from:"John Anderson"

[Freesurfer] Head circumference

2015-10-24 Thread John Anderson


Dear FS experts,

I want to inquire if there is any tool or method in Freesurfer that can help to calculate the head circumference from MPRAGE ?

Thanks for any advice!

 

 
 

Bests,
John 

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[Freesurfer] Head circumference

2015-10-23 Thread John Anderson

Dear FS experts,

I want to inquire if there is any script in Freesurfer that can help to calculate the head circumference from MPRAGE ?

Thanks for any advice!

 

 
 

Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419
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Re: [Freesurfer] recon-all

2015-11-17 Thread John Anderson

Hi Doug,

Thanks you very much for your great and detailed answered.

Kindly one more thing:

when I am tring to run recon-all on "001.mgz" (under the folder mri/orig). If the fov is more than 256 ( e.g 320) recon-all failed. I checked the "recon-all.log" file and I found that it failed because the fov is more than 320 and it says that I need to run recon -all with the flag -cw256.

How can the fov affect the segmentation? in other words is it better to run recon-all on a file with fov less than 256 or more than 256 ? what is the difference in the final output?

 Bests,

John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419

Sent: Thursday, November 05, 2015 at 9:39 AM
From: "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all

On 11/5/15 8:37 AM, John Anderson wrote:

Thanks a lot Doug!

Kindly  ...

1. What do you mean by intensity normalized?

Removing non-biological intensity fluctuations such as darkening/brightening from multiple head coils

2. What is the purpose of conforming the inputs to 256^3 1mm3

This is something that was done when FS was first programmed to make it easier to program by assuring that all inputs were the same size.

3. In order to move mask to diffusion space (FA map) or PET space I do the following:

           3.1 I register FA map to T1 ( after converting the DICOMs to T1.nii - the voxel dimentions here are 176X256X256)

           3.2 I create mask of interest using mri_binarize ( from the wmparc.mgz atals the voxel dimentions here 256X256X256 )

           3.3 I register FA map to T1 image using FLIRT

           3.4 I register the mask to T1 using FLIRT

           3.5 I use reversed matrix to move the mask to FA map.

Probably works, but very compilcated. You should use bbregister to register the FA or PET directly to the conformed space, then use mri_label2vol to map the mask into FA/PET space.

The problem in this approach is the voxel dimentions ( between the mask and the T1). Can I use norm.mgz ( which has the same voxel dimentions of the mask ) istead of T1 to do the previous steps?

Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419

Sent: Wednesday, November 04, 2015 at 3:44 PM
From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all

On 11/04/2015 10:22 AM, John Anderson wrote:
> Hi freesurfers,
> Following recon-all I have a collection of folders inside the subject
> folder.
> Inside the folder "mri" I have collection of files:
> 1. What is the differnce between the file "orig.mgz" and the file
> "norm.mgz" ?
norm has been skull stripped and intensity normalized
> 2. Why the voxel dimentions are differnt? (i.e In norm.mgz the voxel
> dimentions are equal while in orig.mgz it is not)?
They should be the same. It might be differnt than rawavg.mgz or your
input data because we "conform" all inputs to 256^3 1mm3
> 3. Is it correct if I convert norm.mgz to "nii" file and use it as a
> "T1" for further processing?
I don't know without knowing more about the "further processing". It is
not a T1 image itself (ie, the voxel intensities are not T1 in msec).
> bests,
> John Anderson
>
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
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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: 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/

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[Freesurfer] Voxel based vs surface based

2015-10-30 Thread John Anderson

Hi Doug and Bruce,
Kindly, I have question regarding the difference between voxel based ( VBM/ FSL pipeline) and surface based analysis ( Freesurfer ).
 
I have two groups of subjects Group A and Group B
I ran morphometric analysis in Freesurfer ( recon-all then manual edits) to check the difference in cortical thickness between the groups. Then I used Qdec to correct the results for multiple comparisons and to visualize the significant clusters.
Then I ran VBM analysis between the groups ( the same subjects) to study the difference in gray matter volume between the groups.
 
I got significant difference between the groups in both methods but in different areas of the brain ( the significant clusters are not in the same location ).
 
What is the difference between surface based analysis and voxel based analysis technically. Is it right to get different results?
 
Thanks in advance

 

 

 

Bests,
John 

 
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[Freesurfer] recon-all

2015-11-04 Thread John Anderson

Hi freesurfers,

Following recon-all I have a collection of folders inside the subject folder.

Inside the folder "mri" I have collection of files:

 

1. What is the differnce between the file "orig.mgz" and the file "norm.mgz" ? 

2. Why the voxel dimentions are differnt? (i.e In norm.mgz the voxel dimentions are equal while in orig.mgz it is not)?

3. Is it correct if I convert norm.mgz to "nii" file and use it as a "T1" for further processing?

 

bests,

John Anderson

 
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Re: [Freesurfer] recon-all

2015-11-05 Thread John Anderson

Thanks a lot Doug!

Kindly  ...

1. What do you mean by intensity normalized?
2. What is the purpose of conforming the inputs to 256^3 1mm3

3. In order to move mask to diffusion space (FA map) or PET space I do the following:

           3.1 I register FA map to T1 ( after converting the DICOMs to T1.nii - the voxel dimentions here are 176X256X256)

           3.2 I create mask of interest using mri_binarize ( from the wmparc.mgz atals the voxel dimentions here 256X256X256 )

           3.3 I register FA map to T1 image using FLIRT

           3.4 I register the mask to T1 using FLIRT

           3.5 I use reversed matrix to move the mask to FA map.

The problem in this approach is the voxel dimentions ( between the mask and the T1). Can I use norm.mgz ( which has the same voxel dimentions of the mask ) istead of T1 to do the previous steps?

Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419

Sent: Wednesday, November 04, 2015 at 3:44 PM
From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all

On 11/04/2015 10:22 AM, John Anderson wrote:
> Hi freesurfers,
> Following recon-all I have a collection of folders inside the subject
> folder.
> Inside the folder "mri" I have collection of files:
> 1. What is the differnce between the file "orig.mgz" and the file
> "norm.mgz" ?
norm has been skull stripped and intensity normalized
> 2. Why the voxel dimentions are differnt? (i.e In norm.mgz the voxel
> dimentions are equal while in orig.mgz it is not)?
They should be the same. It might be differnt than rawavg.mgz or your
input data because we "conform" all inputs to 256^3 1mm3
> 3. Is it correct if I convert norm.mgz to "nii" file and use it as a
> "T1" for further processing?
I don't know without knowing more about the "further processing". It is
not a T1 image itself (ie, the voxel intensities are not T1 in msec).
> bests,
> John Anderson
>
>
>
> ___
> 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: 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/

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Re: [Freesurfer] MPRAGE SNR

2015-10-19 Thread John Anderson

Dear Jürgen

This really helps!

I highly appreciate your input on this.

Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419

Sent: Monday, October 19, 2015 at 1:30 AM
From: JuergenHaenggi <j.haen...@psychologie.uzh.ch>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] MPRAGE SNR

Dear John

FS's QA tools provide the SNR

see https://surfer.nmr.mgh.harvard.edu/fswiki/QATools

there is also a FS function called wm-anat-snr that can be used for that.

Hope this helps

Cheers

Jürgen

-
Jürgen Hänggi, Ph.D.
Division of 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)
0041 44 635 74 09 (fax office)
BIN 4.D.04 (office room number)
j.haen...@psychologie.uzh.ch (email)
http://www.psychologie.uzh.ch/neuropsy/ (website)
http://www.juergenhaenggi.ch (private website)

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Am 18.10.2015 um 16:48 schrieb John Anderson:

Dear Experts,

Is there any tool in Freesurfer that can help to evaluate the SNR for T1 MPRAGE images directly ( i.e script). If not knidly can any help me to figure out the best way to dao it.

I highly appreciate your help!

Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419

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Re: [Freesurfer] MPRAGE SNR

2015-10-19 Thread John Anderson

Hi All,

Thank you very much for your comments!

 

Is it advisable to include SNR as a covariate when we use Qdec to run the final statistics on volumetrics, surfaces and cortical thickness?

Does it make sence ?

 

Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419

 
 

Sent: Monday, October 19, 2015 at 11:48 AM
From: "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] MPRAGE SNR

This has been my experience as well. Not much seems to predict which
scans will need to be edited.

On 10/19/15 10:23 AM, Harms, Michael wrote:
> Hi,
>
> FWIW, I've looked at a number of these measures in 500+ subjects from HCP
> data -- wm-anat-snr, pctsurfcon, G/W cnr, G/CSF cnr -- to see how they
> relate to each other, and whether they correlate with mean cortical
> thickness, white matter surface area, or number of SurfaceHoles (prior to
> topology correction).
>
> I didn't find much of note. e.g., the highest correlations were:
>
> r = -0.32 between mean cortical thickness and G/CSF cnr (from norm.mgz)
> r = -0.25 between white surface area and wmanatsnr
> r = -0.39 between SurfaceHoles and pctsurfcon (and same with G/W cnr from
> norm.mgz)
>
> Not surprisingly, pctsurfcon and G/W cnr are reasonably correlated (r =
> 0.49).
>
> G/W cnr from norm.mgz and orig.mgz are correlated at r=0.80.
> G/CSF cnr from norm.mgz and orig.mgz are correlated at r=0.97
>
> In another context (but smaller number of subjects), I've looked to see if
> these various snr, cnr measures from FS were related to manual quality
> ratings, and the relationship was rather weak.
>
> All-in-all, I haven't seen much that would indicate that these measures
> can be used as a sort of "automated" QC measure. Manual review of the
> structurals and FS results is still needed.
>
> That said, the structurals from the HCP 500 release were all of reasonably
> good quality to begin with. So, it is possible that these snr/cnr
> measures might be more informative in identifying truly awful scans in a
> clinical population with a wider variability in MPRAGE scan quality.
>
> I'd certainly be interested in hearing from anyone if they have found that
> to be the case in their data.
>
> BTW: Average value for G/W cnr for the HCP 500 is 1.99 and 1.81 from
> orig.mgz and norm.mgz respectively.
> Average value for G/CSF cnr for the same is 0.78 and 0.79, respectively.
>
> cheers,
> -MH
>
> --
> Michael Harms, Ph.D.
>
> ---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave.Tel: 314-747-6173
> St. Louis, MO 63110Email: mha...@wustl.edu
>
>
>
>
> On 10/19/15 8:09 AM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote:
>
> probably similar, although maybe Doug can comment. You probably want to
> run
> it on the orig.mgz as the intensity normalization can artificially
> increase
> the SNR (which is kind of the point)
> Bruce
>
>
> On Mon, 19 Oct 2015, John
> Anderson wrote:
>
>> Hi Bruce,
>> Thanks a lot!! this is really great!
>> I ran the command as the following :
>>
>> mri_cnr subj_01/surf subj_01/mri/norm.mgz
>> processing MRI volume subj_01/mri/norm.mgz...
>> white = 97.2+-9.5, gray = 69.0+-16.1, csf = 47.8+-16.5
>> gray/white CNR = 2.291, gray/csf CNR = 0.848
>> lh CNR = 1.569
>> white = 97.2+-9.3, gray = 69.4+-15.9, csf = 48.6+-17.0
>> gray/white CNR = 2.278, gray/csf CNR = 0.798
>> rh CNR = 1.538
>> total CNR = 1.554
>>
>>
>> I noticed that the normal range for the SNR (15-20) when using the
>> command
>> "wm-anat-snr"
>>
>> What is the normal range for cnr generated by the binary "mri_cnr"?
>>
>>
>> Bests,
>> John Anderson
>>
>> Senior Research Associate
>> Psychological and Brain Sciences Dept.
>> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
>> Phone: +1 (603) 646-9834
>> Fax: +1 (603) 646-1419
>> Sent: Monday, October 19, 2015 at 8:36 AM
>> From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
>> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
>> Cc: j.haen...@psychologie.uzh.ch
>> Subject: Re: [Freesurfer] MPRAGE SNR
>> Hi John
>>
>> there is also a binary called mri_cnr that will compute the
>> contrast-to-noise ratio (CNR), which

[Freesurfer] recon-all stripped brains

2015-10-16 Thread John Anderson

Dear experts,

I want to run recon-all on a stripped brains ( T1 images after applying bet tool).

Do I need to add any flags to the command recon -all -all subjid 

 

 


 

Bests,
John

 
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[Freesurfer] MPRAGE SNR

2015-10-18 Thread John Anderson

Dear Experts,

Is there any tool in Freesurfer that can help to evaluate the SNR for T1 MPRAGE images directly ( i.e script). If not knidly can any help me to figure out the best way to dao it.

 

I highly appreciate your help!

 

Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419
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Re: [Freesurfer] MPRAGE SNR

2015-10-19 Thread John Anderson

Thanks MH,

Let's say that we have 100 MPRAGEs and we want to include them in a cross sectional analysis.

Depending on your experience, do you recommend any criterion to (include/ exclude) these images  in the analysis? As I see visualizing the images alone is not enough to say that the quality of the image is fine. Also calculating the SNR, CNR want help a lot!

 

any suggestions?
 

Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419

 
 

Sent: Monday, October 19, 2015 at 12:24 PM
From: "Harms, Michael" <mha...@wustl.edu>
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] MPRAGE SNR




 

At best that would probably be harmless (if you have a decent number of subjects), but unless SNR, CNR actually relates to those measures in some fashion, you aren't really accomplishing anything by including it as a covariate.  You certainly wouldn't be able to claim that including SNR as a covariate has somehow "controlled" for MPRAGE data quality because there doesn't appear to be much of a relationship in the first place.

 

cheers,

-MH

 



-- 

Michael Harms, Ph.D.


---

Conte Center for the Neuroscience of Mental Disorders

Washington University School of Medicine

Department of Psychiatry, Box 8134

660 South Euclid Ave.  Tel: 314-747-6173

St. Louis, MO  63110  Email: mha...@wustl.edu



 

From: John Anderson <j.ander...@publicist.com>
Reply-To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, October 19, 2015 10:57 AM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] MPRAGE SNR

 




Hi All,

Thank you very much for your comments!

 

Is it advisable to include SNR as a covariate when we use Qdec to run the final statistics on volumetrics, surfaces and cortical thickness?

Does it make sence ?

 

Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419

  

  


Sent: Monday, October 19, 2015 at 11:48 AM
From: "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] MPRAGE SNR

This has been my experience as well. Not much seems to predict which
scans will need to be edited.

On 10/19/15 10:23 AM, Harms, Michael wrote:
> Hi,
>
> FWIW, I've looked at a number of these measures in 500+ subjects from HCP
> data -- wm-anat-snr, pctsurfcon, G/W cnr, G/CSF cnr -- to see how they
> relate to each other, and whether they correlate with mean cortical
> thickness, white matter surface area, or number of SurfaceHoles (prior to
> topology correction).
>
> I didn't find much of note. e.g., the highest correlations were:
>
> r = -0.32 between mean cortical thickness and G/CSF cnr (from norm.mgz)
> r = -0.25 between white surface area and wmanatsnr
> r = -0.39 between SurfaceHoles and pctsurfcon (and same with G/W cnr from
> norm.mgz)
>
> Not surprisingly, pctsurfcon and G/W cnr are reasonably correlated (r =
> 0.49).
>
> G/W cnr from norm.mgz and orig.mgz are correlated at r=0.80.
> G/CSF cnr from norm.mgz and orig.mgz are correlated at r=0.97
>
> In another context (but smaller number of subjects), I've looked to see if
> these various snr, cnr measures from FS were related to manual quality
> ratings, and the relationship was rather weak.
>
> All-in-all, I haven't seen much that would indicate that these measures
> can be used as a sort of "automated" QC measure. Manual review of the
> structurals and FS results is still needed.
>
> That said, the structurals from the HCP 500 release were all of reasonably
> good quality to begin with. So, it is possible that these snr/cnr
> measures might be more informative in identifying truly awful scans in a
> clinical population with a wider variability in MPRAGE scan quality.
>
> I'd certainly be interested in hearing from anyone if they have found that
> to be the case in their data.
>
> BTW: Average value for G/W cnr for the HCP 500 is 1.99 and 1.81 from
> orig.mgz and norm.mgz respectively.
> Average value for G/CSF cnr for the same is 0.78 and 0.79, respectively.
>
> cheers,
> -MH
>
> --
> Michael Harms, Ph.D.
>
> ---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box

Re: [Freesurfer] mri_volsynth

2015-08-31 Thread John Anderson

Thank you for the quick response.

I wanted to create volume has the following dimentions in mm ( 6.25 X 6.25 X 7.5) in a position where the coordinates (in mm) are X=-15 Y= -4 Z= 13

is this command line correct:

mri_volsynth --dim 6.25 6.25 7.5 1 --c_ras -15 -4.3 13 --o voxel.nii

 

Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419

 
 

Sent: Monday, August 31, 2015 at 11:30 AM
From: "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_volsynth


some of this is answered if you run the command with --help
 
On 8/31/15 3:33 PM, John Anderson wrote:




Hi Freesurfers,

I want to create volume 6.25 X 6.25 X 7.5 in this position in scanner space ( x=48, y= 48, z=10)

I used the following command line to create the volume but I don't know how to choose it is position in scanner space.

 

mri_volsynth --dim 6.25 6.25 7.5 0 --o voxel.nii

 

 

I have the following question because i didn't find enough information in FS wiki about this command:

 

1. If the flag  --dim (nc nr ns nf)  is reffering to the volume dimentions. What is the fourth number  (nf ) is standing for  ?



Number of frames (the time dimension)




2. what is the meaning of voxel resolution ( the flag --res (dc dr ds df) ) and what is the meaning of the numbers dc dr ds df ?



How big the voxel is in mm




3. Is the flag c_ras ( c_r c_a c_s) reffering to the volume position. If yes is it in mm or in voxels?



The "center" of the volume in mm, where "center" is defined as (Nvoxels-1)/2 where Nvoxels is the number rows, cols, or slices.




 

 

Thanks in advance ,

John


 

 
 

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Re: [Freesurfer] mri_volsynth

2015-08-31 Thread John Anderson

Thank you!

Actually when I run mri_volsynth --help

I can't find --revol. is it the same flag --res?

also what is the relationship between --dim and --volres?

 

Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419

 
 

Sent: Monday, August 31, 2015 at 4:06 PM
From: "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_volsynth


No, you will need to decide how big you want your voxels to be. If you use --volres 1 1 1 1 then that should work. It will put the center of the volume at that coordiate. If you want a single voxel, then use --dim 1 1 1 1 and --volres 6.25 6.25 7.5 1

 
On 8/31/15 7:52 PM, John Anderson wrote:



Thank you for the quick response.

I wanted to create volume has the following dimentions in mm ( 6.25 X 6.25 X 7.5) in a position where the coordinates (in mm) are X=-15 Y= -4 Z= 13

is this command line correct:

mri_volsynth --dim 6.25 6.25 7.5 1 --c_ras -15 -4.3 13 --o voxel.nii

 

Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419

 
 

Sent: Monday, August 31, 2015 at 11:30 AM
From: "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_volsynth


some of this is answered if you run the command with --help
 
On 8/31/15 3:33 PM, John Anderson wrote:




Hi Freesurfers,

I want to create volume 6.25 X 6.25 X 7.5 in this position in scanner space ( x=48, y= 48, z=10)

I used the following command line to create the volume but I don't know how to choose it is position in scanner space.

 

mri_volsynth --dim 6.25 6.25 7.5 0 --o voxel.nii

 

 

I have the following question because i didn't find enough information in FS wiki about this command:

 

1. If the flag  --dim (nc nr ns nf)  is reffering to the volume dimentions. What is the fourth number  (nf ) is standing for  ?



Number of frames (the time dimension)




2. what is the meaning of voxel resolution ( the flag --res (dc dr ds df) ) and what is the meaning of the numbers dc dr ds df ?



How big the voxel is in mm




3. Is the flag c_ras ( c_r c_a c_s) reffering to the volume position. If yes is it in mm or in voxels?



The "center" of the volume in mm, where "center" is defined as (Nvoxels-1)/2 where Nvoxels is the number rows, cols, or slices.




 

 

Thanks in advance ,

John


 

 
 

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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 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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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
dispose of the e-mail.

Re: [Freesurfer] mri_volsynth

2015-08-31 Thread John Anderson

Perfect!

Thank you very much for your help.

Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419

 
 

Sent: Monday, August 31, 2015 at 4:30 PM
From: "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_volsynth


sorry, --res (not --volres). res is the voxel size (volume resolution). dim is the number of voxels in each dimension
 
On 8/31/15 10:16 PM, John Anderson wrote:



Thank you!

Actually when I run mri_volsynth --help

I can't find --revol. is it the same flag --res?

also what is the relationship between --dim and --volres?

 

Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419

 
 

Sent: Monday, August 31, 2015 at 4:06 PM
From: "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_volsynth


No, you will need to decide how big you want your voxels to be. If you use --volres 1 1 1 1 then that should work. It will put the center of the volume at that coordiate. If you want a single voxel, then use --dim 1 1 1 1 and --volres 6.25 6.25 7.5 1

 
On 8/31/15 7:52 PM, John Anderson wrote:



Thank you for the quick response.

I wanted to create volume has the following dimentions in mm ( 6.25 X 6.25 X 7.5) in a position where the coordinates (in mm) are X=-15 Y= -4 Z= 13

is this command line correct:

mri_volsynth --dim 6.25 6.25 7.5 1 --c_ras -15 -4.3 13 --o voxel.nii

 

Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419

 
 

Sent: Monday, August 31, 2015 at 11:30 AM
From: "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_volsynth


some of this is answered if you run the command with --help
 
On 8/31/15 3:33 PM, John Anderson wrote:




Hi Freesurfers,

I want to create volume 6.25 X 6.25 X 7.5 in this position in scanner space ( x=48, y= 48, z=10)

I used the following command line to create the volume but I don't know how to choose it is position in scanner space.

 

mri_volsynth --dim 6.25 6.25 7.5 0 --o voxel.nii

 

 

I have the following question because i didn't find enough information in FS wiki about this command:

 

1. If the flag  --dim (nc nr ns nf)  is reffering to the volume dimentions. What is the fourth number  (nf ) is standing for  ?



Number of frames (the time dimension)




2. what is the meaning of voxel resolution ( the flag --res (dc dr ds df) ) and what is the meaning of the numbers dc dr ds df ?



How big the voxel is in mm




3. Is the flag c_ras ( c_r c_a c_s) reffering to the volume position. If yes is it in mm or in voxels?



The "center" of the volume in mm, where "center" is defined as (Nvoxels-1)/2 where Nvoxels is the number rows, cols, or slices.




 

 

Thanks in advance ,

John


 

 
 

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[Freesurfer] mri_volsynth

2015-08-31 Thread John Anderson


Hi Freesurfers,

I want to create volume 6.25 X 6.25 X 7.5 in this position in scanner space ( x=48, y= 48, z=10)

I used the following command line to create the volume but I don't know how to choose it is position in scanner space.

 

mri_volsynth --dim 6.25 6.25 7.5 0 --o voxel.nii

 

 

I have the following question because i didn't find enough information in FS wiki about this command:

 

1. If the flag  --dim (nc nr ns nf)  is reffering to the volume dimentions. What is the fourth number  (nf ) is standing for  ?

2. what is the meaning of voxel resolution ( the flag --res (dc dr ds df) ) and what is the meaning of the numbers dc dr ds df ?

3. Is the flag c_ras ( c_r c_a c_s) reffering to the volume position. If yes is it in mm or in voxels?

 

 

Thanks in advance ,

John

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contains patient information, please contact the Partners Compliance HelpLine at
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dispose of the e-mail.

[Freesurfer] recon-all

2015-09-04 Thread John Anderson

Hi freesurfers,

I am interested in studying the difference between the outer and deep white matter volume in my study groups.

I am thinking in the following procedures:

1. If there is any way in Freesurfer to do segmentation for the white matter (only in the depth of 3 cm) starting from the cortex. Then second segmentation for the deep white matter.

2. Creating a mask ( using mri_binarize) for all the superficial white matter Freesurfer's labels and another mask for the deep white matter ( how can I find the Freesurfer deep white matter labels and the outer white matter labels ?)

3. If there is any atlas that can separate the outer and deep white matter then do the segmentation depending on this new atlas.

Thanks in advance for any suggestion,

John

Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419
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Re: [Freesurfer] Segmenting deep and outer white matter

2015-09-05 Thread John Anderson

Hi Bruce,

Thank you for your response!

Actually, after reviewing  multiple papers ( segmentation in Freesurfer) I found that using "wmparc.mgz"  as an input in the command "mri_binarize" will enable me to create two mask ( depending on the white matter parcellate mentioned in wmparc.mgz): The first mask is for deep white matter and the second mask is for the outer white matter.

I am facing one problem right now. I don't know how to divide the white matter parcellates mentioned in "wmparc.mgz" into deep and outer parcellates. Is there any reference that can help. The number of the parcellate is very big and for the purposes of publication I need a reference to divide them.

Any help is highly appreciated.

Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419

Sent: Saturday, September 05, 2015 at 4:23 PM
From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Segmenting deep and outer white matter

Hi John

sorry, meant to respond but spaced it. Have you checked out the
wmparc.mgz? It may have what you need.

cheers
Bruce
On Sat, 5 Sep 2015, John Anderson
wrote:

> Hi Freesurfers,
> I am interested in studying the difference between the outer and deep white
> matter volume in my study groups.
>  
> I am thinking in the following procedures:
> 1. If there is any way in Freesurfer to do segmentation for the white matter
> (only in the depth of 3 cm) starting from the cortex. Then  second
> segmentation for the deep white matter. Is this possible in Freesurfer?
> 2. Creating a mask ( using mri_binarize) for all the superficial white
> matter Freesurfer's labels and another mask for the deep white matter  ( how
> can I find the Freesurfer  deep white matter labels and the outer white
> matter labels ?)
> 3. If there is any atlas that can separate the outer and deep white matter
> then running recon-all depending on this new atlas.
>  
> Thanks in advance for any suggestion.
> John 
>
>  
> Bests,
> John Anderson
>
> Senior Research Associate
> Psychological and Brain Sciences Dept.
> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> Phone: +1 (603) 646-9834
> Fax: +1 (603) 646-1419
>
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[Freesurfer] Segmenting deep and outer white matter

2015-09-05 Thread John Anderson

Hi Freesurfers,

I am interested in studying the difference between the outer and deep white matter volume in my study groups.

I am thinking in the following procedures:

1. If there is any way in Freesurfer to do segmentation for the white matter (only in the depth of 3 cm) starting from the cortex. Then second segmentation for the deep white matter. Is this possible in Freesurfer?

3. If there is any atlas that can separate the outer and deep white matter then running recon-all depending on this new atlas.

Thanks in advance for any suggestion.

John

Bests,
John Anderson

Re: [Freesurfer] Segmenting deep and outer white matter

2015-09-07 Thread John Anderson

Hi Doug,

Thank you for your response.

When we open "wmparc.mgz" in freeview we can see clearly  that we have labels for cortical parcellations and it is white matter parcellations as well as the unsegmented white matter

What is really confusing me is that deep structures like the thalamus, amygdala, putamen, caudate, hypocampus .etc  are also labeled in "wmparc.mgz". Are these labels means the white matter part of these segments or it is gray and white matter together like the segments mentioed in "aseg.mgz" ?!

Please see the attached list of labels for one of my subjects.

Bests,
John Anderson

Senior Research Associate 
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419

Sent: Monday, September 07, 2015 at 1:02 PM
From: "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Segmenting deep and outer white matter

The best thing is to take a look at the wmparc. It was not really designed to be deep and superficial. There is only one "deep"  WM seg which is called "Unsgemented White Matter" or something like that.
doug

On 9/5/15 5:54 PM, Bruce Fischl wrote:

Hi John

I defer to Doug. Not sure he ever published it though
Bruce
On Sat, 5 Sep 2015, John Anderson wrote:

Hi Bruce,
Thank you for your response!
Actually, after reviewing  multiple papers ( segmentation in Freesurfer) I
found that using "wmparc.mgz"  as an input in the command "mri_binarize"
will enable me to create two mask ( depending on the white matter parcellate
mentioned in wmparc.mgz): The first mask is for deep white matter and the
second mask is for the outer white matter.

I am facing one problem right now. I don't know how to divide the white
matter parcellates mentioned in "wmparc.mgz" into deep and outer
parcellates. Is there any reference that can help. The number of the
parcellate is very big and for the purposes of publication I need a
reference to divide them.

Any help is highly appreciated.

Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419
    Sent: Saturday, September 05, 2015 at 4:23 PM
From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Segmenting deep and outer white matter
Hi John

sorry, meant to respond but spaced it. Have you checked out the
wmparc.mgz? It may have what you need.

cheers
Bruce
On Sat, 5 Sep 2015, John Anderson
wrote:

> Hi Freesurfers,
> I am interested in studying the difference between the outer and deep
white
> matter volume in my study groups.
>  
> I am thinking in the following procedures:
> 1. If there is any way in Freesurfer to do segmentation for the white
matter
> (only in the depth of 3 cm) starting from the cortex. Then  second
> segmentation for the deep white matter. Is this possible in Freesurfer?
> 2. Creating a mask ( using mri_binarize) for all the superficial white
> matter Freesurfer's labels and another mask for the deep white matter  (
how
> can I find the Freesurfer  deep white matter labels and the outer white
> matter labels ?)
> 3. If there is any atlas that can separate the outer and deep white matter
> then running recon-all depending on this new atlas.
>  
> Thanks in advance for any suggestion.
> John 
>
>  
> Bests,
> John Anderson
>
> Senior Research Associate
> Psychological and Brain Sciences Dept.
> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> Phone: +1 (603) 646-9834
> Fax: +1 (603) 646-1419
>
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[Freesurfer] White matter volume

2015-09-12 Thread John Anderson

Hi Bruce,

Kindly I want to inquire about the difference between white matter volume generated by freesurfer ( specifically the white matter parcellations volume mentioned in wmparc.stats) and the vwhite matter volume generated by other tools like fslstats. 

For example:

If I use a binarized mask from wmparc.mgz for the precentral gyrus in the command : fslstats -i MPRAGE.nii.gz ( reoriented and skull stripped) -k  -V 

Then

What is the differecne between this volume generated by "fslstats" and the precenral gyrus volume mentioned in wmparc.stats. Which one is more accurate?

 

 

Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 4and the white matter volume generated by other methods like using fslstats19 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419
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[Freesurfer] Tracula_weighted dti metrics values

2015-09-16 Thread John Anderson

Hi Anastasia,

How the script "dmri_pathstats" compute the weighted FA, MD, AD, and RD values?

I checked the command "dmri_pathstats" inside the file "trac-all.log" but I was unable to figure out how this weighting is working. Is it by multiplying the mean DTI metrics by the number of voxel?

 

If my FA maps is "dtifit_FA.nii.gz" and my probabilistic distribution map for the cortico spinal tract is "path.pd.nii.gz" and I want to compute FA value using the command "fslstats" like:

 

fslstats dtifit_FA.nii.gz -k path.pd.nii.gz -m  >This command will output the mean FA for the probabilistic distribution map. How can I weight this FA value using the previous command line?

 

Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419
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[Freesurfer] Basal ganglia

2015-09-21 Thread John Anderson

Hi Experts,

I want to do tractography for the cortico spinal tract between two ROIs ( ROI1: precentral gyrus; ROI2: basal ganglia). I created the first ROI using mask form wmparc.mgz. How can I create mask for the basal ganglia ( there is no label for it). Do I need to segmenta the basal ganglia separatly? Is there any tool in Freesurfer that can help? Thanks for any suggestion.

 

Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419
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[Freesurfer] Tracula Tracts density

2015-10-06 Thread John Anderson

Hi Anastasia,

How can I calculate the tract density from the output of tracula.

For example in the final stats file for the cortico spinal tract I can see the number of sample paths in the WM tract. Is this number refer to the tract density ( number of DTI fibers comprising the tract - in other words the number of distinct tracts that pass through the manually constructed sets of ROIs) ?

 

 

Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419
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[Freesurfer] Longitudinal data analysis

2016-01-02 Thread John Anderson

Hi Freesurfer experts,

I am working on a logitudinal data analysis using freesurfer pipeline. I followed all the steps like in WIKI and the analysis was great. Kindly I have the following questions:

1. In wiki "http://freesurfer.net/fswiki/LinearMixedEffectsModels"-- in the example mentioned there, the command "

lme_lowessPlot(M(:,1),Y(:,1)+Y(:,2),0.70,M(:,2));"

What is the Y(:,2) refer to ?

2. Can I plot multiple measures at the same time ( for example if I have in my qdec table multiple columns for multiple measures ( left precentral gyrus cortical thickness, right precentral gyrus cortical thickness, LH mean thickness , RH mean thickness) can I plot all these measures at the same time instead of running the previous command multiple times?

3. If I have three groups in my qdec table. The previous command line is plotting three lines. Are these lines in th esame order of the groups in qdec tables?

4. The BW in this command was chosen 0.7 and the default is 0.6 how can I choose this number correctly?

Thanks for your support!

Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419

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[Freesurfer] P files

2016-01-06 Thread John Anderson

Dear Freesurfer experts,

I want to inquire if there is any tool in Freesurfer that can help to convert the p files ( raw data generated by GE scanner ) to DICOMs

 

 

Thanks for any advice!
 

Bests,
John 
 
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[Freesurfer] transform statistical map in MNI to surface

2016-01-08 Thread John Anderson

Hi Experts,

I have statistical map in MNI space and I want to view it using tksurfer how can i transform this map to a surface ?

 


 

Bests,
John 
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Re: [Freesurfer] transform statistical map in MNI to surface

2016-01-08 Thread John Anderson

Thanks Bruce,

 if my statistical map "stat1.nii.gz"  is in MNI152 standard space what are the command lines that I need ( or if possible any link to wiki)

Thanks a lot!

 

 

John 




Sent: Friday, January 08, 2016 at 2:49 PM
From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] transform statistical map in MNI to surface

you wouldn't run it on the stats map - you would run it on the
T1-weighted MNI152 volume

On Fri, 8 Jan 2016, John Anderson wrote:

> Thanks you Doug,
> Kindly how can I run recon-all on the statistical map ? my statistical map
> is an output of TBSS analysis
>  
> Bests,
> John 
>   Sent: Friday, January 08, 2016 at 1:41 PM
> From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] transform statistical map in MNI to surface
> If it is in mni152 space, then you can run recon-all on the mni152 T1
> map, then use mri_vol2surf with --regheader to map the volume tothe
> surface, then use tksurfer or freeview to view the resulting map
>
> On 01/08/2016 12:49 PM, John Anderson wrote:
> > Hi Experts,
> > I have statistical map in MNI space and I want to view it using
> > tksurfer how can i transform this map to a surface ?
> >
> > Bests,
> > John
> >
> >
> > ___
> > 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: 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/
>
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>
>
> 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] transform statistical map in MNI to surface

2016-01-08 Thread John Anderson

Thanks you Doug,

Kindly how can I run recon-all on the statistical map ? my statistical map is an output of TBSS analysis

Bests,
John 

Sent: Friday, January 08, 2016 at 1:41 PM
From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] transform statistical map in MNI to surface

If it is in mni152 space, then you can run recon-all on the mni152 T1
map, then use mri_vol2surf with --regheader to map the volume tothe
surface, then use tksurfer or freeview to view the resulting map

On 01/08/2016 12:49 PM, John Anderson wrote:
> Hi Experts,
> I have statistical map in MNI space and I want to view it using
> tksurfer how can i transform this map to a surface ?
>
> Bests,
> John
>
>
> ___
> 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: https://gate.nmr.mgh.harvard.edu/filedrop2
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[Freesurfer] Longitudinal data analysis

2015-12-30 Thread John Anderson

Hi Martin,

I am working on a logitudinal data analysis using freesurfer pipeline. I followed all the steps like in WIKI and the analysis was great. Kindly I have the following questions:

1. In wiki "http://freesurfer.net/fswiki/LinearMixedEffectsModels"-- in the example mentioned there, the command "
lme_lowessPlot(M(:,1),Y(:,1)+Y(:,2),0.70,M(:,2));"

What is the Y(:,2) refer to ?

3. The BW in this command was chosen 0.7 and the default is 0.6 how can I choose this number correctly?

Tanks for your support!

Bests,
John Anderson

Re: [Freesurfer] Qdec visualization

2015-12-21 Thread John Anderson

Hi Doug,

Given that the  standard variance can be calculated using the command "mris_calc" and the flag "-sqrt" what is the correct command to do this calculation?

I tried: 

mris_calc gammavar.mgz -sqrt output.txt but it didn't work. Kindly what I am doing wrong?

 

 

Bests,
John




Sent: Monday, December 21, 2015 at 2:20 PM
From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Qdec visualization

QDEC cannot but the information may be in the output folder. There
should be a file called gammavar.mgh. This will be the standard variance
(so take the square root)

On 12/21/2015 02:08 PM, John Anderson wrote:
> Thanks you very much Doug,
> Please one more question. Is there any way in Qdec to get the stamdard
> error (SE) ?
> Bests,
> John
> *Sent:* Monday, December 21, 2015 at 11:43 AM
> *From:* "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] Qdec visualization
> The correction for multiple comparisons is cluster-based. Each cluster
> gets a single number. In the display, all the vertices get that same
> number.
>
> On 12/18/2015 03:17 PM, John Anderson wrote:
> > Hi Freesurfer experts,
> > I am using Qdec in Freesurfer 5.3 to do some cortical thickness
> > comparisons between two groups.
> >
> > Before corrcting the results for multiple comparisons ( monte carlo
> > simulation) the significant differnce between the groups is visualized
> > as a range of color while after correcting for multiple copmparisons
> > the color of the statistical map is usinform ( Attached)
> > Is ther any way to visualze the results as a range of color after
> > correcting the results for multiple comparsiosn
> >
> > Thanks in advance for any advice
> > Bests,
> > John Anderson
> >
> > Senior Research Associate
> > Psychological and Brain Sciences Dept.
> > Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> > Phone: +1 (603) 646-9834
> > Fax: +1 (603) 646-1419
> >
> >
> > ___
> > 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: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
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> 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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--
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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: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] Qdec visualization

2015-12-21 Thread John Anderson

Thanks Doug,

I used the command "mris_calc gammavar.mgh sqrt" and the output was: "Saving result to 'out.mgz' (type = MGH )"

Then I ran  the command "mris_calc out.mgz stats" and the output was :

         Size                   [ 163842 ]
       Min@(index)        [ 0.00 (161385) ]
      Max@(index)         [ 0.259395 (18208) ]
       Mean                 [ 0.097956 ]
         Std                 [ 0.040943 ]
         Sum             [ 16049.365234 ]
         Prod                 [ 0.00 ]

 

 

In order to calculate the standard error is it fine if I use mris_calc gammavar.mgh stats the I divide the Std of gammavar.mgh by the square root of the sample size ( number of subjects included in the analysis)?

 

 

Thanks a lot!

 

 


 

Sent: Monday, December 21, 2015 at 2:44 PM
From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Qdec visualization

it helps to see the error msg, but my guess is that you need to specify
an mgh file, not a txt file. This will give you the voxel-wise stderr,
not a standard error for the cluster (which does not make sense)

On 12/21/2015 02:38 PM, John Anderson wrote:
> Hi Doug,
> Given that the standard variance can be calculated using the command
> "mris_calc" and the flag "-sqrt" what is the correct command to do
> this calculation?
> I tried:
> mris_calc gammavar.mgz -sqrt output.txt but it didn't work. Kindly
> what I am doing wrong?
> Bests,
> John
> *Sent:* Monday, December 21, 2015 at 2:20 PM
> *From:* "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] Qdec visualization
> QDEC cannot but the information may be in the output folder. There
> should be a file called gammavar.mgh. This will be the standard variance
> (so take the square root)
>
> On 12/21/2015 02:08 PM, John Anderson wrote:
> > Thanks you very much Doug,
> > Please one more question. Is there any way in Qdec to get the stamdard
> > error (SE) ?
> > Bests,
> > John
> > *Sent:* Monday, December 21, 2015 at 11:43 AM
> > *From:* "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> > *To:* freesurfer@nmr.mgh.harvard.edu
> > *Subject:* Re: [Freesurfer] Qdec visualization
> > The correction for multiple comparisons is cluster-based. Each cluster
> > gets a single number. In the display, all the vertices get that same
> > number.
> >
> > On 12/18/2015 03:17 PM, John Anderson wrote:
> > > Hi Freesurfer experts,
> > > I am using Qdec in Freesurfer 5.3 to do some cortical thickness
> > > comparisons between two groups.
> > >
> > > Before corrcting the results for multiple comparisons ( monte carlo
> > > simulation) the significant differnce between the groups is visualized
> > > as a range of color while after correcting for multiple copmparisons
> > > the color of the statistical map is usinform ( Attached)
> > > Is ther any way to visualze the results as a range of color after
> > > correcting the results for multiple comparsiosn
> > >
> > > Thanks in advance for any advice
> > > Bests,
> > > John Anderson
> > >
> > > Senior Research Associate
> > > Psychological and Brain Sciences Dept.
> > > Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> > > Phone: +1 (603) 646-9834
> > > Fax: +1 (603) 646-1419
> > >
> > >
> > > ___
> > > 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: https://gate.nmr.mgh.harvard.edu/filedrop2
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> >
> > ___
> > 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

Re: [Freesurfer] Qdec visualization

2015-12-21 Thread John Anderson

Thanks you very much Doug,

Please one more question. Is there any way in Qdec to get the stamdard error (SE) ?

Bests,
John 

Sent: Monday, December 21, 2015 at 11:43 AM
From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Qdec visualization

The correction for multiple comparisons is cluster-based. Each cluster
gets a single number. In the display, all the vertices get that same number.

On 12/18/2015 03:17 PM, John Anderson wrote:
> Hi Freesurfer experts,
> I am using Qdec in Freesurfer 5.3 to do some cortical thickness
> comparisons between two groups.
>
> Before corrcting the results for multiple comparisons ( monte carlo
> simulation) the significant differnce between the groups is visualized
> as a range of color while after correcting for multiple copmparisons
> the color of the statistical map is usinform ( Attached)
> Is ther any way to visualze the results as a range of color after
> correcting the results for multiple comparsiosn
>
> Thanks in advance for any advice
> Bests,
> John Anderson
>
> Senior Research Associate
> Psychological and Brain Sciences Dept.
> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> Phone: +1 (603) 646-9834
> Fax: +1 (603) 646-1419
>
>
> ___
> 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: 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/

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Re: [Freesurfer] Break 3D volume

2016-06-08 Thread John Anderson

Hi Bruce, 

Thank you for the quick response. it is really highly appreciated!

I have 3D mask in the form of nifti file and it has the shape of large square( the black big square in my figure). I wanted to divid it to a smaller and equale volumes. It iseems that mri_extract can support my objectives:

Please how can I use this command. I was unable to find any instructions:

If my 3D maks is "mask.nii" and the command is mri_extract  x0 y0 z0 dx dy dz  how can I use the command properly?

: is this where my file is located?

x0 y0 z0 dx dy dz: What I should use here?

Thank you very much for your help

John 

Sent: Wednesday, June 08, 2016 at 9:13 AM
From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Break 3D volume

Hi John

I'm not exactly sure what you mean, but you can use mri_extract to pull
out rectangular subvolumes.

cheers
Bruce
On Wed, 8 Jun 2016, John Anderson wrote:

> Dear FS Experts,
> Are there any tools in Freesurfer or Matlab scripts that can help to break
> down a 3D volume ( created using mri_volsynth) to a multiple equal sub
> volumes ( like the attached figure )
> Thanks in a dvance for any suggestion!
> John Anderson
>
> Senior Research Associate
> Psychological and Brain Sciences Dept.
> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> Phone: +1 (603) 646-9834
> Fax: +1 (603) 646-1419
>  
>  
>  
> [IMAGE]
>
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Re: [Freesurfer] Break 3D volume

2016-06-08 Thread John Anderson

Thank you Bruce... This is very helpful!
 

Bests,
John




Sent: Wednesday, June 08, 2016 at 9:32 AM
From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Break 3D volume

the help is old!  should be . (x0,y0,z0) is the
starting point of your bounding box, and (dx,dy,dz) is the extent of it (in
voxels)

On Wed, 8 Jun 2016, John
Anderson wrote:

> Hi Bruce, 
> Thank you for the quick response. it is really highly appreciated!
> I have 3D mask in the form of nifti file and it has the shape of large
> square( the black big square in my figure). I wanted to divid it to a
> smaller and equale volumes. It iseems that mri_extract can support my
> objectives:
> Please how can I use this command. I was unable to find any instructions:
> If my 3D maks is "mask.nii" and the command is mri_extract  x0 y0
> z0 dx dy dz  how can I use the command properly?
> : is this where my file is located?
> x0 y0 z0 dx dy dz: What I should use here?
>  
> Thank you very much for your help
>  
>  
> John 
>   Sent: Wednesday, June 08, 2016 at 9:13 AM
> From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] Break 3D volume
> Hi John
>
> I'm not exactly sure what you mean, but you can use mri_extract to pull
> out rectangular subvolumes.
>
> cheers
> Bruce
> On Wed, 8 Jun 2016, John Anderson wrote:
>
> > Dear FS Experts,
> > Are there any tools in Freesurfer or Matlab scripts that can help to break
> > down a 3D volume ( created using mri_volsynth) to a multiple equal sub
> > volumes ( like the attached figure )
> > Thanks in a dvance for any suggestion!
> > John Anderson
> >
> > Senior Research Associate
> > Psychological and Brain Sciences Dept.
> > Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> > Phone: +1 (603) 646-9834
> > Fax: +1 (603) 646-1419
> >  
> >  
> >  
> > [IMAGE]
> >
> >___
> 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] Break 3D volume

2016-06-08 Thread John Anderson

Dear FS Experts,

Are there any tools in Freesurfer or Matlab scripts that can help to break down a 3D volume ( created using mri_volsynth) to a multiple equal sub volumes ( like the attached figure )

Thanks in a dvance for any suggestion!
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419

 

 

 

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[Freesurfer] smoothing T1 images

2016-06-21 Thread John Anderson


Hi FS experts,

I have T1 images with low quality (noise and artifacts). I am wondering if smoothing these images, before runing the command "Recon-all", can help to improve the segmentation and parcellation process for these images.

Thanks for any advice!

Bests,
John
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[Freesurfer] Qdec-correction for multiple comparison

2016-06-23 Thread John Anderson

Dear FS experts,

I ran cortical thickness analysis between two groups using Qdec and I want to correct the results for multiple comparison.

In Qdec there are two choices to correct the data for multiple comparison (FDR and montecarlo) . Which method do you recommend montecarlo or FDR. Are there any rules that I need to follow when I choose my method to correct the results for multiple comparison ( i.e FDR or montecarlo)

 

Thank you very much for any comment!
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419
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[Freesurfer] Longitudinal analysis_covariates

2016-01-13 Thread John Anderson

Dear Dr Martin,

I have longitudinal database for subjects scanned multiple times. I want to study the changes in cortical thickness over time. I prepared my longitudinal table  ( column#1 fsid column#2 fsid-base column#3 group column#4 bilateral motor cortex thickness column#5 time (years) column#6 disease duration)

Then I followed the instructions like in wiki... and I plot the changes in motor cortex over time using the command :

 

lme_lowessPlot(M:,5),Y(:,1)m0.7,M(:,3))

 

My questions are:

1. How can I regress the effect of disease duration  (column#6) ? is it by running the previous command line by replaceing M(:,5) ( time) by M(:,6) disease duration?

2. If I am interested in studying the change in cortical thickness by the change in clinical scale over time is it correct to replce the coloumn #5 ( time) by a column for the clinical scales? 

 

 

Thanks in advance for any advice!

 

Bests,
John 
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[Freesurfer] Cortical thickness parcellates

2016-01-13 Thread John Anderson

Dear experts,

I am wondering if there is any way to divide the cortical thickness parcellates in the atlas "?h.aparc.annot" by lobe. I highly appreciate any suggestion.


 

Bests,
John 
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Re: [Freesurfer] Cortical thickness parcellates

2016-01-13 Thread John Anderson

Thanks Doug,

I aim to create masks for the frontal lobe , parietal lobe, occipital lobe and temporal lobe including all the parcellates in every lobe in one maks.

I was thinking to use mri_binarize but the number of the parcellates is very big. Is there a way that can give a direct maks for cortical thickness by lobe?

Sent: Wednesday, January 13, 2016 at 12:41 PM
From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Cortical thickness parcellates

Try mris_divide_parcellation

On 01/13/2016 12:18 PM, John Anderson wrote:
> Dear experts,
> I am wondering if there is any way to divide the cortical thickness
> parcellates in the atlas "?h.aparc.annot" by lobe. I highly appreciate
> any suggestion.
>
> Bests,
> John
>
>
> ___
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--
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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
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[Freesurfer] register image to mni152

2016-01-17 Thread John Anderson

 







Dear experts,

I wanted to register T1 mprage image to the standard space MNI152. The output of FLIRT at dof 12 is not effective. How can I get better results using bbregister? What are the commands that I need to use ?

 

thanks for any help!
John 





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[Freesurfer] Qdec-correction for multiple comparison

2016-06-25 Thread John Anderson


Dear FS experts,

I will re post this thread again looking for your help and support:

 

I ran cortical thickness analysis between two groups using Qdec and I want to correct the results for multiple comparison.

In Qdec there are two choices to correct the data for multiple comparison (FDR and montecarlo) . Which method do you recommend to correct the results of cortical thickness analysis? Are there any rules that I need to follow when I choose my method to correct the results for multiple comparison ( i.e FDR or montecarlo)

 

Thank you very much for any comment!
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419

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Re: [Freesurfer] Longitudinal analysis--mass univariate

2016-01-28 Thread John Anderson

Thanks a lot D martin for your quick answer.

Regarding my patients I have two groups but the subject in every group have differnt time points. i.e Group-patients 1: I have 100 patients some scanned three times and some four times the rest at least two times.

Group-Patients 2: is consisted of 75 patients some also some scanned three times and some four times the rest at least two times.

Is LME -- mas usnivariate still workable with out a bias ?

Bests,
John

Sent: Thursday, January 28, 2016 at 6:51 AM
From: "Martin Reuter" <mreu...@nmr.mgh.harvard.edu>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Longitudinal analysis--mass univariate

Hi John,

you should check if the number of time points per subject is relatively random across your two patient groups. You don’t want a bias, let’s say one patient group with 2 tp and the other with 3.

You can compare the atrophy across these two groups easily with LME. Or you can also test if the rate is different from zero in each individual group.

You will never be able to compute atrophy rates for your control group (as you only have a single time point for them) so you cannot compare with them either.

Best, Martin

On Jan 28, 2016, at 12:23 PM, John Anderson <j.ander...@publicist.com> wrote:

Hi Dr Martin,

I have two groups of patients and one group of controls.

The patients scanned multiple times but the number of time points is different between the subjects.

The controls have only one time point.

I aim to :

1. I wanted to study the changes in cortical thickness over time in each group of patients.

2. I wanted to compare the change in cortical thickness between patients and controls over time.

I followed wiki and I choose LME to run the analysis.

My questions are:

1. Can I use mass univariate analysis to check the changes in cortical thickness over time in only one group of patients. The example In wiki was for four groups.

2. Can I do a comparison in cortical thickness over time between controls ( who have only one time point ) and patients using mass univariate approach.

Bests,
John

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[Freesurfer] Longitudinal analysis--mass univariate

2016-01-28 Thread John Anderson

Hi Dr Martin,

I have two groups of patients and one group of controls.

The patients scanned multiple times but the number of time points is different between the subjects.

The controls have only one time point.

 

I aim to :

1. I wanted to study the changes in cortical thickness over time in each group of patients.

2. I wanted to compare the change in cortical thickness between patients and controls over time.

 

I followed wiki and I choose LME to run the analysis.

My questions are:

1. Can I use mass univariate analysis to check the changes in cortical thickness over time in only one group of patients. The example In wiki was for four groups.

2. Can I do a comparison in cortical thickness over time between controls ( who have  only one time point ) and patients using mass univariate approach.
 

Bests,
John 
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Re: [Freesurfer] Longitudinal analysis--mass univariate {Disarmed}

2016-02-01 Thread John Anderson

Dear Dr Martin ,

Thanks a lot for your kindness and your great answers!!

Please I have one more question regarding the design matrix:

If I use my design matrix for LME depending on the exampels mentioned in FS wiki https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples

Is this correct?

Bests,
John

Sent: Saturday, January 30, 2016 at 5:51 AM
From: "Martin Reuter" <mreu...@nmr.mgh.harvard.edu>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Longitudinal analysis--mass univariate {Disarmed}

Hi John,

What I mean is there could be a bias in your study design if 99% of group 1 have three or more time points and 99% of group 2 have only two time points. This is something you should check. If distributions are approximately similar, you’d be fine. LME can be used in either case. If there is any biases (also age, gender etc) you’d probably want to control for it via additional co-variates in your LME model.

Best, Martin

On Jan 28, 2016, at 1:12 PM, John Anderson <j.ander...@publicist.com> wrote:

Thanks a lot D martin for your quick answer.

Group-Patients 2: is consisted of 75 patients some also some scanned three times and some four times the rest at least two times.

Is LME -- mas usnivariate still workable with out a bias ?

Bests,
John

Hi John,

you should check if the number of time points per subject is relatively random across your two patient groups. You don’t want a bias, let’s say one patient group with 2 tp and the other with 3.

You can compare the atrophy across these two groups easily with LME. Or you can also test if the rate is different from zero in each individual group.

You will never be able to compute atrophy rates for your control group (as you only have a single time point for them) so you cannot compare with them either.

Best, Martin

On Jan 28, 2016, at 12:23 PM, John Anderson <MailScanner has detected a possible fraud attempt from "x-msg:" claiming to be j.ander...@publicist.com> wrote:

Hi Dr Martin,

I have two groups of patients and one group of controls.

The patients scanned multiple times but the number of time points is different between the subjects.

The controls have only one time point.

I aim to :

1. I wanted to study the changes in cortical thickness over time in each group of patients.

2. I wanted to compare the change in cortical thickness between patients and controls over time.

I followed wiki and I choose LME to run the analysis.

My questions are:

1. Can I use mass univariate analysis to check the changes in cortical thickness over time in only one group of patients. The example In wiki was for four groups.

2. Can I do a comparison in cortical thickness over time between controls ( who have only one time point ) and patients using mass univariate approach.

Bests,
John

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Re: [Freesurfer] transform statistical map in MNI to surface

2016-01-22 Thread John Anderson

Hi Bruce,

I carefully followed your orientations. Kindly I still need more clarification regarding the following point:

 

I have statistical map in MNI152 space (volume) as an output of permutation analysis using " randomise/FSL". I want to visualize this map on an inflated surface in Freesurfer. 

 

1. Can I directly use the command "






tksurfer fsaverage rh inflated -overlay-reg $FREESURFER_HOME/average/mni152.register.dat -o "my tstat map"

 




2. Whay I need to do segmentation to MNI152 then running the command mri_vol2surf? Whar are the cons and pros of doing or not doing these steps?

 

Thanks a lot!
John 

 
 

Sent: Friday, January 08, 2016 at 2:57 PM
From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] transform statistical map in MNI to surface

Hi John

you would run recon-all on the MNI 152 T1 image (NOT your map), then use
mri_vol2surf to map the stats map onto the resulting surfaces. Note that
this won't give you great results as a bunch of your clusters will
probably not be near the cortical surface (since in general subjects
cortices don't align well in MNI 152)

cheers
Bruce
On Fri, 8 Jan 2016, John Anderson
wrote:

> Thanks Bruce,
>  if my statistical map "stat1.nii.gz"  is in MNI152 standard space what are
> the command lines that I need ( or if possible any link to wiki)
> Thanks a lot!
>  
>  
> John 
> Sent: Friday, January 08, 2016 at 2:49 PM
> From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] transform statistical map in MNI to surface
> you wouldn't run it on the stats map - you would run it on the
> T1-weighted MNI152 volume
>
> >   Sent: Friday, January 08, 2016 at 1:41 PM
> > From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> > To: freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] transform statistical map in MNI to surface
> > If it is in mni152 space, then you can run recon-all on the mni152 T1
> > map, then use mri_vol2surf with --regheader to map the volume tothe
> > surface, then use tksurfer or freeview to view the resulting map
> >
> > On 01/08/2016 12:49 PM, John Anderson wrote:
> > > Hi Experts,
> > > I have statistical map in MNI space and I want to view it using
> > > tksurfer how can i transform this map to a surface ?
> > >
> > > Bests,
> > > John
> > >
> > >
> > > ___
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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: 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/
> >
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htt

[Freesurfer] Fw: mri_glmfit-sim

2016-03-14 Thread John Anderson

 






Hi FS experts,

I am trying to correct the results of groups analysis using mri_glmfit-sim

the command is :

 

mri_glmfit-sim --glmdir lh_10mm --cache 3 pos --cwpvalthresh .0166

 

I receive the follwoing error :

 

ERROR: cannot find /usr/local/freesurfer/stable6/average/mult-comp-cor/fsaverage/lh/cortex/fwhm35/pos/th30/mc-z.csd

 

Thanks you for any suggestion!

 

 

Bests,
John 





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[Freesurfer] mri_glmfit-sim

2016-03-13 Thread John Anderson

Hi experts,

I am trying to correct the results of groups analysis using mri_glmfit-sim

the command is :

mri_glmfit-sim --glmdir lh_10mm --cache 3 pos --cwpvalthresh .0166

I receive the follwoing error :

 

ERROR: cannot find /usr/local/freesurfer/stable6/average/mult-comp-cor/fsaverage/lh/cortex/fwhm35/pos/th30/mc-z.csd

 

Thanks you for any suggestion!

 

 

Bests,
John 
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[Freesurfer] voxel vs surface based morphometric analysis

2016-03-14 Thread John Anderson

Hi Doug,

I ran voxel based analysis in FSL to check the differnce in PET signal between two groups. The results are totally differnt than surface based analysis in Freesurfer.  I this real or I am doing something wrong? I tried to do the same but using FA maps and also I got totally differnt results.

 

I have special interest in understanding why these two methods leads to differnt results?!

I have read this refernce http://cds.ismrm.org/protected/11MProceedings/files/ISMRM2011-8410.pdf and actually I was unable to reach the point that can explain this differnce in th results. I highly appreciate if you clarify that to me.

 

 

Bests,
John
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[Freesurfer] FA maps surface based analysis

2016-03-11 Thread John Anderson

Hi FS experts,

How can ai do surface based analysis on FA maps.

In other wods:

I have 20 subjects( two groups 10/10) and FA map for every subject. How can I dtufy the differnce between the groups in FA on surface?
 

Best,
John
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[Freesurfer] mri_glmfit

2016-03-11 Thread John Anderson

Hi FS experts,

I am trying to run OSGM analysis between two groups using mri_glmfit as follow :

mri_glmfit --y lh_10mm.mgh --fsgd fsgd.dat --glmdir lh_10mm --surf fsaverage lh --osgm 

 

it keep returning as:

ERROR: DOF = 0
 

my FSGD is as follow 

GroupDescriptorFile 1
Title OSGM
Class group1
Class group2

Input 001 group1

Input 002 group1

Input 003 group1

Input 004  group1

.

.

.
Input C001 group2

Input C002 group2

Input C003 group2

Input C004 group2

.

.

.

 

please what I am doing wrong?!

Bests,
John 
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[Freesurfer] mri_glmfit

2016-03-19 Thread John Anderson

Hi Experts,

What is the meaning of this error as an output of the command mri_glmfit

 

Found 0 voxels in mask
ERROR: no voxels found in the mask
  make sure at least one voxel has a non-zero value for each input
 

in other words what are therrors that can lead to such like error message

 

 

Bests,
John 
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Re: [Freesurfer] tksurfer

2016-03-19 Thread John Anderson

Thank you doug,

Please what do you suggesst me to do?

Is this related to something wrong in the analysis?
 

Bests,
John

 

Sent: Wednesday, March 16, 2016 at 10:42 AM
From: "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] tksurfer





it looks like the cluster is covering most of the brain, including precentral gyrus. The precentral gyrus ROI in the table file indicates that is where the peak of the cluster is and does not mean that the cluster is confined to that ROI
 
On 3/16/16 9:43 AM, John Anderson wrote:



Dear experts,

I am running into a trouble visualizing my data in tksurfer. I highly appreciate any advice that can help!

I ran group analysis between two groups using GLM analysis (mri_glmfit) and I corrected the results for multiple comparison using (mri_glmfit-sim), then I ran this command to visualize the results:

 

tksurfer fsaverage lh inflated -overlay cache.th13.pos.sig.cluster.mgh 

 

The result attached. In my summary file I see that I have significant differnce only in the precentral gyrus. But the results in tksurger is not showing precentral gyrus. I tried to play with the thresholds and nothing changed.

 

Any advice is highly appreciated!!

Bests,
John 

 

 
 

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[Freesurfer] mri_fwhm

2016-03-20 Thread John Anderson

Hi FS experts,

I am trying to use the folowing command: 

mri_fwhm --i lh.mgh --auto-mask 0.2 --sum lh.fwhm5.sum --fwhm 5 --o lh_5mm.mgh

 

I keep receiving an error message as follow:

 

voxelvolume 1 mm3
Computing mask, relative threshold = 0.2, gmean = 0.501858, absthresh = 0.100372
Search region is 163842 voxels = 163842.00 mm3
Polynomial detrending, order = 0
Detrending
Smoothing input by fwhm=5.00, gstd=2.123305
Segmentation fault (core dumped)
 

Any suggestion?


 

Bests,
John 
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[Freesurfer] longitudinal data analysis

2016-03-21 Thread John Anderson

Hi Dr Martin
I want to study the change in cortical thickness overtime in one group of subjects.


I have only one group of subjects who scanned multiple times ( two time points and more)

I followed the pipeline exactly as in wiki.

I want to inquire about  X in this case . Is it supposed to be 1 ( one group)

In wiki they used the follwoing x=[ones(length(M),1) M M(:,1).M*(:2)] how this formulla will be for one group of subjects?

 

 

Bests,
John
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Re: [Freesurfer] longitudinal data analysis

2016-03-21 Thread John Anderson

Dear Dr Martin,

Thanks you very much for your awesome clarification and your kindness!!

Bests,
John

Hi John,

X is the design matrix. The rows are the total number of time points for all subjects, the columns the different parameters of your model.

In the wiki example, the first column is all 1s (intercept) the second is the time_from_baseline and other parameters that are in the matrix M (M was read from the qdec table file), the last column is the interaction between the first and second column in M (so probably time X group interaction).

So for you, you probably have
column of ones, time_from_baseline and potentially other control variables (age_at_baseline, gender, scores? IQ.. whatever you want).
Only having 2 columns (ones for the intercept and time for the slope) allow you to test
- if whatever you test is different from zero (intercept), usually that is the case, as you measure volume or thickness
- if the longitudinal slope is different from zero, usually that is also the case, but sometimes you don't have enough power to find that effect.

So that does not really tell you much. For most interesting questions you need two groups.

Best, Martin

On 03/21/2016 12:40 PM, John Anderson wrote:

Hi Dr Martin
I want to study the change in cortical thickness overtime in one group of subjects.

I have only one group of subjects who scanned multiple times ( two time points and more)

I followed the pipeline exactly as in wiki.

I want to inquire about X in this case . Is it supposed to be 1 ( one group)

In wiki they used the follwoing x=[ones(length(M),1) M M(:,1).M*(:2)] how this formulla will be for one group of subjects?

Bests,
John

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[Freesurfer] Qdec-statistical map

2016-03-03 Thread John Anderson

Dear FS experts,

I am using Qdec to study the differnce in cortical thicnkess between two groups.

Qdec is running a GLM analysis. This will output a statistical map (sig.mgh) for the differnce between the groups in cortical thicnkess.

How can I extract the numbers of cortical thickness for every subject (depending on the order of subjects in Qdec table) from this statistical map ?
 

Bests,
John 
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Re: [Freesurfer] Qdec-statistical map

2016-03-03 Thread John Anderson

Hi Doug,

How can I use this statistical map ( e.g. as a mask) to calculate the mean cortical thickness only in the areas of significant differnce between the groups for every subject?

Bests,
John 

Sent: Thursday, March 03, 2016 at 12:37 PM
From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Qdec-statistical map

not sure what you mean. the statistical map will have a single value,
not a value for each subject

On 03/03/2016 12:31 PM, John Anderson wrote:
> Dear FS experts,
> I am using Qdec to study the differnce in cortical thicnkess between
> two groups.
> Qdec is running a GLM analysis. This will output a statistical map
> (sig.mgh) for the differnce between the groups in cortical thicnkess.
> How can I extract the numbers of cortical thickness for every
> subject (depending on the order of subjects in Qdec table) from this
> statistical map ?
> Bests,
> John
>
>
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--
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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
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Re: [Freesurfer] Qdec-statistical map

2016-03-03 Thread John Anderson

This si Great!!! Thanks Doug. One more question:

What is the correct input in the command mri_surfcluster. Is it the image "sig.mgh" ?

 


 

Bests,
John 


 

Sent: Thursday, March 03, 2016 at 12:47 PM
From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Qdec-statistical map

You will have to extract clusters (mri_surfcluster) to create an
annotation, then use mri_segstats with the --annot option and specifying
the y.mgh file as input and the output using something like --avgwf
output.txt (also add --exludeid 0). The output will have a row for each
frame in y.mgh (ie, each subject) and a column for each cluster

On 03/03/2016 12:43 PM, John Anderson wrote:
> Hi Doug,
> How can I use this statistical map ( e.g. as a mask) to calculate the
> mean cortical thickness only in the areas of significant differnce
> between the groups for every subject?
> Bests,
> John
> *Sent:* Thursday, March 03, 2016 at 12:37 PM
> *From:* "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] Qdec-statistical map
> not sure what you mean. the statistical map will have a single value,
> not a value for each subject
>
> On 03/03/2016 12:31 PM, John Anderson wrote:
> > Dear FS experts,
> > I am using Qdec to study the differnce in cortical thicnkess between
> > two groups.
> > Qdec is running a GLM analysis. This will output a statistical map
> > (sig.mgh) for the differnce between the groups in cortical thicnkess.
> > How can I extract the numbers of cortical thickness for every
> > subject (depending on the order of subjects in Qdec table) from this
> > statistical map ?
> > Bests,
> > John
> >
> >
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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
>
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[Freesurfer] V1 Atlas ( brodman maps)

2016-05-11 Thread John Anderson


Dear experts,

 I want to use the atlas V1 to calculate PET signal for Brodman areas. How can I create this atlas in the form of “aseg.mgz” or ”wmparc.mgz” ( i.e all the BAs in one file) to feed it in the command “mri-segstat”?


Bests,
John 
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[Freesurfer] V1 Atlas ( brodman maps)

2016-05-13 Thread John Anderson


Dear Experts,






I want to calculate PET signal within each Brodman map! I will give an example: If I want to caclulate PET singal for every parcellate and segment in the brain I do the following:

 

bbregister  --t1 --mov T1_MPRAGE.nii.gz --init-fsl --reg t1.reg.dat --s SUBJID 

 

mri_vol2vol --mov PET_MAP.nii --reg t1.reg.dat --fstarg --interp nearest --o PET_MAP.anat.nii 
mri_segstats --seg $SUBJECTS_DIR/SUBJID/mri/wmparc.mgz  --ctab-default --i PET_MAP.anat.nii --mask PET_MAP.anat.nii --sum PET_MAP.summary.dat 

 

How can I do the same previous steps ( or something similar) on the atlas V1. I.e how can I replace the atalas "wmparc" in the command "mri_segstat" with the atals V1 to get PET signal for every brodman?. I can't locate the atals V1 as a file like wmparc.mgz or aseg.mgz is there any method to creat this atlas?

 

 

 

Many thanks for any advice!

 

John 


 

 








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[Freesurfer] white and gray matter masks

2016-08-10 Thread John Anderson

Dear FS experts,

I need to crate a mask for whole white matter in the brain including the cerebellum. Also I need a mask for the whoe gray matter.

Can I binzarize ( i.e. use mri_binarize) and input the files:

 

wm.seg.mgz from the output of recon-all to create a a mask for global white matter

and the file ribbon.mgz the output of recon-all to create a a mask for global gray matter

 

Thank you for any advice!

 

Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419
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Re: [Freesurfer] Qdec-correction for multiple comparison

2016-07-06 Thread John Anderson

Hi Doug,

thank you veru much for the answr.

Please what do you mean by " an emperical question that depends on your data"? For example:

 I have two groups of participants. I ran cortical thickness analysis in Qdec to study the differnce between the groups in cortical thickness: 

1. Monte carlo simulation reported differnce between the groups ( p<0.05 ) in the precentral gyrus and the paracentral gyrus

2. FDR reported no diffwernce between the groups ( p<0.05)

Depending on pathology. I expect a differnce in the orecentral gyrus. How can I explain the results of FDR and mote carlo simulation? Does "empirical " means to follow the results that support the hypothesis?

John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419

Sent: Wednesday, July 06, 2016 at 1:44 PM
From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Qdec-correction for multiple comparison

There is no recommendation between FDR and monte carlo. The question of
which one is "better" is an emperical question that depends on your data.

On 06/29/2016 06:38 AM, John Anderson wrote:
> Dear FS experts,
> I will re post this thread again looking for your help and support:
> I ran cortical thickness analysis between two groups using Qdec and I
> want to correct the results for multiple comparison.
> In Qdec there are two choices to correct the data for multiple
> comparison (FDR and montecarlo) . Which method do you recommend to
> correct the results of cortical thickness analysis? Are there any
> rules that I need to follow when I choose my method to correct the
> results for multiple comparison ( i.e FDR or montecarlo)
> Thank you very much for any comment!
> John Anderson
>
> Senior Research Associate
> Psychological and Brain Sciences Dept.
> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> Phone: +1 (603) 646-9834
> Fax: +1 (603) 646-1419
>
>
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gr...@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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[Freesurfer] Qdec-correction for multiple comparison

2016-07-02 Thread John Anderson




Hi Doug,

I ran cortical thickness analysis between two groups using Qdec and I want to correct the results for multiple comparison.

In Qdec there are two choices to correct the data for multiple comparison (FDR and montecarlo) . Which method do you recommend to correct the results of cortical thickness analysis? Are there any rules that I need to follow when I choose my method to correct the results for multiple comparison ( i.e FDR or montecarlo)

 

Thank you very much for any comment!
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419



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[Freesurfer] Qdec-correction for multiple comparison

2016-06-29 Thread John Anderson



Dear FS experts,

I will re post this thread again looking for your help and support:

 

I ran cortical thickness analysis between two groups using Qdec and I want to correct the results for multiple comparison.

In Qdec there are two choices to correct the data for multiple comparison (FDR and montecarlo) . Which method do you recommend to correct the results of cortical thickness analysis? Are there any rules that I need to follow when I choose my method to correct the results for multiple comparison ( i.e FDR or montecarlo)

 

Thank you very much for any comment!
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419


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[Freesurfer] surface based analysis

2017-01-26 Thread John Anderson

Hello Freesurfers,

I am working on a PET surface based analysis between two groups. I did the following:

1. I concatentaed the PET images using the command "mris_preproce" and I got the file (lh.mgh) for left hemisphere and (rh.mgh) for right hemisphere.

2. I smoothed "lh.mgh and rh.mgh) using the command:

mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval lh.mgh --tval lh_sm10.mgh

3. I studdied the diffence between the groups usiing the command:

mri_glmfit --y lh_sm10.mgh --fsgd fsgd.dat --C contrast.mtx --surf fsaverage lh --cortex --glmdir lh

4. I corrected the results for multiple comparison using the command:

mri_glmfit-sim --glmdir lh --cache 30 pos --cwp 0.01 --2spaces

I want to narrow (reduce the strictness) of the correction for multiple comparision to a specific label (e.g. precentral gyrus). I changed the commands "mri_glmfit" and "mri_glmfit-sim" as follow:

mri_glmfit --y lh_sm10.mgh --fsgd fsgd.dat --C contrast.mtx --surf fsaverage lh --label precentral --glmdir lh

mri_glmfit-sim --glmdir lh --cache 30 pos --cache-label precentral --cwp 0.01 --2spaces

I got error that the label "precentral" is not exist. I was unable to find this label in the folder "fsaverage". Kindly:

1. whct I am doing wrong?

2. How can I create this label ? and in whcih folder it must be placed?

Best,
John
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Re: [Freesurfer] surface based analysis

2017-01-26 Thread John Anderson

Thank you Doug,

Actually I was trying to apply what was mentioned in this link by replicating the method on  the command "mri_glmfit" and not  using the command "mri_mcsim".

 I tried to use for example the label "BA4a" (it is available in the folder/fsaverage/label), but the command "mriglm_fit failed to see it!! I ran the command as follow:

mri_glmfit --y lh_sm10.mgh --fsgd fsgd.dat --C contrast.mtx --surf fsaverage lh --label BA4a --glmdir lh

Kindly, what I am doing wrong in this command ? and how can I create label? What command I need? Can I use mri_binarize for example and save the output as a label?

John

Sent: Thursday, January 26, 2017 at 1:15 PM
From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] surface based analysis

FS does not come with correction tables for all labels. You'll have to
build your own. here are the instructions:

http://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo

On 01/26/2017 01:09 PM, John Anderson wrote:
> Hello Freesurfers,
> I am working on a PET surface based analysis between two groups. I did
> the following:
> 1. I concatentaed the PET images using the command "mris_preproce"
> and I got the file (lh.mgh) for left hemisphere and (rh.mgh) for right
> hemisphere.
> 2. I smoothed "lh.mgh and rh.mgh) using the command:
> mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval lh.mgh --tval
> lh_sm10.mgh
> 3. I studdied the diffence between the groups usiing the command:
> mri_glmfit --y lh_sm10.mgh --fsgd fsgd.dat --C contrast.mtx --surf
> fsaverage lh --cortex --glmdir lh
> 4. I corrected the results for multiple comparison using the command:
> mri_glmfit-sim --glmdir lh --cache 30 pos --cwp 0.01 --2spaces
> I want to narrow (reduce the strictness) of the correction for
> multiple comparision to a specific label (e.g. precentral gyrus). I
> changed the commands "mri_glmfit" and "mri_glmfit-sim" as follow:
> mri_glmfit --y lh_sm10.mgh --fsgd fsgd.dat --C contrast.mtx --surf
> fsaverage lh --label precentral --glmdir lh
> mri_glmfit-sim --glmdir lh --cache 30 pos --cache-label precentral
> --cwp 0.01 --2spaces
> I got error that the label "precentral" is not exist. I was unable to
> find this label in the folder "fsaverage". Kindly:
> 1. whct I am doing wrong?
> 2. How can I create this label ? and in whcih folder it must be placed?
> Best,
> John
>
>
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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
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[Freesurfer] bbregister vs spmregister vs mri_coreg

2017-02-25 Thread John Anderson

Dear Freesurfer experts,
I see that the tool "mri_coreg" has been implemented recently in Free Surfer 6 
and I really wanted to know what are the differences between the registration 
tools "bbregister", " spmregister" and "mri_coreg"! Kindly:
1. Are these tools similar? if not what are the differences ?
2. Is there any preference of using a tool over the others for specific type of 
data. For example:
A. If I want to register FA map to T1 image which tool is more robust?
B. if I want to register FA map to MNI space which tool is more robust?


I highly appreciate your input on this!

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[Freesurfer] mri_segstats

2017-02-24 Thread John Anderson

Dear Freesurfer experts,

I have used the following commandline to generate the final statistics in my 
analysis:
mri_segstats --seg aseg.mgz --ctab-default --i suvr.nii --mask mask.nii --sum 
stats.dat

The final output of this command is (attached). Depedning on the anatomical 
location of the mask, I expect that I will get two structures in the stats 
file. What is the "unknown" label means? is it CSF? Do I need to include it in 
my next statistcal analses?

I highly appreciate your input!


Best,
John



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[Freesurfer] Fw: Re: bbregister

2017-02-14 Thread John Anderson

Thank you very much!

Kindly, I have one follow up question:

I have VOI 20X20X20 mm have been created during an MR spectroscopy session. This VOI was placed in specific loacation on the T1 image. I have created this VOI using the command "mri_volsynth"  and I want to move it from native space (T1) to Freesurfer space (e.g. wmparc.mgz) so I can generrat somestatistics using the command "mri_segstats".

I ran the following commands:

bbregister  --t1 --mov T1.nii --init-fsl --reg t1.reg.dat --s subj
tkregister2 --mov VOI.nii --int T1.nii t1.reg.dat --reg VOI.reg.dat --noedit --subject subj 

mri_vol2vol --mov VOI.nii --reg t1.reg.dat --fstarg --interp nearest --o VOI.anat.nii

Are these stpes correct?

When I open T1.nii and the VOI.nii in  freeview, I can see the VOI in it is correct position. But when I open "wmparc.mgz" and "VOI.anat.nii" then VOI is not showing in the correct position. I suspet that I am doing something wrong in the previous steps and I highly appreciate any feedback!

Best,
John 

For version 6, it should not matter.

Sent: Friday, February 10, 2017 at 4:03 PM
From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] bbregister

Hi John

one of the many nice things about bbregister is that it is quite
resistant to non-brain tissue, since it's just trying to place the
gray/white (and optionally the pial surface) at a reasonable spot in the
volume. I guess it might make the initialization less robust, not sure, but
I expect it works pretty well without doing brain extraction

cheers
Bruce

On Fri, 10 Feb 2017, John Anderson wrote:

> Hi FS experts,
> I want to register T1 image to its freesurfer space (i.e. wmparc.mgz) using
> the command 
> bbregister  --t1 --mov T1.nii --init-fsl --reg t1.reg.dat --s subj
>  
> do I need to apply brain extraction tools before this step or bb register
> can accept non-brain extracted images?
>  
> Best,
> John
>
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[Freesurfer] bbregister

2017-02-10 Thread John Anderson

Hi FS experts,

I want to register T1 image to its freesurfer space (i.e. wmparc.mgz) using the command 

bbregister  --t1 --mov T1.nii --init-fsl --reg t1.reg.dat --s subj

 

do I need to apply brain extraction tools before this step or bb register can accept non-brain extracted images?

 

Best,
John
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[Freesurfer] bbregister

2017-02-15 Thread John Anderson

Thank you very much!

Kindly, I have one follow up question:

I have VOI 20X20X20 mm have been created during an MR spectroscopy session. This VOI was placed in specific loacation on the T1 image. I have created this VOI using the command "mri_volsynth"  and I want to move it from native space (T1) to Freesurfer space (e.g. wmparc.mgz) so I can generrat somestatistics using the command "mri_segstats".

I ran the following commands:

bbregister  --t1 --mov T1.nii --init-fsl --reg t1.reg.dat --s subj
tkregister2 --mov VOI.nii --int T1.nii t1.reg.dat --reg VOI.reg.dat --noedit --subject subj 

mri_vol2vol --mov VOI.nii --reg t1.reg.dat --fstarg --interp nearest --o VOI.anat.nii

Are these stpes correct?

When I open T1.nii and the VOI.nii in  freeview, I can see the VOI in it is correct position. But when I open "wmparc.mgz" and "VOI.anat.nii" then VOI is not showing in the correct position. I suspet that I am doing something wrong in the previous steps and I highly appreciate any feedback!

Best,
John 

For version 6, it should not matter.

Sent: Friday, February 10, 2017 at 4:03 PM
From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] bbregister

Hi John

one of the many nice things about bbregister is that it is quite
resistant to non-brain tissue, since it's just trying to place the
gray/white (and optionally the pial surface) at a reasonable spot in the
volume. I guess it might make the initialization less robust, not sure, but
I expect it works pretty well without doing brain extraction

cheers
Bruce

On Fri, 10 Feb 2017, John Anderson wrote:

> Hi FS experts,
> I want to register T1 image to its freesurfer space (i.e. wmparc.mgz) using
> the command 
> bbregister  --t1 --mov T1.nii --init-fsl --reg t1.reg.dat --s subj
>  
> do I need to apply brain extraction tools before this step or bb register
> can accept non-brain extracted images?
>  
> Best,
> John
>
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Re: [Freesurfer] bbregister vs spmregister vs mri_coreg

2017-02-25 Thread John Anderson

Hi Doug, thank you for the detailed response. Highly appreciated!
Kindly. I want to register FA map to structural T1 image using the command 
mri_spmregister as follow:

mri_spmregister move FA.nii --s subj1 --reg reg dat --o FA_2_T1.nii.gz

Is this correct?







 Original Message 
Subject: bbregister vs spmregister vs mri_coreg
Local Time: February 25, 2017 8:49 AM
UTC Time: February 25, 2017 1:49 PM
From: john.ande...@protonmail.com
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>

mri_coreg is the FS implementation of spm_coreg (spmregister) both of which use 
normalized mutual info. bbregister uses the BBR cost function and is preferred 
for all MRI. For registration to MNI space, we usually use mni152reg (a wrapper 
around fsl's flirt)





On 2/25/17 8:49 AM, John Anderson wrote:


Dear Freesurfer experts,


I see that the tool "mri_coreg" has been implemented recently in Free Surfer 6 
and I really wanted to know what are the differences between the registration 
tools "bbregister", " spmregister" and "mri_coreg"! Kindly:


1. Are these tools similar? if not what are the differences ?


2. Is there any preference of using a tool over the others for specific type of 
data. For example:


A. If I want to register FA map to T1 image which tool is more robust?


B. if I want to register FA map to MNI space which tool is more robust?








I highly appreciate your input on this!




John t?e�?�Z�׮
Dear Freesurfer experts,
I see that the tool "mri_coreg" has been implemented recently in Free Surfer 6 
and I really wanted to know what are the differences between the registration 
tools "bbregister", " spmregister" and "mri_coreg"! Kindly:
1. Are these tools similar? if not what are the differences ?
2. Is there any preference of using a tool over the others for specific type of 
data. For example:
A. If I want to register FA map to T1 image which tool is more robust?
B. if I want to register FA map to MNI space which tool is more robust?


I highly appreciate your input on this!

John___
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[Freesurfer] QA tools

2016-09-13 Thread John Anderson

Hello, FS experts,

I am trying to use QA tool:

I ran the following command

recon_checker -snaps-only -s-file subjects.txt

The script output the following:

X11 connection rejected because of wrong authentication.
GLUT: Fatal Error in tkmedit.bin: could not open display: localhost:12.0
X11 connection rejected because of wrong authentication.
GLUT: Fatal Error in tksurfer.bin: could not open display: localhost:12.0
X11 connection rejected because of wrong authentication.
GLUT: Fatal Error in tksurfer.bin: could not open display: localhost:12.0

Taking snapshots for subject ALS-0038
X11 connection rejected because of wrong authentication.
GLUT: Fatal Error in tkmedit.bin: could not open display: localhost:12.0
X11 connection rejected because of wrong authentication.
GLUT: Fatal Error in tksurfer.bin: could not open display: localhost:12.0
X11 connection rejected because of wrong authentication.
GLUT: Fatal Error in tksurfer.bin: could not open display: localhost:12.0

At the end it said that he process finshed. I checked the AQ folder and the snaps where not there

Any suggestions!

Bests,
John
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Re: [Freesurfer] Fw: Re: surface based analysis for subcortical structures

2016-10-28 Thread John Anderson

Hi Doug,

Yes! Thank you for the offer to share the script.

Actually I want to run surface based analysis for sub cortical structres 

I tried the command 
mri_glmfit-sim --glmdir subc.glmdir --cache 1.3 pos --cwp 0.05 --3spaces

 

But it failed (I don't know why!) and this is the reason why I want to use "mri_glmfit-sim --glmdir subc.glmdir --grf 3 pos --cwpvalthresh .0166"

 

Bests,
John 




Sent: Friday, October 28, 2016 at 11:53 AM
From: "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Fw: Re: surface based analysis for subcortical structures



If you want to use GRF, then I should get you new versions of some of the programs as the volume-based GRF used the Friston 1994 algorithm that was not as accurate as the Worsley 1996 algorithm. I just updated my code last week (better late than never:). But in the end, you probably want to use permutation if your group analysis allows it.

 
 

On 10/23/16 10:25 AM, John Anderson wrote:



Thank you very much Doug,

The codes worked very well. I was using the wrong command to correct the data.

My command was 

mri_glmfit-sim --glmdir subc.glmdir --cache 1.3 pos --cwp 0.05 --3spaces

 

and for subcortical structures it must be 


mri_glmfit-sim --glmdir subc.glmdir --grf 3 pos --cwpvalthresh .0166


All the bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419

 
 

Sent: Thursday, October 20, 2016 at 9:20 PM
From: "John Anderson" <j.ander...@publicist.com>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] surface based analysis for subcortical structures



Dear Doug,

Thank you very much for this detailed explaination. I highly appreciate your help

Kindly I have the following question:

The command mri_vol2vol ran smoothly without any errors

The command mri_mask output the following :

 

mri_mask suvr.tal2mm.nii $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz suvr.tal2mm.subc.nii 
freadFloat: fread failed
DoAbs = 0
Writing masked volume to suvr.tal2mm.subc.nii...done.

 

Should I worry about this error ?

 

 

I ignored this error and I continued the following steps. They went fine but when I correct for multiple comparisons using the command "mri_glmfit-sim" I get the following:

 

 


mri_glmfit-sim --glmdir subc.glmdir --cache 1.3 pos --cwp 0.05 --3spaces
cmdline mri_glmfit --y all.pet.tal2mm.subc.sm5.nii --fsgd fsgd.dat --C 2G0C.mtx --glmdir subc.glmdir
log file is subc.glmdir/cache.mri_glmfit-sim.log

cd /analyses/pet_scan/SBM/sm
/usr/local/freesurfer/stable5_3_0/bin/mri_glmfit-sim
--glmdir subc.glmdir --cache 1.3 pos --cwp 0.05 --3spaces

$Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $
Thu Oct 20 21:10:31 EDT 2016
Linux sven 2.6.32-642.3.1.el6.x86_64 #1 SMP Tue Jul 12 18:30:56 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
malshikh
setenv SUBJECTS_DIR /analyses/recons
FREESURFER_HOME /usr/local/freesurfer/stable5_3_0

Original mri_glmfit command line:
cmdline mri_glmfit --y all.pet.tal2mm.subc.sm5.nii --fsgd fsgd.dat --C 2G0C.mtx --glmdir subc.glmdir

DoSim = 0
UseCache = 1
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 10.682767
ERROR: cannot find /usr/local/freesurfer/stable5_3_0/average/mult-comp-cor///cortex/fwhm11/pos/th13/mc-z.csd
 


I smoothed just fwhm = 1

 

Kindly how can I troubleshoo? thank you for any advice

 

Bests,
John 


 

Sent: Thursday, October 20, 2016 at 12:16 PM
From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] surface based analysis for subcortical structures


After spmregister, you can run

mri_vol2vol --mov pet.nii --reg reg.dat --tal --talres 2 --talxfm
talairach.xfm --nearest --no-save-reg --o pet.tal2mm.nii

# mask out the cortical structures

mri_mask pet.tal2mm.nii
$FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz
pet.tal2mm.subc.nii

# Concatenate all subjects together

mri_concat s1/pet.tal2mm.subc.nii s2/pet.tal2mm.subc.nii ... --o
all.pet.tal2mm.subc.nii --prune

# smooth

mri_fwhm --i all.pet.tal2mm.subc.nii --mask
$FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz --fwhm X
--smooth-only --o all.pet.tal2mm.subc.smoothed.nii

mri_glmfit --y all.pet.tal2mm.subc.smoothed.nii --fsgd fsgd.txt--C
2gc0.mtx --glmdir subc.glmdir



On 10/19/2016 05:09 PM, John Anderson wrote:
> Dear experts,
> I ran surface based analysis using PET maps. As the following:
> spmregister --s subj --mov pet.nii --reg reg.dat --out pet_t1.mgh
> mris_preproc --target fsaverage --hemi lh --iv subj1/ubject1_pet.nii subject1/pet/pet_2_T1_register.dat . --projfrac 0.5 --out lh.mgh
> mri_surf2surf --hemi lh --s fsaverage --fwhm 6 --cortex --sval lh.mgh --tval lh.sm6.mgh
> mri_glmfit--y

[Freesurfer] recon all

2016-11-10 Thread John Anderson


Dear Freesurfer experts,

I ran the following command on a T1 image

recon-all -subjid 089 -all -qcache

 

and I got the following error message:

 

talairach_afd -T 0.005 -xfm transforms/talairach.xfm

 

ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0344, pval=0.0034 < threshold=0.0050)

 

 

I highly appreciate an explanation for the meaning of this error and how to fix it.

 

 


Best
John 
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[Freesurfer] surface based analysis for subcortical structures

2016-10-19 Thread John Anderson

Dear experts,

I ran surface based analysis using PET maps. As the following:

 


spmregister --s subj --mov pet.nii --reg reg.dat --out pet_t1.mgh
mris_preproc --target fsaverage --hemi lh --iv subj1/ubject1_pet.nii subject1/pet/pet_2_T1_register.dat . --projfrac 0.5 --out lh.mgh
mri_surf2surf --hemi lh --s fsaverage --fwhm 6 --cortex --sval lh.mgh --tval lh.sm6.mgh
mri_glmfit--y lh.sm6.mgh--fsgd fsgd.txt--C 2gc0.mtx --surf fsaverage lh --cortex --glmdir lh.glmdir



then mri_glmfit-sim to correct for multiple comparison.

 

I want to study the subcortical regions and map it on MNI305. How can I resume tha analysis for subcortical structures?

Thank you for any help!


Bests,
John
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[Freesurfer] de-identify DICOM

2016-10-20 Thread John Anderson


Hi FS experts,

I wanted to inquire if there are any tools in FS that can help to de-identify DICOMs?

 

 

Thank you for any comment
John 
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[Freesurfer] Fw: Re: surface based analysis for subcortical structures

2016-10-23 Thread John Anderson

Thank you very much Doug,

The codes worked very well. I was using the wrong command to correct the data.

My command was 

mri_glmfit-sim --glmdir subc.glmdir --cache 1.3 pos --cwp 0.05 --3spaces

 

and for subcortical structures it must be 


mri_glmfit-sim --glmdir subc.glmdir --grf 3 pos --cwpvalthresh .0166


All the bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419

 
 

Sent: Thursday, October 20, 2016 at 9:20 PM
From: "John Anderson" <j.ander...@publicist.com>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] surface based analysis for subcortical structures



Dear Doug,

Thank you very much for this detailed explaination. I highly appreciate your help

Kindly I have the following question:

The command mri_vol2vol ran smoothly without any errors

The command mri_mask output the following :

 

mri_mask suvr.tal2mm.nii $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz suvr.tal2mm.subc.nii 
freadFloat: fread failed
DoAbs = 0
Writing masked volume to suvr.tal2mm.subc.nii...done.

 

Should I worry about this error ?

 

 

I ignored this error and I continued the following steps. They went fine but when I correct for multiple comparisons using the command "mri_glmfit-sim" I get the following:

 

 


mri_glmfit-sim --glmdir subc.glmdir --cache 1.3 pos --cwp 0.05 --3spaces
cmdline mri_glmfit --y all.pet.tal2mm.subc.sm5.nii --fsgd fsgd.dat --C 2G0C.mtx --glmdir subc.glmdir
log file is subc.glmdir/cache.mri_glmfit-sim.log

cd /analyses/pet_scan/SBM/sm
/usr/local/freesurfer/stable5_3_0/bin/mri_glmfit-sim
--glmdir subc.glmdir --cache 1.3 pos --cwp 0.05 --3spaces

$Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $
Thu Oct 20 21:10:31 EDT 2016
Linux sven 2.6.32-642.3.1.el6.x86_64 #1 SMP Tue Jul 12 18:30:56 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
malshikh
setenv SUBJECTS_DIR /analyses/recons
FREESURFER_HOME /usr/local/freesurfer/stable5_3_0

Original mri_glmfit command line:
cmdline mri_glmfit --y all.pet.tal2mm.subc.sm5.nii --fsgd fsgd.dat --C 2G0C.mtx --glmdir subc.glmdir

DoSim = 0
UseCache = 1
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 10.682767
ERROR: cannot find /usr/local/freesurfer/stable5_3_0/average/mult-comp-cor///cortex/fwhm11/pos/th13/mc-z.csd
 


I smoothed just fwhm = 1

 

Kindly how can I troubleshoo? thank you for any advice

 

Bests,
John 


 

Sent: Thursday, October 20, 2016 at 12:16 PM
From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] surface based analysis for subcortical structures


After spmregister, you can run

mri_vol2vol --mov pet.nii --reg reg.dat --tal --talres 2 --talxfm
talairach.xfm --nearest --no-save-reg --o pet.tal2mm.nii

# mask out the cortical structures

mri_mask pet.tal2mm.nii
$FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz
pet.tal2mm.subc.nii

# Concatenate all subjects together

mri_concat s1/pet.tal2mm.subc.nii s2/pet.tal2mm.subc.nii ... --o
all.pet.tal2mm.subc.nii --prune

# smooth

mri_fwhm --i all.pet.tal2mm.subc.nii --mask
$FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz --fwhm X
--smooth-only --o all.pet.tal2mm.subc.smoothed.nii

mri_glmfit --y all.pet.tal2mm.subc.smoothed.nii --fsgd fsgd.txt--C
2gc0.mtx --glmdir subc.glmdir



On 10/19/2016 05:09 PM, John Anderson wrote:
> Dear experts,
> I ran surface based analysis using PET maps. As the following:
> spmregister --s subj --mov pet.nii --reg reg.dat --out pet_t1.mgh
> mris_preproc --target fsaverage --hemi lh --iv subj1/ubject1_pet.nii subject1/pet/pet_2_T1_register.dat . --projfrac 0.5 --out lh.mgh
> mri_surf2surf --hemi lh --s fsaverage --fwhm 6 --cortex --sval lh.mgh --tval lh.sm6.mgh
> mri_glmfit--y lh.sm6.mgh--fsgd fsgd.txt--C 2gc0.mtx --surf fsaverage lh --cortex --glmdir lh.glmdir//
> then mri_glmfit-sim to correct for multiple comparison.
> I want to study the subcortical regions and map it on MNI305. How can
> I resume tha analysis for subcortical structures?
> Thank you for any help!
> Bests,
> John
>
>
> ___
> 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: 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/

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The in

[Freesurfer] Volume or surface?

2016-10-17 Thread John Anderson

Dear FS experts,

I want to know what is the output (volume or surface) of the following scripts.

(The input is file.nii.gz which is a volumetric )

1. spmregister --s subj --mov file.nii.gz --reg reg.dat --o file_t1.mgh #is the output file (file_t1.mgh) is a volume or a surface 

 

2. mris_preproc --target fsaverage --hemi lh --projfrac 0.5 --iv file1_t1.mgh reg1.dat --iv file2_t1.mgh reg  --out lh.mgh #is the output file (lh.mgh) is a volume or a surface

 

where I must feed the output of "mris_preproc"? to "mri_vol2surf or mri_surf2surf

 

Thank you for your help

 

 

Bests,
John 
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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] surface based analysis for subcortical structures

2016-10-20 Thread John Anderson

Dear Doug,

Thank you very much for this detailed explaination. I highly appreciate your help

Kindly I have the following question:

The command mri_vol2vol ran smoothly without any errors

The command mri_mask output the following :

 

mri_mask suvr.tal2mm.nii $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz suvr.tal2mm.subc.nii 
freadFloat: fread failed
DoAbs = 0
Writing masked volume to suvr.tal2mm.subc.nii...done.

 

Should I worry about this error ?

 

 

I ignored this error and I continued the following steps. They went fine but when I correct for multiple comparisons using the command "mri_glmfit-sim" I get the following:

 

 


mri_glmfit-sim --glmdir subc.glmdir --cache 1.3 pos --cwp 0.05 --3spaces
cmdline mri_glmfit --y all.pet.tal2mm.subc.sm5.nii --fsgd fsgd.dat --C 2G0C.mtx --glmdir subc.glmdir
log file is subc.glmdir/cache.mri_glmfit-sim.log

cd /analyses/pet_scan/SBM/sm
/usr/local/freesurfer/stable5_3_0/bin/mri_glmfit-sim
--glmdir subc.glmdir --cache 1.3 pos --cwp 0.05 --3spaces

$Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $
Thu Oct 20 21:10:31 EDT 2016
Linux sven 2.6.32-642.3.1.el6.x86_64 #1 SMP Tue Jul 12 18:30:56 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
malshikh
setenv SUBJECTS_DIR /analyses/recons
FREESURFER_HOME /usr/local/freesurfer/stable5_3_0

Original mri_glmfit command line:
cmdline mri_glmfit --y all.pet.tal2mm.subc.sm5.nii --fsgd fsgd.dat --C 2G0C.mtx --glmdir subc.glmdir

DoSim = 0
UseCache = 1
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 10.682767
ERROR: cannot find /usr/local/freesurfer/stable5_3_0/average/mult-comp-cor///cortex/fwhm11/pos/th13/mc-z.csd
 


I smoothed just fwhm = 1

 

Kindly how can I troubleshoo? thank you for any advice

 

Bests,
John 


 

Sent: Thursday, October 20, 2016 at 12:16 PM
From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] surface based analysis for subcortical structures


After spmregister, you can run

mri_vol2vol --mov pet.nii --reg reg.dat --tal --talres 2 --talxfm
talairach.xfm --nearest --no-save-reg --o pet.tal2mm.nii

# mask out the cortical structures

mri_mask pet.tal2mm.nii
$FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz
pet.tal2mm.subc.nii

# Concatenate all subjects together

mri_concat s1/pet.tal2mm.subc.nii s2/pet.tal2mm.subc.nii ... --o
all.pet.tal2mm.subc.nii --prune

# smooth

mri_fwhm --i all.pet.tal2mm.subc.nii --mask
$FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz --fwhm X
--smooth-only --o all.pet.tal2mm.subc.smoothed.nii

mri_glmfit --y all.pet.tal2mm.subc.smoothed.nii --fsgd fsgd.txt--C
2gc0.mtx --glmdir subc.glmdir



On 10/19/2016 05:09 PM, John Anderson wrote:
> Dear experts,
> I ran surface based analysis using PET maps. As the following:
> spmregister --s subj --mov pet.nii --reg reg.dat --out pet_t1.mgh
> mris_preproc --target fsaverage --hemi lh --iv subj1/ubject1_pet.nii subject1/pet/pet_2_T1_register.dat . --projfrac 0.5 --out lh.mgh
> mri_surf2surf --hemi lh --s fsaverage --fwhm 6 --cortex --sval lh.mgh --tval lh.sm6.mgh
> mri_glmfit--y lh.sm6.mgh--fsgd fsgd.txt--C 2gc0.mtx --surf fsaverage lh --cortex --glmdir lh.glmdir//
> then mri_glmfit-sim to correct for multiple comparison.
> I want to study the subcortical regions and map it on MNI305. How can
> I resume tha analysis for subcortical structures?
> Thank you for any help!
> Bests,
> John
>
>
> ___
> 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: 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/

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The information in this e-mail is intended only for the person to whom it is
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conta

[Freesurfer] dtrecon

2016-11-12 Thread John Anderson

Dear Freesurfer experts,

I want to analyze DTI data using the command 

dt_recon --i dwi.nii --b bvals bvecs --s subj1 --o /subj1

 

Under Fressurfer 5.3, the analysis fail showing this error message:

nifti1Read(): unsupported slice timing pattern 5 in /data/anaconda/mesgp/dtrecon3/subj1/dwi.nii


I re-run the same previous comand line under freesurfer 6 and the nalysis went fine.

 

The problem is that all my recons are prepared under freesurfer 5.3. If I use dt_recon under FS6 does this affect the results?

 

Thank you for any advice you provide!

 

Bests,
John 
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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.

Re: [Freesurfer] Fw: Re: surface based analysis for subcortical structures

2016-11-14 Thread John Anderson

Thank you very much Doug. You are so awsome :)

 

Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419

 
 

Sent: Monday, November 14, 2016 at 1:00 PM
From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Fw: Re: surface based analysis for subcortical structures

Hi, I just found a bug in mri_glmfit-sim in regards to GRF on
volume-based data. I put a fixed version at the same location. Please
use the new version


On 11/04/2016 10:25 AM, Douglas N Greve wrote:
> oops, sorry,
>
> download these files
>
> https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_glmfit-sim
>
> https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_volcluster
>
> https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_surfcluster
>
> Copy them into $FREESURFER_HOME/bin (after making a backup of the
> previous files).
>
> Edit mri_glmfit-sim to remove
>
> source $FREESURFER_HOME/sources.csh
>
> then hopefully everything should work
>
> doug
>
>
> On 11/04/2016 06:11 AM, John Anderson wrote:
>> Hi Doug,
>> I want to use GRF. Will you be willing to share the new versions of
>> the programs? Your help is highly appreciated.
>> Thanks!
>> Jon
>> *on:* Friday, October 28, 2016 at 11:53 AM
>> *From:* "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
>> *To:* freesurfer@nmr.mgh.harvard.edu
>> *Subject:* Re: [Freesurfer] Fw: Re: surface based analysis for
>> subcortical structures
>>
>> If you want to use GRF, then I should get you new versions of some of
>> the programs as the volume-based GRF used the Friston 1994 algorithm
>> that was not as accurate as the Worsley 1996 algorithm. I just
>> updated my code last week (better late than never:). But in the end,
>> you probably want to use permutation if your group analysis allows it.
>>
>> On 10/23/16 10:25 AM, John Anderson wrote:
>>
>> Thank you very much Doug,
>> The codes worked very well. I was using the wrong command to
>> correct the data.
>> My command was
>> mri_glmfit-sim --glmdir subc.glmdir --cache 1.3 pos --cwp 0.05
>> --3spaces
>> and for subcortical structures it must be
>>
>> mri_glmfit-sim --glmdir subc.glmdir --grf 3 pos --cwpvalthresh .0166
>>
>> All the bests,
>> John Anderson
>>
>> Senior Research Associate
>> Psychological and Brain Sciences Dept.
>> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH
>> 03755
>> Phone: +1 (603) 646-9834
>> Fax: +1 (603) 646-1419
>> *Sent:* Thursday, October 20, 2016 at 9:20 PM
>> *From:* "John Anderson" <j.ander...@publicist.com>
>> *To:* freesurfer@nmr.mgh.harvard.edu
>> *Subject:* Re: [Freesurfer] surface based analysis for subcortical
>> structures
>> Dear Doug,
>> Thank you very much for this detailed explaination. I highly
>> appreciate your help
>> Kindly I have the following question:
>> The command mri_vol2vol ran smoothly without any errors
>> The command mri_mask output the following :
>> mri_mask suvr.tal2mm.nii
>> $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz
>> suvr.tal2mm.subc.nii
>> freadFloat: fread failed
>> DoAbs = 0
>> Writing masked volume to suvr.tal2mm.subc.nii...done.
>> Should I worry about this error ?
>> I ignored this error and I continued the following steps. They
>> went fine but when I correct for multiple comparisons using the
>> command "mri_glmfit-sim" I get the following:
>> mri_glmfit-sim --glmdir subc.glmdir --cache 1.3 pos --cwp 0.05
>> --3spaces
>> cmdline mri_glmfit --y all.pet.tal2mm.subc.sm5.nii --fsgd fsgd.dat
>> --C 2G0C.mtx --glmdir subc.glmdir
>> log file is subc.glmdir/cache.mri_glmfit-sim.log
>> cd /analyses/pet_scan/SBM/sm
>> /usr/local/freesurfer/stable5_3_0/bin/mri_glmfit-sim
>> --glmdir subc.glmdir --cache 1.3 pos --cwp 0.05 --3spaces
>> $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $
>> Thu Oct 20 21:10:31 EDT 2016
>> Linux sven 2.6.32-642.3.1.el6.x86_64 #1 SMP Tue Jul 12 18:30:56
>> UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
>> malshikh
>> setenv SUBJECTS_DIR /analyses/recons
>> FREESURFER_HOME /usr/local/freesurfer/stable5_3_0
>> Original mri_glmfit command line:
>> cmdline mri_glmfit --y all.pet.tal2mm.subc.sm5.nii --fsgd fsgd.dat
>> --C 2G0C.mtx --glmdir subc.glmdir
>> DoSim = 0
>> UseCache = 1
>> DoPoll = 0
>> DoPBSubmit = 0
>> DoB

[Freesurfer] Re: surface based analysis for subcortical structures

2016-11-28 Thread John Anderson

Hi Doug,

I have one additional question regarding surface based analyses:

Let's say that we have two types of brain lesions:

1. The first one is located in the cortical parcellates ( the labels in freesurfer atlas (wmparc.mgz) are named ctx-lh-? and ctx-rh-?).

2. The second lesion is located in the white matter parcellates ( the labels in freesurfer atlas (wmparc.mgz) are named  wm-lh-? and wm-rh-?).

Depedning on the location of these lesions the study subjects are divided into three groups ( normal people, those who have lesions in the cortical parcellates and those who have lesions in the white matter parcellates)

I want to invistigate the position of these lesions by runnig two surface based analyses (using PET images and the pipelines mentioned bellow) to show the location of these lesions (superfecial and deeper):

1. The first surface based analysis is between normal people and those who have supperfecial lesions in the cortical parcellates

2. The second surface based analysis is betweem normal people and those who have deep lesions in the white matter parcellates

In this case can the surface based analysis be able to find these differnces (between lesions in the cortical parcellates vs lesions in the white matter parcellates) using the same projection factor? Or I need to change the projection factor to include more deeper structures in the analysis?

Thank you for any advice!
John

Sent: Monday, November 14, 2016 at 1:29 PM
From: "John Anderson" <j.ander...@publicist.com>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Fw: Re: surface based analysis for subcortical structures

Thank you very much Doug. You are so awsome :)

Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419

Sent: Monday, November 14, 2016 at 1:00 PM
From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Fw: Re: surface based analysis for subcortical structures

Hi, I just found a bug in mri_glmfit-sim in regards to GRF on
volume-based data. I put a fixed version at the same location. Please
use the new version

On 11/04/2016 10:25 AM, Douglas N Greve wrote:
> oops, sorry,
>
> download these files
>
> https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_glmfit-sim
>
> https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_volcluster
>
> https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_surfcluster
>
> Copy them into $FREESURFER_HOME/bin (after making a backup of the
> previous files).
>
> Edit mri_glmfit-sim to remove
>
> source $FREESURFER_HOME/sources.csh
>
> then hopefully everything should work
>
> doug
>
>
> On 11/04/2016 06:11 AM, John Anderson wrote:
>> Hi Doug,
>> I want to use GRF. Will you be willing to share the new versions of
>> the programs? Your help is highly appreciated.
>> Thanks!
>> Jon
>> *on:* Friday, October 28, 2016 at 11:53 AM
>> *From:* "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
>> *To:* freesurfer@nmr.mgh.harvard.edu
>> *Subject:* Re: [Freesurfer] Fw: Re: surface based analysis for
>> subcortical structures
>>
>> If you want to use GRF, then I should get you new versions of some of
>> the programs as the volume-based GRF used the Friston 1994 algorithm
>> that was not as accurate as the Worsley 1996 algorithm. I just
>> updated my code last week (better late than never:). But in the end,
>> you probably want to use permutation if your group analysis allows it.
>>
>> On 10/23/16 10:25 AM, John Anderson wrote:
>>
>> Thank you very much Doug,
>> The codes worked very well. I was using the wrong command to
>> correct the data.
>> My command was
>> mri_glmfit-sim --glmdir subc.glmdir --cache 1.3 pos --cwp 0.05
>> --3spaces
>> and for subcortical structures it must be
>>
>> mri_glmfit-sim --glmdir subc.glmdir --grf 3 pos --cwpvalthresh .0166
>>
>> All the bests,
>> John Anderson
>>
>> Senior Research Associate
>> Psychological and Brain Sciences Dept.
>> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH
>> 03755
>> Phone: +1 (603) 646-9834
>> Fax: +1 (603) 646-1419
>> *Sent:* Thursday, October 20, 2016 at 9:20 PM
>> *From:* "John Anderson" <j.ander...@publicist.com>
>> *To:* freesurfer@nmr.mgh.harvard.edu
>> *Subject:* Re: [Freesurfer] surface based analysis for subcortical
>> structures
>> Dear Doug,
>> Thank you very much for this detailed explaination. I highly
>> appreciate your help
>> Kindly I have the following question:
&

Re: [Freesurfer] recon all

2016-11-11 Thread John Anderson

Thank you very much Doug,

Kindly, what do you suggest me to use instead of fslswapidim. What is your choice in this case? I highly appreciate your experience !
 

Bests,
John


 

Sent: Friday, November 11, 2016 at 4:42 PM
From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon all

On this volume as the head is almost at a 45deg angle perhaps causing
the nominal SI and AP to swap. Even after swap dim, the angle is pretty
extreme, but maybe better than the original so the tal check does not
fail. In general, I don't like to use swapdim as I'm afraid that it
might left-right rev the volume. In either case, you can manually check
the tal reg to see if it looks ok.


On 11/11/2016 03:56 PM, John Anderson wrote:
> Thank you Doug,
> Attched are to snapshots
> #1 is for the original T1 ( i.e. as aquired) and this image what
> output the error message mentioned in my previous email.
> #2 is after correcting the orientation using the command "*fslswapdim
> 001.nii RL PA IS T1-2mm_orientOK.nii"*
> I re run the same command "recon-all" on the newly corrected T1 image.
> The analysis is runnig fine right now, but when I checked the file
> "recon-all" I found similar error to what terminated my previous
> analysis. The differnce here is that the analysis didn't fail!
> Here is what I have in "recon.log"
> talairach_afd -T 0.005 -xfm transforms/talairach.xfm
> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
> ***FAILED*** (p=0.0386, pval=0.0034 < threshold=0.0050)
> INFO: Attempting MINC mritotal to perform Talairach align
> Do I need to warry about this error? I appreciate any suggestion to
> improve analyzing this image.
> Bests,
> John
> *Sent:* Friday, November 11, 2016 at 3:19 PM
> *From:* "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] recon all
> This can also happen if the head is oriented in a strange way. This can
> happen with older patients that tend to tilt their head back.
>
>
> On 11/10/2016 08:27 PM, Bruce Fischl wrote:
> > Hi John
> >
> > it means that the talairach transform that was computed was extremely
> > unlikely and deemed to be probably incorrect. Frequently this happens
> > if you start with images (like analyze) that don't contain accurate
> > direction cosine information. You can check this by bringing one of
> > the volumes in freeview and checking to make sure that the anatomical
> > directions we show
> > (e.g. anterior/posterior) correspond to the true anatomy. Sometimes
> > abnormal anatomiies like huge ventricles can also make it fail, but
> > you need to figure out which one it is before deciding what to do
> >
> > cheers
> > Bruce
> >
> >
> > On Fri, 11 Nov 2016, John Anderson wrote:
> >
> >> Dear Freesurfer experts,
> >> I ran the following command on a T1 image
> >> recon-all -subjid 089 -all -qcache
> >>
> >> and I got the following error message:
> >>
> >> talairach_afd -T 0.005 -xfm transforms/talairach.xfm
> >>
> >> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
> >> ***FAILED*** (p=0.0344, pval=0.0034 < threshold=0.0050)
> >>
> >>
> >> I highly appreciate an explanation for the meaning of this error and
> >> how to
> >> fix it.
> >>
> >>
> >> Best
> >> John
> >>
> >>
> >
> >
> > ___
> > 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: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> 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

Re: [Freesurfer] Fw: Re: surface based analysis for subcortical structures

2016-11-04 Thread John Anderson









Hi Doug,

I want to use GRF. Will you be willing to share the new versions of the programs? Your help is highly appreciated. 

 

Thanks!

Jon

 

on: Friday, October 28, 2016 at 11:53 AM
From: "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Fw: Re: surface based analysis for subcortical structures



If you want to use GRF, then I should get you new versions of some of the programs as the volume-based GRF used the Friston 1994 algorithm that was not as accurate as the Worsley 1996 algorithm. I just updated my code last week (better late than never:). But in the end, you probably want to use permutation if your group analysis allows it.

 
 

On 10/23/16 10:25 AM, John Anderson wrote:



Thank you very much Doug,

The codes worked very well. I was using the wrong command to correct the data.

My command was 

mri_glmfit-sim --glmdir subc.glmdir --cache 1.3 pos --cwp 0.05 --3spaces

 

and for subcortical structures it must be 


mri_glmfit-sim --glmdir subc.glmdir --grf 3 pos --cwpvalthresh .0166


All the bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419

 
 

Sent: Thursday, October 20, 2016 at 9:20 PM
From: "John Anderson" <j.ander...@publicist.com>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] surface based analysis for subcortical structures



Dear Doug,

Thank you very much for this detailed explaination. I highly appreciate your help

Kindly I have the following question:

The command mri_vol2vol ran smoothly without any errors

The command mri_mask output the following :

 

mri_mask suvr.tal2mm.nii $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz suvr.tal2mm.subc.nii 
freadFloat: fread failed
DoAbs = 0
Writing masked volume to suvr.tal2mm.subc.nii...done.

 

Should I worry about this error ?

 

 

I ignored this error and I continued the following steps. They went fine but when I correct for multiple comparisons using the command "mri_glmfit-sim" I get the following:

 

 


mri_glmfit-sim --glmdir subc.glmdir --cache 1.3 pos --cwp 0.05 --3spaces
cmdline mri_glmfit --y all.pet.tal2mm.subc.sm5.nii --fsgd fsgd.dat --C 2G0C.mtx --glmdir subc.glmdir
log file is subc.glmdir/cache.mri_glmfit-sim.log

cd /analyses/pet_scan/SBM/sm
/usr/local/freesurfer/stable5_3_0/bin/mri_glmfit-sim
--glmdir subc.glmdir --cache 1.3 pos --cwp 0.05 --3spaces

$Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $
Thu Oct 20 21:10:31 EDT 2016
Linux sven 2.6.32-642.3.1.el6.x86_64 #1 SMP Tue Jul 12 18:30:56 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
malshikh
setenv SUBJECTS_DIR /analyses/recons
FREESURFER_HOME /usr/local/freesurfer/stable5_3_0

Original mri_glmfit command line:
cmdline mri_glmfit --y all.pet.tal2mm.subc.sm5.nii --fsgd fsgd.dat --C 2G0C.mtx --glmdir subc.glmdir

DoSim = 0
UseCache = 1
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 10.682767
ERROR: cannot find /usr/local/freesurfer/stable5_3_0/average/mult-comp-cor///cortex/fwhm11/pos/th13/mc-z.csd
 


I smoothed just fwhm = 1

 

Kindly how can I troubleshoo? thank you for any advice

 

Bests,
John 


 

Sent: Thursday, October 20, 2016 at 12:16 PM
From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] surface based analysis for subcortical structures


After spmregister, you can run

mri_vol2vol --mov pet.nii --reg reg.dat --tal --talres 2 --talxfm
talairach.xfm --nearest --no-save-reg --o pet.tal2mm.nii

# mask out the cortical structures

mri_mask pet.tal2mm.nii
$FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz
pet.tal2mm.subc.nii

# Concatenate all subjects together

mri_concat s1/pet.tal2mm.subc.nii s2/pet.tal2mm.subc.nii ... --o
all.pet.tal2mm.subc.nii --prune

# smooth

mri_fwhm --i all.pet.tal2mm.subc.nii --mask
$FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz --fwhm X
--smooth-only --o all.pet.tal2mm.subc.smoothed.nii

mri_glmfit --y all.pet.tal2mm.subc.smoothed.nii --fsgd fsgd.txt--C
2gc0.mtx --glmdir subc.glmdir



On 10/19/2016 05:09 PM, John Anderson wrote:
> Dear experts,
> I ran surface based analysis using PET maps. As the following:
> spmregister --s subj --mov pet.nii --reg reg.dat --out pet_t1.mgh
> mris_preproc --target fsaverage --hemi lh --iv subj1/ubject1_pet.nii subject1/pet/pet_2_T1_register.dat . --projfrac 0.5 --out lh.mgh
> mri_surf2surf --hemi lh --s fsaverage --fwhm 6 --cortex --sval lh.mgh --tval lh.sm6.mgh
> mri_glmfit--y lh.sm6.mgh--fsgd fsgd.txt--C 2gc0.mtx --surf fsaverage lh --cortex --glmdir lh.glmdir//
> then mri_glmfit-sim to correct for multiple comparison.
> I want to study the subcortical regions and map it on MNI305. How can
> I resu

Re: [Freesurfer] surface based analysis (projfrac)

2017-01-13 Thread John Anderson

Thank you Doug for the advice ,

I will follow your pipeline, I see that the command  "gtmseg " is part of Freesurfer 6. Can I apply it on recons generated by Freesurfer 5.3 ?
 

Best,
John




Sent: Friday, January 13, 2017 at 3:16 PM
From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] surface based analysis (projfrac)

These differences are hard to track down because they are so subtle.

You may want to use our PET module, which includes PVC

http://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer


On 01/13/2017 03:10 PM, John Anderson wrote:
> I am working on surface-based analysis to study the differnce in PET
> signal in the cortex between two groups.
> When I used "projfrac=0.5 " there was no differnce between the groups
> at "cwp 0.05", and when I changed the "projfrac to 0" I got
> significant differnce between the groups in specific areas at "cwp
> 0.01". How can I check that this differnce is a real differnce and
> not related to partial volume effect?
> Best,
> John
> *Sent:* Friday, January 13, 2017 at 2:46 PM
> *From:* "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] surface based analysis (projfrac)
> What is the modality you are looking at?
>
>
> On 01/13/2017 02:08 PM, John Anderson wrote:
> > Thank you very much Doug,
> > Kindly, do you suggest me any steps to avoid patial volume effects in
> > surface based analyses ?
> > Best,
> > John
> > *Sent:* Friday, January 13, 2017 at 12:21 PM
> > *From:* "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> > *To:* freesurfer@nmr.mgh.harvard.edu
> > *Subject:* Re: [Freesurfer] surface based analysis (projfrac)
> >
> >
> > On 01/12/2017 05:20 PM, John Anderson wrote:
> > > Thank you very much Doug and thank you for briniging the issue of
> > > "partial volume effect " to my attention. Kindly, I have one last
> > > question.
> > > I found in wiki that the default values for projfrc value are between
> > > 0 and 1. Are there negative values? I mean for example "-2, -1, 0 , 1,
> > > 2 ", In other words, less than zero means the surface based analysis
> > > is running at a lower level of the white matter.
> > Yes
> > > Can the issue of the partial volume effect be avoided by using larger
> > > numbers for "projfrac" ?
> > No, PVEs can't be avoided that way.
> > > Bests,
> > > John
> > > *Sent:* Thursday, January 12, 2017 at 5:08 PM
> > > *From:* "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> > > *To:* freesurfer@nmr.mgh.harvard.edu
> > > *Subject:* Re: [Freesurfer] surface based analysis (projfrac)
> > > yes, that is correct. However, understand that there might only be a
> > > difference of 1mm between those two locations, so it could easily be a
> > > partial volume effect
> > >
> > >
> > > On 01/11/2017 08:50 AM, John Anderson wrote:
> > > > Thank you Doug,
> > > > Exactly! I meant GM near the CC.
> > > > When I used "projfrac=0.5 " there was no differnce between the
> groups
> > > > at "cwp 0.05", and when I changed the "projfrac to 0" I got
> > > > significant differnce between the groups in specific areas at "cwp
> > > > 0.01". Kindly, how can this be explained? I highly appreciate if you
> > > > help me to understand this point:
> > > > For "projfrac =0" I expect the surface based analysis to
> > > > be running close to white matter. Right? and when I used
> > > > "projfrac=0.5" the analysis is running in the middle area
> between pial
> > > > and white. When the analysis is not showing any differne between the
> > > > groups for "projfrac 0.5" and showing differnce for "projfrac 0"
> that
> > > > means the differnce between the groups is deeper and closer to white
> > > > matter. Is this correct?
> > > > Thank you for any input and clarification!
> > > > Bests,
> > > > John
> > > > *Sent:* Tuesday, January 10, 2017 at 10:51 AM
> > > > *From:* "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
> > > > *To:* freesurfer@nmr.mgh.harvard.edu
> > > > *Subject:* Re: [Freesurfer] surface based analysis (projfrac)
> > > >
> > > > When you say in the corpus callosum, do you mean in WM? The
> > >

Re: [Freesurfer] surface based analysis (projfrac)

2017-01-13 Thread John Anderson

I am working on surface-based analysis to study the differnce in PET signal in the cortex between two groups.

When I used "projfrac=0.5 " there was no differnce between the groups at "cwp 0.05", and when I changed the "projfrac to 0" I got significant differnce between the groups in specific areas at "cwp 0.01".  How can I check that this differnce is a real differnce and not related to partial volume effect?

Best,
John 


 

Sent: Friday, January 13, 2017 at 2:46 PM
From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] surface based analysis (projfrac)

What is the modality you are looking at?


On 01/13/2017 02:08 PM, John Anderson wrote:
> Thank you very much Doug,
> Kindly, do you suggest me any steps to avoid patial volume effects in
> surface based analyses ?
> Best,
> John
> *Sent:* Friday, January 13, 2017 at 12:21 PM
> *From:* "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] surface based analysis (projfrac)
>
>
> On 01/12/2017 05:20 PM, John Anderson wrote:
> > Thank you very much Doug and thank you for briniging the issue of
> > "partial volume effect " to my attention. Kindly, I have one last
> > question.
> > I found in wiki that the default values for projfrc value are between
> > 0 and 1. Are there negative values? I mean for example "-2, -1, 0 , 1,
> > 2 ", In other words, less than zero means the surface based analysis
> > is running at a lower level of the white matter.
> Yes
> > Can the issue of the partial volume effect be avoided by using larger
> > numbers for "projfrac" ?
> No, PVEs can't be avoided that way.
> > Bests,
> > John
> > *Sent:* Thursday, January 12, 2017 at 5:08 PM
> > *From:* "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> > *To:* freesurfer@nmr.mgh.harvard.edu
> > *Subject:* Re: [Freesurfer] surface based analysis (projfrac)
> > yes, that is correct. However, understand that there might only be a
> > difference of 1mm between those two locations, so it could easily be a
> > partial volume effect
> >
> >
> > On 01/11/2017 08:50 AM, John Anderson wrote:
> > > Thank you Doug,
> > > Exactly! I meant GM near the CC.
> > > When I used "projfrac=0.5 " there was no differnce between the groups
> > > at "cwp 0.05", and when I changed the "projfrac to 0" I got
> > > significant differnce between the groups in specific areas at "cwp
> > > 0.01". Kindly, how can this be explained? I highly appreciate if you
> > > help me to understand this point:
> > > For "projfrac =0" I expect the surface based analysis to
> > > be running close to white matter. Right? and when I used
> > > "projfrac=0.5" the analysis is running in the middle area between pial
> > > and white. When the analysis is not showing any differne between the
> > > groups for "projfrac 0.5" and showing differnce for "projfrac 0" that
> > > means the differnce between the groups is deeper and closer to white
> > > matter. Is this correct?
> > > Thank you for any input and clarification!
> > > Bests,
> > > John
> > > *Sent:* Tuesday, January 10, 2017 at 10:51 AM
> > > *From:* "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
> > > *To:* freesurfer@nmr.mgh.harvard.edu
> > > *Subject:* Re: [Freesurfer] surface based analysis (projfrac)
> > >
> > > When you say in the corpus callosum, do you mean in WM? The
> > > surface-based analysis is only for cortical GM. If you mean in GM near
> > > the CC, then the analysis is appropriate. The projfrac parameter sets
> > > the sampling location between the white and pial surfaces where 0.5
> > > means half way.
> > >
> > > On 1/10/17 8:07 AM, John Anderson wrote:
> > >
> > > Dear FS experts,
> > > I am working on surface based analysis using freesurfer. I want to
> > > inquire about the flag "projfrac" in the command "mris_preproc"
> > > I ran voxel wise analysis including the same subjects. I found
> > > differnce between the groups in areas close to the corpus
> > > callosum. I want to get the same results using surface based
> > > analysis. If I use the projfrac=0.5 is this able to show the same
> > > results that I got in voxel wise analysis at the level of the
> > > corpus callosum. Do I need to use differnt n

Re: [Freesurfer] surface based analysis (projfrac)

2017-01-13 Thread John Anderson

Thank you very much Doug,

Kindly, do you suggest me any steps to avoid patial volume effects in surface based analyses ?
 

Best,
John 


 

Sent: Friday, January 13, 2017 at 12:21 PM
From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] surface based analysis (projfrac)



On 01/12/2017 05:20 PM, John Anderson wrote:
> Thank you very much Doug and thank you for briniging the issue of
> "partial volume effect " to my attention. Kindly, I have one last
> question.
> I found in wiki that the default values for projfrc value are between
> 0 and 1. Are there negative values? I mean for example "-2, -1, 0 , 1,
> 2 ", In other words, less than zero means the surface based analysis
> is running at a lower level of the white matter.
Yes
> Can the issue of the partial volume effect be avoided by using larger
> numbers for "projfrac" ?
No, PVEs can't be avoided that way.
> Bests,
> John
> *Sent:* Thursday, January 12, 2017 at 5:08 PM
> *From:* "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] surface based analysis (projfrac)
> yes, that is correct. However, understand that there might only be a
> difference of 1mm between those two locations, so it could easily be a
> partial volume effect
>
>
> On 01/11/2017 08:50 AM, John Anderson wrote:
> > Thank you Doug,
> > Exactly! I meant GM near the CC.
> > When I used "projfrac=0.5 " there was no differnce between the groups
> > at "cwp 0.05", and when I changed the "projfrac to 0" I got
> > significant differnce between the groups in specific areas at "cwp
> > 0.01". Kindly, how can this be explained? I highly appreciate if you
> > help me to understand this point:
> > For "projfrac =0" I expect the surface based analysis to
> > be running close to white matter. Right? and when I used
> > "projfrac=0.5" the analysis is running in the middle area between pial
> > and white. When the analysis is not showing any differne between the
> > groups for "projfrac 0.5" and showing differnce for "projfrac 0" that
> > means the differnce between the groups is deeper and closer to white
> > matter. Is this correct?
> > Thank you for any input and clarification!
> > Bests,
> > John
> > *Sent:* Tuesday, January 10, 2017 at 10:51 AM
> > *From:* "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
> > *To:* freesurfer@nmr.mgh.harvard.edu
> > *Subject:* Re: [Freesurfer] surface based analysis (projfrac)
> >
> > When you say in the corpus callosum, do you mean in WM? The
> > surface-based analysis is only for cortical GM. If you mean in GM near
> > the CC, then the analysis is appropriate. The projfrac parameter sets
> > the sampling location between the white and pial surfaces where 0.5
> > means half way.
> >
> > On 1/10/17 8:07 AM, John Anderson wrote:
> >
> > Dear FS experts,
> > I am working on surface based analysis using freesurfer. I want to
> > inquire about the flag "projfrac" in the command "mris_preproc"
> > I ran voxel wise analysis including the same subjects. I found
> > differnce between the groups in areas close to the corpus
> > callosum. I want to get the same results using surface based
> > analysis. If I use the projfrac=0.5 is this able to show the same
> > results that I got in voxel wise analysis at the level of the
> > corpus callosum. Do I need to use differnt number for projfrac ?
> > Thank you for any advice.
> >
> > Best,
> > John
> >
> > ___
> > Freesurfer mailing list
> > 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 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.
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@

Re: [Freesurfer] surface based analysis (projfrac)

2017-01-11 Thread John Anderson

Thank you Doug,

Exactly! I meant GM near the CC.

When I used "projfrac=0.5 " there was no differnce between the groups at "cwp 0.05", and when I changed the "projfrac to 0" I got significant differnce between the groups in specific areas at "cwp 0.01". Kindly, how can this be explained? I highly appreciate if you help me to understand this point:

For "projfrac =0" I expect the surface based analysis to be running close to white matter. Right? and when I used "projfrac=0.5" the analysis is running in the middle area between pial and white. When the analysis is not showing any differne between the groups for "projfrac 0.5" and showing differnce for "projfrac 0" that means the differnce between the groups is deeper and closer to white matter. Is this correct?

Thank you for any input and clarification!

Bests,
John

Sent: Tuesday, January 10, 2017 at 10:51 AM
From: "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] surface based analysis (projfrac)

When you say in the corpus callosum, do you mean in WM? The surface-based analysis is only for cortical GM. If you mean in GM near the CC, then the analysis is appropriate. The projfrac parameter sets the sampling location between the white and pial surfaces where 0.5 means half way.

On 1/10/17 8:07 AM, John Anderson wrote:

Dear FS experts,

I am working on surface based analysis using freesurfer. I want to inquire about the flag "projfrac" in the command "mris_preproc"

I ran voxel wise analysis including the same subjects. I found differnce between the groups in areas close to the corpus callosum. I want to get the same results using surface based analysis. If I use the projfrac=0.5 is this able to show the same results that I got in voxel wise analysis at the level of the corpus callosum. Do I need to use differnt number for projfrac ?

Thank you for any advice.

Best,
John

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Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] surface based analysis (projfrac)

2017-01-12 Thread John Anderson

Thank you very much Doug and thank you for briniging the issue of "partial volume effect " to my attention. Kindly, I have one last question.

 

I found in wiki that the default values for projfrc value are between 0 and 1. Are there negative values? I mean for example "-2, -1, 0 , 1, 2 ", In other words, less than zero means the surface based analysis is running at a lower level of the white matter. Can the issue of the partial volume effect be avoided by using larger numbers for "projfrac" ?

 

Bests,
John 

 
 

Sent: Thursday, January 12, 2017 at 5:08 PM
From: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] surface based analysis (projfrac)

yes, that is correct. However, understand that there might only be a
difference of 1mm between those two locations, so it could easily be a
partial volume effect


On 01/11/2017 08:50 AM, John Anderson wrote:
> Thank you Doug,
> Exactly! I meant GM near the CC.
> When I used "projfrac=0.5 " there was no differnce between the groups
> at "cwp 0.05", and when I changed the "projfrac to 0" I got
> significant differnce between the groups in specific areas at "cwp
> 0.01". Kindly, how can this be explained? I highly appreciate if you
> help me to understand this point:
> For "projfrac =0" I expect the surface based analysis to
> be running close to white matter. Right? and when I used
> "projfrac=0.5" the analysis is running in the middle area between pial
> and white. When the analysis is not showing any differne between the
> groups for "projfrac 0.5" and showing differnce for "projfrac 0" that
> means the differnce between the groups is deeper and closer to white
> matter. Is this correct?
> Thank you for any input and clarification!
> Bests,
> John
> *Sent:* Tuesday, January 10, 2017 at 10:51 AM
> *From:* "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] surface based analysis (projfrac)
>
> When you say in the corpus callosum, do you mean in WM? The
> surface-based analysis is only for cortical GM. If you mean in GM near
> the CC, then the analysis is appropriate. The projfrac parameter sets
> the sampling location between the white and pial surfaces where 0.5
> means half way.
>
> On 1/10/17 8:07 AM, John Anderson wrote:
>
> Dear FS experts,
> I am working on surface based analysis using freesurfer. I want to
> inquire about the flag "projfrac" in the command "mris_preproc"
> I ran voxel wise analysis including the same subjects. I found
> differnce between the groups in areas close to the corpus
> callosum. I want to get the same results using surface based
> analysis. If I use the projfrac=0.5 is this able to show the same
> results that I got in voxel wise analysis at the level of the
> corpus callosum. Do I need to use differnt number for projfrac ?
> Thank you for any advice.
>
> Best,
> John
>
> ___
> Freesurfer mailing list
> 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 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.
>
>
> ___
> 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: 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/

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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.

[Freesurfer] surface based analysis (projfrac)

2017-01-10 Thread John Anderson

Dear FS experts,

I am working on surface based analysis using freesurfer. I want to inquire about the flag "projfrac" in the command "mris_preproc"

 

I ran voxel wise analysis including the same subjects. I found differnce between the groups in areas close to the corpus callosum. I want to get the same results using surface based analysis. If I use the projfrac=0.5 is this able to show the same results that I got in voxel wise analysis at the level of the corpus callosum. Do I need to use differnt number for projfrac ?

 

Thank you for any advice.


 

Best,
John
___
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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.

[Freesurfer] Moving fa map from talairach to MNI

2017-03-27 Thread John Anderson

Hi Freesurfer experts,
I followed "dt_recon" pipeline 
https://surfer.nmr.mgh.harvard.edu/fswiki/dt_recon to analyze DTI data. The 
analysis ran smoothly without any issues.
I want to inquire waht is the correct method to move "fa-tal.nii" to MNI152_2mm
Is this command correct"?
mri_vol2vol --mov fa-tal.nii --targ MNI152_2mm --regheader --o fa-MNI 
--no-save-reg

Thank you for any advice
John

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[Freesurfer] Volume vs cortical thickness

2017-04-10 Thread John Anderson

Dear Freesurfer experts,
I highly appreciate if anybody clarify how Freesurfer calculate cortical 
thickness and gray matter volume.
If the cortical thickness of e.g. precentral gurus is measured as the closest 
distance from the gray-white boundary to the gray-CSF boundray at each vertex 
on the tessellated surface (Fischl and Dale. 2000).
How the gray matter volume for the precentral gyrus was measured?

Thank you for any clarification!

John___
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Re: [Freesurfer] manual edits

2017-04-13 Thread John Anderson

Hi David,
Thank you for the feedback! I followed your advice's and everything has been 
resolved. Highly appreciated!

Cheers,
John

Sent with [ProtonMail](https://protonmail.com) Secure Email.

 Original Message 
Subject: Re: [Freesurfer] manual edits
Local Time: April 12, 2017 11:04 AM
UTC Time: April 12, 2017 3:04 PM
From: seman...@nyspi.columbia.edu
To: John Anderson <john.ande...@protonmail.com>, freesurfer@nmr.mgh.harvard.edu 
<freesurfer@nmr.mgh.harvard.edu>

Hi John,

Yes understanding how freesurfer deals with edits can be a bit confusing. I 
have a lot of experience doing edits to the wm.mgz and brainmask.mgz for cross 
sectional data in Freesurfer 5.3 so perhaps I can help.

Recon-all is basically a script which runs a series of about 25 or so 
processing steps in a defined sequence. The software generally will be able to 
recognize when an edit has been done at a particular intervention point and 
will take those edits into account when running that step unless you 
specifically instruct it not to.

The most common types of edits are edits to the wm.mgz to fix white matter 
defects and tissue incorrectly identified as white matter, and edits to the 
brainmask.mgz to fix cases where the skull strip is insufficient to prevent 
dura and other non-cortical tissue from making it into the gray matter/pial 
surfaces. White matter edits need to be done directly on the wm.mgz and gray 
matter/skull strip edits need to be done on the brainmask.mgz. Editing those 
two files and saving them directly in freeview is sufficient to register those 
edits for recon-all.

If you have edited only the brainmask.mgz, it is sufficient to run 
–autorecon-pial since the white matter surfaces will not need to be 
regenerated. If you have edited the wm.mgz, you must run –autorecon2-wm (or 
–autorecon2-cp if you used control points as well as white matter edits). If 
you have edited both the brainmask.mgz and the wm.mgz, then you only need to 
run –autorecon2-wm since the pial surfaces will be regenerated taking into 
account the brainmask.mgz edits as part of that workflow. Keep in mind that you 
still need to run –autorecon3 to complete the reprocessing of these data 
(-autorecon-pial includes the steps from –autorecon3) but that can be done when 
you are happy with your final surfaces if you want to save processing time on 
iterative edits.

Here is the wiki page referring to edits: 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData

I hope this is helpful.

Best,

David P. Semanek, HCISPP

Research Technician, Posner Lab

Division of Child and Adolescent Psychiatry

Columbia University Medical Center

New York State Psychiatric Institute

1051 Riverside Drive, Pardes Bldg. Rm. 2424

New York, NY 10032

PH: (646) 774-5885

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From:  John Anderson <john.ande...@protonmail.com>
Reply-To: John Anderson <john.ande...@protonmail.com>
Date: Wednesday, April 12, 2017 at 6:45 AM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] manual edits

Dear Freesurfer experts,

I am not an expert in manual edits, so I highly appreciate any feedback 
regarding the issues in my questions below. I ran the following command line 
“recon-all -s subjid -all” on T1 image for one of the subjects. when reviewing 
the output images (i.e. wm.mgz, brainmask.mgz) I found issues as attached.

Attached is an output of the command: "Freeveiw orig.mgz wmparc.mgz wm.mgz"

1. When I reviewed “wm.mgz” I see interactions between the white matter (wm), 
and the cortex (yellow arrows). To fix this, I edited “wm.mgz” by removing the 
wm voxels from the cortex, and the data was saved in the file “wm.seg.mgz”

2. I found many holes in many slices similar to the (black arrow). I filled all 
these holes. The data saved in “wm.seg.mgz”

3. I fixed some issues related to dura and bad skullstipping

Then I ran the command:

“recon-all -autorecon2-wm -autorecon3 -subjid ” which output the file 
“brain.finalsurfs.mgz”

and the command

“recon-all -autorecon-pial -subjid ”

Now, I want to understand where Freesurfer implement the new edits? Which files 
will be used as the main files that include the new edits. Logically, the edits 
must be implemented in "wm.mgz" and "brainmask.mgz". What confuses me is when I 
open orig.mgz wm.mgz and brainmask.mgz in freesview. I see the original 
non-edited files

[Freesurfer] White matter atrophy

2017-04-20 Thread John Anderson

Dear Freesurfer experts,
I know how to do cortical thickness group analysis using Freesurfer, also I 
know how to use Qdec to compare groups regarding gray matter volume 
differences, cortical thickness, curvatures, area,... etc.
I am wondering if there is any way in Freesurfer to study the difference in 
white matter volume between two groups?

I highly appreciate any suggestion!
John___
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Re: [Freesurfer] White matter atrophy

2017-04-20 Thread John Anderson

Thank you a.y,
I am sorry if my question was not clear enough!
In Qdec/ tab "design" the user have the choice to choose the analyses that he 
wants to conduct on aseg,mgz, wmparc.mgz or aparc+aseg.mgz.
These atlases report white and gray matter volumes.

in Qdec, if I choose volume from the dropdown menu "measure" under the tab 
"design" to conduct surface based analyses. Dose this means surface based 
analyses for gray matter volume or white matter volume?
In aseg you can find both volumes for whit matter and gray matter. so which 
volume is Qdec referring to? If Qdec compute surface based analysis of gray 
matter volume, then how can I do surface based analysis using the whiate matter 
volume of the parcellates instead of the gray matter voluem of the parcellaets? 
Is this feasible

J.

 Original Message 
Subject: RE: [Freesurfer] White matter atrophy
Local Time: April 20, 2017 10:04 AM
UTC Time: April 20, 2017 2:04 PM
From: ayend...@mgh.harvard.edu
To: John Anderson <john.ande...@protonmail.com>, Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu>

Hi John - Unless someone else has a better idea, the aseg (subcortical 
segmentation) contains left and right cerebral and cerebellar white matter 
labels. You can look at the ROI analysis tutorial for how to extract stats from 
aseg labels.

Best,
a.y

---

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of John Anderson 
[john.ande...@protonmail.com]
Sent: Thursday, April 20, 2017 7:42 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] White matter atrophy

Dear Freesurfer experts,
I know how to do cortical thickness group analysis using Freesurfer, also I 
know how to use Qdec to compare groups regarding gray matter volume 
differences, cortical thickness, curvatures, area,... etc.
I am wondering if there is any way in Freesurfer to study the difference in 
white matter volume between two groups?

I highly appreciate any suggestion!
John

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[Freesurfer] Reslice image

2017-03-03 Thread John Anderson

Dear experts:
I have nifti file with 96 slices. I want to re-slice it to form nifti file with 
200 slice. Are there any tools in Freesurfer that can help to achieve this?

Many thanks for any suggestion

John___
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Re: [Freesurfer] FW: MPRAGE images dimension different {Disarmed}

2017-04-03 Thread John Anderson

Dear Dhaval,
when your recon-all finishs the process you will get images 256^3 and 1mm 
isootropic.
The you can simply follow the instructions mentioned here 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat to send your 
images back to native space.

All the best,
John

>

> On Mon, Apr 3, 2017 at 4:35 PM, Dhaval Shah  wrote:
> Hi All,
>
> I am new and a very basic question about freesurfer processing.
>
> I ran recon-all on a high res-T1 image(128x128x80 matrix size), but
> after recon-all the folder mri contains resulted (brain.mgz and
> orig.mgz) T1 images has (127x128x128 matrix size).
>
> 1) how come the dimensions are changed? Is it normal?
> 2) how can i keep the dimensions same as the original?
> 3) is it possible that i will always get the higher matrix size image
> data?
>
> for simplicity, i converted resulted orig.mgz to nii format and loaded
> it in to fslview. Please find the first image (Original) and the
> second image (after recon-all but orig.mgz).
>
> Your help is greatly appreciated.
>
> --
> Kind regards,
> Dhaval Shah
>
> MRI Research fellow,MRI Physicist,Clinical Trial Research Staff
> Buffalo Neuroimaging Analysis Center
> State University of New York at Buffalo
> Department of Neurology
> 100 High St., D-2, Buffalo, NY 14203
> [MailScanner has detected a possible fraud attempt from "ds...@bnac.net" 
> claiming to be MailScanner has detected a possible fraud attempt from 
> "ds...@bnac.net" claiming to be 
> ds...@bnac.net//http://mbl.bnac.net](http://ds...@bnac.net/http:/mbl.bnac.net)
>
>
>
>
> --
> Kind regards,
> Dhaval Shah
>
> MRI Research fellow,MRI Physicist,Clinical Trial Research Staff
> Buffalo Neuroimaging Analysis Center
> State University of New York at Buffalo
> Department of Neurology
> 100 High St., D-2, Buffalo, NY 14203
> [MailScanner has detected a possible fraud attempt from "ds...@bnac.net" 
> claiming to be MailScanner has detected a possible fraud attempt from 
> "ds...@bnac.net" claiming to be 
> ds...@bnac.net//http://mbl.bnac.net](http://ds...@bnac.net/http:/mbl.bnac.net)
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>

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--

Kind regards,

Dhaval Shah

MRI Research fellow,MRI Physicist,Clinical Trial Research Staff

Buffalo Neuroimaging Analysis Center

State University of New York at Buffalo

Department of Neurology

100 High St., D-2, Buffalo, NY 14203

ds...@bnac.net
//
http://mbl.bnac.net___
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[Freesurfer] FSFAST (plot-twf-sess)

2017-07-31 Thread John Anderson

Dear Dr Greeve,
I am new to FSFAST so I highly appreciate your response.
I have resting state fMRI data and I am following the steps as reported in wiki.
My questions is regarding motion evaluation. The attached figure is an output 
of "plot-twf-sess".
1. Given the plotted data can we say that including run 003 is more reliable 
that all the other runs?
2. In the attached figure the command "plot-twf-sess" provide the maximum and 
minimum motion for every run on Y axes. I am wondering if there is any way to 
create a cutoff value of motion parameters for all the runs in the study were 
data can be included/excluded depending on lower/upper than this cutoff?
Thank you for help
John___
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