[Freesurfer] How to calculate the surface area of a vertex ?

[Zhiliang Long]

Hi FS experts:
I am studying the vertex-level group analysis on surface area between 
groups. I know that the cortical thickness of a vertex is computed as the 
distance between white matter surface and pial surface. But I have no idea how 
to calculate the surface area of a vertex. In my understanding, surface area is 
a measurement of a face instead of a vertex.


Best,
Zhiliang___
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Re: [Freesurfer] Differences in aseg volumes between FreeSurfer 5.3.0 and FreeSurfer 6.0

[Bruce Fischl]

Include the orig.mgz and voxel cords and I'll see if I have already fixed it

> On May 5, 2017, at 10:11 AM, Knut J Bjuland  wrote:
> 
> Hi Bruce
> 
> I found some filled-in occipital horn and some in the anterior parts. I can 
> upload nu.mgz and aseg.mgz for a subject with problems with lateral 
> ventricle.   
> 
> Cheers
> Knut Jørgen
> 
> 
> 
> 
>> On 4 May 2017, at 16:54, Bruce Fischl  wrote:
>> 
>> Hi Knut
>> 
>> where is it being filled? If it is the occipital horn we may soon have a 
>> patch for it
>> 
>> cheers
>> Bruce
>> On Thu, 4 May 2017, Knut J Bjuland wrote:
>> 
>>> Hi
>>> Are there any options that I can use in Freesurfer 6.0 that can prevent lef
>>> t lateral ventricle from being filled with WM? Should I send the MPRAGE seq
>>> uence information?   
>>> Knut Jørgen
>>> 
>>>  On 2 May 2017, at 17:57, Douglas Greve
>>>   wrote:
>>> This is a test we do before we release. The averages don't look out of
>>> line. Putamen should be smaller because we now try to remove
>>> claustrum. Small structures may have some large percent differences.
>>> Some structures are not that meaningful (like the CC because it has no
>>> real boundaries). The left lateral ventricle may be a problem. I've
>>> seen cases where it totally gets filled in with WM in v6. Others are
>>> hard to define -- when I would look at the scans there would not be a
>>> good case for rejecting one and accepting the other (eg, pallidum and
>>> thalamus don't have good contrast at typical mprage acq parameters).
>>> On 5/2/17 3:56 AM, Knut J Bjuland wrote:
>>>  Dear FreeSurfer experts,
>>>  
>>> When I ran Freesurfer 5.3 and Freesurfer 6.0 I ran with default settings us
>>> ing this command. recon-all -s (id) -all for both Freesurfer 5.3 and FreeSu
>>> rfer 6.0.
>>> Are these differences larger than one would expect? I think that 100% may b
>>> e a little high? The difference in volume between Freesurfer 5.3 and Freesu
>>> rfer 6.0 is shown in the table below calculated using asegstatsdiff.
>>>  
>>> Knut Jørgen Bjuland 
>>> Volume name
>>> Mean(range)
>>> Left-Lateral-Ventricle
>>> 7.4  (-0.13,130.72)
>>> Left-Cerebellum-White-Matter
>>> 0.64  (-22.9,56.15)
>>> Left-Cerebellum-Cortex
>>> 7.56  (-10.3,19.17)
>>> Left-Thalamus-Proper
>>> 0.12  (-16.31,32.42)
>>> Left-Caudate
>>> -4.25  (-12,33.64)
>>> Left-Putamen
>>> -16.72  (-27.99,8.3)
>>> Left-Pallidum
>>> 16.23  (-22.94,84.75)
>>> Left-Hippocampus
>>> -1.74  (-13.53,15.93)
>>> Left-Amygdala
>>> 2.29  (-19.28,41.04)
>>> Right-Lateral-Ventricle
>>> 4.6  (-24.77,102.12)
>>> Right-Cerebellum-White-Matter
>>> -3.2  (-20.87,49.37)
>>> Right-Cerebellum-Cortex
>>> 4.88  (-12.99,14.36)
>>> Right-Thalamus-Proper
>>> 1.06  (-22.34,19.99)
>>> Right-Caudate
>>> -6.08  (-14.59,6.13)
>>> Right-Putamen
>>> -12.87  (-31.37,10.17)
>>> Right-Pallidum
>>> 14.01  (-27.79,89.19)
>>> Right-Hippocampus
>>> -1.71  (-9.29,12.02)
>>> Right-Amygdala
>>> 3.74  (-18.6,51.01)
>>> Right-Accumbens-area
>>> -9.14  (-37.89,61.02)
>>> CC_Posterior
>>> 22.07  (-47.04,525.51)
>>> CC_Mid_Posterior
>>> 53.59  (-11.3,537.3)
>>> CC_Central
>>> 36.77  (-21.36,317.24)
>>> CC_Mid_Anterior
>>> 24.09  (-18.86,128.31)
>>> CC_Anterior
>>> 10.64  (-33.71,152.33)
>>> lhCortexVol
>>> 3.13  (-1.31,12.37)
>>> rhCortexVol
>>> 3.16  (-0.36,14.2)
>>> CortexVol
>>> 3  (-4.47,13.26)
>>> EstimatedTotalIntraCranialVol
>>> 0.65  (-0.05,26.52)
>>> 
>>>  On 21 Apr 2017, at 20:01, Knut J Bjuland
>>>   wrote:
>>> Dear FreeSurfer expert, 
>>>  
>>> I have compared the aseg volume between FreeSurfer 5.3 and FreeSurfer 6.0 w
>>> ith asegstatsdiff from FreeSurfer 6.0 for each subject in my data set. I ha
>>> ve enclosed the range for some of the volume. I found the largest differenc
>>> es in subcortical structures, especially in Corpus callosum(CC). I found th
>>> at FreeSurfer 6.0 CC posterior volume was 525.51 % larger than in FreeSurfe
>>> r 5.3. Nevertheless, these differences were much smaller for lhCortex, but
>> ?? ?also here FreeSurfer 6.0 was on average larger than FreeSurfer 5.3. I 
>> ran t
>>> he FreeSurfer 6.0 using the same option as FreeSurfer 5.30. Both versions o
>>> f FreeSurfer were run on Centos. I am also enclosing a
>>> table with mean values along with min and max  for
>>> differences between FreeSurfer 5.3 and FreeSurfer 6.0 aseg
>>> volumes.
>>>  
>>>  
>>> Best regards
>>> Knut Jørgen Bjuland PhD
>>> NTNU
>>> Left-Lateral-Ventricle
>>> 7.4  (-0.13,130.72)
>>> Left-Cerebellum-White-Matter
>>> 0.64  (-22.9,56.15)
>>> Left-Cerebellum-Cortex
>>> 7.56  (-10.3,19.17)
>>> Left-Thalamus-Proper
>>> 0.12  (-16.31,32.42)
>>> Left-Caudate
>>> -4.25  (-12,33.64)
>>> Left-Putamen
>>> -16.72  (-27.99,8.3)
>>> Left-Pallidum
>>> 16.23  (-22.94,84.75)
>>> Left-Hippocampus
>>> -1.74  (-13.53,15.93)
>>> Left-Amygdala
>>> 2.29  (-19.28,41.04)
>>> Right-Lateral-Ventricle
>>> 4.6  (-24.77,102.12)
>>> Right-Cerebellum-White-Matter
>>> -3.2  (-20.87,49.37)
>>> Right-Cerebellum-Cortex
>>> 4.88  (-12.99,14.36)
>>> Right-Thalamu

Re: [Freesurfer] Differences in aseg volumes between FreeSurfer 5.3.0 and FreeSurfer 6.0

[Knut J Bjuland]

Hi Bruce

I found some filled-in occipital horn and some in the anterior parts. I can 
upload nu.mgz and aseg.mgz for a subject with problems with lateral ventricle.

Cheers
Knut Jørgen




On 4 May 2017, at 16:54, Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>> wrote:

Hi Knut

where is it being filled? If it is the occipital horn we may soon have a patch 
for it

cheers
Bruce
On Thu, 4 May 2017, Knut J Bjuland wrote:

Hi
Are there any options that I can use in Freesurfer 6.0 that can prevent lef
t lateral ventricle from being filled with WM? Should I send the MPRAGE seq
uence information?
Knut Jørgen

 On 2 May 2017, at 17:57, Douglas Greve
 mailto:gr...@nmr.mgh.harvard.edu>> wrote:
This is a test we do before we release. The averages don't look out of
line. Putamen should be smaller because we now try to remove
claustrum. Small structures may have some large percent differences.
Some structures are not that meaningful (like the CC because it has no
real boundaries). The left lateral ventricle may be a problem. I've
seen cases where it totally gets filled in with WM in v6. Others are
hard to define -- when I would look at the scans there would not be a
good case for rejecting one and accepting the other (eg, pallidum and
thalamus don't have good contrast at typical mprage acq parameters).
On 5/2/17 3:56 AM, Knut J Bjuland wrote:
 Dear FreeSurfer experts,

When I ran Freesurfer 5.3 and Freesurfer 6.0 I ran with default settings us
ing this command. recon-all -s (id) -all for both Freesurfer 5.3 and FreeSu
rfer 6.0.
Are these differences larger than one would expect? I think that 100% may b
e a little high? The difference in volume between Freesurfer 5.3 and Freesu
rfer 6.0 is shown in the table below calculated using asegstatsdiff.

Knut Jørgen Bjuland
Volume name
Mean(range)
Left-Lateral-Ventricle
7.4  (-0.13,130.72)
Left-Cerebellum-White-Matter
0.64  (-22.9,56.15)
Left-Cerebellum-Cortex
7.56  (-10.3,19.17)
Left-Thalamus-Proper
0.12  (-16.31,32.42)
Left-Caudate
-4.25  (-12,33.64)
Left-Putamen
-16.72  (-27.99,8.3)
Left-Pallidum
16.23  (-22.94,84.75)
Left-Hippocampus
-1.74  (-13.53,15.93)
Left-Amygdala
2.29  (-19.28,41.04)
Right-Lateral-Ventricle
4.6  (-24.77,102.12)
Right-Cerebellum-White-Matter
-3.2  (-20.87,49.37)
Right-Cerebellum-Cortex
4.88  (-12.99,14.36)
Right-Thalamus-Proper
1.06  (-22.34,19.99)
Right-Caudate
-6.08  (-14.59,6.13)
Right-Putamen
-12.87  (-31.37,10.17)
Right-Pallidum
14.01  (-27.79,89.19)
Right-Hippocampus
-1.71  (-9.29,12.02)
Right-Amygdala
3.74  (-18.6,51.01)
Right-Accumbens-area
-9.14  (-37.89,61.02)
CC_Posterior
22.07  (-47.04,525.51)
CC_Mid_Posterior
53.59  (-11.3,537.3)
CC_Central
36.77  (-21.36,317.24)
CC_Mid_Anterior
24.09  (-18.86,128.31)
CC_Anterior
10.64  (-33.71,152.33)
lhCortexVol
3.13  (-1.31,12.37)
rhCortexVol
3.16  (-0.36,14.2)
CortexVol
3  (-4.47,13.26)
EstimatedTotalIntraCranialVol
0.65  (-0.05,26.52)

 On 21 Apr 2017, at 20:01, Knut J Bjuland
 mailto:knutjor...@outlook.com>> wrote:
Dear FreeSurfer expert,

I have compared the aseg volume between FreeSurfer 5.3 and FreeSurfer 6.0 w
ith asegstatsdiff from FreeSurfer 6.0 for each subject in my data set. I ha
ve enclosed the range for some of the volume. I found the largest differenc
es in subcortical structures, especially in Corpus callosum(CC). I found th
at FreeSurfer 6.0 CC posterior volume was 525.51 % larger than in FreeSurfe
r 5.3. Nevertheless, these differences were much smaller for lhCortex, but
?? ?also here FreeSurfer 6.0 was on average larger than FreeSurfer 5.3. I ran t
he FreeSurfer 6.0 using the same option as FreeSurfer 5.30. Both versions o
f FreeSurfer were run on Centos. I am also enclosing a
table with mean values along with min and max  for
differences between FreeSurfer 5.3 and FreeSurfer 6.0 aseg
volumes.


Best regards
Knut Jørgen Bjuland PhD
NTNU
Left-Lateral-Ventricle
7.4  (-0.13,130.72)
Left-Cerebellum-White-Matter
0.64  (-22.9,56.15)
Left-Cerebellum-Cortex
7.56  (-10.3,19.17)
Left-Thalamus-Proper
0.12  (-16.31,32.42)
Left-Caudate
-4.25  (-12,33.64)
Left-Putamen
-16.72  (-27.99,8.3)
Left-Pallidum
16.23  (-22.94,84.75)
Left-Hippocampus
-1.74  (-13.53,15.93)
Left-Amygdala
2.29  (-19.28,41.04)
Right-Lateral-Ventricle
4.6  (-24.77,102.12)
Right-Cerebellum-White-Matter
-3.2  (-20.87,49.37)
Right-Cerebellum-Cortex
4.88  (-12.99,14.36)
Right-Thalamus-Proper
1.06  (-22.34,19.99)
Right-Caudate
-6.08  (-14.59,6.13)
Right-Putamen
-12.87  (-31.37,10.17)
Right-Pallidum
14.01  (-27.79,89.19)
Right-Hippocampus
-1.71  (-9.29,12.02)
Right-Amygdala
3.74  (-18.6,51.01)
Right-Accumbens-area
-9.14  (-37.89,61.02)
CC_Posterior
22.07  (-47.04,525.51)
CC_Mid_Posterior
53.59  (-11.3,537.3)
CC_Central
36.77  (-21.36,317.24)
CC_Mid_Anterior
24.09  (-18.86,128.31)
CC_Anterior
10.64  (-33.71,152.33)
lhCortexVol
3.13  (-1.31,12.37)
rhCortexVol
3.16  (-0.36,14.2)
CortexVol
3  (-4.47,13.26)
EstimatedTotalIntraCranialVol
0.65  (-0.05,26.52)
___
Freesurfer mai

Re: [Freesurfer] FSFAST

[Douglas Greve]

On 5/5/17 5:06 AM, John Anderson wrote:

Dear Doug,
I have Bold fMRI data (6 minutes of acquisition which is equal to 180 
volume for every run). The total number for images is 140 (50 controls 
and 90 patients). I plan to use FSFAST (FS V6.0) to study:

1. The difference between the groups in global functional connectivity
2. Seed-based functional connectivity analysis depending on an ROI 
 for a difference in a voxel-wise analysis between PET images for the 
same subjects.

My questions are:
1. In this data set I have only one run for every subject. I am 
wondering if FSFAST  can analyze fMRI data (one run per subject).

Yes, no problem
2. FSFAST depends on  the recons, meaning it depends on the ROIs in 
wmparc, aseg and apare+aseg atlases. Can FSFAST accept an external ROI 
for seed based functional connectivity analysis?
Yes, just create an ROI as a mask in the conformed anatomical space and 
put the volume in the subject/mri folder. Then when you run fcseed-sess, 
spec that volume with -seg and specify the ROI code with -segid. Eg, if 
your volume was myroi.mgz and the value that the roi takes in that 
volume was 3, then -seg myroi.mgz -segid 3


I highly appreciate your advice
John






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Re: [Freesurfer] perform group analysis on user defined maps

[Douglas Greve]

Hi Ladan, please include previous correspondence so that we know what 
this is referring to


doug


On 5/5/17 1:58 AM, Ladan Shahshahani wrote:

​
It didn't crash. I got the following line in the terminal window:

Invalid argument
WARNING: 319 NaNs found in subjid.map.mgh

When the NaNs were common in all the subjects, mri_glmfit did not end 
successfully. After I omitted the common NaN values, there were still 
a few subjects with NaN values, in this case, it printed the above 
lines in the terminal; but the mri_glmfit proceeded and sig.mgh was 
created alongside other outputs.



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Re: [Freesurfer] Freeview libpng warning

[Kanoff, Kristen Elise]

Freeview stills runs but none of the toolbar icon graphics are visible (see 
attached screenshot).

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Ruopeng Wang
Sent: Thursday, May 04, 2017 5:51 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freeview libpng warning

Does freeview still run? If it does, you can just ignore the warning.

Best,
Ruopeng

On May 4, 2017, at 12:39 PM, Kanoff, Kristen Elise 
mailto:kkan...@mgh.harvard.edu>> wrote:

Hello FreeSurfer community,

I am having an issue with the icon graphics displaying properly in freeview 
(Linux virtual machine – Ubuntu).  I receive the following warning when opening 
the application:

“libpng warning: Application built with libpng-1.2.7 but running with 1.6.25”

The newer version of libpng was downloaded as part of the Miniconda 2 package 
(which I need to run the MNE-Python pipeline).  I’ve been unable to find a way 
to revert back to the older version of libpng.  If anyone else has dealt with 
this compatibility issue before, suggestions on how to proceed would be very 
much appreciated!

Thank you in advance,

Kristen
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[Freesurfer] TRACULA exports white matter tract labels without DTI data

[Yong Li]

Dear Anastasia,
Dear Bruce,

As a newbie in using freesurfer, I would like to ask for help to output
white matter tract labels of each subject without DTI data. This topic was
briefly discussed last April by Holleran, Laurena (
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg46459.html),
but I don't find how to do it. To be specific, I would like using TRACULA
'to mapping the tracts from the atlas onto the individual subject' as
suggested by Bruce in his reply to Laurena.

Other questions are:
How to view the extracted white matter tract labels in the individual
space? freeview or trackvis or other viewers?

Could TRACULA deal with DTI data in Nifti format? If not, is there a way to
reliably convert DTI data from Nifti to DICOM (*.dcm)?

Hope I make myself clear. Thank you very much in advance!

Best regards,

Yong
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[Freesurfer] FSFAST

[John Anderson]

Dear Doug,
I have Bold fMRI data (6 minutes of acquisition which is equal to 180 volume 
for every run). The total number for images is 140 (50 controls and 90 
patients). I plan to use FSFAST (FS V6.0) to study:
1. The difference between the groups in global functional connectivity
2. Seed-based functional connectivity analysis depending on an ROI for a 
difference in a voxel-wise analysis between PET images for the same subjects.
My questions are:
1. In this data set I have only one run for every subject. I am wondering if 
FSFAST can analyze fMRI data (one run per subject).
2. FSFAST depends on the recons, meaning it depends on the ROIs in wmparc, aseg 
and apare+aseg atlases. Can FSFAST accept an external ROI for seed based 
functional connectivity analysis?

I highly appreciate your advice
John___
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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