Re: [Freesurfer] White matter volume

[Alshikho, Mohamad J.]

Thanks a lot!!


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Friday, October 31, 2014 11:49 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] White matter volume

yes. Partial volume correction helps both accuracy and repeatability. You
can certainly use our (partial-volume) corrected WM volumes and the FA
from FSL if you want

cheers
Bruce
On Fri, 31 Oct 2014, Alshikho, Mohamad J. wrote:

> Hi Bruce,
> Actually I am totally confused and this is the reason for my question!
> What is the best  and trusted approach in this case?
> I want to  study the relationship between the FA and the right and left 
> hemispheric white matter. I generated the DTI metrics and volume using FSL. I 
> am sure that the calculated white matter volume in FSL is not correct because 
> it is closer to what I am thinking about.
> in this case can I use and is it valid if I use the volume from the output of 
> Freesurfer  and the metrics from FSL in my analsysis?
>
> Thanks
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Friday, October 31, 2014 11:35 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] White matter volume
>
> Hi Mohamad
>
> this is probably due to the partial-volume correction that we typically
> compute when we estimate volumes in the stats files.
>
> cheers
> Bruce
> On Fri, 31 Oct 2014,
> Alshikho, Mohamad J. wrote:
>
>> Thanks Doug,
>> In order to improve my understanding for the analysis that I am working on 
>> and in the process of my learning I am tring to calculate the volume in many 
>> different ways. Actually It is very easy, simple  and possible to use the 
>> numbers mentioned in aseg.stats but what if we got different results when we 
>> use different methods?
>> I caclated the right and left hemispheric white matter volume in FSL using a 
>> mask deriverd from the T1 segmentation in Freesurfer "lh.dwhite.mgz , 
>> rh.dwhite.mgz" then I binarized those masks and I registered them to my T1 
>> then I used the command line "fslstats  -k my mask -V"  What surprised 
>> me is that the volume was totally different from the one mentioned in 
>> aseg.stats (attached)
>>
>> I highly appreciate any advice.
>> looking forward to learn from you
>> Mohamad
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Friday, October 31, 2014 11:04 AM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] White matter volume
>>
>> I would suggest using the value in aseg.stats. Is that not possible?
>>
>> On 10/31/2014 10:06 AM, Alshikho, Mohamad J. wrote:
>>> Thanks Doug!
>>> So do you suggest to use "lh.dwhite.mgz , rh.dwhite.mgz" the output of 
>>> mris_volmask?
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>>> [gr...@nmr.mgh.harvard.edu]
>>> Sent: Friday, October 31, 2014 10:02 AM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] White matter volume
>>>
>>> The aseg is not surface-based and will not be as accurate
>>> doug
>>>
>>> On 10/31/2014 09:14 AM, Alshikho, Mohamad J. wrote:
 Hi Bruce,
 I wanted to calculate the right and left hemispheric white matter
 volume using a mask.
 Is there any difference between "lh.dwhite.mgz , rh.dwhite.mgz" (the
 outputs of mris_volmmask after binarize them) and the right and left
 hemispheric white matter masks from aseg.mgz atlas (the output of
 mri_binarize command line)?
 I am asking this question because those masks gave me different
 estimation for the volume?

 Thanks!
 Mohamad


 ___
 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/
>>>
>>> ___
>>> 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
>>>
>>>

Re: [Freesurfer] White matter volume

[Bruce Fischl]

yes. Partial volume correction helps both accuracy and repeatability. You 
can certainly use our (partial-volume) corrected WM volumes and the FA 
from FSL if you want

cheers
Bruce
On Fri, 31 Oct 2014, Alshikho, Mohamad J. wrote:

> Hi Bruce,
> Actually I am totally confused and this is the reason for my question!
> What is the best  and trusted approach in this case?
> I want to  study the relationship between the FA and the right and left 
> hemispheric white matter. I generated the DTI metrics and volume using FSL. I 
> am sure that the calculated white matter volume in FSL is not correct because 
> it is closer to what I am thinking about.
> in this case can I use and is it valid if I use the volume from the output of 
> Freesurfer  and the metrics from FSL in my analsysis?
>
> Thanks
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Friday, October 31, 2014 11:35 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] White matter volume
>
> Hi Mohamad
>
> this is probably due to the partial-volume correction that we typically
> compute when we estimate volumes in the stats files.
>
> cheers
> Bruce
> On Fri, 31 Oct 2014,
> Alshikho, Mohamad J. wrote:
>
>> Thanks Doug,
>> In order to improve my understanding for the analysis that I am working on 
>> and in the process of my learning I am tring to calculate the volume in many 
>> different ways. Actually It is very easy, simple  and possible to use the 
>> numbers mentioned in aseg.stats but what if we got different results when we 
>> use different methods?
>> I caclated the right and left hemispheric white matter volume in FSL using a 
>> mask deriverd from the T1 segmentation in Freesurfer "lh.dwhite.mgz , 
>> rh.dwhite.mgz" then I binarized those masks and I registered them to my T1 
>> then I used the command line "fslstats  -k my mask -V"  What surprised 
>> me is that the volume was totally different from the one mentioned in 
>> aseg.stats (attached)
>>
>> I highly appreciate any advice.
>> looking forward to learn from you
>> Mohamad
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Friday, October 31, 2014 11:04 AM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] White matter volume
>>
>> I would suggest using the value in aseg.stats. Is that not possible?
>>
>> On 10/31/2014 10:06 AM, Alshikho, Mohamad J. wrote:
>>> Thanks Doug!
>>> So do you suggest to use "lh.dwhite.mgz , rh.dwhite.mgz" the output of 
>>> mris_volmask?
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>>> [gr...@nmr.mgh.harvard.edu]
>>> Sent: Friday, October 31, 2014 10:02 AM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] White matter volume
>>>
>>> The aseg is not surface-based and will not be as accurate
>>> doug
>>>
>>> On 10/31/2014 09:14 AM, Alshikho, Mohamad J. wrote:
 Hi Bruce,
 I wanted to calculate the right and left hemispheric white matter
 volume using a mask.
 Is there any difference between "lh.dwhite.mgz , rh.dwhite.mgz" (the
 outputs of mris_volmmask after binarize them) and the right and left
 hemispheric white matter masks from aseg.mgz atlas (the output of
 mri_binarize command line)?
 I am asking this question because those masks gave me different
 estimation for the volume?

 Thanks!
 Mohamad


 ___
 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/
>>>
>>> ___
>>> 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
>>>
>>>
>>
>> --
>> 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
>> Outg

Re: [Freesurfer] White matter volume

[Alshikho, Mohamad J.]

Hi Bruce,
Actually I am totally confused and this is the reason for my question!
What is the best  and trusted approach in this case? 
I want to  study the relationship between the FA and the right and left 
hemispheric white matter. I generated the DTI metrics and volume using FSL. I 
am sure that the calculated white matter volume in FSL is not correct because 
it is closer to what I am thinking about. 
in this case can I use and is it valid if I use the volume from the output of 
Freesurfer  and the metrics from FSL in my analsysis?

Thanks


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Friday, October 31, 2014 11:35 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] White matter volume

Hi Mohamad

this is probably due to the partial-volume correction that we typically
compute when we estimate volumes in the stats files.

cheers
Bruce
On Fri, 31 Oct 2014,
Alshikho, Mohamad J. wrote:

> Thanks Doug,
> In order to improve my understanding for the analysis that I am working on 
> and in the process of my learning I am tring to calculate the volume in many 
> different ways. Actually It is very easy, simple  and possible to use the 
> numbers mentioned in aseg.stats but what if we got different results when we 
> use different methods?
> I caclated the right and left hemispheric white matter volume in FSL using a 
> mask deriverd from the T1 segmentation in Freesurfer "lh.dwhite.mgz , 
> rh.dwhite.mgz" then I binarized those masks and I registered them to my T1 
> then I used the command line "fslstats  -k my mask -V"  What surprised me 
> is that the volume was totally different from the one mentioned in aseg.stats 
> (attached)
>
> I highly appreciate any advice.
> looking forward to learn from you
> Mohamad
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Friday, October 31, 2014 11:04 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] White matter volume
>
> I would suggest using the value in aseg.stats. Is that not possible?
>
> On 10/31/2014 10:06 AM, Alshikho, Mohamad J. wrote:
>> Thanks Doug!
>> So do you suggest to use "lh.dwhite.mgz , rh.dwhite.mgz" the output of 
>> mris_volmask?
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Friday, October 31, 2014 10:02 AM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] White matter volume
>>
>> The aseg is not surface-based and will not be as accurate
>> doug
>>
>> On 10/31/2014 09:14 AM, Alshikho, Mohamad J. wrote:
>>> Hi Bruce,
>>> I wanted to calculate the right and left hemispheric white matter
>>> volume using a mask.
>>> Is there any difference between "lh.dwhite.mgz , rh.dwhite.mgz" (the
>>> outputs of mris_volmmask after binarize them) and the right and left
>>> hemispheric white matter masks from aseg.mgz atlas (the output of
>>> mri_binarize command line)?
>>> I am asking this question because those masks gave me different
>>> estimation for the volume?
>>>
>>> Thanks!
>>> Mohamad
>>>
>>>
>>> ___
>>> 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/
>>
>> ___
>> 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
>>
>>
>
> --
> 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/
>
> ___
> 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/

Re: [Freesurfer] permission denied

[zkaufman]

Yes, please try running as root and get back when you have the chance.
This is a very odd issue and your results when running as root will
provide insight.

-Zeke

> Hi Z K,
>
> Yes I am sure as I have tried the same MPRGAE image on all 16 PCs. The one
> installed with the latest freesurfer version did not work while others
> finished the processing in a reasonable processing time and I got the
> results.
>
> Also, I have a PC at my office installed with the latest freesurfer
> version
> and it works fine. So I have two PCs installed with the latest Freesurfer
> (one of them which does not work is in the lab).
>
>
> To summarize:
> All PCs (16 PCs in the lab and 1 in my office) are installed with latest
> Ubuntu version 14.04 64 bits
> 15 PCs in the lab are installed with freesurfer 5.0.0 version
> 1 PC in the lab is installed with the latest freesurfer version (does not
> work, permission denied)
> 1 PC in my office is installed with the latest freesurfer version (works
> fine)
>
> All these PCs have Ubuntu 14.04 64bit installed on them.
>
>
>
> No, I am not using any vitual machine.
>
> Regarding the root user, I will try it on Sunday as I am away for a couple
> of days.
>
> Many thanks for your continuous support.
>
> Ali
>
>
>
>
> On Thu, Oct 30, 2014 at 6:34 PM, Z K  wrote:
>
>> Ali,
>>
>> First, are you ABSOLUTELY sure the PCs running freesurfer v5.0 are
>> working properly? I am under the impression that versions of freesurfer
>> pre-version 5.3 will not work on newer linux distributions?
>>
>>
>> In regards to your current permision denied issue... What happens if you
>> try and run tkmedit as root user? Also, you not using virtual machine
>> setup are you?
>>
>> -Zeke
>>
>> On 10/30/2014 06:27 AM, Ali Radaideh wrote:
>> > It does not work. This is really strange
>> >
>> > On Thu, Oct 30, 2014 at 12:53 AM, Z K > > > wrote:
>> >
>> > I beleive it should have a lower case X, as in:
>> >
>> > chmod -R a+x freesurfer/bin
>> >
>> > -Zeke
>> >
>> > On 10/28/2014 01:19 AM, Ali Radaideh wrote:
>> >  > Dear Douglas
>> >  >
>> >  > Thanks for your reply. unfortunatey I still get the same error.
>> > Here is
>> >  > the terminal output. Is there anything else I can do?
>> >  >
>> >  >  freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
>> 
>> >  > Setting up environment for FreeSurfer/FS-FAST (and FSL)
>> >  > FREESURFER_HOME   /usr/local/freesurfer
>> >  > FSFAST_HOME   /usr/local/freesurfer/fsfast
>> >  > FSF_OUTPUT_FORMAT nii.gz
>> >  > SUBJECTS_DIR  /usr/local/freesurfer/subjects
>> >  > MNI_DIR   /usr/local/freesurfer/mni
>> >  > FSL_DIR   /usr/local/fsl
>> >  > imaging@imaging-ThinkCentre-23:~$ tcsh
>> >  > imaging-ThinkCentre-23:~> tkmedit
>> >  > /usr/local/freesurfer/bin/tkmedit: Permission denied.
>> >  > imaging-ThinkCentre-23:~>
>> >  >
>> >  >
>> >  > On Mon, Oct 27, 2014 at 5:21 AM, Douglas Greve
>> >  > mailto:gr...@nmr.mgh.harvard.edu>
>> > > > >> wrote:
>> >  >
>> >  >
>> >  > Try chmod -R a+X freesurfer/bin
>> >  >
>> >  >
>> >  > On 10/26/14 1:57 PM, Ali Radaideh wrote:
>> >  >> Dear FreeSurfer users,
>> >  >>
>> >  >> I am using freesurfer on 16 PCs (Ubuntu 14.04 64 bit). One
>> > of the
>> >  >> PCs has the latest version of freesurfer 5.3.0 while the
>> others
>> >  >> have the version 5.0.0. The PC that is installed with the
>> latest
>> >  >> version freesurfer 5.3.0 does not allow me to run any
>> > command and
>> >  >> everytime I try a command such such as tkmedit i get the
>> > following
>> >  >> error
>> >  >> /usr/local/freesurfer/bin/tkmedit: permission denied.
>> >  >>
>> >  >> I have tried to change the permission settings
>> >  >> sudo chown -R imaging:imaging freesurfer
>> >  >>
>> >  >> but did not work.
>> >  >>
>> >  >> Any ideas why is this happening although I have done the
>> same
>> >  >> thing to other PCs and they are working fine.
>> >  >>
>> >  >> ​Thanks in advance,
>> >  >> Ali​
>> >  >>
>> >  >> --
>> >  >> /Ali M. Al-Radaideh. PhD
>> >  >> Assistant Professor
>> >  >> Head of Department of Medical Imaging
>> >  >> Vice Dean of the Faculty of Allied Health Sciences
>> >  >> The Hashemite University,
>> >  >> Zarqa, Jordan
>> >  >> W.phone +962 5 390 ext.5422, 5355, 5364
>> >  >> Email: ali.radai...@hu.edu.jo
>> >  > > >
>> >  >> /
>> >  >> /webpage:
>> http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/
>> >  >>
>> >  >>

Re: [Freesurfer] White matter volume

[Bruce Fischl]

Hi Mohamad

this is probably due to the partial-volume correction that we typically 
compute when we estimate volumes in the stats files.

cheers
Bruce
On Fri, 31 Oct 2014, 
Alshikho, Mohamad J. wrote:

> Thanks Doug,
> In order to improve my understanding for the analysis that I am working on 
> and in the process of my learning I am tring to calculate the volume in many 
> different ways. Actually It is very easy, simple  and possible to use the 
> numbers mentioned in aseg.stats but what if we got different results when we 
> use different methods?
> I caclated the right and left hemispheric white matter volume in FSL using a 
> mask deriverd from the T1 segmentation in Freesurfer "lh.dwhite.mgz , 
> rh.dwhite.mgz" then I binarized those masks and I registered them to my T1 
> then I used the command line "fslstats  -k my mask -V"  What surprised me 
> is that the volume was totally different from the one mentioned in aseg.stats 
> (attached)
>
> I highly appreciate any advice.
> looking forward to learn from you
> Mohamad
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Friday, October 31, 2014 11:04 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] White matter volume
>
> I would suggest using the value in aseg.stats. Is that not possible?
>
> On 10/31/2014 10:06 AM, Alshikho, Mohamad J. wrote:
>> Thanks Doug!
>> So do you suggest to use "lh.dwhite.mgz , rh.dwhite.mgz" the output of 
>> mris_volmask?
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Friday, October 31, 2014 10:02 AM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] White matter volume
>>
>> The aseg is not surface-based and will not be as accurate
>> doug
>>
>> On 10/31/2014 09:14 AM, Alshikho, Mohamad J. wrote:
>>> Hi Bruce,
>>> I wanted to calculate the right and left hemispheric white matter
>>> volume using a mask.
>>> Is there any difference between "lh.dwhite.mgz , rh.dwhite.mgz" (the
>>> outputs of mris_volmmask after binarize them) and the right and left
>>> hemispheric white matter masks from aseg.mgz atlas (the output of
>>> mri_binarize command line)?
>>> I am asking this question because those masks gave me different
>>> estimation for the volume?
>>>
>>> Thanks!
>>> Mohamad
>>>
>>>
>>> ___
>>> 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/
>>
>> ___
>> 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
>>
>>
>
> --
> 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/
>
> ___
> 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.

Re: [Freesurfer] White matter volume

[Douglas N Greve]

I would suggest using the value in aseg.stats. Is that not possible?

On 10/31/2014 10:06 AM, Alshikho, Mohamad J. wrote:
> Thanks Doug!
> So do you suggest to use "lh.dwhite.mgz , rh.dwhite.mgz" the output of 
> mris_volmask?
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Friday, October 31, 2014 10:02 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] White matter volume
>
> The aseg is not surface-based and will not be as accurate
> doug
>
> On 10/31/2014 09:14 AM, Alshikho, Mohamad J. wrote:
>> Hi Bruce,
>> I wanted to calculate the right and left hemispheric white matter
>> volume using a mask.
>> Is there any difference between "lh.dwhite.mgz , rh.dwhite.mgz" (the
>> outputs of mris_volmmask after binarize them) and the right and left
>> hemispheric white matter masks from aseg.mgz atlas (the output of
>> mri_binarize command line)?
>> I am asking this question because those masks gave me different
>> estimation for the volume?
>>
>> Thanks!
>> Mohamad
>>
>>
>> ___
>> 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/
>
> ___
> 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
>
>

-- 
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/

___
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.

Re: [Freesurfer] Longitudinal prediction

[Alex Hanganu]

I see. Thank you Doug !

Now I used the command lines from the qdec output in the terminal and I 
constructed the next contrasts using them as a starting point. Now the results 
seem more reliable and I can perform the Monte-Carlo with 5000 iterations.
 I'll verify them once again with LME.

Alex.

 

 On Friday, October 31, 2014 10:05 AM, Douglas N Greve 
 wrote:
   

 
--osgm is for one-sample group mean which is the simplest design 
possible. It is probably not appropriate for your design. If you have 
different inputs and different labels then you will get different results

On 10/30/2014 03:08 PM, Alex Hanganu wrote:
> Hi Martin,
>
> could you please confirm whether the glm analysis was correctly 
> performed ?
>
> the command line is:
> /mri_glmfit --glmdir DIR --y lh.thickness-pc1.stack.fwhm15.mgh 
> //--label lh.fsaverage.cortex.label //--fsgd FSGD_FILE --C 
> Contrast-010..0.mtx --surf fsaverage lh /
>
> I get results, but I when I do the same command for the analysis from 
> the 2-stage-model webpage, the results are different. For example, on 
> the webpage the cmd is:
> /mri_glmfit --osgm --glmdir DIR --y Y.mgh --label LABEL.label --surf 
> fsaverage lh/
>
> I tried to receive the same result with:
> /mri_glmfit --glmdir DIR --y Y.mgh //--label LABEL.label //--fsgd 
> FSGD_FILE --C Contrast-100...0.mtx --surf fsaverage lh /
>
> but the results are different. In this case, how can I be sure that 
> the first analysis was performed correctly ?
>
> the /fsgd/ file was constructed using the base-subjects and the values 
> were taken as in the "/cross/" file that is used by qdec.
>
> Thanks,
> Alex
>
>
>
>
> On Thursday, October 23, 2014 2:52 PM, Martin Reuter 
>  wrote:
>
>
> Hi Alex,
>
> you are not looking at a "one sample group mean" (osgd) so don't pass 
> that flag. Your design is probably something like
> 1 A other_co_vars_to_regress_out
> (these are column vectors).
>
> so contrast in that case would be [ 0 1 0... ]
>
> That should create all outputs. All of this is really cross sectional 
> analysis where the depending variable is simply the 'change in 
> thickness' instead of thickness itself. Take a look at the glm 
> tutorial on the wiki, which describes the process.
>
> Best, Martin
>
>
> On 10/23/2014 02:40 PM, Alex Hanganu wrote:
>> Hi Martin,
>>
>> thanks for confirming. I duplicated the parameter and got good 
>> results in qdec.
>>
>> I also tried to repeat the analysis with mri_glmfit but I can't 
>> manage to come to an end.
>> In order to analyse the correlation between pc1 and parameter 'A', it 
>> seems that I have to construct an fsgd file, that is different from 
>> the .qdec file included in the "long_mris_slopes" command. 
>> Nevertheless, after doing so (presumably all "Inputs" were attibuted 
>> to subject.long.base-time1 and subject.long.base-time2) I thought 
>> that a contrast is needed, yet the "--C" and the "--osgm" flags 
>> cannot be used together.
>> - How can the correlation between -pc1 and parameter 'A' be performed 
>> in this case ?
>>
>> Additionally, after performing the "mri_glmfit" described in the 
>> 2-stage-model page, in the tksurfer  how can I see the plot ? The 
>> y.fsgd file wasn't created. Is there another method ?
>>
>> Thanks,
>> Alex
>>
>>
>>
>>
>> Le mardi 21 octobre 2014 16h40, Martin Reuter 
>>   a 
>> écrit :
>>
>>
>> Hi Alex,
>>
>> you have to duplicate the parameter (it is basically fixed across 
>> time). If you put 0 for tp2, it will average the two values, which is 
>> not what you want. Otherwise I think it is the correct approach.
>>
>> Best, Martin
>>
>>
>> On 10/21/2014 04:31 PM, Alex Hanganu wrote:
>>> Dear Martin,
>>>
>>> thank you very much for your answer ! and thanks for all the details !
>>> - yes, we have exactly 2 time points in all subjects and the 
>>> parameter is a single number.
>>>
>>> In qdec - it seems that qdec table has to include the parameter 'A' 
>>> both at time 1 and at time 2 in order for "long_qdec_table" command 
>>> to create the "cross" file. I put a zero at time 2. In qdec design 
>>> we analyzed parameter 'A' with -pc1 and -spc. I'm not sure that this 
>>> is the correct approach.
>>>
>>> I'll continue with LME and mri_glmfit.
>>>
>>> Sincerely,
>>> Alex
>>>
>>>
>>> Le mardi 21 octobre 2014 9h19, Martin Reuter 
>>>   a 
>>> écrit :
>>>
>>>
>>> Hi Alex,
>>>
>>> the parameter is a single number that happens to be measured at time 
>>> 1 right, eg baseline age? Lets call that parameter 'A' for the 
>>> discussion below.  Also you have exactly 2 time points in all subjects?
>>>
>>> There is two alternatives:
>>>
>>> 1. Simple approach (2-stage-model): You compute the atrophy rate 
>>> (e.g. percent thickness change) on the cortex (long_mris_slopes) for 
>>> each subject. At this point you have 1 measure per subject and work 
>>> cross-sectionally. You can use qdec or mri_glmfit to correlate 'A' 
>>> (independent parameter) with t

Re: [Freesurfer] White matter volume

[Alshikho, Mohamad J.]

Thanks Doug! 
So do you suggest to use "lh.dwhite.mgz , rh.dwhite.mgz" the output of 
mris_volmask?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Friday, October 31, 2014 10:02 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] White matter volume

The aseg is not surface-based and will not be as accurate
doug

On 10/31/2014 09:14 AM, Alshikho, Mohamad J. wrote:
> Hi Bruce,
> I wanted to calculate the right and left hemispheric white matter
> volume using a mask.
> Is there any difference between "lh.dwhite.mgz , rh.dwhite.mgz" (the
> outputs of mris_volmmask after binarize them) and the right and left
> hemispheric white matter masks from aseg.mgz atlas (the output of
> mri_binarize command line)?
> I am asking this question because those masks gave me different
> estimation for the volume?
>
> Thanks!
> Mohamad
>
>
> ___
> 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/

___
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.

Re: [Freesurfer] Longitudinal prediction

[Douglas N Greve]

--osgm is for one-sample group mean which is the simplest design 
possible. It is probably not appropriate for your design. If you have 
different inputs and different labels then you will get different results

On 10/30/2014 03:08 PM, Alex Hanganu wrote:
> Hi Martin,
>
> could you please confirm whether the glm analysis was correctly 
> performed ?
>
> the command line is:
> /mri_glmfit --glmdir DIR --y lh.thickness-pc1.stack.fwhm15.mgh 
> //--label lh.fsaverage.cortex.label //--fsgd FSGD_FILE --C 
> Contrast-010..0.mtx --surf fsaverage lh /
>
> I get results, but I when I do the same command for the analysis from 
> the 2-stage-model webpage, the results are different. For example, on 
> the webpage the cmd is:
> /mri_glmfit --osgm --glmdir DIR --y Y.mgh --label LABEL.label --surf 
> fsaverage lh/
>
> I tried to receive the same result with:
> /mri_glmfit --glmdir DIR --y Y.mgh //--label LABEL.label //--fsgd 
> FSGD_FILE --C Contrast-100...0.mtx --surf fsaverage lh /
>
> but the results are different. In this case, how can I be sure that 
> the first analysis was performed correctly ?
>
> the /fsgd/ file was constructed using the base-subjects and the values 
> were taken as in the "/cross/" file that is used by qdec.
>
> Thanks,
> Alex
>
>
>
>
> On Thursday, October 23, 2014 2:52 PM, Martin Reuter 
>  wrote:
>
>
> Hi Alex,
>
> you are not looking at a "one sample group mean" (osgd) so don't pass 
> that flag. Your design is probably something like
> 1 A other_co_vars_to_regress_out
> (these are column vectors).
>
> so contrast in that case would be [ 0 1 0... ]
>
> That should create all outputs. All of this is really cross sectional 
> analysis where the depending variable is simply the 'change in 
> thickness' instead of thickness itself. Take a look at the glm 
> tutorial on the wiki, which describes the process.
>
> Best, Martin
>
>
> On 10/23/2014 02:40 PM, Alex Hanganu wrote:
>> Hi Martin,
>>
>> thanks for confirming. I duplicated the parameter and got good 
>> results in qdec.
>>
>> I also tried to repeat the analysis with mri_glmfit but I can't 
>> manage to come to an end.
>> In order to analyse the correlation between pc1 and parameter 'A', it 
>> seems that I have to construct an fsgd file, that is different from 
>> the .qdec file included in the "long_mris_slopes" command. 
>> Nevertheless, after doing so (presumably all "Inputs" were attibuted 
>> to subject.long.base-time1 and subject.long.base-time2) I thought 
>> that a contrast is needed, yet the "--C" and the "--osgm" flags 
>> cannot be used together.
>> - How can the correlation between -pc1 and parameter 'A' be performed 
>> in this case ?
>>
>> Additionally, after performing the "mri_glmfit" described in the 
>> 2-stage-model page, in the tksurfer  how can I see the plot ? The 
>> y.fsgd file wasn't created. Is there another method ?
>>
>> Thanks,
>> Alex
>>
>>
>>
>>
>> Le mardi 21 octobre 2014 16h40, Martin Reuter 
>>   a 
>> écrit :
>>
>>
>> Hi Alex,
>>
>> you have to duplicate the parameter (it is basically fixed across 
>> time). If you put 0 for tp2, it will average the two values, which is 
>> not what you want. Otherwise I think it is the correct approach.
>>
>> Best, Martin
>>
>>
>> On 10/21/2014 04:31 PM, Alex Hanganu wrote:
>>> Dear Martin,
>>>
>>> thank you very much for your answer ! and thanks for all the details !
>>> - yes, we have exactly 2 time points in all subjects and the 
>>> parameter is a single number.
>>>
>>> In qdec - it seems that qdec table has to include the parameter 'A' 
>>> both at time 1 and at time 2 in order for "long_qdec_table" command 
>>> to create the "cross" file. I put a zero at time 2. In qdec design 
>>> we analyzed parameter 'A' with -pc1 and -spc. I'm not sure that this 
>>> is the correct approach.
>>>
>>> I'll continue with LME and mri_glmfit.
>>>
>>> Sincerely,
>>> Alex
>>>
>>>
>>> Le mardi 21 octobre 2014 9h19, Martin Reuter 
>>>   a 
>>> écrit :
>>>
>>>
>>> Hi Alex,
>>>
>>> the parameter is a single number that happens to be measured at time 
>>> 1 right, eg baseline age? Lets call that parameter 'A' for the 
>>> discussion below.  Also you have exactly 2 time points in all subjects?
>>>
>>> There is two alternatives:
>>>
>>> 1. Simple approach (2-stage-model): You compute the atrophy rate 
>>> (e.g. percent thickness change) on the cortex (long_mris_slopes) for 
>>> each subject. At this point you have 1 measure per subject and work 
>>> cross-sectionally. You can use qdec or mri_glmfit to correlate 'A' 
>>> (independent parameter) with the thickness change (dependent 
>>> variable). This is OK if you have the same number of time points and 
>>> the same time distance in all subjects. Details here:
>>> https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel
>>>
>>> 2. Better approach: use Linear Mixed Effects models (we have matlab 
>>> tools for that). This model is more flexible (different many

Re: [Freesurfer] White matter volume

[Douglas N Greve]

The aseg is not surface-based and will not be as accurate
doug

On 10/31/2014 09:14 AM, Alshikho, Mohamad J. wrote:
> Hi Bruce,
> I wanted to calculate the right and left hemispheric white matter 
> volume using a mask.
> Is there any difference between "lh.dwhite.mgz , rh.dwhite.mgz" (the 
> outputs of mris_volmmask after binarize them) and the right and left 
> hemispheric white matter masks from aseg.mgz atlas (the output of 
> mri_binarize command line)?
> I am asking this question because those masks gave me different 
> estimation for the volume?
>
> Thanks!
> Mohamad
>
>
> ___
> 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/

___
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] White matter volume

[Alshikho, Mohamad J.]

Hi Bruce,
I wanted to calculate the right and left hemispheric white matter volume using 
a mask.
Is there any difference between "lh.dwhite.mgz , rh.dwhite.mgz" (the outputs of 
mris_volmmask after binarize them) and the right and left hemispheric white 
matter masks from aseg.mgz atlas (the output of mri_binarize command line)?
I am asking this question because those masks gave me different estimation for 
the volume?

Thanks!
Mohamad
___
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.