Re: [Freesurfer] Measuring cortical thickness

[Bruce Fischl]

Hi Vasudev

no, there is no alternative. Computing resources are cheap these days. 
Most cluster would let you run all your subjects in a single night.


cheers
Bruce
On Thu, 
14 Jul 2016, Dev vasu wrote:



 

Dear Sir / madam,


I have 50 subjects (25 healthy controls and 25 patients with BLVP) , I would
like to know how could i generate cortical thickness maps for multi subject
group analysis.

The initial pre-processing with recon-all takes several hours for single
subject, is there any alternate way to approach this problem in a limited
amount of time?.


Any help would be greatly appreciated.


Thanks
Vasudev


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[Freesurfer] Measuring cortical thickness

[Dev vasu]

Dear Sir / madam,


I have 50 subjects (25 healthy controls and 25 patients with BLVP) , I
would like to know how could i generate cortical thickness maps for multi
subject group analysis.

The initial pre-processing with recon-all takes several hours for single
subject, is there any alternate way to approach this problem in a limited
amount of time?.


Any help would be greatly appreciated.


Thanks
Vasudev
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Re: [Freesurfer] Measuring cortical thickness at a specific location

[pfotiad]

Hi Bruce,

Thanks again for your help so far. I had a few follow up questions:

1) As far as mapping the average thickness to fsaverage coords, when I was
constructing the average thickness map I used mris_preproc with --target
fsaverage (and then mri_concat), so it's already in fsaverage coordinates
right? Or do I need to apply mri_surf2surf?

2) I used read_curv to load it into matlab which gives a  matrix
where I'm assuming that n is the number of total vertices of the cortex,
right?

3) Concerning the binning in matlab, I know how to do it in the order of
increasing vertex number, but I had trouble incorporating the [xyz]
fsaverage coordinates. Is there a way to rearrange the matrix (that is the
result of read_curv) into another matrix where the thickness values are
sorted based on the fsaverage coordinates?

Best,
Panos



> Hi Panos
>
> no, mris_anatomical_stats won't do it. I would map the average thickness
> to fsaverage coords, then load that into matlab and go from there using
> the [xyz] coords of fsaverage for the binning, which is pretty much
> MNI305
>
> cheers
> Bruce
> On Tue, 13 May 2014, pfot...@nmr.mgh.harvard.edu wrote:
>
>> Hi Bruce,
>>
>> Sorry, I had a last follow up question. I just realized that the
>> resulting
>> bins will be in the fsaverage space, and hence I wouldn't be able to use
>> mris_anatomical_stats to calculate the average thickness of the bins,
>> since the fsaverage "subject" does not have a wm.mgz file. Did you have
>> another way in mind to calculate the thickness of each bin, or do you
>> believe that mris_anatomical stats should do the trick with a specific
>> flag?
>>
>> Thanks a ton,
>> Panos
>>
>>> Hi Bruce,
>>>
>>> I see, that's really helpful, thank you!
>>>
>>> Best,
>>> Panos
>>>
>>>
 Hi Panos

 I would make an average thickness map in fsaverage space, then in
 matlab
 divvy up the a-p direction into bins (say 100 of them) and compute the
 average in each bin based on the a/p coordinate

 cheers
 Bruce
 On Tue, 13 May 2014,
 pfot...@nmr.mgh.harvard.edu wrote:

> Hi Bruce,
>
> Just to clarify, when you say "average the thickness along each A/P
> coordinate" do you mean by looking up at the average cortical
> thickness
> of
> each parcellation and then calculating their average from P->A, or is
> there another way to find the average thickness of each slice and
> then
> see
> how that average changes from P->A?
> Thanks again for your time,
> Panos
>
>> I see. Then measure the thickness normally, then see how it changes
>> in
>> those directions. You could average the thickness along each A/P
>> coordinate
>> - that wouldn't be a problem. You just don't want to measure it that
>> way
>>
>> cheers
>> Bruce
>>
>>
>> On Mon, 12 May 2014,
>> pfot...@nmr.mgh.harvard.edu wrote:
>>
>>> Hi Bruce,
>>>
>>> Thank you for your reply. I was interested in looking how the
>>> thickness
>>> changes from the posterior to the anterior side of the brain and
>>> vice
>>> versa (the thickness gradient).
>>>
>>> Thank you again for your time!
>>> Panos
>>>
>>>
 Hi Panos

 it would certainly be possible to make that measurement, but it
 wouldn't
 tell you anything biologically interesting. Why would you want to
 do
 such
 a
 thing? It will reflect the (arbitrary) image slice orientation and
 not
 the
 brain.

 cheers
 Bruce


 On Mon, 12 May 2014, pfot...@nmr.mgh.harvard.edu wrote:

> Hi FS experts,
>
> I was wondering whether it would be possible to measure the
> average
> cortical thickness at a specific slice (either axial, coronal, or
> sagittal). I read in Bruce's paper: "Measuring the thickness of
> the
> human
> cerebral cortex from magnetic resonance images" that "Measuring
> the
> thickness from the coronal slice at the point indicated by the
> green
> cross
> would result in an estimate in excess of 1 cm." Is that always
> the
> case,
> or has there been a way to bypass that issue?
>
> Thank you for your time,
> Panos
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Re: [Freesurfer] Measuring cortical thickness at a specific location

[pfotiad]

Hi Bruce,

I was having issues with the part after that, that is how to calculate the
average thickness of those bins, after I create them. Thanks again
Best,
Panos

> Hi Panos
>
> no, mris_anatomical_stats won't do it. I would map the average thickness
> to fsaverage coords, then load that into matlab and go from there using
> the [xyz] coords of fsaverage for the binning, which is pretty much
> MNI305
>
> cheers
> Bruce
> On Tue, 13 May 2014, pfot...@nmr.mgh.harvard.edu wrote:
>
>> Hi Bruce,
>>
>> Sorry, I had a last follow up question. I just realized that the
>> resulting
>> bins will be in the fsaverage space, and hence I wouldn't be able to use
>> mris_anatomical_stats to calculate the average thickness of the bins,
>> since the fsaverage "subject" does not have a wm.mgz file. Did you have
>> another way in mind to calculate the thickness of each bin, or do you
>> believe that mris_anatomical stats should do the trick with a specific
>> flag?
>>
>> Thanks a ton,
>> Panos
>>
>>> Hi Bruce,
>>>
>>> I see, that's really helpful, thank you!
>>>
>>> Best,
>>> Panos
>>>
>>>
 Hi Panos

 I would make an average thickness map in fsaverage space, then in
 matlab
 divvy up the a-p direction into bins (say 100 of them) and compute the
 average in each bin based on the a/p coordinate

 cheers
 Bruce
 On Tue, 13 May 2014,
 pfot...@nmr.mgh.harvard.edu wrote:

> Hi Bruce,
>
> Just to clarify, when you say "average the thickness along each A/P
> coordinate" do you mean by looking up at the average cortical
> thickness
> of
> each parcellation and then calculating their average from P->A, or is
> there another way to find the average thickness of each slice and
> then
> see
> how that average changes from P->A?
> Thanks again for your time,
> Panos
>
>> I see. Then measure the thickness normally, then see how it changes
>> in
>> those directions. You could average the thickness along each A/P
>> coordinate
>> - that wouldn't be a problem. You just don't want to measure it that
>> way
>>
>> cheers
>> Bruce
>>
>>
>> On Mon, 12 May 2014,
>> pfot...@nmr.mgh.harvard.edu wrote:
>>
>>> Hi Bruce,
>>>
>>> Thank you for your reply. I was interested in looking how the
>>> thickness
>>> changes from the posterior to the anterior side of the brain and
>>> vice
>>> versa (the thickness gradient).
>>>
>>> Thank you again for your time!
>>> Panos
>>>
>>>
 Hi Panos

 it would certainly be possible to make that measurement, but it
 wouldn't
 tell you anything biologically interesting. Why would you want to
 do
 such
 a
 thing? It will reflect the (arbitrary) image slice orientation and
 not
 the
 brain.

 cheers
 Bruce


 On Mon, 12 May 2014, pfot...@nmr.mgh.harvard.edu wrote:

> Hi FS experts,
>
> I was wondering whether it would be possible to measure the
> average
> cortical thickness at a specific slice (either axial, coronal, or
> sagittal). I read in Bruce's paper: "Measuring the thickness of
> the
> human
> cerebral cortex from magnetic resonance images" that "Measuring
> the
> thickness from the coronal slice at the point indicated by the
> green
> cross
> would result in an estimate in excess of 1 cm." Is that always
> the
> case,
> or has there been a way to bypass that issue?
>
> Thank you for your time,
> Panos
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>
>
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>

Re: [Freesurfer] Measuring cortical thickness at a specific location

[Bruce Fischl]

Hi Panos

no, mris_anatomical_stats won't do it. I would map the average thickness 
to fsaverage coords, then load that into matlab and go from there using 
the [xyz] coords of fsaverage for the binning, which is pretty much 
MNI305

cheers
Bruce
On Tue, 13 May 2014, pfot...@nmr.mgh.harvard.edu wrote:

> Hi Bruce,
>
> Sorry, I had a last follow up question. I just realized that the resulting
> bins will be in the fsaverage space, and hence I wouldn't be able to use
> mris_anatomical_stats to calculate the average thickness of the bins,
> since the fsaverage "subject" does not have a wm.mgz file. Did you have
> another way in mind to calculate the thickness of each bin, or do you
> believe that mris_anatomical stats should do the trick with a specific
> flag?
>
> Thanks a ton,
> Panos
>
>> Hi Bruce,
>>
>> I see, that's really helpful, thank you!
>>
>> Best,
>> Panos
>>
>>
>>> Hi Panos
>>>
>>> I would make an average thickness map in fsaverage space, then in matlab
>>> divvy up the a-p direction into bins (say 100 of them) and compute the
>>> average in each bin based on the a/p coordinate
>>>
>>> cheers
>>> Bruce
>>> On Tue, 13 May 2014,
>>> pfot...@nmr.mgh.harvard.edu wrote:
>>>
 Hi Bruce,

 Just to clarify, when you say "average the thickness along each A/P
 coordinate" do you mean by looking up at the average cortical thickness
 of
 each parcellation and then calculating their average from P->A, or is
 there another way to find the average thickness of each slice and then
 see
 how that average changes from P->A?
 Thanks again for your time,
 Panos

> I see. Then measure the thickness normally, then see how it changes in
> those directions. You could average the thickness along each A/P
> coordinate
> - that wouldn't be a problem. You just don't want to measure it that
> way
>
> cheers
> Bruce
>
>
> On Mon, 12 May 2014,
> pfot...@nmr.mgh.harvard.edu wrote:
>
>> Hi Bruce,
>>
>> Thank you for your reply. I was interested in looking how the
>> thickness
>> changes from the posterior to the anterior side of the brain and vice
>> versa (the thickness gradient).
>>
>> Thank you again for your time!
>> Panos
>>
>>
>>> Hi Panos
>>>
>>> it would certainly be possible to make that measurement, but it
>>> wouldn't
>>> tell you anything biologically interesting. Why would you want to do
>>> such
>>> a
>>> thing? It will reflect the (arbitrary) image slice orientation and
>>> not
>>> the
>>> brain.
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>> On Mon, 12 May 2014, pfot...@nmr.mgh.harvard.edu wrote:
>>>
 Hi FS experts,

 I was wondering whether it would be possible to measure the average
 cortical thickness at a specific slice (either axial, coronal, or
 sagittal). I read in Bruce's paper: "Measuring the thickness of the
 human
 cerebral cortex from magnetic resonance images" that "Measuring the
 thickness from the coronal slice at the point indicated by the
 green
 cross
 would result in an estimate in excess of 1 cm." Is that always the
 case,
 or has there been a way to bypass that issue?

 Thank you for your time,
 Panos
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>>>
>>>
>>
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>>
>>
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Re: [Freesurfer] Measuring cortical thickness at a specific location

[pfotiad]

Hi Bruce,

Sorry, I had a last follow up question. I just realized that the resulting
bins will be in the fsaverage space, and hence I wouldn't be able to use
mris_anatomical_stats to calculate the average thickness of the bins,
since the fsaverage "subject" does not have a wm.mgz file. Did you have
another way in mind to calculate the thickness of each bin, or do you
believe that mris_anatomical stats should do the trick with a specific
flag?

Thanks a ton,
Panos

> Hi Bruce,
>
> I see, that's really helpful, thank you!
>
> Best,
> Panos
>
>
>> Hi Panos
>>
>> I would make an average thickness map in fsaverage space, then in matlab
>> divvy up the a-p direction into bins (say 100 of them) and compute the
>> average in each bin based on the a/p coordinate
>>
>> cheers
>> Bruce
>> On Tue, 13 May 2014,
>> pfot...@nmr.mgh.harvard.edu wrote:
>>
>>> Hi Bruce,
>>>
>>> Just to clarify, when you say "average the thickness along each A/P
>>> coordinate" do you mean by looking up at the average cortical thickness
>>> of
>>> each parcellation and then calculating their average from P->A, or is
>>> there another way to find the average thickness of each slice and then
>>> see
>>> how that average changes from P->A?
>>> Thanks again for your time,
>>> Panos
>>>
 I see. Then measure the thickness normally, then see how it changes in
 those directions. You could average the thickness along each A/P
 coordinate
 - that wouldn't be a problem. You just don't want to measure it that
 way

 cheers
 Bruce


 On Mon, 12 May 2014,
 pfot...@nmr.mgh.harvard.edu wrote:

> Hi Bruce,
>
> Thank you for your reply. I was interested in looking how the
> thickness
> changes from the posterior to the anterior side of the brain and vice
> versa (the thickness gradient).
>
> Thank you again for your time!
> Panos
>
>
>> Hi Panos
>>
>> it would certainly be possible to make that measurement, but it
>> wouldn't
>> tell you anything biologically interesting. Why would you want to do
>> such
>> a
>> thing? It will reflect the (arbitrary) image slice orientation and
>> not
>> the
>> brain.
>>
>> cheers
>> Bruce
>>
>>
>> On Mon, 12 May 2014, pfot...@nmr.mgh.harvard.edu wrote:
>>
>>> Hi FS experts,
>>>
>>> I was wondering whether it would be possible to measure the average
>>> cortical thickness at a specific slice (either axial, coronal, or
>>> sagittal). I read in Bruce's paper: "Measuring the thickness of the
>>> human
>>> cerebral cortex from magnetic resonance images" that "Measuring the
>>> thickness from the coronal slice at the point indicated by the
>>> green
>>> cross
>>> would result in an estimate in excess of 1 cm." Is that always the
>>> case,
>>> or has there been a way to bypass that issue?
>>>
>>> Thank you for your time,
>>> Panos
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>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
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>>>
>>>
>>>
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>>
>>
>
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Re: [Freesurfer] Measuring cortical thickness at a specific location

[pfotiad]

Hi Bruce,

I see, that's really helpful, thank you!

Best,
Panos


> Hi Panos
>
> I would make an average thickness map in fsaverage space, then in matlab
> divvy up the a-p direction into bins (say 100 of them) and compute the
> average in each bin based on the a/p coordinate
>
> cheers
> Bruce
> On Tue, 13 May 2014,
> pfot...@nmr.mgh.harvard.edu wrote:
>
>> Hi Bruce,
>>
>> Just to clarify, when you say "average the thickness along each A/P
>> coordinate" do you mean by looking up at the average cortical thickness
>> of
>> each parcellation and then calculating their average from P->A, or is
>> there another way to find the average thickness of each slice and then
>> see
>> how that average changes from P->A?
>> Thanks again for your time,
>> Panos
>>
>>> I see. Then measure the thickness normally, then see how it changes in
>>> those directions. You could average the thickness along each A/P
>>> coordinate
>>> - that wouldn't be a problem. You just don't want to measure it that
>>> way
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>> On Mon, 12 May 2014,
>>> pfot...@nmr.mgh.harvard.edu wrote:
>>>
 Hi Bruce,

 Thank you for your reply. I was interested in looking how the
 thickness
 changes from the posterior to the anterior side of the brain and vice
 versa (the thickness gradient).

 Thank you again for your time!
 Panos


> Hi Panos
>
> it would certainly be possible to make that measurement, but it
> wouldn't
> tell you anything biologically interesting. Why would you want to do
> such
> a
> thing? It will reflect the (arbitrary) image slice orientation and
> not
> the
> brain.
>
> cheers
> Bruce
>
>
> On Mon, 12 May 2014, pfot...@nmr.mgh.harvard.edu wrote:
>
>> Hi FS experts,
>>
>> I was wondering whether it would be possible to measure the average
>> cortical thickness at a specific slice (either axial, coronal, or
>> sagittal). I read in Bruce's paper: "Measuring the thickness of the
>> human
>> cerebral cortex from magnetic resonance images" that "Measuring the
>> thickness from the coronal slice at the point indicated by the green
>> cross
>> would result in an estimate in excess of 1 cm." Is that always the
>> case,
>> or has there been a way to bypass that issue?
>>
>> Thank you for your time,
>> Panos
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
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>
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Re: [Freesurfer] Measuring cortical thickness at a specific location

[Bruce Fischl]

Hi Panos

I would make an average thickness map in fsaverage space, then in matlab 
divvy up the a-p direction into bins (say 100 of them) and compute the 
average in each bin based on the a/p coordinate

cheers
Bruce
On Tue, 13 May 2014, 
pfot...@nmr.mgh.harvard.edu wrote:

> Hi Bruce,
>
> Just to clarify, when you say "average the thickness along each A/P
> coordinate" do you mean by looking up at the average cortical thickness of
> each parcellation and then calculating their average from P->A, or is
> there another way to find the average thickness of each slice and then see
> how that average changes from P->A?
> Thanks again for your time,
> Panos
>
>> I see. Then measure the thickness normally, then see how it changes in
>> those directions. You could average the thickness along each A/P
>> coordinate
>> - that wouldn't be a problem. You just don't want to measure it that way
>>
>> cheers
>> Bruce
>>
>>
>> On Mon, 12 May 2014,
>> pfot...@nmr.mgh.harvard.edu wrote:
>>
>>> Hi Bruce,
>>>
>>> Thank you for your reply. I was interested in looking how the thickness
>>> changes from the posterior to the anterior side of the brain and vice
>>> versa (the thickness gradient).
>>>
>>> Thank you again for your time!
>>> Panos
>>>
>>>
 Hi Panos

 it would certainly be possible to make that measurement, but it
 wouldn't
 tell you anything biologically interesting. Why would you want to do
 such
 a
 thing? It will reflect the (arbitrary) image slice orientation and not
 the
 brain.

 cheers
 Bruce


 On Mon, 12 May 2014, pfot...@nmr.mgh.harvard.edu wrote:

> Hi FS experts,
>
> I was wondering whether it would be possible to measure the average
> cortical thickness at a specific slice (either axial, coronal, or
> sagittal). I read in Bruce's paper: "Measuring the thickness of the
> human
> cerebral cortex from magnetic resonance images" that "Measuring the
> thickness from the coronal slice at the point indicated by the green
> cross
> would result in an estimate in excess of 1 cm." Is that always the
> case,
> or has there been a way to bypass that issue?
>
> Thank you for your time,
> Panos
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
 ___
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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
>>>
>>>
>>>
>> ___
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>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
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>
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Re: [Freesurfer] Measuring cortical thickness at a specific location

[pfotiad]

Hi Bruce,

Just to clarify, when you say "average the thickness along each A/P
coordinate" do you mean by looking up at the average cortical thickness of
each parcellation and then calculating their average from P->A, or is
there another way to find the average thickness of each slice and then see
how that average changes from P->A?
Thanks again for your time,
Panos

> I see. Then measure the thickness normally, then see how it changes in
> those directions. You could average the thickness along each A/P
> coordinate
> - that wouldn't be a problem. You just don't want to measure it that way
>
> cheers
> Bruce
>
>
> On Mon, 12 May 2014,
> pfot...@nmr.mgh.harvard.edu wrote:
>
>> Hi Bruce,
>>
>> Thank you for your reply. I was interested in looking how the thickness
>> changes from the posterior to the anterior side of the brain and vice
>> versa (the thickness gradient).
>>
>> Thank you again for your time!
>> Panos
>>
>>
>>> Hi Panos
>>>
>>> it would certainly be possible to make that measurement, but it
>>> wouldn't
>>> tell you anything biologically interesting. Why would you want to do
>>> such
>>> a
>>> thing? It will reflect the (arbitrary) image slice orientation and not
>>> the
>>> brain.
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>> On Mon, 12 May 2014, pfot...@nmr.mgh.harvard.edu wrote:
>>>
 Hi FS experts,

 I was wondering whether it would be possible to measure the average
 cortical thickness at a specific slice (either axial, coronal, or
 sagittal). I read in Bruce's paper: "Measuring the thickness of the
 human
 cerebral cortex from magnetic resonance images" that "Measuring the
 thickness from the coronal slice at the point indicated by the green
 cross
 would result in an estimate in excess of 1 cm." Is that always the
 case,
 or has there been a way to bypass that issue?

 Thank you for your time,
 Panos
 ___
 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
>>>
>>>
>>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
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>
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Re: [Freesurfer] Measuring cortical thickness at a specific location

[Bruce Fischl]

I see. Then measure the thickness normally, then see how it changes in 
those directions. You could average the thickness along each A/P coordinate 
- that wouldn't be a problem. You just don't want to measure it that way

cheers
Bruce


On Mon, 12 May 2014, 
pfot...@nmr.mgh.harvard.edu wrote:

> Hi Bruce,
>
> Thank you for your reply. I was interested in looking how the thickness
> changes from the posterior to the anterior side of the brain and vice
> versa (the thickness gradient).
>
> Thank you again for your time!
> Panos
>
>
>> Hi Panos
>>
>> it would certainly be possible to make that measurement, but it wouldn't
>> tell you anything biologically interesting. Why would you want to do such
>> a
>> thing? It will reflect the (arbitrary) image slice orientation and not the
>> brain.
>>
>> cheers
>> Bruce
>>
>>
>> On Mon, 12 May 2014, pfot...@nmr.mgh.harvard.edu wrote:
>>
>>> Hi FS experts,
>>>
>>> I was wondering whether it would be possible to measure the average
>>> cortical thickness at a specific slice (either axial, coronal, or
>>> sagittal). I read in Bruce's paper: "Measuring the thickness of the
>>> human
>>> cerebral cortex from magnetic resonance images" that "Measuring the
>>> thickness from the coronal slice at the point indicated by the green
>>> cross
>>> would result in an estimate in excess of 1 cm." Is that always the case,
>>> or has there been a way to bypass that issue?
>>>
>>> Thank you for your time,
>>> Panos
>>> ___
>>> 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
>>
>>
>>
>
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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Re: [Freesurfer] Measuring cortical thickness at a specific location

[pfotiad]

Hi Bruce,

Thank you for your reply. I was interested in looking how the thickness
changes from the posterior to the anterior side of the brain and vice
versa (the thickness gradient).

Thank you again for your time!
Panos


> Hi Panos
>
> it would certainly be possible to make that measurement, but it wouldn't
> tell you anything biologically interesting. Why would you want to do such
> a
> thing? It will reflect the (arbitrary) image slice orientation and not the
> brain.
>
> cheers
> Bruce
>
>
> On Mon, 12 May 2014, pfot...@nmr.mgh.harvard.edu wrote:
>
>> Hi FS experts,
>>
>> I was wondering whether it would be possible to measure the average
>> cortical thickness at a specific slice (either axial, coronal, or
>> sagittal). I read in Bruce's paper: "Measuring the thickness of the
>> human
>> cerebral cortex from magnetic resonance images" that "Measuring the
>> thickness from the coronal slice at the point indicated by the green
>> cross
>> would result in an estimate in excess of 1 cm." Is that always the case,
>> or has there been a way to bypass that issue?
>>
>> Thank you for your time,
>> Panos
>> ___
>> 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
>
>
>

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Re: [Freesurfer] Measuring cortical thickness at a specific location

[Bruce Fischl]

Hi Panos

it would certainly be possible to make that measurement, but it wouldn't 
tell you anything biologically interesting. Why would you want to do such a 
thing? It will reflect the (arbitrary) image slice orientation and not the 
brain.

cheers
Bruce


On Mon, 12 May 2014, pfot...@nmr.mgh.harvard.edu wrote:

> Hi FS experts,
>
> I was wondering whether it would be possible to measure the average
> cortical thickness at a specific slice (either axial, coronal, or
> sagittal). I read in Bruce's paper: "Measuring the thickness of the human
> cerebral cortex from magnetic resonance images" that "Measuring the
> thickness from the coronal slice at the point indicated by the green cross
> would result in an estimate in excess of 1 cm." Is that always the case,
> or has there been a way to bypass that issue?
>
> Thank you for your time,
> Panos
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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[Freesurfer] Measuring cortical thickness at a specific location

[pfotiad]

Hi FS experts,

I was wondering whether it would be possible to measure the average
cortical thickness at a specific slice (either axial, coronal, or
sagittal). I read in Bruce's paper: "Measuring the thickness of the human
cerebral cortex from magnetic resonance images" that "Measuring the
thickness from the coronal slice at the point indicated by the green cross
would result in an estimate in excess of 1 cm." Is that always the case,
or has there been a way to bypass that issue?

Thank you for your time,
Panos
___
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Re: [Freesurfer] measuring cortical thickness using FreeSurfer

[Pedro Paulo de Magalhães Oliveira Junior]

I usually can run one instance of FreeSurfer with 1GB if I use the -no-gut
flag

I have a benchmark of 4 recon-all running in a 4 Core AMD with 4GB RAM that
took only 10% more time than one recon-all alone.

2011/7/6 John Jan Drozd 

> Hi Bruce,
>
> Thanks for pointing this out to me about the RAM.
>
> I have 8 Gb of RAM. So I guess I can safely run 3 or 4 subjects
> simultaneously if each subject requires 2 to 3 Gb of RAM.
>
> Thanks,
> John
>
> Sent from my iPhone
>
> On 2011-07-05, at 6:08 PM, Bruce Fischl 
> wrote:
>
> > how much ram do you have? You'll need at least 2G/subject if not 3
> > On Tue, 5 Jul 2011, John Drozd wrote:
> >
> >> Hi Bruce,
> >> Thanks for the suggestion, Bruce. I'll run 8 different subjects at once.
> >> Take care,
> >> John
> >> 2011/7/5 Bruce Fischl 
> >> Sorry, that won't help a single subject much, although there are
> >> options to run the hemis in parallel. You can run multiple
> >> subjects at the same time, which is what we usually do. Or you
> >> can use cuss
> >> On Jul 5, 2011, at 5:11 PM, John Drozd  wrote:
> >>
> >> Hi Bruce,
> >>
> >> Okay, thank you. I understand and can see that to do an
> >> accurate job, the pipeline must be complicated.
> >> I have eight processors on my linux desktop computer.
> >> Maybe some parts of recon-all are multi-threaded which
> >> could speed things up for me :-)
> >>
> >> Thank you,
> >> John
> >>
> >> 2011/7/5 Bruce Fischl 
> >> sorry, but the majority of the time is
> >> required. We're working to speed things up,
> >> but it is complicated software with multiple
> >> nonlinear warps, segmentation procedures,
> >> etc
> >> Bruce
> >> On Tue, 5 Jul 2011, John Drozd wrote:
> >>
> >> Hi Bruce and Pedro,
> >>
> >> Thank you both for sending me your
> >> suggestions.
> >> Just to let you know, because my .dcm (dicom)
> >> files had a space and two dots
> >> in the filenames:
> >> (e.g. "2008_12_08.ek -0035-0001-1.dcm" )
> >> (and using quotes around the file name or "\ "
> >> within the filename without
> >> the quotes did not work with recon-all),
> >> recon-all truncated the filename
> >> before the space as "2008_12_08.ek" feeding it
> >> to an mri_convert command and
> >> gave an error message.
> >>
> >> So I worked around this problem as follows: I
> >> converted the .dcm series to a
> >> nifti .nii volume using 3D Slicer, and then
> >> used mri_convert to convert the
> >> .nii format to .mgz format. Then I ran
> >> recon-all on the .mgz formatted file
> >> and it is now running successfully.
> >>
> >> I see on the online tutorials and slides, that
> >> this process takes about 20
> >> hours. Is there a way to only run partial
> >> steps pertaining only to the
> >> cortical thickness?
> >>
> >> Pedro also suggested that I go through the
> >> FreeSurferBeginnersGuide wiki
> >> which I am doing now.
> >>
> >> Also, reading some mailing lists emails, I
> >> noticed that matlab can be used
> >> to analyze the cortical thickness statistiics,
> >> and also freesurfer comes
> >> with matlab scripts. I will try these tools
> >> out as well.
> >>
> >> Thank you for your time,
> >> John
> >>
> >> On Tue, Jul 5, 2011 at 1:18 PM, Bruce Fischl
> >> 
> >> wrote:
> >> recon-all \
> >> -i  >> dicom series> \
> >> -s  \
> >> -sd  >> folder in> \
> >> -all
> >>
> >> cheers
> >> Bruce
> >>
> >> On Tue, 5 Jul 2011, John Drozd wrote:
> >>
> >> Hi,
> >>
> >> I am running freesurfer on 64 bit Fedora
> >> 10 linux.
> >> I am using version:
> >>
> >> freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0.
> >> Can anyone point me to a reference web
> >> page listing what
> >> steps I need to
> >> type to process
> >> a series of MRI dicom slices and use
> >> FreeSurfer to measure
> >> cortical
> >> thickness for this dicom series?
> >>
> >> Thank you,
> >> John
> >>
> >> --
> >> John Drozd
> >> Post-Doctoral Fellow, Robarts Research
> >> Institute
> >> The University of Western Ontario
> >> London, ON, Canada
> >> http://publish.uwo.ca/~jdrozd2/index.htm
> >>
> >>
> >> ___
> >> 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.
> >>
> >> --
> >> John Drozd
> >> Post-Doctoral Fellow, Robarts Research
> >> Institute
> >> The University of Western Ontario
> >> London, ON, Canada
> >> http://publish.uwo.ca/~jdrozd2/index.htm
> >>
> >> --
> >> John Drozd
> >> Post-Doctoral Fellow, Robarts Research Institute
> >> The University of Western Ontari

Re: [Freesurfer] measuring cortical thickness using FreeSurfer

[John Jan Drozd]

Hi Bruce,

Thanks for pointing this out to me about the RAM.

I have 8 Gb of RAM. So I guess I can safely run 3 or 4 subjects simultaneously 
if each subject requires 2 to 3 Gb of RAM.  

Thanks,
John

Sent from my iPhone

On 2011-07-05, at 6:08 PM, Bruce Fischl  wrote:

> how much ram do you have? You'll need at least 2G/subject if not 3
> On Tue, 5 Jul 2011, John Drozd wrote:
> 
>> Hi Bruce,
>> Thanks for the suggestion, Bruce. I'll run 8 different subjects at once.
>> Take care,
>> John
>> 2011/7/5 Bruce Fischl 
>>  Sorry, that won't help a single subject much, although there are
>>  options to run the hemis in parallel. You can run multiple
>>  subjects at the same time, which is what we usually do. Or you
>>  can use cuss
>> On Jul 5, 2011, at 5:11 PM, John Drozd  wrote:
>> 
>>  Hi Bruce,
>> 
>>  Okay, thank you. I understand and can see that to do an
>>  accurate job, the pipeline must be complicated.
>>  I have eight processors on my linux desktop computer.
>>  Maybe some parts of recon-all are multi-threaded which
>>  could speed things up for me :-)
>> 
>>  Thank you,
>>  John
>> 
>>  2011/7/5 Bruce Fischl 
>>sorry, but the majority of the time is
>>required. We're working to speed things up,
>>but it is complicated software with multiple
>>nonlinear warps, segmentation procedures,
>>etc
>> Bruce
>> On Tue, 5 Jul 2011, John Drozd wrote:
>> 
>>  Hi Bruce and Pedro,
>> 
>>  Thank you both for sending me your
>>  suggestions. 
>>  Just to let you know, because my .dcm (dicom)
>>  files had a space and two dots
>>  in the filenames:
>>  (e.g. "2008_12_08.ek -0035-0001-1.dcm" )
>>  (and using quotes around the file name or "\ "
>>  within the filename without
>>  the quotes did not work with recon-all),
>>  recon-all truncated the filename
>>  before the space as "2008_12_08.ek" feeding it
>>  to an mri_convert command and
>>  gave an error message.
>> 
>>  So I worked around this problem as follows: I
>>  converted the .dcm series to a
>>  nifti .nii volume using 3D Slicer, and then
>>  used mri_convert to convert the
>>  .nii format to .mgz format.  Then I ran
>>  recon-all on the .mgz formatted file
>>  and it is now running successfully.
>> 
>>  I see on the online tutorials and slides, that
>>  this process takes about 20
>>  hours. Is there a way to only run partial
>>  steps pertaining only to the
>>  cortical thickness? 
>> 
>>  Pedro also suggested that I go through the
>>  FreeSurferBeginnersGuide wiki
>>  which I am doing now. 
>> 
>>  Also, reading some mailing lists emails, I
>>  noticed that matlab can be used
>>  to analyze the cortical thickness statistiics,
>>  and also freesurfer comes
>>  with matlab scripts.  I will try these tools
>>  out as well.
>> 
>>  Thank you for your time,
>>  John
>> 
>>  On Tue, Jul 5, 2011 at 1:18 PM, Bruce Fischl
>>  
>>  wrote:
>>   recon-all \
>>  -i >  dicom series> \
>>  -s  \
>>  -sd >  folder in> \
>>  -all
>> 
>>   cheers
>>   Bruce
>> 
>>  On Tue, 5 Jul 2011, John Drozd wrote:
>> 
>>   Hi,
>> 
>>   I am running freesurfer on 64 bit Fedora
>>  10 linux.
>>   I am using version: 
>> 
>>   freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0.
>>   Can anyone point me to a reference web
>>  page listing what
>>   steps I need to
>>   type to process
>>   a series of MRI dicom slices and use
>>  FreeSurfer to measure
>>   cortical
>>   thickness for this dicom series?
>> 
>>   Thank you,
>>   John
>> 
>>   --
>>   John Drozd
>>   Post-Doctoral Fellow, Robarts Research
>>  Institute
>>   The University of Western Ontario
>>   London, ON, Canada
>>   http://publish.uwo.ca/~jdrozd2/index.htm
>>
>> 
>>  ___
>>  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.
>> 
>>  --
>>  John Drozd
>>  Post-Doctoral Fellow, Robarts Research

Re: [Freesurfer] measuring cortical thickness using FreeSurfer

[Bruce Fischl]

how much ram do you have? You'll need at least 2G/subject if not 3
On Tue, 5 
Jul 2011, John Drozd wrote:



Hi Bruce,

Thanks for the suggestion, Bruce. I'll run 8 different subjects at once.

Take care,
John

2011/7/5 Bruce Fischl 
  Sorry, that won't help a single subject much, although there are
  options to run the hemis in parallel. You can run multiple
  subjects at the same time, which is what we usually do. Or you
  can use cuss



On Jul 5, 2011, at 5:11 PM, John Drozd  wrote:

  Hi Bruce,

  Okay, thank you. I understand and can see that to do an
  accurate job, the pipeline must be complicated.
  I have eight processors on my linux desktop computer.
  Maybe some parts of recon-all are multi-threaded which
  could speed things up for me :-)

  Thank you,
  John

  2011/7/5 Bruce Fischl 
sorry, but the majority of the time is
required. We're working to speed things up,
but it is complicated software with multiple
nonlinear warps, segmentation procedures,
etc


Bruce



On Tue, 5 Jul 2011, John Drozd wrote:

  Hi Bruce and Pedro,

  Thank you both for sending me your
  suggestions. 
  Just to let you know, because my .dcm (dicom)
  files had a space and two dots
  in the filenames:
  (e.g. "2008_12_08.ek -0035-0001-1.dcm" )
  (and using quotes around the file name or "\ "
  within the filename without
  the quotes did not work with recon-all),
  recon-all truncated the filename
  before the space as "2008_12_08.ek" feeding it
  to an mri_convert command and
  gave an error message.

  So I worked around this problem as follows: I
  converted the .dcm series to a
  nifti .nii volume using 3D Slicer, and then
  used mri_convert to convert the
  .nii format to .mgz format.  Then I ran
  recon-all on the .mgz formatted file
  and it is now running successfully.

  I see on the online tutorials and slides, that
  this process takes about 20
  hours. Is there a way to only run partial
  steps pertaining only to the
  cortical thickness? 

  Pedro also suggested that I go through the
  FreeSurferBeginnersGuide wiki
  which I am doing now. 

  Also, reading some mailing lists emails, I
  noticed that matlab can be used
  to analyze the cortical thickness statistiics,
  and also freesurfer comes
  with matlab scripts.  I will try these tools
  out as well.

  Thank you for your time,
  John

  On Tue, Jul 5, 2011 at 1:18 PM, Bruce Fischl
  
  wrote:
       recon-all \
              -i  \
              -s  \
              -sd  \
              -all


       cheers
       Bruce



  On Tue, 5 Jul 2011, John Drozd wrote:

       Hi,

       I am running freesurfer on 64 bit Fedora
  10 linux.
       I am using version: 
     
   freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0.
       Can anyone point me to a reference web
  page listing what
       steps I need to
       type to process
       a series of MRI dicom slices and use
  FreeSurfer to measure
       cortical
       thickness for this dicom series?

       Thank you,
       John

       --
       John Drozd
       Post-Doctoral Fellow, Robarts Research
  Institute
       The University of Western Ontario
       London, ON, Canada
       http://publish.uwo.ca/~jdrozd2/index.htm
        



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  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.




  --
  John Drozd
  Post-Doctoral Fellow, Robarts Research
  Institute
  The University of Western Ontario
  London, ON, Canada
  http://publish.uwo.ca/~jdrozd2/index.htm
   





--
John Drozd
Post-Doctoral Fellow, Robarts Research Institute
The University of Western Ontario
London, ON, Canada
http://publish.uwo.ca/~jdrozd2/index.htm
 




--
John Drozd
Post-Doctoral Fellow, Robarts Research Institute
The University of Western Ontario
London, ON, Canada
http://publish.uwo.ca/~jdrozd2/index.htm
 


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Re: [Freesurfer] measuring cortical thickness using FreeSurfer

[John Drozd]

Hi Bruce,

Thanks for the suggestion, Bruce. I'll run 8 different subjects at once.

Take care,
John

2011/7/5 Bruce Fischl 

> Sorry, that won't help a single subject much, although there are options to
> run the hemis in parallel. You can run multiple subjects at the same time,
> which is what we usually do. Or you can use cuss
>
>
>
> On Jul 5, 2011, at 5:11 PM, John Drozd  wrote:
>
> Hi Bruce,
>
> Okay, thank you. I understand and can see that to do an accurate job, the
> pipeline must be complicated.
> I have eight processors on my linux desktop computer.
> Maybe some parts of recon-all are multi-threaded which could speed things
> up for me :-)
>
> Thank you,
> John
>
> 2011/7/5 Bruce Fischl < 
> fis...@nmr.mgh.harvard.edu>
>
>> sorry, but the majority of the time is required. We're working to speed
>> things up, but it is complicated software with multiple nonlinear warps,
>> segmentation procedures, etc
>>
>>
>> Bruce
>>
>>
>>
>> On Tue, 5 Jul 2011, John Drozd wrote:
>>
>>  Hi Bruce and Pedro,
>>>
>>> Thank you both for sending me your suggestions.
>>> Just to let you know, because my .dcm (dicom) files had a space and two
>>> dots
>>> in the filenames:
>>> (e.g. "2008_12_08.ek -0035-0001-1.dcm" )
>>> (and using quotes around the file name or "\ " within the filename
>>> without
>>> the quotes did not work with recon-all), recon-all truncated the filename
>>> before the space as "2008_12_08.ek" feeding it to an mri_convert command
>>> and
>>> gave an error message.
>>>
>>> So I worked around this problem as follows: I converted the .dcm series
>>> to a
>>> nifti .nii volume using 3D Slicer, and then used mri_convert to convert
>>> the
>>> .nii format to .mgz format.  Then I ran recon-all on the .mgz formatted
>>> file
>>> and it is now running successfully.
>>>
>>> I see on the online tutorials and slides, that this process takes about
>>> 20
>>> hours. Is there a way to only run partial steps pertaining only to the
>>> cortical thickness?
>>>
>>> Pedro also suggested that I go through the FreeSurferBeginnersGuide wiki
>>> which I am doing now.
>>>
>>> Also, reading some mailing lists emails, I noticed that matlab can be
>>> used
>>> to analyze the cortical thickness statistiics, and also freesurfer comes
>>> with matlab scripts.  I will try these tools out as well.
>>>
>>> Thank you for your time,
>>> John
>>>
>>> On Tue, Jul 5, 2011 at 1:18 PM, Bruce Fischl <
>>> fis...@nmr.mgh.harvard.edu>
>>> wrote:
>>>  recon-all \
>>> -i  \
>>> -s  \
>>> -sd  \
>>> -all
>>>
>>>
>>>  cheers
>>>  Bruce
>>>
>>>
>>>
>>> On Tue, 5 Jul 2011, John Drozd wrote:
>>>
>>>  Hi,
>>>
>>>  I am running freesurfer on 64 bit Fedora 10 linux.
>>>  I am using version:
>>>  freesurfer-Linux-centos4_x86_**64-stable-pub-v4.3.0.
>>>  Can anyone point me to a reference web page listing what
>>>  steps I need to
>>>  type to process
>>>  a series of MRI dicom slices and use FreeSurfer to measure
>>>  cortical
>>>  thickness for this dicom series?
>>>
>>>  Thank you,
>>>  John
>>>
>>>  --
>>>  John Drozd
>>>  Post-Doctoral Fellow, Robarts Research Institute
>>>  The University of Western Ontario
>>>  London, ON, Canada
>>>   
>>> http://publish.uwo.ca/~**jdrozd2/index.htm
>>>
>>>
>>>
>>>
>>> __**_
>>> 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.
>>>
>>>
>>>
>>>
>>> --
>>> John Drozd
>>> Post-Doctoral Fellow, Robarts Research Institute
>>> The University of Western Ontario
>>> London, ON, Canada
>>>  http://publish.uwo.ca/~**
>>> jdrozd2/index.htm
>>>
>>>
>>>
>>>
>
>
> --
> John Drozd
> Post-Doctoral Fellow, Robarts Research Institute
> The University of Western Ontario
> London, ON, Canada
> 
> http://publish.uwo.ca/~jdrozd2/index.htm
>
>
>


-- 
John Drozd
Post-Doctoral Fellow, Robarts Research Institute
The University of Western Ontario
London, ON, Canada
http://publish.uwo.ca/~jdrozd2/index.htm
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T

Re: [Freesurfer] measuring cortical thickness using FreeSurfer

[Bruce Fischl]

Sorry, that won't help a single subject much, although there are options to run 
the hemis in parallel. You can run multiple subjects at the same time, which is 
what we usually do. Or you can use cuss



On Jul 5, 2011, at 5:11 PM, John Drozd  wrote:

> Hi Bruce,
> 
> Okay, thank you. I understand and can see that to do an accurate job, the 
> pipeline must be complicated.
> I have eight processors on my linux desktop computer. 
> Maybe some parts of recon-all are multi-threaded which could speed things up 
> for me :-)
> 
> Thank you,
> John
> 
> 2011/7/5 Bruce Fischl 
> sorry, but the majority of the time is required. We're working to speed 
> things up, but it is complicated software with multiple nonlinear warps, 
> segmentation procedures, etc
> 
> 
> Bruce
> 
> 
> 
> On Tue, 5 Jul 2011, John Drozd wrote:
> 
> Hi Bruce and Pedro,
> 
> Thank you both for sending me your suggestions. 
> Just to let you know, because my .dcm (dicom) files had a space and two dots
> in the filenames:
> (e.g. "2008_12_08.ek -0035-0001-1.dcm" )
> (and using quotes around the file name or "\ " within the filename without
> the quotes did not work with recon-all), recon-all truncated the filename
> before the space as "2008_12_08.ek" feeding it to an mri_convert command and
> gave an error message.
> 
> So I worked around this problem as follows: I converted the .dcm series to a
> nifti .nii volume using 3D Slicer, and then used mri_convert to convert the
> .nii format to .mgz format.  Then I ran recon-all on the .mgz formatted file
> and it is now running successfully.
> 
> I see on the online tutorials and slides, that this process takes about 20
> hours. Is there a way to only run partial steps pertaining only to the
> cortical thickness? 
> 
> Pedro also suggested that I go through the FreeSurferBeginnersGuide wiki
> which I am doing now. 
> 
> Also, reading some mailing lists emails, I noticed that matlab can be used
> to analyze the cortical thickness statistiics, and also freesurfer comes
> with matlab scripts.  I will try these tools out as well.
> 
> Thank you for your time,
> John
> 
> On Tue, Jul 5, 2011 at 1:18 PM, Bruce Fischl 
> wrote:
>  recon-all \
> -i  \
> -s  \
> -sd  \
> -all
> 
> 
>  cheers
>  Bruce
> 
> 
> 
> On Tue, 5 Jul 2011, John Drozd wrote:
> 
>  Hi,
> 
>  I am running freesurfer on 64 bit Fedora 10 linux.
>  I am using version: 
>  freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0.
>  Can anyone point me to a reference web page listing what
>  steps I need to
>  type to process
>  a series of MRI dicom slices and use FreeSurfer to measure
>  cortical
>  thickness for this dicom series?
> 
>  Thank you,
>  John
> 
>  --
>  John Drozd
>  Post-Doctoral Fellow, Robarts Research Institute
>  The University of Western Ontario
>  London, ON, Canada
>  http://publish.uwo.ca/~jdrozd2/index.htm
>   
> 
> 
> 
> ___
> 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.
> 
> 
> 
> 
> --
> John Drozd
> Post-Doctoral Fellow, Robarts Research Institute
> The University of Western Ontario
> London, ON, Canada
> http://publish.uwo.ca/~jdrozd2/index.htm
>  
> 
> 
> 
> 
> 
> -- 
> John Drozd
> Post-Doctoral Fellow, Robarts Research Institute
> The University of Western Ontario
> London, ON, Canada
> http://publish.uwo.ca/~jdrozd2/index.htm
>  
> 
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Re: [Freesurfer] measuring cortical thickness using FreeSurfer

[John Drozd]

Hi Bruce,

Okay, thank you. I understand and can see that to do an accurate job, the
pipeline must be complicated.
I have eight processors on my linux desktop computer.
Maybe some parts of recon-all are multi-threaded which could speed things up
for me :-)

Thank you,
John

2011/7/5 Bruce Fischl 

> sorry, but the majority of the time is required. We're working to speed
> things up, but it is complicated software with multiple nonlinear warps,
> segmentation procedures, etc
>
>
> Bruce
>
>
>
> On Tue, 5 Jul 2011, John Drozd wrote:
>
>  Hi Bruce and Pedro,
>>
>> Thank you both for sending me your suggestions.
>> Just to let you know, because my .dcm (dicom) files had a space and two
>> dots
>> in the filenames:
>> (e.g. "2008_12_08.ek -0035-0001-1.dcm" )
>> (and using quotes around the file name or "\ " within the filename without
>> the quotes did not work with recon-all), recon-all truncated the filename
>> before the space as "2008_12_08.ek" feeding it to an mri_convert command
>> and
>> gave an error message.
>>
>> So I worked around this problem as follows: I converted the .dcm series to
>> a
>> nifti .nii volume using 3D Slicer, and then used mri_convert to convert
>> the
>> .nii format to .mgz format.  Then I ran recon-all on the .mgz formatted
>> file
>> and it is now running successfully.
>>
>> I see on the online tutorials and slides, that this process takes about 20
>> hours. Is there a way to only run partial steps pertaining only to the
>> cortical thickness?
>>
>> Pedro also suggested that I go through the FreeSurferBeginnersGuide wiki
>> which I am doing now.
>>
>> Also, reading some mailing lists emails, I noticed that matlab can be used
>> to analyze the cortical thickness statistiics, and also freesurfer comes
>> with matlab scripts.  I will try these tools out as well.
>>
>> Thank you for your time,
>> John
>>
>> On Tue, Jul 5, 2011 at 1:18 PM, Bruce Fischl 
>> wrote:
>>  recon-all \
>> -i  \
>> -s  \
>> -sd  \
>> -all
>>
>>
>>  cheers
>>  Bruce
>>
>>
>>
>> On Tue, 5 Jul 2011, John Drozd wrote:
>>
>>  Hi,
>>
>>  I am running freesurfer on 64 bit Fedora 10 linux.
>>  I am using version:
>>  freesurfer-Linux-centos4_x86_**64-stable-pub-v4.3.0.
>>  Can anyone point me to a reference web page listing what
>>  steps I need to
>>  type to process
>>  a series of MRI dicom slices and use FreeSurfer to measure
>>  cortical
>>  thickness for this dicom series?
>>
>>  Thank you,
>>  John
>>
>>  --
>>  John Drozd
>>  Post-Doctoral Fellow, Robarts Research Institute
>>  The University of Western Ontario
>>  London, ON, Canada
>>  
>> http://publish.uwo.ca/~**jdrozd2/index.htm
>>
>>
>>
>>
>> __**_
>> 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.
>>
>>
>>
>>
>> --
>> John Drozd
>> Post-Doctoral Fellow, Robarts Research Institute
>> The University of Western Ontario
>> London, ON, Canada
>> http://publish.uwo.ca/~**jdrozd2/index.htm
>>
>>
>>
>>


-- 
John Drozd
Post-Doctoral Fellow, Robarts Research Institute
The University of Western Ontario
London, ON, Canada
http://publish.uwo.ca/~jdrozd2/index.htm
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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] measuring cortical thickness using FreeSurfer

[Bruce Fischl]

sorry, but the majority of the time is required. We're working to speed 
things up, but it is complicated software with multiple nonlinear warps, 
segmentation procedures, etc


Bruce



On Tue, 5 Jul 2011, John Drozd wrote:


Hi Bruce and Pedro,

Thank you both for sending me your suggestions. 
Just to let you know, because my .dcm (dicom) files had a space and two dots
in the filenames:
(e.g. "2008_12_08.ek -0035-0001-1.dcm" )
(and using quotes around the file name or "\ " within the filename without
the quotes did not work with recon-all), recon-all truncated the filename
before the space as "2008_12_08.ek" feeding it to an mri_convert command and
gave an error message.

So I worked around this problem as follows: I converted the .dcm series to a
nifti .nii volume using 3D Slicer, and then used mri_convert to convert the
.nii format to .mgz format.  Then I ran recon-all on the .mgz formatted file
and it is now running successfully.

I see on the online tutorials and slides, that this process takes about 20
hours. Is there a way to only run partial steps pertaining only to the
cortical thickness? 

Pedro also suggested that I go through the FreeSurferBeginnersGuide wiki
which I am doing now. 

Also, reading some mailing lists emails, I noticed that matlab can be used
to analyze the cortical thickness statistiics, and also freesurfer comes
with matlab scripts.  I will try these tools out as well.

Thank you for your time,
John

On Tue, Jul 5, 2011 at 1:18 PM, Bruce Fischl 
wrote:
  recon-all \
         -i  \
         -s  \
         -sd  \
         -all


  cheers
  Bruce



On Tue, 5 Jul 2011, John Drozd wrote:

  Hi,

  I am running freesurfer on 64 bit Fedora 10 linux.
  I am using version: 
  freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0.
  Can anyone point me to a reference web page listing what
  steps I need to
  type to process
  a series of MRI dicom slices and use FreeSurfer to measure
  cortical
  thickness for this dicom series?

  Thank you,
  John

  --
  John Drozd
  Post-Doctoral Fellow, Robarts Research Institute
  The University of Western Ontario
  London, ON, Canada
  http://publish.uwo.ca/~jdrozd2/index.htm
   



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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.




--
John Drozd
Post-Doctoral Fellow, Robarts Research Institute
The University of Western Ontario
London, ON, Canada
http://publish.uwo.ca/~jdrozd2/index.htm
 


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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] measuring cortical thickness using FreeSurfer

[John Drozd]

Hi Bruce and Pedro,

Thank you both for sending me your suggestions.
Just to let you know, because my .dcm (dicom) files had a space and two dots
in the filenames:
(e.g. "2008_12_08.ek -0035-0001-1.dcm" )
(and using quotes around the file name or "\ " within the filename without
the quotes did not work with recon-all), recon-all truncated the filename
before the space as "2008_12_08.ek" feeding it to an mri_convert command and
gave an error message.

So I worked around this problem as follows: I converted the .dcm series to a
nifti .nii volume using 3D Slicer, and then used mri_convert to convert the
.nii format to .mgz format.  Then I ran recon-all on the .mgz formatted file
and it is now running successfully.

I see on the online tutorials and slides, that this process takes about 20
hours. Is there a way to only run partial steps pertaining only to the
cortical thickness?

Pedro also suggested that I go through the FreeSurferBeginnersGuide wiki
which I am doing now.

Also, reading some mailing lists emails, I noticed that matlab can be used
to analyze the cortical thickness statistiics, and also freesurfer comes
with matlab scripts.  I will try these tools out as well.

Thank you for your time,
John

On Tue, Jul 5, 2011 at 1:18 PM, Bruce Fischl wrote:

> recon-all \
>-i  \
>-s  \
>-sd  \
>-all
>
>
> cheers
> Bruce
>
>
>
> On Tue, 5 Jul 2011, John Drozd wrote:
>
>  Hi,
>>
>> I am running freesurfer on 64 bit Fedora 10 linux.
>> I am using version:  freesurfer-Linux-centos4_x86_**64-stable-pub-v4.3.0.
>> Can anyone point me to a reference web page listing what steps I need to
>> type to process
>> a series of MRI dicom slices and use FreeSurfer to measure cortical
>> thickness for this dicom series?
>>
>> Thank you,
>> John
>>
>> --
>> John Drozd
>> Post-Doctoral Fellow, Robarts Research Institute
>> The University of Western Ontario
>> London, ON, Canada
>> http://publish.uwo.ca/~**jdrozd2/index.htm
>>
>>
>>
>>
> ___
> 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.
>
>


-- 
John Drozd
Post-Doctoral Fellow, Robarts Research Institute
The University of Western Ontario
London, ON, Canada
http://publish.uwo.ca/~jdrozd2/index.htm
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Re: [Freesurfer] measuring cortical thickness using FreeSurfer

[Bruce Fischl]

recon-all \
-i  \
-s  \
-sd  \
-all


cheers
Bruce


On Tue, 5 Jul 2011, John Drozd wrote:


Hi,

I am running freesurfer on 64 bit Fedora 10 linux.
I am using version:  freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0.
Can anyone point me to a reference web page listing what steps I need to
type to process
a series of MRI dicom slices and use FreeSurfer to measure cortical
thickness for this dicom series?

Thank you,
John

--
John Drozd
Post-Doctoral Fellow, Robarts Research Institute
The University of Western Ontario
London, ON, Canada
http://publish.uwo.ca/~jdrozd2/index.htm
 


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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] measuring cortical thickness using FreeSurfer

[Pedro Paulo de Magalhães Oliveira Junior]

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

On Tue, Jul 5, 2011 at 13:14, John Drozd  wrote:

> Hi,
>
> I am running freesurfer on 64 bit Fedora 10 linux.
> I am using version:  freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0.
> Can anyone point me to a reference web page listing what steps I need to
> type to process
> a series of MRI dicom slices and use FreeSurfer to measure cortical
> thickness for this dicom series?
>
> Thank you,
> John
>
> --
> John Drozd
> Post-Doctoral Fellow, Robarts Research Institute
> The University of Western Ontario
> London, ON, Canada
> http://publish.uwo.ca/~jdrozd2/index.htm
>
>
>
> ___
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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
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> properly
> dispose of the e-mail.
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>
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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] measuring cortical thickness using FreeSurfer

[John Drozd]

Hi,

I am running freesurfer on 64 bit Fedora 10 linux.
I am using version:  freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0.
Can anyone point me to a reference web page listing what steps I need to
type to process
a series of MRI dicom slices and use FreeSurfer to measure cortical
thickness for this dicom series?

Thank you,
John

-- 
John Drozd
Post-Doctoral Fellow, Robarts Research Institute
The University of Western Ontario
London, ON, Canada
http://publish.uwo.ca/~jdrozd2/index.htm
___
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] Measuring cortical thickness with high resolution data

[Nick Schmansky]

Falk,

Because the -hires switch disables the use the atlas during the skull-
strip step, skull-stripping is more subject to stripping too much or too
little brain (which is why use of the atlas was introduced).  See this
tutorial for ways to correct badly stripped skull:

http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix

I had to add the switch -wsthresh 30 to get your sample subject to
skull-strip (although it still left bits and pieces which affected the
white matter tesselation step).

Nick


On Wed, 2009-04-08 at 15:07 +0200, Falk Lüsebrink wrote:
> Hi Nick,
> 
> First I wanted to give you a little bit of feedback. I'm still processing
> one volume with .6mm which is working perfectly fine until now. The skull
> stripping was done really well and no manual intervention was needed. I'm
> currently running autorecon3 and will have a look at the final results
> pretty soon. Thanks again for your modification and the help you offered.
> 
> But I recently tried to process the data I send to you simultaneously to see
> the results of the erroneous segmentation for myself. I just ran autorecon1
> to view the brainmask.mgz and the result isn't as bad as the one you send to
> me in terms of remaining dura and skull, but only the right hemisphere is
> being shown and a small piece on the anterior is missing.
> 
> I also created a new subject so no older files could somehow influence the
> new process. The result is the same. The flags I used were simply -hires and
> -autorecon1 (and -clean in case for the older subject), so I don't know what
> might have caused this issue.
> 
> Regards,
> Falk
> 
> 
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Doug Greve
> Sent: Monday, April 06, 2009 6:25 PM
> To: Falk Lüsebrink
> Cc: freesurfer@nmr.mgh.harvard.edu; 'Nick Schmansky'
> Subject: RE: [Freesurfer] Measuring cortical thickness with high resolution
> data
> 
> 
> Falk,  it looks like that file was somehow converted to DOS. try:
> 
> dos2unix recon-all
> chmod a+x recon-all
> 
> then re-run
> 
> doug
> 
> 
> On Mon, 6 Apr 2009, Falk Lüsebrink wrote:
> 
> > Hi Nick,
> >
> > I tried using your modified recon-all today but as soon as I try to
> process any data I receive following error message:
> >
> > 'nknown option: `-
> > Usage: tcsh [ -bcdefilmnqstvVxX ] [argument ...].
> >
> > Also it doesn't matter at all which flags I add to recon-all or if I don't
> use any flags at all, the error is the same. The unmodified recon-all
> performs well.
> >
> > Regards,
> > Falk
> >
> > -Original Message-----
> > From: freesurfer-boun...@nmr.mgh.harvard.edu 
> > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Nick 
> > Schmansky
> > Sent: Thursday, April 02, 2009 3:28 PM
> > To: Falk Lüsebrink
> > Cc: Freesurfer Mailing List
> > Subject: RE: [Freesurfer] Measuring cortical thickness with high 
> > resolution data
> >
> > Falk,
> >
> > There are no plans in the near future, but in the long term we'd like to
> remove the dependence on conforming the data.
> >
> > It just occurred to me that you could have the best of both worlds:
> > first run your data through the normal stream (conforming) up through
> autorecon1, then use mri_vol2vol to create a brainmask.mgz at the same
> resolution as that created using the -hires stream, and copy it over.
> > At least that would eliminate having to edit the original hires brainmask,
> which would save hours of work.  If i get few minutes i will try this.
> >
> > You can copy that recon-all over top your existing v4.x freesurfer
> installation (attached again for the list).
> >
> > Nick
> >
> >
> > On Thu, 2009-04-02 at 10:58 +0200, Falk Lüsebrink wrote:
> >> Hi Nick,
> >>
> >> Thank you very much. I'll have to look into that and try to process some
> other volumes which might work a bit better, with less manual intervention.
> >>
> >> Are there any plans to improve Freesurfer in the (near) future so that
> hires data can be processed within the currently available stream?
> >>
> >> Regards,
> >> Falk
> >>
> >> -Original Message-
> >> From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu]
> >> Sent: Wednesday, April 01, 2009 7:53 PM
> >> To: Falk Lüsebrink
> >> Cc: Freesurfer Mailing List
> >> Subject: Re: [Freesurfer] Measuring cortical thickness with high 
> >> resolution data
> 

RE: [Freesurfer] Measuring cortical thickness with high resolution data

[Falk Lüsebrink]

Hi Nick,

First I wanted to give you a little bit of feedback. I'm still processing
one volume with .6mm which is working perfectly fine until now. The skull
stripping was done really well and no manual intervention was needed. I'm
currently running autorecon3 and will have a look at the final results
pretty soon. Thanks again for your modification and the help you offered.

But I recently tried to process the data I send to you simultaneously to see
the results of the erroneous segmentation for myself. I just ran autorecon1
to view the brainmask.mgz and the result isn't as bad as the one you send to
me in terms of remaining dura and skull, but only the right hemisphere is
being shown and a small piece on the anterior is missing.

I also created a new subject so no older files could somehow influence the
new process. The result is the same. The flags I used were simply -hires and
-autorecon1 (and -clean in case for the older subject), so I don't know what
might have caused this issue.

Regards,
Falk


-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Doug Greve
Sent: Monday, April 06, 2009 6:25 PM
To: Falk Lüsebrink
Cc: freesurfer@nmr.mgh.harvard.edu; 'Nick Schmansky'
Subject: RE: [Freesurfer] Measuring cortical thickness with high resolution
data


Falk,  it looks like that file was somehow converted to DOS. try:

dos2unix recon-all
chmod a+x recon-all

then re-run

doug


On Mon, 6 Apr 2009, Falk Lüsebrink wrote:

> Hi Nick,
>
> I tried using your modified recon-all today but as soon as I try to
process any data I receive following error message:
>
> 'nknown option: `-
> Usage: tcsh [ -bcdefilmnqstvVxX ] [argument ...].
>
> Also it doesn't matter at all which flags I add to recon-all or if I don't
use any flags at all, the error is the same. The unmodified recon-all
performs well.
>
> Regards,
> Falk
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Nick 
> Schmansky
> Sent: Thursday, April 02, 2009 3:28 PM
> To: Falk Lüsebrink
> Cc: Freesurfer Mailing List
> Subject: RE: [Freesurfer] Measuring cortical thickness with high 
> resolution data
>
> Falk,
>
> There are no plans in the near future, but in the long term we'd like to
remove the dependence on conforming the data.
>
> It just occurred to me that you could have the best of both worlds:
> first run your data through the normal stream (conforming) up through
autorecon1, then use mri_vol2vol to create a brainmask.mgz at the same
resolution as that created using the -hires stream, and copy it over.
> At least that would eliminate having to edit the original hires brainmask,
which would save hours of work.  If i get few minutes i will try this.
>
> You can copy that recon-all over top your existing v4.x freesurfer
installation (attached again for the list).
>
> Nick
>
>
> On Thu, 2009-04-02 at 10:58 +0200, Falk Lüsebrink wrote:
>> Hi Nick,
>>
>> Thank you very much. I'll have to look into that and try to process some
other volumes which might work a bit better, with less manual intervention.
>>
>> Are there any plans to improve Freesurfer in the (near) future so that
hires data can be processed within the currently available stream?
>>
>> Regards,
>> Falk
>>
>> -Original Message-
>> From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu]
>> Sent: Wednesday, April 01, 2009 7:53 PM
>> To: Falk Lüsebrink
>> Cc: Freesurfer Mailing List
>> Subject: Re: [Freesurfer] Measuring cortical thickness with high 
>> resolution data
>>
>> Falk,
>>
>> Attached is a modified recon-all script where I've added a -hires switch
to force the stream to not conform the data to 1mm^3, and to not use the
atlases.
>>
>> Note that you should add the -clean flag to delete any work that had been
done prior (namely, -clean deletes brainmask.mgz, aseg.mgz and wm.mgz).
>>
>> However, in working with the .8mm data that you sent me, working with
hires data will require quite a bit of manual intervention due to the fact
that the atlases normally used cannot be used.  The first problem occurs in
skull-stripping, where quite a bit of dura and skull remains, and seems to
have intensity values close to gray matter.  This would have to be manually
erased on each of the slices.  If it is not erased (I did not do this
because of the amount of time required), then the wm.mgz file, which is what
is tessellated to create the initial surface, will be very wrong (it
tessellates the garbage surrounding the gray matter).
>>
>> See also Bruce's prior posting on the problems of working with hires da

RE: [Freesurfer] Measuring cortical thickness with high resolution data

[Falk Lüsebrink]

Hi Doug,

Thanks! Now recon-all is processing well.

Regards,
Falk

-Original Message-
From: Doug Greve [mailto:gr...@nmr.mgh.harvard.edu] 
Sent: Monday, April 06, 2009 6:25 PM
To: Falk Lüsebrink
Cc: 'Nick Schmansky'; freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] Measuring cortical thickness with high resolution
data


Falk,  it looks like that file was somehow converted to DOS. try:

dos2unix recon-all
chmod a+x recon-all

then re-run

doug


On Mon, 6 Apr 2009, Falk Lüsebrink wrote:

> Hi Nick,
>
> I tried using your modified recon-all today but as soon as I try to
process any data I receive following error message:
>
> 'nknown option: `-
> Usage: tcsh [ -bcdefilmnqstvVxX ] [argument ...].
>
> Also it doesn't matter at all which flags I add to recon-all or if I don't
use any flags at all, the error is the same. The unmodified recon-all
performs well.
>
> Regards,
> Falk
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Nick Schmansky
> Sent: Thursday, April 02, 2009 3:28 PM
> To: Falk Lüsebrink
> Cc: Freesurfer Mailing List
> Subject: RE: [Freesurfer] Measuring cortical thickness with high
resolution data
>
> Falk,
>
> There are no plans in the near future, but in the long term we'd like to
remove the dependence on conforming the data.
>
> It just occurred to me that you could have the best of both worlds:
> first run your data through the normal stream (conforming) up through
autorecon1, then use mri_vol2vol to create a brainmask.mgz at the same
resolution as that created using the -hires stream, and copy it over.
> At least that would eliminate having to edit the original hires brainmask,
which would save hours of work.  If i get few minutes i will try this.
>
> You can copy that recon-all over top your existing v4.x freesurfer
installation (attached again for the list).
>
> Nick
>
>
> On Thu, 2009-04-02 at 10:58 +0200, Falk Lüsebrink wrote:
>> Hi Nick,
>>
>> Thank you very much. I'll have to look into that and try to process some
other volumes which might work a bit better, with less manual intervention.
>>
>> Are there any plans to improve Freesurfer in the (near) future so that
hires data can be processed within the currently available stream?
>>
>> Regards,
>> Falk
>>
>> -Original Message-
>> From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu]
>> Sent: Wednesday, April 01, 2009 7:53 PM
>> To: Falk Lüsebrink
>> Cc: Freesurfer Mailing List
>> Subject: Re: [Freesurfer] Measuring cortical thickness with high
>> resolution data
>>
>> Falk,
>>
>> Attached is a modified recon-all script where I've added a -hires switch
to force the stream to not conform the data to 1mm^3, and to not use the
atlases.
>>
>> Note that you should add the -clean flag to delete any work that had been
done prior (namely, -clean deletes brainmask.mgz, aseg.mgz and wm.mgz).
>>
>> However, in working with the .8mm data that you sent me, working with
hires data will require quite a bit of manual intervention due to the fact
that the atlases normally used cannot be used.  The first problem occurs in
skull-stripping, where quite a bit of dura and skull remains, and seems to
have intensity values close to gray matter.  This would have to be manually
erased on each of the slices.  If it is not erased (I did not do this
because of the amount of time required), then the wm.mgz file, which is what
is tessellated to create the initial surface, will be very wrong (it
tessellates the garbage surrounding the gray matter).
>>
>> See also Bruce's prior posting on the problems of working with hires data
in freesurfer.
>>
>> Nick
>>
>>
>> On Wed, 2009-03-25 at 13:04 +0100, Falk Lüsebrink wrote:
>>> Hi Freesurfers,
>>>
>>>
>>>
>>> Iÿÿm trying to evaluate the usefulness of high resolution scans
>>> acquired at 7T with an isometric voxel size of .6mm for the
>>> measurement of cortical thickness. The inhomogeneities are taken
>>> care of by dividing the scans with another scan of another sequence,
>>> so they are not an issue anymore.
>>>
>>>
>>>
>>> My problem is that Freesurfer usually conforms the voxel size to 1mm
>>> which is not desirable. I tried using the ÿÿcm and ÿÿnoaseg flags for
>>> the recon-all process to avoid the conformation and to skip the
>>> subcortical segmentation, but another problem arises while using
>>> these flags.
>>>
>>>
>>>
>>> The error I receive is occurring after the WM Segmentation a

RE: [Freesurfer] Measuring cortical thickness with high resolution data

[Doug Greve]

Falk,  it looks like that file was somehow converted to DOS. try:

dos2unix recon-all
chmod a+x recon-all

then re-run

doug


On Mon, 6 Apr 2009, Falk Lüsebrink wrote:


Hi Nick,

I tried using your modified recon-all today but as soon as I try to process any 
data I receive following error message:

'nknown option: `-
Usage: tcsh [ -bcdefilmnqstvVxX ] [argument ...].

Also it doesn't matter at all which flags I add to recon-all or if I don't use 
any flags at all, the error is the same. The unmodified recon-all performs well.

Regards,
Falk

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Nick Schmansky
Sent: Thursday, April 02, 2009 3:28 PM
To: Falk Lüsebrink
Cc: Freesurfer Mailing List
Subject: RE: [Freesurfer] Measuring cortical thickness with high resolution data

Falk,

There are no plans in the near future, but in the long term we'd like to remove 
the dependence on conforming the data.

It just occurred to me that you could have the best of both worlds:
first run your data through the normal stream (conforming) up through 
autorecon1, then use mri_vol2vol to create a brainmask.mgz at the same 
resolution as that created using the -hires stream, and copy it over.
At least that would eliminate having to edit the original hires brainmask, 
which would save hours of work.  If i get few minutes i will try this.

You can copy that recon-all over top your existing v4.x freesurfer installation 
(attached again for the list).

Nick


On Thu, 2009-04-02 at 10:58 +0200, Falk Lüsebrink wrote:

Hi Nick,

Thank you very much. I'll have to look into that and try to process some other 
volumes which might work a bit better, with less manual intervention.

Are there any plans to improve Freesurfer in the (near) future so that hires 
data can be processed within the currently available stream?

Regards,
Falk

-Original Message-
From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu]
Sent: Wednesday, April 01, 2009 7:53 PM
To: Falk Lüsebrink
Cc: Freesurfer Mailing List
Subject: Re: [Freesurfer] Measuring cortical thickness with high
resolution data

Falk,

Attached is a modified recon-all script where I've added a -hires switch to 
force the stream to not conform the data to 1mm^3, and to not use the atlases.

Note that you should add the -clean flag to delete any work that had been done 
prior (namely, -clean deletes brainmask.mgz, aseg.mgz and wm.mgz).

However, in working with the .8mm data that you sent me, working with hires 
data will require quite a bit of manual intervention due to the fact that the 
atlases normally used cannot be used.  The first problem occurs in 
skull-stripping, where quite a bit of dura and skull remains, and seems to have 
intensity values close to gray matter.  This would have to be manually erased 
on each of the slices.  If it is not erased (I did not do this because of the 
amount of time required), then the wm.mgz file, which is what is tessellated to 
create the initial surface, will be very wrong (it tessellates the garbage 
surrounding the gray matter).

See also Bruce's prior posting on the problems of working with hires data in 
freesurfer.

Nick


On Wed, 2009-03-25 at 13:04 +0100, Falk Lüsebrink wrote:

Hi Freesurfers,



Iÿÿm trying to evaluate the usefulness of high resolution scans
acquired at 7T with an isometric voxel size of .6mm for the
measurement of cortical thickness. The inhomogeneities are taken
care of by dividing the scans with another scan of another sequence,
so they are not an issue anymore.



My problem is that Freesurfer usually conforms the voxel size to 1mm
which is not desirable. I tried using the ÿÿcm and ÿÿnoaseg flags for
the recon-all process to avoid the conformation and to skip the
subcortical segmentation, but another problem arises while using
these flags.



The error I receive is occurring after the WM Segmentation and
states as follows:



#

#...@# WM Segmentation Wed Mar 18 10:14:42 CET 2009



 cp wm.mgz wm.seg.mgz





 mri_segment -keep brain.mgz wm.seg.mgz



preserving editing changes in output volume...

doing initial intensity segmentation...

using local statistics to label ambiguous voxels...

computing class statistics for intensity windows...

WM (106.0): 106.9 +- 5.8 [80.0 --> 125.0]

GM (69.0) : 66.3 +- 11.6 [30.0 --> 96.0]

setting bottom of white matter range to 77.9

setting top of gray matter range to 89.4

doing initial intensity segmentation...

using local statistics to label ambiguous voxels...

using local geometry to label remaining ambiguous voxels...



reclassifying voxels using Gaussian border classifier...



removing voxels with positive offset direction...

smoothing T1 volume with sigma = 0.250

removing 1-dimensional structures...

thickening thin strands

20 segments, 4813 filled

10270 bright non-wm voxels segmented

RE: [Freesurfer] Measuring cortical thickness with high resolution data

[Falk Lüsebrink]

Hi Nick,

I tried using your modified recon-all today but as soon as I try to process any 
data I receive following error message:

'nknown option: `-
Usage: tcsh [ -bcdefilmnqstvVxX ] [argument ...].

Also it doesn't matter at all which flags I add to recon-all or if I don't use 
any flags at all, the error is the same. The unmodified recon-all performs well.

Regards,
Falk

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Nick Schmansky
Sent: Thursday, April 02, 2009 3:28 PM
To: Falk Lüsebrink
Cc: Freesurfer Mailing List
Subject: RE: [Freesurfer] Measuring cortical thickness with high resolution data

Falk,

There are no plans in the near future, but in the long term we'd like to remove 
the dependence on conforming the data.

It just occurred to me that you could have the best of both worlds:
first run your data through the normal stream (conforming) up through 
autorecon1, then use mri_vol2vol to create a brainmask.mgz at the same 
resolution as that created using the -hires stream, and copy it over.
At least that would eliminate having to edit the original hires brainmask, 
which would save hours of work.  If i get few minutes i will try this.

You can copy that recon-all over top your existing v4.x freesurfer installation 
(attached again for the list).

Nick


On Thu, 2009-04-02 at 10:58 +0200, Falk Lüsebrink wrote:
> Hi Nick,
> 
> Thank you very much. I'll have to look into that and try to process some 
> other volumes which might work a bit better, with less manual intervention.
> 
> Are there any plans to improve Freesurfer in the (near) future so that hires 
> data can be processed within the currently available stream?
> 
> Regards,
> Falk
> 
> -Original Message-
> From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu]
> Sent: Wednesday, April 01, 2009 7:53 PM
> To: Falk Lüsebrink
> Cc: Freesurfer Mailing List
> Subject: Re: [Freesurfer] Measuring cortical thickness with high 
> resolution data
> 
> Falk,
> 
> Attached is a modified recon-all script where I've added a -hires switch to 
> force the stream to not conform the data to 1mm^3, and to not use the atlases.
> 
> Note that you should add the -clean flag to delete any work that had been 
> done prior (namely, -clean deletes brainmask.mgz, aseg.mgz and wm.mgz).
> 
> However, in working with the .8mm data that you sent me, working with hires 
> data will require quite a bit of manual intervention due to the fact that the 
> atlases normally used cannot be used.  The first problem occurs in 
> skull-stripping, where quite a bit of dura and skull remains, and seems to 
> have intensity values close to gray matter.  This would have to be manually 
> erased on each of the slices.  If it is not erased (I did not do this because 
> of the amount of time required), then the wm.mgz file, which is what is 
> tessellated to create the initial surface, will be very wrong (it tessellates 
> the garbage surrounding the gray matter).
> 
> See also Bruce's prior posting on the problems of working with hires data in 
> freesurfer.
> 
> Nick
> 
> 
> On Wed, 2009-03-25 at 13:04 +0100, Falk Lüsebrink wrote:
> > Hi Freesurfers,
> > 
> >  
> > 
> > I’m trying to evaluate the usefulness of high resolution scans 
> > acquired at 7T with an isometric voxel size of .6mm for the 
> > measurement of cortical thickness. The inhomogeneities are taken 
> > care of by dividing the scans with another scan of another sequence, 
> > so they are not an issue anymore.
> > 
> >  
> > 
> > My problem is that Freesurfer usually conforms the voxel size to 1mm 
> > which is not desirable. I tried using the –cm and –noaseg flags for 
> > the recon-all process to avoid the conformation and to skip the 
> > subcortical segmentation, but another problem arises while using 
> > these flags.
> > 
> >  
> > 
> > The error I receive is occurring after the WM Segmentation and 
> > states as follows:
> > 
> >  
> > 
> > #
> > 
> > #...@# WM Segmentation Wed Mar 18 10:14:42 CET 2009
> > 
> >  
> > 
> >  cp wm.mgz wm.seg.mgz
> > 
> >  
> > 
> >  
> > 
> >  mri_segment -keep brain.mgz wm.seg.mgz
> > 
> >  
> > 
> > preserving editing changes in output volume...
> > 
> > doing initial intensity segmentation...
> > 
> > using local statistics to label ambiguous voxels...
> > 
> > computing class statistics for intensity windows...
> > 
> > WM (106.0): 106.9 +- 5.8 [80.0 --> 125.0]
> &

RE: [Freesurfer] Measuring cortical thickness with high resolution data

[Falk Lüsebrink]

Hi Nick,

Thank you very much. I'll have to look into that and try to process some other 
volumes which might work a bit better, with less manual intervention.

Are there any plans to improve Freesurfer in the (near) future so that hires 
data can be processed within the currently available stream?

Regards,
Falk

-Original Message-
From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu] 
Sent: Wednesday, April 01, 2009 7:53 PM
To: Falk Lüsebrink
Cc: Freesurfer Mailing List
Subject: Re: [Freesurfer] Measuring cortical thickness with high resolution data

Falk,

Attached is a modified recon-all script where I've added a -hires switch to 
force the stream to not conform the data to 1mm^3, and to not use the atlases.

Note that you should add the -clean flag to delete any work that had been done 
prior (namely, -clean deletes brainmask.mgz, aseg.mgz and wm.mgz).

However, in working with the .8mm data that you sent me, working with hires 
data will require quite a bit of manual intervention due to the fact that the 
atlases normally used cannot be used.  The first problem occurs in 
skull-stripping, where quite a bit of dura and skull remains, and seems to have 
intensity values close to gray matter.  This would have to be manually erased 
on each of the slices.  If it is not erased (I did not do this because of the 
amount of time required), then the wm.mgz file, which is what is tessellated to 
create the initial surface, will be very wrong (it tessellates the garbage 
surrounding the gray matter).

See also Bruce's prior posting on the problems of working with hires data in 
freesurfer.

Nick


On Wed, 2009-03-25 at 13:04 +0100, Falk Lüsebrink wrote:
> Hi Freesurfers,
> 
>  
> 
> I’m trying to evaluate the usefulness of high resolution scans 
> acquired at 7T with an isometric voxel size of .6mm for the 
> measurement of cortical thickness. The inhomogeneities are taken care 
> of by dividing the scans with another scan of another sequence, so 
> they are not an issue anymore.
> 
>  
> 
> My problem is that Freesurfer usually conforms the voxel size to 1mm 
> which is not desirable. I tried using the –cm and –noaseg flags for 
> the recon-all process to avoid the conformation and to skip the 
> subcortical segmentation, but another problem arises while using these 
> flags.
> 
>  
> 
> The error I receive is occurring after the WM Segmentation and states 
> as follows:
> 
>  
> 
> #
> 
> #...@# WM Segmentation Wed Mar 18 10:14:42 CET 2009
> 
>  
> 
>  cp wm.mgz wm.seg.mgz
> 
>  
> 
>  
> 
>  mri_segment -keep brain.mgz wm.seg.mgz
> 
>  
> 
> preserving editing changes in output volume...
> 
> doing initial intensity segmentation...
> 
> using local statistics to label ambiguous voxels...
> 
> computing class statistics for intensity windows...
> 
> WM (106.0): 106.9 +- 5.8 [80.0 --> 125.0]
> 
> GM (69.0) : 66.3 +- 11.6 [30.0 --> 96.0]
> 
> setting bottom of white matter range to 77.9
> 
> setting top of gray matter range to 89.4
> 
> doing initial intensity segmentation...
> 
> using local statistics to label ambiguous voxels...
> 
> using local geometry to label remaining ambiguous voxels...
> 
>  
> 
> reclassifying voxels using Gaussian border classifier...
> 
>  
> 
> removing voxels with positive offset direction...
> 
> smoothing T1 volume with sigma = 0.250
> 
> removing 1-dimensional structures...
> 
> thickening thin strands
> 
> 20 segments, 4813 filled
> 
> 10270 bright non-wm voxels segmented.
> 
> 5589 diagonally connected voxels added...
> 
> white matter segmentation took 2.4 minutes
> 
> writing output to wm.seg.mgz...
> 
> ERROR: mri_segment-MRIcheckVolDims: volume1 height=256 != volume2 
> height=320.
> 
>  
> 
> The dimensions of the data I’m trying to process is 320 x 320 x 224 
> and is changed to 320 x 320 x 320 while using the –cm flag. It seems 
> the mri_segment process can’t handle any dimensions above 256 or I’m 
> missing another flag.
> 
>  
> 
> Does someone has any ideas about that issue?
> 
>  
> 
> Regards,
> 
> Falk
> 
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] Measuring cortical thickness with high resolution data

[Nick Schmansky]

Falk,

Is it possible to send me an example hires volume that you are working
with?  I'd like to send it through the stream myself so that I can fix
the problems encountered (with using hires data) first-hand.  You can
upload the dicom or the 001.mgz file to me here:

https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html

Nick



On Wed, 2009-03-25 at 13:04 +0100, Falk Lüsebrink wrote:
> Hi Freesurfers,
> 
>  
> 
> I’m trying to evaluate the usefulness of high resolution scans
> acquired at 7T with an isometric voxel size of .6mm for the
> measurement of cortical thickness. The inhomogeneities are taken care
> of by dividing the scans with another scan of another sequence, so
> they are not an issue anymore.
> 
>  
> 
> My problem is that Freesurfer usually conforms the voxel size to 1mm
> which is not desirable. I tried using the –cm and –noaseg flags for
> the recon-all process to avoid the conformation and to skip the
> subcortical segmentation, but another problem arises while using these
> flags.
> 
>  
> 
> The error I receive is occurring after the WM Segmentation and states
> as follows:
> 
>  
> 
> #
> 
> #...@# WM Segmentation Wed Mar 18 10:14:42 CET 2009
> 
>  
> 
>  cp wm.mgz wm.seg.mgz 
> 
>  
> 
>  
> 
>  mri_segment -keep brain.mgz wm.seg.mgz 
> 
>  
> 
> preserving editing changes in output volume...
> 
> doing initial intensity segmentation...
> 
> using local statistics to label ambiguous voxels...
> 
> computing class statistics for intensity windows...
> 
> WM (106.0): 106.9 +- 5.8 [80.0 --> 125.0]
> 
> GM (69.0) : 66.3 +- 11.6 [30.0 --> 96.0]
> 
> setting bottom of white matter range to 77.9
> 
> setting top of gray matter range to 89.4
> 
> doing initial intensity segmentation...
> 
> using local statistics to label ambiguous voxels...
> 
> using local geometry to label remaining ambiguous voxels...
> 
>  
> 
> reclassifying voxels using Gaussian border classifier...
> 
>  
> 
> removing voxels with positive offset direction...
> 
> smoothing T1 volume with sigma = 0.250
> 
> removing 1-dimensional structures...
> 
> thickening thin strands
> 
> 20 segments, 4813 filled
> 
> 10270 bright non-wm voxels segmented.
> 
> 5589 diagonally connected voxels added...
> 
> white matter segmentation took 2.4 minutes
> 
> writing output to wm.seg.mgz...
> 
> ERROR: mri_segment-MRIcheckVolDims: volume1 height=256 != volume2
> height=320.
> 
>  
> 
> The dimensions of the data I’m trying to process is 320 x 320 x 224
> and is changed to 320 x 320 x 320 while using the –cm flag. It seems
> the mri_segment process can’t handle any dimensions above 256 or I’m
> missing another flag.
> 
>  
> 
> Does someone has any ideas about that issue?
> 
>  
> 
> Regards,
> 
> Falk
> 
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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[Freesurfer] Measuring cortical thickness with high resolution data

[Falk Lüsebrink]

Hi Freesurfers,

 

I’m trying to evaluate the usefulness of high resolution scans acquired at
7T with an isometric voxel size of .6mm for the measurement of cortical
thickness. The inhomogeneities are taken care of by dividing the scans with
another scan of another sequence, so they are not an issue anymore.

 

My problem is that Freesurfer usually conforms the voxel size to 1mm which
is not desirable. I tried using the –cm and –noaseg flags for the recon-all
process to avoid the conformation and to skip the subcortical segmentation,
but another problem arises while using these flags.

 

The error I receive is occurring after the WM Segmentation and states as
follows:

 

#

#...@# WM Segmentation Wed Mar 18 10:14:42 CET 2009

 

 cp wm.mgz wm.seg.mgz 

 

 

 mri_segment -keep brain.mgz wm.seg.mgz 

 

preserving editing changes in output volume...

doing initial intensity segmentation...

using local statistics to label ambiguous voxels...

computing class statistics for intensity windows...

WM (106.0): 106.9 +- 5.8 [80.0 --> 125.0]

GM (69.0) : 66.3 +- 11.6 [30.0 --> 96.0]

setting bottom of white matter range to 77.9

setting top of gray matter range to 89.4

doing initial intensity segmentation...

using local statistics to label ambiguous voxels...

using local geometry to label remaining ambiguous voxels...

 

reclassifying voxels using Gaussian border classifier...

 

removing voxels with positive offset direction...

smoothing T1 volume with sigma = 0.250

removing 1-dimensional structures...

thickening thin strands

20 segments, 4813 filled

10270 bright non-wm voxels segmented.

5589 diagonally connected voxels added...

white matter segmentation took 2.4 minutes

writing output to wm.seg.mgz...

ERROR: mri_segment-MRIcheckVolDims: volume1 height=256 != volume2
height=320.

 

The dimensions of the data I’m trying to process is 320 x 320 x 224 and is
changed to 320 x 320 x 320 while using the –cm flag. It seems the
mri_segment process can’t handle any dimensions above 256 or I’m missing
another flag.

 

Does someone has any ideas about that issue?

 

Regards,

Falk

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