date:20170322

[Freesurfer] Correcting Skull-Strip Errors - Watershed Algorithm Question

2017-03-22 Thread Abhinav Kurada

The initial running of recon-all autorecon-1 autorecon-2 for a sample scan 
resulted in a bad skull strip. I am attempting to troubleshoot the issue 
through running just the skull strip portion of the recon-all pipeline again, 
followed by adjusting the watershed parameters. 

During re-running -skullstrip, I am given a 

mri_watershed Error: read failed

 (the em_register portion of the -skullstrip flag ran without interruption). I 
have attached the corresponding log.

Is there a way to fix this watershed error (when I have tried to run the 
watershed command by itself, the command is not recognized)?

https://share.polymail.io/v1/z/f/NThkMzUzYTU4ODA4/Vp21pl8rsUD4Tvw7tgnoOONDLHvyqODHm-JuJ2CuYvbpNRv74VHiIXFW2sq1hbb-_IVq_gsswxsr7C_ze5rXaYdUNPgZe62f-6Nkfl5OYuq3oGTdw0D4lWWL-eF5CxE20aCbJXC_5RQpmTiuFb46yJ13lSZ5Dvo3xeSo4ogTr6_M5umIcZTfK7sFK3yjPIXu2Cc=/recon-all.log

https://share.polymail.io/v1/z/f/NThkMzUzYTU4ODA4/Vp21pl8rsUD4Tvw7tgnoOONDLHvyqODHm-JuJ2CuYvbpNRv74VHiIXFW2sq1hbb-_IVq_gsswxsr7C_ze5rXaYdUNPgZe62f-6Nkfl5OYuq3oGTdw0D4lWWL-eF5CxE20aCbJXC_5RQpmTiuFb46yJ13lSZ5Dvo3xeSo4ogTr6_M5umIcZTfK7sFK3yjPIXu2Cc=/recon-all.log___
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Re: [Freesurfer] Qdec 1.5

2017-03-22 Thread Duy Nguyen

Dear Douglas

Thank you for your response.  I cannot run asegstats2table and
aparcstats2table command outside of qdec.

Best regards,
Duy Nguyen

*--v-- Peace --v--*
*Duy Nguyễn *
*Biomedical Engineering Department- IU HCMC*
*Cell: (+84)90056*
*Email: duy.nguyen...@gmail.com *

On Thu, Mar 23, 2017 at 5:07 AM, Douglas Greve 
wrote:

> don't know what is going on there. Can you run the asegstats2table command
> outside of qdec?
>
> On 3/17/17 8:29 AM, Duy Nguyen wrote:
>
> Dear FS Expert
>
> I am doing analysis from the group_analysis_tutorial data to practice and
> learn.  However, I come across the error window like it shows on the
> attached picture (please see the attachment) when I press the button
> "Generate Stats Data Table." Please help me how can I can find the file
> aseg.volume.stats.dat.  If the file does not exist, how can I create one?
>
> Thank you for your response. Any help would be appreciated!!!
> *--v-- Peace --v--*
> *Duy Nguyễn *
> *Biomedical Engineering Department- IU HCMC*
> *Cell: (+84)90056*
> *Email: duy.nguyen...@gmail.com *
>
>
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> is
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> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
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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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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] LME mass univariate model

2017-03-22 Thread Bronwyn Overs

Hi Mailing List,

I am fitting an LME model with random effects for B0 and B2, so I am using the 
following to fit a spatiotemporal model:

lhstats = lme_mass_fit_Rgw(X,[1 3],Y,ni,lhTh0,lhRgs,lhsphere);

However, prior to this when i am computing the initial temporal covariance 
estimates, do the square bracketed numbers refer to the random effects as well? 
So would this be run for random effects at B0 and B2:

[lhTh0,lhRe] = lme_mass_fit_EMinit(X,[1 3],Y,ni,lhcortex,3);

Kind regards,
Bronwyn Overs
Research Assistant

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265

neura.edu.au  
  
 

> On 7 Mar 2017, at 11:57 pm, Martin Reuter  wrote:
> 
> Hi Bronwyn, 
> 
> to shorten equations, lets set t = years_form_baseline
> a = age
> g = group
> s = sex
> 
> so your model is
> Y_ij = b0 + b1 t_ij + b2 a_i + b3 g_i + b4 s_i + b5 t_ij a_i + b6 t_ij g_i + 
> b7 a_i g_i + b8 t_ij a_i g_i
> (as a fist step, I would consider simplifying it, by dropping the age 
> interactions). 
> 
> Anyway
> 
> for male (s_i =0) and controls (g_i = 0) this reduces to
> Y_ij = b0 + b1 t_ij + b2 a_i + b5 t_ij a_i 
> so b1 is the slope for male controls, controlling for age and the slope age 
> interaction. (0 1 0….)
> 
> Now for female (s=1) patients (g=1) we get this:
> 
> Y_ij = b0 + b1 t_ij + b2 a_i + b3  + b4 + b5 t_ij a_i + b6 t_ij + b7 a_i + b8 
> t_ij
>= (b0+b3+b4) + (b1 + b6 + b8 ) t_ij + (b2+b7) a_i + b5 t_ij a_i 
> So the slope for female patients (controlling for age and age time 
> interaction) would be
> (b1 + b6 + b8)
> 0 1 0 0 0 0 1 0 1
> 
> The difference in slope between female patients and male controls would be
> 0 0 0 0 0 0 1 0 1 (or the negative of that depending which way you subtract). 
> Similarly you can look at group differences (controlling for age gender and 
> interactions). 
> 
> Always write out the full model to make sure you understand what you are 
> doing. 
> 
> To complete the picture, here is the contrast for the slope of male patients
> 0 1 0 0 0 0 1 0 1 (it is the same as for female patients, because you don’t 
> have a timeXgender interaction. So that is your patient slope )
> Therefore the 
> 0 0 0 0 0 0 1 0 1  is the slope difference between the groups. 
> 
> I would recommend you talk to a local biostatistician, to make sure you are 
> actually modelling what you want to model. And that you are interpreting the 
> results correctly.  
> 
> Grüße, Martin
> 
>> On 06 Mar 2017, at 18:56, Bronwyn Overs > > wrote:
>> 
>> Hi Martin,
>> 
>> Thank you for your response, that is much clearer. 
>> 
>> I am also a little confused about how to specify the exact contrasts we wish 
>> to test and was hoping to get some advice. My design matrix X includes the 
>> following columns:
>> 1. Intercept
>> 2. Years from baseline
>> 3. Age at baseline
>> 4. Group (patients labelled 1, controls 0)
>> 5. Gender (females labelled 1, males 0)
>> 6. Col 2 (years) * Col 3 (age)
>> 7. Col 2 (years) * Col 4 (group)
>> 8. Col 3 (age) * Col 4 (group)
>> 9. Col 2 (years) * Col 3 (age) * Col 4 (group)
>> 
>> If I test the following contrast, is it giving me the effect of years across 
>> all groups and genders, or just years for male controls:
>> CM.C = [0 1 0 0 0 0 0 0 0]
>> 
>> Also, what contrast should I use to examine the effect of years in my 
>> patient group irrespective of gender?
>> 
>> Kind regards,
>> Bronwyn Overs
>> Research Assistant
>> 
>> Neuroscience Research Australia
>> Margarete Ainsworth Building
>> Barker Street Randwick Sydney NSW 2031 Australia
>> M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265
>> 
>> neura.edu.au  
>>   
>>  
>> 
>>> On 4 Mar 2017, at 12:43 am, Martin Reuter >> > wrote:
>>> 
>>> Hi Bronwyn, 
>>> 
>>> I think years-between-scans should be years-from-baseline-scans . You may 
>>> need to compute that if what you have is really years between neighbouring 
>>> scans.
>>> 
>>> 1. Usually people use intercept and maybe years-from-baseline as random 
>>> effects. I would not include too many random effects, as it each adds a lot 
>>> of free parameters and you need a lot of data to fit all that in a 
>>> meaningful way. Which of your columns are random effects can be passed 
>>> lme_fit_FS(X,[1 2],Y(:,1)+Y(:,2),ni);
>>> for example has column 1 and 2 as random effects. 
>>> 
>>> 2. You can do a model comparison as described on our wiki 
>>>

Re: [Freesurfer] Fw: PETsurfer surface based analysis

2017-03-22 Thread miracooloz

Hello Doug, I was able to solve the problem. It had to do with the gtmseg part of the pipeline. I had to re-run gtmseg again and mri_gtmpvc exited without error and produced all output. Thank you Best, Paul Sent from my BlackBerry 10 smartphone.From: Douglas GreveSent: Wednesday, March 22, 2017 5:10 PMTo: freesurfer@nmr.mgh.harvard.eduReply To: Freesurfer support listSubject: Re: [Freesurfer] Fw: PETsurfer surface based analysis

Can you tar up the output folder and send it to me at our file
drop?

https://gate.nmr.mgh.harvard.edu/filedrop2
Also, please send the following 3 files
/net/synapse/nt/paul/Analysis/C6_01_001_140813/mri/gtmseg.mgz
/net/synapse/nt/paul/Analysis/C6_01_001_140813/mri/gtmseg.ctab
/net/synapse/nt/paul/Analysis/C6_01_001_140813/mri/gtmseg.lta

On 3/22/17 3:34 PM, miracle ozzoude
wrote:

Thank you Doug. I am trying to perform pvc for my
pet data based on the tutorial however, I keep getting this
error:

" mri_gtmpvc --i
C6_01_001_140813_PET_AV45_coreg_avg.nii.gz --reg
C6_01_001_140813_PET_AV45_coreg_avg.reg.lta --psf 6mm --seg
gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx
0.01 --o C6_01_001_140813.gtmpvc.output
Loading input C6_01_001_140813_PET_AV45_coreg_avg.nii.gz
done loading input 1 frames

$Id: mri_gtmpvc.c,v 1.69.2.1 2016/07/08 19:50:25 zkaufman
Exp $
setenv SUBJECTS_DIR /net/synapse/nt/paul/Analysis
cd /net/synapse/nt/paul/Analysis
mri_gtmpvc --i C6_01_001_140813_PET_AV45_coreg_avg.nii.gz
--reg C6_01_001_140813_PET_AV45_coreg_avg.reg.lta --psf 6mm
--seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01
--mgx 0.01 --o C6_01_001_140813.gtmpvc.output
sysname Linux
hostname neuron2.sri.utoronto.ca
machine x86_64
user paul
vgthresh 0.001000
nReplace 18
0. 0. 0. 0. 0. 0.
24 avail.processors, using 1
Creating output directory C6_01_001_140813.gtmpvc.output
Loading seg for gtm
/net/synapse/nt/paul/Analysis/C6_01_001_140813/mri/gtmseg.mgz
Loading seg ctab
/net/synapse/nt/paul/Analysis/C6_01_001_140813/mri/gtmseg.ctab
Reading
/net/synapse/nt/paul/Analysis/C6_01_001_140813/mri/gtmseg.lta
Replacing 18
Pruning ctab
ERROR: CTABpruneCTab(): ctab does not have segid 192
Checking tissue type
Segmentation fault"

Step 1 and 2 were successful. Please can you tell me what
is wrong. Thanks
Best,
Paul

On Wed, Mar 22, 2017 at 3:07 PM,
Douglas Greve
wrote:

On
3/22/17 2:02 PM, miracle ozzoude wrote:

Hello Doug,
Thank you for the detailed reply. I do have
other questions.

1) Can you confirm if this is the correct use
of mris_preproc for Uncached PET data.
mris_preproc --fsgd your.fsgd --target fsaverage
--hemi lh --meas Pet --out lh.your.pet.00.mgh.
This modification was made from the thickness
thickness data. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis

You need to specify the pet input data. See for
example the fMRI analysis tutorial here
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_freeview

2) if both the thickness and pet maps have the
same contrast matrices, can I use one of them as
my matrix for multimodal analysis?

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