 AM

Hi Tricia,

I don't think you can use that subject. It will only have 39% of the SNR 
of the others. Sorry :<

Bruce
On Wed, 9 Mar 2011, Tricia Merkley wrote:

> The native resolution of the other subjects is (1,1,1)mm voxel size and 
> (256,256,160) voxels, whereas this subject is (0.7,0.7,0.8) mm voxel size and 
> (288,288,165) voxels.  Sorry that wasn't clear in my previous email.  I'd 
> appreciate any insight that anyone might be able to share.
>
> Thanks,
> Tricia
>
> --- On Wed, 3/9/11, Bruce Fischl  wrote:
>
> From: Bruce Fischl 
> Subject: Re: [Freesurfer] Small voxel size
> To: "Tricia Merkley" 
> Cc: "freesurfer@nmr.mgh.harvard.edu" 
> Date: Wednesday, March 9, 2011, 5:01 PM
>
> What is the resolution of your other subjects?
>
>
>
> On Mar 9, 2011, at 5:21 PM, Tricia Merkley  wrote:
>
> Hello,
>
> One of our subjects was scanned with (0.7,0.7,0.8) mm voxel size, although 
> all other acquisition parameters were the same as the other subjects.  I'm 
> wondering to what extent this might affect the results of the subcortical 
> segmentation, cortical thickness measurements, etc., as compared to 1mm cubic 
> voxels.  When would it be appropriate to use the '-cm' flag for mri_convert?
>
> Thanks,
> Tricia Merkley
>
>
>
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>
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> properly
> dispose of the e-mail.
>
>
>
>


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Re: [Freesurfer] mri_glmfit-sim error

2011-03-10 Thread Douglas N Greve

You can make a soft link. Don't worry about that warning (it's not 
important, and I've fixed it for the next version).
doug

GREGORY R KIRK wrote:
> hi folks,
>
> when i run mri_glmfit-sim --glmdir rh.measure_t7cort.glmdir --cache 2.0 neg
> i get an error message ERROR: cannot find 
> /apps/x86_64_sci5/freesurfer-latest/average/mult-comp-cor/average/rh/cortex/fwhm14/neg/th20/mc-z.csd
>
> there is fsaverage... should i just make a soft link ?
> also when i run the mri_glmfit-sim with or without --cache i get
> WARNING: unrecognized mri_glmfit cmd option doss, the glm fit anal was -doss 
> and went without problem or complaints.
> and using sim without --cache the simulations are running.
>
> is this a nuisance error message that i should just ignore ?
>
> thanks
>
> greg
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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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[Freesurfer] mri_glmfit-sim error

2011-03-10 Thread GREGORY R KIRK


hi folks,

when i run mri_glmfit-sim --glmdir rh.measure_t7cort.glmdir --cache 2.0 neg
i get an error message ERROR: cannot find 
/apps/x86_64_sci5/freesurfer-latest/average/mult-comp-cor/average/rh/cortex/fwhm14/neg/th20/mc-z.csd

there is fsaverage... should i just make a soft link ?
also when i run the mri_glmfit-sim with or without --cache i get
WARNING: unrecognized mri_glmfit cmd option doss, the glm fit anal was -doss 
and went without problem or complaints.
and using sim without --cache the simulations are running.

is this a nuisance error message that i should just ignore ?

thanks

greg
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Re: [Freesurfer] DODS and DOSS

2011-03-10 Thread Michael Harms


Hi Chris,
If you run an ANCOVA model with an interaction (which is what DODS is)
then the interpretation of the group effect is ambiguous because the
"group" effect varies with age.  If there is actually a differential
slope between groups, then the p-value of the contrast of the group
means (i.e., "intercepts") can/will change considerably depending on
whether or not age is demeaned (or centered around any other arbitrary
ages).

Tom Nichols had a helpful explanation of the interpretation of various
models that he posted to the SPM list back in 2008, which I've included
below for your convenience.



Post from Tom Nicols to SPM list 
https://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0803&L=SPM&P=R19616&I=-3&d=No+Match%3BMatch%3BMatches

There is always going to be a huge space of models you can consider, and it is
*not* advisable to check every model under the sun 'just to be safe'.  Rather,
always go for the simplest possible model *unless* there is a concern (backed
by previous data, the literature) that a more complicated model is warranted.

Hence, if you run the ANCOVA-with-interaction model and find no evidence for
an interaction, I'd recommend reverting to the simpler model in which to test
the group main effect, as the interpretation of the group effect is
unambiguous in the simpler model.  If you must test the main effect in the
model with an interaction then, yes, using centering is vital, but realize
that the entire meaning of "main effect" is different, as the very *direction*
of the group effect may flip as you consider different ages.

---
Notation - General Linear Model

Y = X beta + epsilon

Y is response (data), X is design matrix of predictors, beta is vector of
coefficients of predictors, epsilon is random error.

-
Two Sample T Model

Two groups of subjects, 3 in group I, 2 in group II.

Design Matrix Parameterization 1a

 1  0
 1  0
 1  0
 0  1
 0  1

Coefficient Interpretation

beta1:  Mean of Group I
beta2:  Mean of Group II

Contrast Interpretation

[ -1  1 ]   Difference of group means, Group II > Group I

[  1  0 ]   Mean of Group I -- ONLY meaningful group level fMRI

[  0  1 ]   Mean of Group II -- ONLY meaningful group level fMRI


Design Matrix Parameterization 1b

-1  1
-1  1
-1  1
 1  1
 1  1

Coefficient Interpretation

beta1:  Half the group mean difference, Group II > Group I
beta2:  Overall mean WHEN no group difference

Contrast Interpretation

[  1  0 ]   Half difference of group means, Group II > Group I
[  2  0 ]   Difference of group means, Group II > Group I

Both contrasts will give identical T and P-values.

-
Simple Correlation Model

One group of 5 subjects, with age covariate with values:
  20 25 30 35 40

Design Matrix Parameterization 2a (no centering)

 1  20
 1  25
 1  30
 1  35
 1  40

Coefficient Interpretation

beta1:  Expected response for Age of 0
beta2:  Expected change in response with increase of 1 year (no
longitudinal interpretation, only cross-sectional)

Contrast Interpretation

[ 0   1 ]   Increase in response with increasing age

[ 1   0 ]   NOT MEANINGFUL


Design Matrix Parameterization 2b (covariate centering)

 1 -10
 1  -5
 1   0
 1   5
 1  10

Coefficient Interpretation

beta1:  Expected response for (Age-Average(Age)) of 0, i.e. Age = Average(Age)
beta2:  Expected change in response with increase of 1 year (no
longitudinal interpretation, only cross-sectional)

Contrast Interpretation

[ 0   1 ]   Increase in response with increasing age (identical to
previous parameterization).

[ 1   0 ]   Expected response for an individual with average age,
while accounting for (removing from error the) linear
effect of age --  ONLY meaningful group level fMRI


-
ANCOVA Model - No Interaction

Two groups of subjects, 3 in group I, 2 in group II.
Age covariate with values:  20 25 30 35 40

Design Matrix Parameterization 3a

 1  0  20
 1  0  25
 1  0  30
 0  1  35
 0  1  40

Coefficient Interpretation

beta1:  Expected response of Group I for Age of 0
beta2:  Expected response of Group II for Age of 0
beta3:  Expected change in response with increase of 1 year (no
longitudinal interpretation, only cross-sectional)

Contrast Interpretation

[ 1   0   0 ]   NOT MEANINGFUL
[ 0   1   0 ]   NOT MEANINGFUL

[-1   1   0 ]   Difference of group means, Group II > Group I,
while accounting for (removing from error the) linear
effect of age.  (NOTE: No interaction, so differential
group effect doesn't vary with age).

[ 0   0   1 ]   Increase in response with increasing age.  (NOTE: No
interaction, so age effect is same for both groups).


Design Matrix Parameterization 3b - Centering

 1  0 -10
 1  0  -5
 1  0   0
 0  1   5
 0  1  10

Coefficient Interpretation

beta1:  Expected response of Group I for Age = Average(Age)
beta2:  Expected response of Group II for Age = Average(Age)
beta3:  Expected change in respon

Re: [Freesurfer] mri_glmfit allocate memory error

2011-03-10 Thread Douglas N Greve

There appears to be something wrong with the 
lh.paired-diff.thickness.mgh file. How was it created?
doug

Andrew Mendlowitz wrote:
> Hello All,
> I get the following error while trying to run mri_glmfit. I am running 
> a 2.93 
> ghz imac with 8gb of ram. I am also running freesurfer version 5.0.0 
> on Snow
> Leopard OS version 10.6.
>
>
>  /Applications/freesurfer/subjects/qdec$  mri_glmfit  --glmdir 
> lh.paired-diff 
> --fsgd paired-diff.fsgd  --C mean.mtx --y
> lh.paired-diff.thickness.mghgdfReadHeader: reading paired-diff.fsgd
> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
> Continuous Variable Means (all subjects)
> 0 Age 1.5
> Class Means of each Continuous Variable
> 1 Main   1.5000
> INFO: gd2mtx_method is dods
>
> $Id: mri_glmfit.c,v 1.187.2.1 2010/07/26 15:54:39 greve Exp $
> cwd /Applications/freesurfer/subjects/qdec
> cmdline mri_glmfit --glmdir lh.paired-diff --fsgd paired-diff.fsgd --C 
> mean.mtx
> --y lh.paired-diff.thickness.mgh
> sysname  Darwin
> hostname larry
> machine  i386
> user amend
> FixVertexAreaFlag = 1
> UseMaskWithSmoothing 1
> OneSampleGroupMean 0
> y/Applications/freesurfer/subjects/qdec/lh.paired-diff.thickness.mgh
> logyflag 0
> usedti  0
> FSGD paired-diff.fsgd
> glmdir lh.paired-diff
> IllCondOK 0
> DoFFx 0
> Creating output directory lh.paired-diff
> Loading y from
> /Applications/freesurfer/subjects/qdec/lh.paired-diff.thickness.mgh
> mri_glmfit(79576) malloc: *** mmap(size=2563764224) failed (error code=12)
> *** error: can't allocate region
> *** set a breakpoint in malloc_error_break to debug
> MRIallocIndices: could not allocate 1714511945 elt index array
> Cannot allocate memory
>
> The mri_info for the file is :
>
> mghRead(/Applications/freesurfer/subjects/qdec/fsgd_input.mgh, -1): 
> could not
> open file
> amend@larry /Applications/freesurfer/subjects/qdec$  mri_info
> /Applications/freesurfer/subjects/qdec/lh.paired-diff.thickness.mgh
> Volume information for
> /Applications/freesurfer/subjects/qdec/lh.paired-diff.thickness.mgh
>   type: MGH
> dimensions: 1714510945 x 1853057372 x 1634628457 x 1668310833
>voxel sizes: 72950800688805540228332034981888., 0.,
> 70387746064971392794503413760.
>   type: UNKNOWN (842347100)
>fov: inf
>dof: 1668244335
> xstart: -inf, xend: inf
> ystart: -39.8, yend: 39.8
> zstart: -57528904905339976080461439864148066304.0, zend:
> 57528904905339976080461439864148066304.0
> TR: 71446969504754118412748034408448.00 msec, TE:
> 17862977898376175754203558313984.00 msec, TI:
> 4464583905807213894543171649536.00 msec, flip angle:
> 4128358109894647822155776.00 degrees
>nframes: 1668310833
>PhEncDir: UNKNOWN
> ras xform present
> xform info: x_r = 19441367164500690594879212879872., y_r =
> 282670772483715414097920., z_r = 
> 4630517930517356511053742080., c_r =
> 18179207505345150839094025125888.
>   : x_a = 72953300747400503281465327353856., y_a =
> 71756401321839400437789128392704., z_a =
> 4721224652433019196440490016768., c_a = 0.
>   : x_s =   0., y_s = 208210237828607676252160., z_s =
> 42829986963488., c_s = 4622889417339745644740714954752.
>
> talairach xfm :
> Orientation   : AAA
> Primary Slice Direction: coronal
>
> voxel to ras transform:
>inf 12133604733747200.  inf   -inf
>inf 3080133850722982464323584.  inf   -inf
>   36752183205510726549504. 8937395835633664. 
>  inf  
> -inf
> 0.   0.   0. 1.
>
> voxel-to-ras determinant nan
>
> ras to voxel transform:
> mat = NULL!
> Invalid argument
> MatrixFree: NULL mat POINTER!
>
> Invalid argument
>
> -Andrew
> 
>
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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] Mac Pro with 12cores

2011-03-10 Thread Richard G. Edgar


On Thu, 2011-03-10 at 11:29 -0300, Pedro Paulo de Magalhães Oliveira
Junior wrote:
> That's without GPU?

Yes. CPU only stream.

Richard

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Re: [Freesurfer] Mac Pro with 12cores

2011-03-10 Thread Pedro Paulo de Magalhães Oliveira Junior

That's without GPU?


On Thu, Mar 10, 2011 at 11:17, Richard G. Edgar
wrote:

>
> On Thu, 2011-03-10 at 08:27 -0500, Bruce Fischl wrote:
> > If you have enough memory! Maybe Richard can post current CPU recon
> > times with the latest hardware and optimizations. I think they are
> > much shorter than they used to be
>
> My workstation (3.2 GHz Nehalem) can do a recon-all ernie in about 8
> hours. Running four in parallel (one for each core) bumps the total
> walltime up to about eight and a half hours.
>
> Regards,
>
> Richard
>
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Re: [Freesurfer] Mac Pro with 12cores

2011-03-10 Thread Richard G. Edgar

On Thu, 2011-03-10 at 08:27 -0500, Bruce Fischl wrote:
> If you have enough memory! Maybe Richard can post current CPU recon
> times with the latest hardware and optimizations. I think they are
> much shorter than they used to be

My workstation (3.2 GHz Nehalem) can do a recon-all ernie in about 8
hours. Running four in parallel (one for each core) bumps the total
walltime up to about eight and a half hours.

Regards,

Richard

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Re: [Freesurfer] Small voxel size

2011-03-10 Thread Bruce Fischl


Hi Tricia,

I don't think you can use that subject. It will only have 39% of the SNR 
of the others. Sorry :<


Bruce
On Wed, 9 Mar 2011, Tricia Merkley wrote:


The native resolution of the other subjects is (1,1,1)mm voxel size and 
(256,256,160) voxels, whereas this subject is (0.7,0.7,0.8) mm voxel size and 
(288,288,165) voxels.  Sorry that wasn't clear in my previous email.  I'd 
appreciate any insight that anyone might be able to share.

Thanks,
Tricia

--- On Wed, 3/9/11, Bruce Fischl  wrote:

From: Bruce Fischl 
Subject: Re: [Freesurfer] Small voxel size
To: "Tricia Merkley" 
Cc: "freesurfer@nmr.mgh.harvard.edu" 
Date: Wednesday, March 9, 2011, 5:01 PM

What is the resolution of your other subjects?



On Mar 9, 2011, at 5:21 PM, Tricia Merkley  wrote:

Hello,

One of our subjects was scanned with (0.7,0.7,0.8) mm voxel size, although all 
other acquisition parameters were the same as the other subjects.  I'm 
wondering to what extent this might affect the results of the subcortical 
segmentation, cortical thickness measurements, etc., as compared to 1mm cubic 
voxels.  When would it be appropriate to use the '-cm' flag for mri_convert?

Thanks,
Tricia Merkley



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Re: [Freesurfer] Mac Pro with 12cores

2011-03-10 Thread Bruce Fischl

If you have enough memory! Maybe Richard can post current CPU recon times with 
the latest hardware and optimizations. I think they are much shorter than they 
used to be



On Mar 10, 2011, at 3:28 AM, Pedro Paulo de Magalhães Oliveira 
Junior wrote:

> You can run 12 recon-all in parallel.
> 
> You'll have 12 patients processed in each day approximately
> 
> -
> Pedro Paulo de Magalhães Oliveira Junior
> Diretor de Operações
> Netfilter & SpeedComm Telecom
> -- www.netfilter.com.br
> -- For mobile: http://www.netfilter.com.br/mobile
> 
> 
> 
> 
> 2011/3/10 汪贵宏 
> Hi,all:
>As we have too many controls and patients to run the "recon-all",and 
> it is really time-suming,so,how can I reduce the time of recon-all in a group 
> of patients?
> After read the statistic info on the website
>   https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllRunTimes 
> It seems the mac pro will take much more time than others,so ,can anybody 
> give me a suggestion?Is it Mac Pro with 12 cores works?
> http://www.apple.com/macpro/
>  
> Thanks a lot!
>  
> Wang
> 
> 
> 
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Re: [Freesurfer] about recon-all command

2011-03-10 Thread Allison Stevens

That flag is needed if your input is larger than the required size by 
FreeSurfer 256x256x256. You would not use it on input that did not require it 
(ie it is smaller than 256x256x256). 

On Mar 10, 2011, at 4:53 AM, Kenichiro Tanaka  wrote:

> Hello All,
> 
> I have a question about recon-all command with "-cw256" option.
> What is the difference between "recon-all" and "recon-all with -cw256"?
> What is "-cw256 option"?
> 
> When I tried executing recon-all command, I had an error message:
> 
>  ERROR! FOV=320.000 > 256
>  Include the flag -cw256 with recon-all!
> 
> I did the following using another 001.mgz file:
> 
> I compared aseg.stats file after "recon-all" execution with aseg.stats file 
> after 
> "recon-all -cw256" execution using "diff" command.
> aseg.stats file after "recon-all " execution was much different from 
> aseg.stats file after
> "recon-all -cw256" execution.
> What's wrong with it?
> 
> I tried to search information about "-cw256"on internet, but I could not find 
> out.
> Please tell me -cw256.
> 
> Thanks.
> 
> Kenichiro Tanaka
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[Freesurfer] about recon-all command

2011-03-10 Thread Kenichiro Tanaka

Hello All,

I have a question about recon-all command with "-cw256" option.
What is the difference between "recon-all" and "recon-all with -cw256"?
What is "-cw256 option"?

When I tried executing recon-all command, I had an error message:

/
// ERROR! FOV=320.000 > 256
// Include the flag -cw256 with recon-all!
//
/

I did the following using another 001.mgz file:

I compared aseg.stats file after "recon-all" execution with aseg.stats
file after
"recon-all -cw256" execution using "diff" command.
aseg.stats file after "recon-all " execution was much different from
aseg.stats file after
"recon-all -cw256" execution.
What's wrong with it?

I tried to search information about "-cw256"on internet, but I could not
find out.
Please tell me -cw256.

Thanks.

Kenichiro Tanaka
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Re: [Freesurfer] Mac Pro with 12cores

2011-03-10 Thread Pedro Paulo de Magalhães Oliveira Junior

You can run 12 recon-all in parallel.

You'll have 12 patients processed in each day approximately

-
Pedro Paulo de Magalhães Oliveira Junior
Diretor de Operações
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://www.netfilter.com.br/mobile




2011/3/10 汪贵宏 

> Hi,all:
>As we have too many controls and patients to run the "recon-all",and
> it is really time-suming,so,how can I reduce the time of recon-all in a
> group of patients?
> After read the statistic info on the website
>   https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllRunTimes
> It seems the mac pro will take much more time than others,so ,can anybody
> give me a suggestion?Is it Mac Pro  with 12
> cores works?
> http://www.apple.com/macpro/
>
> Thanks a lot!
>
> Wang
>
>
>
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[Freesurfer] effect size for cortical thickness changes

Re: [Freesurfer] extracting thickness values from group level map

[Freesurfer] extracting thickness values from group level map

Re: [Freesurfer] Newbie - Group analysis on a single session with multiple runs.

[Freesurfer] Reconchecker error

Re: [Freesurfer] Newbie - Group analysis on a single session with multiple runs.

Re: [Freesurfer] Newbie - Group analysis on a single session with multiple runs.

[Freesurfer] Newbie - Group analysis on a single session with multiple runs.

Re: [Freesurfer] Small voxel size

Re: [Freesurfer] Small voxel size

Re: [Freesurfer] mri_glmfit-sim error

[Freesurfer] mri_glmfit-sim error

Re: [Freesurfer] DODS and DOSS

Re: [Freesurfer] mri_glmfit allocate memory error

Re: [Freesurfer] Mac Pro with 12cores

Re: [Freesurfer] Mac Pro with 12cores

Re: [Freesurfer] Mac Pro with 12cores

Re: [Freesurfer] Small voxel size

Re: [Freesurfer] Mac Pro with 12cores

Re: [Freesurfer] about recon-all command

[Freesurfer] about recon-all command

Re: [Freesurfer] Mac Pro with 12cores

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