Re: [Freesurfer] Estimate Brain Volume Fraction

[Cheryl McCreary]

Ok.  So then if ventricular volume is already excluded, the brain
parenchymal volume should be:

Total GM + total cortical WM +cerebellar GM + cerebellar WM + brain stem -
CSF?

Cheryl 


On 11-12-15 2:58 PM, "Douglas N Greve"  wrote:

> Yes.
> 
> Alexopoulos, Dimitrios wrote:
>> Just for clarification, the standard output value in the aseg.stats for total
>> cortical WM
>> is detremined with 'mris_wm_volume' which subtracts out the volume of non-wm
>> voxels based on the
>> aseg, correct?
>> 
>> Jim
>> 
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Thursday, December 15, 2011 3:02 PM
>> To: Cheryl McCreary
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Estimate Brain Volume Fraction
>> 
>> total cortical WM should not include the ventricles. If the lateral
>> ventricles are not segmented properly, then they would be included, but
>> this would be an error. Otherwise, I think your equation is correct.
>> doug
>> 
>> Cheryl McCreary wrote:
>>   
>>> Hi Doug,
>>> 
>>> Thanks for the quick reply.  I will re-run the mri_segstats as below to get
>>> the BrainSegNotVent volumes for consistency with the previous version.
>>> 
>>> Just for my own understanding using the default output aseg.stats from
>>> recon-all, could whole brain parenchymal volume be calculated as  [(total
>>> GM, total cortical WM, cerebellar GM, cerebellar WM + brain-stem)-2*(left
>>> lateral ventricle + left Inf Lat Vent + right lateral ventricle+ right inf
>>> lat vent) - CSF)]? I'm assuming that since both the white matter and pial
>>> surfaces include the lateral ventricle, the lateral ventricular volume needs
>>> to be subtracted, while the 3rd and 4th ventricles are not included in the
>>> surfaces and therefore would not need to be subtracted?
>>> 
>>> Kind regards,
>>> Cheryl
>>> 
>>> 
>>> On 11-12-14 12:45 PM, "Douglas N Greve"  wrote:
>>> 
>>> 
>>> 
 Hi Cheryl,
 You can regenerate the asseg.stats file with BrianVolNotVent with:
 
 cd $SUBJECTS_DIR/yoursubject
  mri_segstats --subject yoursubject --seg mri/aseg.mgz --sum
 stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm
 --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm
 --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray
 --ctab /usr/local/freesurfer/dev/ASegStatsLUT.txt  --brain-vol-from-seg
 
 This is the same command that generated the existing aseg.stats file
 with "--brain-vol-from-seg" added.
 
 doug
 
 
 
 
 
 Cheryl McCreary wrote:
 
   
> Hi Freesurfer experts,
> 
> I would like to determine brain parenchymal fraction (ie brain tissue
> volume/estimated ICV) as an estimate of global atrophy.  In previous
> versions of FS, I used the BrianVolNotVent/ICV.  Is this correct?
> 
> I am now using freesurfer version 5.0.0 and BrainVolNotVent is not longer
> available.
> 
> My understanding is that the total gray matter and total cortical white
> matter volumes are determined from the pial and white surfaces (thickness
> *surface area).  Do these volumes include or exclude the ventricular
> volumes? Can the total brain volume be calculated as the sum of the total
> GM, total cortical WM, brain stem, cerebellar GM and WM minus the CSF.  Or
> do the volumes of the ventricles need to be subtracted as well?
> 
> Thanks for your help.
> 
> Cheryl
> 
> 
> 
>>> 
>> 
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>> 
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> 
>> ___
>> 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.
>> 
>> 
>> The materials in this email are private and may contain Protected Health
>> Information. If you are not the intended recipient, be advised that any
>> unauthorized use, disclosure, copying, distribution or the taking of any
>> action in reliance on the contents of this information is strictly
>> prohibited. If you have received this email in error, please immediately
>> notify the sender via telephone or return 

Re: [Freesurfer] Estimate Brain Volume Fraction

[Bruce Fischl]

yes
On Thu, 15 Dec 2011, Alexopoulos, Dimitrios wrote:

> Just for clarification, the standard output value in the aseg.stats for total 
> cortical WM
> is detremined with 'mris_wm_volume' which subtracts out the volume of non-wm 
> voxels based on the
> aseg, correct?
>
> Jim
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Thursday, December 15, 2011 3:02 PM
> To: Cheryl McCreary
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Estimate Brain Volume Fraction
>
> total cortical WM should not include the ventricles. If the lateral
> ventricles are not segmented properly, then they would be included, but
> this would be an error. Otherwise, I think your equation is correct.
> doug
>
> Cheryl McCreary wrote:
>> Hi Doug,
>>
>> Thanks for the quick reply.  I will re-run the mri_segstats as below to get
>> the BrainSegNotVent volumes for consistency with the previous version.
>>
>> Just for my own understanding using the default output aseg.stats from
>> recon-all, could whole brain parenchymal volume be calculated as  [(total
>> GM, total cortical WM, cerebellar GM, cerebellar WM + brain-stem)-2*(left
>> lateral ventricle + left Inf Lat Vent + right lateral ventricle+ right inf
>> lat vent) - CSF)]? I'm assuming that since both the white matter and pial
>> surfaces include the lateral ventricle, the lateral ventricular volume needs
>> to be subtracted, while the 3rd and 4th ventricles are not included in the
>> surfaces and therefore would not need to be subtracted?
>>
>> Kind regards,
>> Cheryl
>>
>>
>> On 11-12-14 12:45 PM, "Douglas N Greve"  wrote:
>>
>>
>>> Hi Cheryl,
>>> You can regenerate the asseg.stats file with BrianVolNotVent with:
>>>
>>> cd $SUBJECTS_DIR/yoursubject
>>>  mri_segstats --subject yoursubject --seg mri/aseg.mgz --sum
>>> stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm
>>> --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm
>>> --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray
>>> --ctab /usr/local/freesurfer/dev/ASegStatsLUT.txt  --brain-vol-from-seg
>>>
>>> This is the same command that generated the existing aseg.stats file
>>> with "--brain-vol-from-seg" added.
>>>
>>> doug
>>>
>>>
>>>
>>>
>>>
>>> Cheryl McCreary wrote:
>>>
 Hi Freesurfer experts,

 I would like to determine brain parenchymal fraction (ie brain tissue
 volume/estimated ICV) as an estimate of global atrophy.  In previous
 versions of FS, I used the BrianVolNotVent/ICV.  Is this correct?

 I am now using freesurfer version 5.0.0 and BrainVolNotVent is not longer
 available.

 My understanding is that the total gray matter and total cortical white
 matter volumes are determined from the pial and white surfaces (thickness
 *surface area).  Do these volumes include or exclude the ventricular
 volumes? Can the total brain volume be calculated as the sum of the total
 GM, total cortical WM, brain stem, cerebellar GM and WM minus the CSF.  Or
 do the volumes of the ventricles need to be subtracted as well?

 Thanks for your help.

 Cheryl


>>
>>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
> ___
> 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.
>
>
> The materials in this email are private and may contain Protected Health 
> Information. If you are not the intended recipient, be advised that any 
> unauthorized use, disclosure, copying, distribution or the taking of any 
> action in reliance on the contents of this information is strictly 
> prohibited. If you have received this email in error, please immediately 
> notify the sender via telephone or return email.
>
> ___
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>
>
>
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Re: [Freesurfer] Estimate Brain Volume Fraction

[Douglas N Greve]

Yes.

Alexopoulos, Dimitrios wrote:
> Just for clarification, the standard output value in the aseg.stats for total 
> cortical WM
> is detremined with 'mris_wm_volume' which subtracts out the volume of non-wm 
> voxels based on the
> aseg, correct?
>
> Jim
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Thursday, December 15, 2011 3:02 PM
> To: Cheryl McCreary
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Estimate Brain Volume Fraction
>
> total cortical WM should not include the ventricles. If the lateral
> ventricles are not segmented properly, then they would be included, but
> this would be an error. Otherwise, I think your equation is correct.
> doug
>
> Cheryl McCreary wrote:
>   
>> Hi Doug,
>>
>> Thanks for the quick reply.  I will re-run the mri_segstats as below to get
>> the BrainSegNotVent volumes for consistency with the previous version.
>>
>> Just for my own understanding using the default output aseg.stats from
>> recon-all, could whole brain parenchymal volume be calculated as  [(total
>> GM, total cortical WM, cerebellar GM, cerebellar WM + brain-stem)-2*(left
>> lateral ventricle + left Inf Lat Vent + right lateral ventricle+ right inf
>> lat vent) - CSF)]? I'm assuming that since both the white matter and pial
>> surfaces include the lateral ventricle, the lateral ventricular volume needs
>> to be subtracted, while the 3rd and 4th ventricles are not included in the
>> surfaces and therefore would not need to be subtracted?
>>
>> Kind regards,
>> Cheryl
>>
>>
>> On 11-12-14 12:45 PM, "Douglas N Greve"  wrote:
>>
>>
>> 
>>> Hi Cheryl,
>>> You can regenerate the asseg.stats file with BrianVolNotVent with:
>>>
>>> cd $SUBJECTS_DIR/yoursubject
>>>  mri_segstats --subject yoursubject --seg mri/aseg.mgz --sum
>>> stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm
>>> --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm
>>> --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray
>>> --ctab /usr/local/freesurfer/dev/ASegStatsLUT.txt  --brain-vol-from-seg
>>>
>>> This is the same command that generated the existing aseg.stats file
>>> with "--brain-vol-from-seg" added.
>>>
>>> doug
>>>
>>>
>>>
>>>
>>>
>>> Cheryl McCreary wrote:
>>>
>>>   
 Hi Freesurfer experts,

 I would like to determine brain parenchymal fraction (ie brain tissue
 volume/estimated ICV) as an estimate of global atrophy.  In previous
 versions of FS, I used the BrianVolNotVent/ICV.  Is this correct?

 I am now using freesurfer version 5.0.0 and BrainVolNotVent is not longer
 available.

 My understanding is that the total gray matter and total cortical white
 matter volumes are determined from the pial and white surfaces (thickness
 *surface area).  Do these volumes include or exclude the ventricular
 volumes? Can the total brain volume be calculated as the sum of the total
 GM, total cortical WM, brain stem, cerebellar GM and WM minus the CSF.  Or
 do the volumes of the ventricles need to be subtracted as well?

 Thanks for your help.

 Cheryl


 
>> 
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
> ___
> 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.
>
>
> The materials in this email are private and may contain Protected Health 
> Information. If you are not the intended recipient, be advised that any 
> unauthorized use, disclosure, copying, distribution or the taking of any 
> action in reliance on the contents of this information is strictly 
> prohibited. If you have received this email in error, please immediately 
> notify the sender via telephone or return email.
>
>
>   

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] Estimate Brain Volume Fraction

[Alexopoulos, Dimitrios]

Just for clarification, the standard output value in the aseg.stats for total 
cortical WM
is detremined with 'mris_wm_volume' which subtracts out the volume of non-wm 
voxels based on the
aseg, correct?

Jim


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Thursday, December 15, 2011 3:02 PM
To: Cheryl McCreary
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Estimate Brain Volume Fraction

total cortical WM should not include the ventricles. If the lateral
ventricles are not segmented properly, then they would be included, but
this would be an error. Otherwise, I think your equation is correct.
doug

Cheryl McCreary wrote:
> Hi Doug,
>
> Thanks for the quick reply.  I will re-run the mri_segstats as below to get
> the BrainSegNotVent volumes for consistency with the previous version.
>
> Just for my own understanding using the default output aseg.stats from
> recon-all, could whole brain parenchymal volume be calculated as  [(total
> GM, total cortical WM, cerebellar GM, cerebellar WM + brain-stem)-2*(left
> lateral ventricle + left Inf Lat Vent + right lateral ventricle+ right inf
> lat vent) - CSF)]? I'm assuming that since both the white matter and pial
> surfaces include the lateral ventricle, the lateral ventricular volume needs
> to be subtracted, while the 3rd and 4th ventricles are not included in the
> surfaces and therefore would not need to be subtracted?
>
> Kind regards,
> Cheryl
>
>
> On 11-12-14 12:45 PM, "Douglas N Greve"  wrote:
>
>
>> Hi Cheryl,
>> You can regenerate the asseg.stats file with BrianVolNotVent with:
>>
>> cd $SUBJECTS_DIR/yoursubject
>>  mri_segstats --subject yoursubject --seg mri/aseg.mgz --sum
>> stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm
>> --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm
>> --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray
>> --ctab /usr/local/freesurfer/dev/ASegStatsLUT.txt  --brain-vol-from-seg
>>
>> This is the same command that generated the existing aseg.stats file
>> with "--brain-vol-from-seg" added.
>>
>> doug
>>
>>
>>
>>
>>
>> Cheryl McCreary wrote:
>>
>>> Hi Freesurfer experts,
>>>
>>> I would like to determine brain parenchymal fraction (ie brain tissue
>>> volume/estimated ICV) as an estimate of global atrophy.  In previous
>>> versions of FS, I used the BrianVolNotVent/ICV.  Is this correct?
>>>
>>> I am now using freesurfer version 5.0.0 and BrainVolNotVent is not longer
>>> available.
>>>
>>> My understanding is that the total gray matter and total cortical white
>>> matter volumes are determined from the pial and white surfaces (thickness
>>> *surface area).  Do these volumes include or exclude the ventricular
>>> volumes? Can the total brain volume be calculated as the sum of the total
>>> GM, total cortical WM, brain stem, cerebellar GM and WM minus the CSF.  Or
>>> do the volumes of the ventricles need to be subtracted as well?
>>>
>>> Thanks for your help.
>>>
>>> Cheryl
>>>
>>>
>
>

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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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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The materials in this email are private and may contain Protected Health 
Information. If you are not the intended recipient, be advised that any 
unauthorized use, disclosure, copying, distribution or the taking of any action 
in reliance on the contents of this information is strictly prohibited. If you 
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Re: [Freesurfer] ICV and regional brain volumes

[Douglas N Greve]

Hi Heather, the ICV is mostly unrelated to the other volumetric 
measures. what do you mean that you are having problems getting ICV to 
fit correctly in your sample?
doug

Lugar, Heather wrote:
>
> We are having a difficult time getting the ICV to fit correctly in our 
> sample, but the segmentions and parcellations look accurate.  I 
> believe that the ICV is generated from the talairach.xfm early on in 
> the processing stream, but then further processing for 
> segmentations/parcellations is done. 
>
>  
>
> So, does the ICV measure affect regional brain volumes in any way, or 
> can we trust the volumetric measures to be accurate even if the ICV is 
> not? 
>
>  
>
> Thank you,
>
> Heather Lugar
>
> 
>
> ___
> Freesurfer mailing list
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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dispose of the e-mail.

[Freesurfer] (no subject)

[Adam Nitenson]

Hi Doug et al,

We have been working on a linear regression-type analysis (see attached
analysis.info for analysis and slopepar for a sample paradigm file) that
involves task-related activation in a working memory test.  For each
participant, there are four conditions: 1, 3, 5, and 7 items that need to
be remembered.  The question that we would like to ask is: for each voxel,
does the slope of activation (i.e., the slope of the best-fit line as you
move from 1 to 3 to 5 to 7 items, as calculated separately for each
subject) differ from zero?  The second-level analysis would determine if
there is a significant difference in activation-related slope between
groups.

Based on previous discussion, the way we have been doing this is to modify
the paradigm file to create the following contrast:

Condition 2: activation during working memory, but weighted by condition –
so the 1 item condition is weighted as “1”, the 3 item condition as “3”,
etc.
Condition 0: fixation
The contrast is Condition 2 minus Condition 0.

However, this method of weighting does not appear to answer the question
about slope, but rather focuses on a weighted average.

Consider the following scenario, involving 5 subjects (A through E):

The SLOPE column is calculated using the slope function of the spreadsheet
(i.e., slope of best fit line, using values of 1...3...5...7 for the
x-axis, and, say, for subject A, the values of 2...4...6...8 for the
y-axis).

The WEIGHTED column is calculated in the way that I think FS-FAST is doing
it, which is as follows:
((1 * 1 item activ. value) + (3 * 3 item activ. value) + (5 * 5 item
activ. value) + (7 * 7 item activ. value))/4

The SLOPE and WEIGHTED values (regardless of their different scale) are
not really comparable.  For example, for Subject A, the SLOPE value is 1
and the WEIGHTED value is 58, while for Subject E, the SLOPE value is 1.1
and the WEIGHTED value is 28.

So when looking at the paradigm file, take the lines

76.57   2   3.4 5
213.42  2   2.297

Does this mean that the activation at the first timepoint is accounted for
5-fold and the second timepoint 7-fold? If this is the case then this
analysis may not best represent what we are looking for.

Is there a way to modify the paradigm file so that the analysis can focus
on slope of the best fit line — as opposed to the weighted average?

Thanks,
Josh



Adam Nitenson, B.S.
Brain Genomics Lab
Massachusetts General Hospital
niten...@nmr.mgh.harvard.edu
Phone: 617-643-3215

slopepar
Description: Binary data


analysis.info
Description: Binary data
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Re: [Freesurfer] Estimate Brain Volume Fraction

[Douglas N Greve]

total cortical WM should not include the ventricles. If the lateral 
ventricles are not segmented properly, then they would be included, but 
this would be an error. Otherwise, I think your equation is correct.
doug

Cheryl McCreary wrote:
> Hi Doug,
>
> Thanks for the quick reply.  I will re-run the mri_segstats as below to get
> the BrainSegNotVent volumes for consistency with the previous version.
>
> Just for my own understanding using the default output aseg.stats from
> recon-all, could whole brain parenchymal volume be calculated as  [(total
> GM, total cortical WM, cerebellar GM, cerebellar WM + brain-stem)-2*(left
> lateral ventricle + left Inf Lat Vent + right lateral ventricle+ right inf
> lat vent) - CSF)]? I'm assuming that since both the white matter and pial
> surfaces include the lateral ventricle, the lateral ventricular volume needs
> to be subtracted, while the 3rd and 4th ventricles are not included in the
> surfaces and therefore would not need to be subtracted?
>
> Kind regards,
> Cheryl
>
>
> On 11-12-14 12:45 PM, "Douglas N Greve"  wrote:
>
>   
>> Hi Cheryl,
>> You can regenerate the asseg.stats file with BrianVolNotVent with:
>>
>> cd $SUBJECTS_DIR/yoursubject
>>  mri_segstats --subject yoursubject --seg mri/aseg.mgz --sum
>> stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm
>> --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm
>> --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray
>> --ctab /usr/local/freesurfer/dev/ASegStatsLUT.txt  --brain-vol-from-seg
>>
>> This is the same command that generated the existing aseg.stats file
>> with "--brain-vol-from-seg" added.
>>
>> doug
>>
>>
>>
>>
>>
>> Cheryl McCreary wrote:
>> 
>>> Hi Freesurfer experts,
>>>
>>> I would like to determine brain parenchymal fraction (ie brain tissue
>>> volume/estimated ICV) as an estimate of global atrophy.  In previous
>>> versions of FS, I used the BrianVolNotVent/ICV.  Is this correct?
>>>
>>> I am now using freesurfer version 5.0.0 and BrainVolNotVent is not longer
>>> available. 
>>>
>>> My understanding is that the total gray matter and total cortical white
>>> matter volumes are determined from the pial and white surfaces (thickness
>>> *surface area).  Do these volumes include or exclude the ventricular
>>> volumes? Can the total brain volume be calculated as the sum of the total
>>> GM, total cortical WM, brain stem, cerebellar GM and WM minus the CSF.  Or
>>> do the volumes of the ventricles need to be subtracted as well?
>>>
>>> Thanks for your help.
>>>
>>> Cheryl  
>>>   
>>>   
>
>   

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] Freesurfer Digest, Vol 94, Issue 13

[Douglas N Greve]

Thanks. I just added it into our code, so new versions will not have 
this problem.
doug

Maryam Vaziri Pashkam wrote:
> Hi,
>
> Following up on the preprocessing error:
> > Can't connect? tcp_connect[connect]: Connection timed out
>
> We figured where the problem is. This error came out when freesurfer 
> calls an afni function. Apparently it tries to check which version of 
> afni it is using against the internet to find out the most recent 
> version.  Suppressing the afni version check solved the problem. I 
> just added this line to my .bashrc file:
> export AFNI_VERSION_CHECK=NO
>
> Maryam
>
> On Mon, Dec 12, 2011 at 12:00 PM, 
>  > wrote:
>
> Send Freesurfer mailing list submissions to
>freesurfer@nmr.mgh.harvard.edu
> 
>
> To subscribe or unsubscribe via the World Wide Web, visit
>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> or, via email, send a message with subject or body 'help' to
>freesurfer-requ...@nmr.mgh.harvard.edu
> 
>
> You can reach the person managing the list at
>freesurfer-ow...@nmr.mgh.harvard.edu
> 
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Freesurfer digest..."
>
>
> Today's Topics:
>
>   1. preprocessing error (Maryam Vaziri Pashkam)
>   2. Re: preprocessing error (Douglas Greve)
>   3. convert surface label on to functional image (Zhangyuanchao)
>   4. References/materials for interaction analysis in  freesurfer
>  (Bhavani Shankara Bagepally)
>   5. Re: dt_recon error (Yuko Yotsumoto)
>   6. Re: dt_recon error (Yuko Yotsumoto)
>   7. Re: run preproc-sess with -nomc (Thunell Evelina)
>   8. Re: mri_ca_register from virtual box (Lorenzo Busti)
>   9. Re: mri_ca_register from virtual box (Lorenzo Busti)
>  10. Converting thickness maps to vtk (Navid Shiee)
>  11. Re: tracula and snow leopard: can't allocate region / memory
>  error (Anastasia Yendiki)
>  12. tracula failed to find header file for -t (Scott Hayes)
>
>
> --
>
> Message: 1
> Date: Sun, 11 Dec 2011 14:34:05 -0500
> From: Maryam Vaziri Pashkam  >
> Subject: [Freesurfer] preprocessing error
> To: freesurfer@nmr.mgh.harvard.edu
> 
> Message-ID:
>  
>   
> >
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
>
> I am running preprocessing on my data using freesurfer 5.1, fsl
> 4.1.7, and
> matlab R2009a (I also tried it with matlab 2007a) on Harvard
> cluster and I
> am receiving an error. I connect to the cluster using terminal and SSH
> connection in mac.
>
> the preprocessing is stalled in the middle with this error:
>
> ++ Max displacement in automask = 0.79 (mm) at sub-brick 3
> Can't connect? tcp_connect[connect]: Connection timed out
> ++ Wrote dataset to disk in 004/tmp.mc-afni2.20850/outvol.nii.gz
> ** Warning: overwriting file 004/fmcpr.mcdat
> Can't connect? tcp_connect[connect]: Connection timed out
> Can't connect? tcp_connect[connect]: Connection timed out
> Can't connect? tcp_connect[connect]: Connection timed out
>
>
> It does not stop running and output an error. But rather keeps
> printing the
> last line and does not move forward. Any idea where the problem
> might be?
>
>
> Thanks,
> Maryam
> -- next part --
> An HTML attachment was scrubbed...
> URL:
> 
> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20111211/c2c91d24/attachment-0001.html
>
> --
>
> Message: 2
> Date: Sun, 11 Dec 2011 15:39:34 -0500
> From: Douglas Greve  >
> Subject: Re: [Freesurfer] preprocessing error
> To: freesurfer@nmr.mgh.harvard.edu
> 
> Message-ID: <4ee51506.6090...@nmr.mgh.harvard.edu
> >
> Content-Type: text/plain; charset="iso-8859-1"
>
> what command are you running (I mean the full command line -- hard to
> debug without it). The preprocessing should not require matlab. Just
> guessing, this does not look like a FS problem.
> doug
>
> On 12/11/11 2:34 PM, Maryam Vaziri Pashkam wrote:
> > Hi,
> >
> > I am running preprocessing on my data using freesurfer 5.1, fsl
> 4.1.7,
> > and matlab R2009a (I also tried it with matlab 2007a) on Harvard
> > cluster and I am receiving an error. I con

[Freesurfer] nWBV

[Lindsay Ercole]

How might we obtain nWBV from the FS data? What variables could be summed
or what variable could be used individually and adjusted to create a nWBV?

Does total gray include cerebellar gray, but total white volume does not
include cerebellar white?

Sincerest thanks!
Lindsay
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Re: [Freesurfer] GLM design question

[Martijn Steenwijk]

Dear Doug,

Thanks again for your reply. Based on that I did some further work.

I first demeaned the age of all subjects. Actually, I have a third group
which I would like to compare to, so my contrast matrices will be
[.5 .5 -.5 -.5 0 0 0 0 0 0 0 0]
[0 0 .5 .5 -.5 -.5 0 0 0 0 0 0]
[.5 .5 0 0 -.5 -.5 0 0 0 0 0 0]
to test for CT differences between all the groups while correcting for age
and sex. Surprisingly, I'm observing a big difference in the results
compared to the results without demeaning. Could you explain the reson for
this? In the FSGD-examples (eg
http://surfer.nmr.mgh.harvard.edu/fswiki/FsgdFormat), age is also not
normalized. Does normalizing the variance to 1 also influence the results?
Given this big difference, I started wondering whether it would maybe be
better to analyze the data in pairs of two groups (and then demean by the
mean of the two groups). Would this be a better approach?

Concerning your second suggestion: if I test the data for differences in
group slope, a number of small area's are significantly different. Regions
popping up are especially in the neighborhood of the insula. Unfortunately
this suggests that I cannot use the DOSS model, or am I wrong?

Looking forward to your reply,
With best regards,
Martijn


On Sat, Dec 10, 2011 at 7:16 PM, Douglas Greve wrote:

>  Yes, that is correct, though I think your matrix should be [.5 .5 -.5 -.5
> 0 0 0 0]. You should also remove the mean from the age (mean computed from
> all subjects). Or even better, first test whether there is a group
> difference in age slope with [0 0 0 0 .5 .5 -.5 -.5]. If there is nothing
> that is significant, then re-run your analysis using the Different Offset
> Same Slope (DOSS) model with this contrast [.5 .5 -.5 -.5 0].
>
> doug
>
>
> On 12/10/11 4:15 AM, Martijn Steenwijk wrote:
>
>  Dear all,
>
> ** **
>
> I’m relatively new with Freesurfer, but slowly getting more and more used
> to it’s great possibilities. To be ‘sure’, I’ve a question about the design
> of a GLM. 
>
> ** **
>
> I want to compare CT in Healthy Controls vs Diseased, and control for age
> and sex. It appears to me that factors (eg sex) cannot be used as
> covariate/variable, which forces me to model them as a separate class
> although I’m not interested in sex differences. This brings me to the
> following FSGD file:
>
> ** **
>
> # HcDis.fsgd
>
> GroupDescriptorFile 1
>
> Title HcDis
>
> Class Hc_Male
>
> Class Hc_Female
>
> Class Dis_Male
>
> Class Dis_Female
>
> Variables Age
>
> Input subjid1 Hc_Male 35
>
> Input subjid2 Dis_Female 30
>
> ….
>
> ** **
>
> Then the difference between Hc and Dis, corrected for age and sex is given
> by the contrast matrix
>
> #Hc-vs-Dis.mtx
>
> 0.5 0.5 -0.5 -0.5 0 0 0 0 0 0 0 0 
>
> ** **
>
> Is this correct? 
>
> ** **
>
> Best,
>
> Martijn
>
> ** **
>
> ** **
>
>
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Re: [Freesurfer] FA interpretation from cvs registration for group analysis

[Antonella Kis]

Dear Lilla,

Thank you very much for your answer and your help. I followed all the 
recommended steps (I introduced a white matter mask that will ensure that I am  
only 
considering diffusion values in the white matter and then also I did corrected 
for multiple comparison running mri_glmfit-sim with the option grf as Doug 
recommend me). 


My question is how can I conclude if there is an increase and/or decrease in 
the FA values in one group (for example Patients) versus another group (example 
controls).

In other words can we conclude on the FA values based on the GLM 
results/clusters  from the 
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Diffusion (I don't see 
anymore the image with red and blue clusters posted on this website. Is 
something going on?)


Thank you very much!
Antonella




 From: Lilla Zollei 
To: Antonella Kis  
Cc: "freesurfer@nmr.mgh.harvard.edu"  
Sent: Tuesday, December 13, 2011 12:02 PM
Subject: Re: [Freesurfer] FA interpretation from cvs registration for group 
analysis
 

Hi Antonella,

> I will appreciate a lot if you can help me understand what is the meaning of 
> the results after running after running mri_cvs_register and the GLM group 
> analysis.
> 
> More exactly, I followed all the instructions from the webpage:
> 
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Diffusion
> 
> and I wonder if based on the cluster's colours I can say something about my 
> FA values in one group related to the other one.
> 
> More exactly I am looking to understand if I have an increase in the FA value 
> for the controls versus patients or the FA in patients is larger than in the 
> control group.
> 
> My contrast matrix is C = [+1.0 -1.0 ] and I have 30 controls and 32 
> patients.

I am not sure how to comment on your outcomes as I don't know anything 
about your data. However, the diffusion tutorial that we put together is 
a very top-level roadmap on how one might go about voxel-based analysis 
of their diffusion data. It is not complete in a sense that you would 
want to make sure that there is some further processing done on your data 
sets before you start interpreting the results. One is that you would 
want to introduce a white matter mask that will ensure that you are only 
considering diffusion values in the white matter and then also you would 
want to correct for multiple comparison running mri_glmfit-sim. We are 
planning on updating this tutorial further for our next course to reflect 
all these additional steps.

> What is the age range for the cvs_avg35 space? I wonder if is the best space 
> to register my subjects if they are children with age between 6-14.

The atlas was constructed from 35 adults, consisting of males and females 
ages 18 to 93.

We have been successul registering pediatric images also in that space, 
but the outcome will also depend on the quality of your images.

--Lilla
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Re: [Freesurfer] Extracting area.pial stats

[Michael Harms]

You need to specify 'pial' as the surface name argument in
mris_anatomical_stats

cheers,
-MH

On Thu, 2011-12-15 at 10:52 -0500, Robustelli, Briana (NIH/NIMH) [F]
wrote:
> Dear FreeSurfer team,
>  I have been looking at area.pial differences in two groups using qdec.  
> I would now like to extract stats for each subject at the gyral level (using 
> the Desikan parcellation).  I used aparcstats2table with the measure flag set 
> to area.  But these numbers seem off.  Is this the correct area or am I 
> somehow getting white matter area and it so how do I get the area of the pial 
> surface?
> 
> Thank you!
> Briana Robustelli
> 
> 
> --
> Briana Robustelli
> Post-Baccalaureate IRTA
> Laboratory of Brain and Cognition, NIMH/NIH/DHHS
> Building 10, Room 4C103
> 10 Center Dr MSC 1366
> Bethesda, MD 20892
> Phone: (301) 435-4491
> briana.robuste...@nih.gov
> 
> 
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[Freesurfer] Extracting area.pial stats

[Robustelli, Briana (NIH/NIMH) [F]]

Dear FreeSurfer team,
 I have been looking at area.pial differences in two groups using qdec.  I 
would now like to extract stats for each subject at the gyral level (using the 
Desikan parcellation).  I used aparcstats2table with the measure flag set to 
area.  But these numbers seem off.  Is this the correct area or am I somehow 
getting white matter area and it so how do I get the area of the pial surface?

Thank you!
Briana Robustelli


--
Briana Robustelli
Post-Baccalaureate IRTA
Laboratory of Brain and Cognition, NIMH/NIH/DHHS
Building 10, Room 4C103
10 Center Dr MSC 1366
Bethesda, MD 20892
Phone: (301) 435-4491
briana.robuste...@nih.gov


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