Re: [Freesurfer] what program generates "path.map.txt" for dmri_pathstats to run?

14 Jul 2017

      Dear DTI experts:
I am wondering if anybody could provide any information to help me out with this constant error that I am desperate to resolve? 
I just need to know what program generates this "path.map.txt" for the tracula script dmri_pathstats to run through?
dmri_pathstats --intrc START_610/dpath/lh.cst_AS_avg33_mni_bbr --dtbase START_610/dmri/dtifit --path lh.cst --subj START_610 --out START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt --outvox START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.byvoxel.txt --debug
cwd /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610
cmdline dmri_pathstats --intrc START_610/dpath/lh.cst_AS_avg33_mni_bbr --dtbase START_610/dmri/dtifit --path lh.cst --subj START_610 --out START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt --outvox START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.byvoxel.txt --debug sysname  Linux hostname node031 machine  x86_64
user     yuwenh
Input tracula directory: /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr
Input DTI fit base: /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dmri/dtifit
Pathway name: lh.cst
Subject name: START_610
Output file for overall measures: /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt
Output file for voxel-by-voxel measures: /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.byvoxel.txt
Lower threshold for probability: 0.200000 Computing statistics on /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr...
ERROR: Could not open /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr/path.map.txt for reading
Your help is being greatly appreciated,
Yuwen
-----Original Message-----
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Subject: Freesurfer Digest, Vol 161, Issue 25
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Today's Topics:
1. Re: PETsurfer AC/TOF (Douglas N Greve)
   2. Re: 3G1V.fsgd (Douglas N Greve)
   3. Re: GLM Analysis Number of vertices and Area (Douglas N Greve)
   4. Regression diagnostic in context of surface-based	analysis
      (Antonin Skoch)
   5. bbregister + mri_vol2vol different results (Paul Glad Mihai)
   6. R: Re:  3G1V.fsgd (stdp82@virgilio.it)
   7. R:  R: Re:  3G1V.fsgd (stdp82@virgilio.it)
   8. Re: R: Re: 3G1V.fsgd (Douglas N Greve)
   9. Mid point on Freeview (Trisanna Sprung-Much)
  10. vertex-wise contra-lateral mapping on an ico surface (Burke Rosen)
  11. Re: Mid point on Freeview (Bruce Fischl)
  12. Re: ERROR: dimension mismatch between input volume and	seg -
      VolumeROICorticalThickness (M Janani)
  13. R: Re:  R: Re: 3G1V.fsgd (stdp82@virgilio.it)
  14. problems with recon-all in 6.0 (Lars M. Rimol)
----------------------------------------------------------------------
Message: 1
Date: Thu, 13 Jul 2017 16:28:24 -0400
From: Douglas N Greve greve@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] PETsurfer AC/TOF
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: d5234734-a0cc-e310-cd02-d73229c9437c@nmr.mgh.harvard.edu
Content-Type: text/plain; charset=utf-8; format=flowed
Sorry, I don't know what the difference is. I always use the mean update volume as the template for registration.
On 07/13/2017 01:57 PM, Fu, Jason (NIH/NINDS) [F] wrote:
...
ac/tof is attenuation corrected/time of flight. Ac/hd is attenuation corrected/head.
-----Original Message-----
From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu]
Sent: Thursday, July 13, 2017 12:52 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] PETsurfer AC/TOF
sorry, what is an ac/tof file?
On 07/13/2017 12:12 PM, Fu, Jason (NIH/NINDS) [F] wrote:
...
Hi,
I am currently using PETsurfer PVC to determine glucose metabolism
differences in certain structures between the brain hemispheres. I am
currently using ac/tof files to coregister to the anatomy. One of the
patients did not have the ac/tof files, would ac/hd files work instead?
Thanks,
Jason Fu

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Douglas N. Greve, Ph.D.
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-- 
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
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------------------------------

Message: 2
Date: Thu, 13 Jul 2017 16:30:54 -0400
From: Douglas N Greve greve@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] 3G1V.fsgd
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: 1139ca82-1846-fbb5-9650-f10a5ad867c4@nmr.mgh.harvard.edu
Content-Type: text/plain; charset=utf-8; format=flowed

On 07/13/2017 10:37 AM, stdp82@virgilio.it wrote:
> Dear FS group,
>
> I don't understand how I should build the contrast for 3 groups 1 
> covariate.
> No specific example is provided within fsgd example and also other 
> colleagues report the same problem in the mail list.
> Please could you provide us details on this topic?
> Especially, how should be the g3v1.intercept and g31v.slope?
>
> 1 -1 0 0 0 0
> 1 0 -1 0 0 0
> for g3v1.intercept.mtx
This is the main effect of group on the intercept regressing out the 
effect of covariate.
>
> and
> 0 0 0 1 -1 0
> 0 0 0 1 0 -1
> for g3v1.slope.mtx
This is the main effect of group on the slope regressing out the effect 
of group intercept.
>
>
> are corrected?
>
> Waiting for you very wellcome suggestions
>
> Thanks and kind regards
>
> Stefano
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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-- 
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: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

------------------------------

Message: 3
Date: Thu, 13 Jul 2017 16:38:21 -0400
From: Douglas N Greve greve@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] GLM Analysis Number of vertices and Area
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: 7ef1f42e-31d6-fe1e-7e89-9e04338a8a9d@nmr.mgh.harvard.edu
Content-Type: text/plain; charset=utf-8; format=flowed

I'm not sure what you mean. Do you want stats for every cluster 
regardless of significance? If so, you can run the monte carlo 
correction with a clusterwise p-value (--cwp in mri_glmfit-sim) of 1.0

On 07/13/2017 11:52 AM, Aman Montazeri wrote:
> Hello Friends,
>
> Sorry for the simple question.
>
> I am doing GLM analysis using QDEC between two groups (one discrete 
> variable), then I run the Monte-Carlo clustering and got the stats of 
> my cluster.
>
> My supervisor asked me to get the Stats of blobs/clusters (area and 
> number of vertices in each area) before applying the Monte-Carlo (only 
> after GLM analysis/comparison)
> I would really appreciate if you could help me with getting those 
> stats, as I can't figure out how to do it.
>
>
> Thank you,
> Aman
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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-- 
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: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

------------------------------

Message: 4
Date: Thu, 13 Jul 2017 22:48:03 +0200
From: Antonin Skoch ansk@ikem.cz
Subject: [Freesurfer] Regression diagnostic in context of
    surface-based	analysis
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: 1034294575-17116@posta.medicon.cz
Content-Type: text/plain; charset="utf-8"

Dear experts,

I am looking for a way how to effectively run a regression model diagnostic in context of surface-based analysis.

My example case is the regression model where response variable is cortical thickness and explanatory variable is continuous (disease duration). The statistical linear modelling uses several principial approaches to find model which best describes the studied relation in the data, namely:

1. model simplification by elimination of insignificant effects
2. transformation of dependent variable to improve normality of residuals
3. transformation of explanatory variable to improve model fit or use of linear combination of various terms in explanatory variable (for example apart from linear term to include also quadratic and higher-order polynomial terms)

My question is, how to effectively exploit methods 2 and 3 in context of vertex-wise surface-based analysis? Could you please comment on what tools inside FreeSurfer framework can be used for this purpose? What is your common aproach to find regression model which best approximates the relation present in the data?

Thank you in advance for pointing me to right direction.

Regards,

Antonin Skoch

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Re: [Freesurfer] what program generates "path.map.txt" for dmri_pathstats to run?