Re: [Freesurfer] excluding labels

[Adam, Ruth]

Hi,I would like to exclude areas which were incorrectly segmented and could not be corrected after editing and re-running recon-all from the cortical thickness measure. Thank you again.Best,ruthiOn 09 Oct 2014, at 19:57, Douglas Greve  wrote:
  

  
  
What analysis?

On 10/9/14 11:35 AM, Adam, Ruth wrote:


  
  Hi all,
  

  
Would be great is someone can tell me
how to exclude user-defined labels from the analysis.

  

  As far as I
  understand after creating all labels, mris_label2annot
  with a custom colortable should be used.

-Is this correct or
is there a more efficient way to exclude labels form
analysis?
-How can the new
annotation file be incorporated with old annotation files to
mark what should be excluded/included in the analysis? 
-Can a similar operation be done
directly for labels created in Tkmedit and volumes?


Thank you very much  in advance!

  
Best,
ruthi
  
  
  
  
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Re: [Freesurfer] rawfunc2surf-sess with a limited set of surface files

[Douglas Greve]

No, use fmc.sm2.F99.lh.iter05

On 10/10/14 1:55 AM, Reza Rajimehr wrote:
> Thanks Doug! I got it to work. The outputs are like
> fmc.sm2.F99.lh.iter05.nii.gz
>
> Should I still specify stem as fmc.iter05 in mkanalysis-sess?
>
> Reza
>
>
> Try added something like "-expkey iter05". When  you make the analysis
> you will have to spec "-stem fmc.iter05"
> doug
>
>
>
> On 10/09/2014 12:12 AM, Reza Rajimehr wrote:
>> Hi Doug,
>>
>> Removing -i fmc did not help, and I still get the same error.
>>
>> By looking at the rawfunc2surf-sess script, it looks like specifying an
>> argument for -surfreg makes ExpKeyNeeded = 1. Can I just specify something
>> for -expkey? Is this something that is used only in the name of log file?
>>
>> Thanks,
>> Reza
>>
>>
>> Try it without -i fmc
>>
>>
>> On 10/08/2014 04:38 AM, Reza Rajimehr wrote:
>>> One more question:
>>>
>>> I tried to run:
>>>
>>> rawfunc2surf-sess -s oz_fparc -i fmc -trgsubject F99 -surfreg
>>> iter05.sphere.reg -fwhm 2 -per-session
>>>
>>> And I got this:
>>>
>>> ERROR: experts key needed (-expkey)
>>>
>>> Not sure what this flag is.
>>>
>>> Reza
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Re: [Freesurfer] WM & Pial Segmentation Errors

[Smith, Michael]

We re-ran that subject and it seemed to fix the problem, thanks! We will test 
it out on the other subjects with the same issue and see how that goes, but it 
looks like everything is good.  Thanks again!

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Varjabedian, Ani
Sent: Thursday, October 09, 2014 10:02 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] WM & Pial Segmentation Errors

Hi Michael, 

I took a look at your data and it seems that you paired a T2 image with a T1 
image when you submitted to recon all. Recon-all will try to average these 
together, and since they have such different contrasts, you will end up with a 
poor template for surfaces later on. 

Try running recon-all again without the T2 and see if that helps.


-Ani 


On Wed, 2014-10-08 at 17:21 +, Smith, Michael wrote:
> Ah, sorry for some reason it just wasn’t clicking before.  I was able 
> to upload a dataset.  Thanks!
> 
> On 10/8/14, 10:59 AM, "Bruce Fischl"  wrote:
> 
> >Hi Michael
> >
> >you need to follow the directions on this page:
> >
> >http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
> >
> >in particular, make sure you change directories before trying to put
> >
> >cheers
> >Bruce
> >
> >On Wed,
> >8 Oct 2014,
> >Smith,
> >Michael wrote:
> >
> >> See attached
> >>
> >> On 10/8/14, 10:46 AM, "Bruce Fischl"  wrote:
> >>
> >>> can you send us the details of your ftp command?
> >>> On Wed, 8 Oct 2014, Smith,
> >>> Michael wrote:
> >>>
>  Hi Bruce,
> 
>  Do I not have permission to transfer files to the remote machine? 
> I can  login fine as an anonymous user but when I attempt to use 
> the put  command  it says it could not create the file.
> 
>  On 10/7/14, 7:33 PM, "Bruce Fischl" 
> wrote:
> 
> > Hi Michael
> >
> > sure, the T2 can help if you have it (although you'll need to 
> >download  some  updated binaries), but it is impossible to tell 
> >from these images what  is  going on. Looks either the intensity 
> >normalization, mri_segment or  mris_make_surfaces failed. You can 
> >try the expert options for each one  to  prespecify the range of 
> >allowable intensities for gray and white  matter.
> > If
> > you upload the subject to our ftp site (the whole subject 
> >directory  tarred  and gzipped) we will take a look
> >
> > cheers
> > Bruce
> >
> > On Mon, 6 Oct 2014, Smith, Michael wrote:
> >
> >> Hi,
> >>
> >> I¹ve been having trouble on a few of our subjects with getting 
> >>the  white  matter and pial surface files to ³line up² correctly 
> >>with the volume  files.
> >>  I¹ve attached a screenshot of what is happening: the pial 
> >>surface is  in red  and the white matter surface file is in 
> >>yellow. I have also attached  an  example of a ³good² subject 
> >>for comparison.
> >>
> >> I¹ve tried looking through the tutorials online but didn¹t see  
> >>anything  that  was really related to my issue and I was 
> >>wondering what the best way  to  correct this.  We have T2 
> >>weighted images for several subjects is well  if  that helps.  
> >>Not sure if Freesurfer can use T2 images instead of T1 in  the  
> >>­reconall script but I thought I would mention it.  Thank you 
> >>very  much  in  advance!
> >>
> >> Best,
> >>
> >> Michael S.
> >>
> 
> 
> 
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> 
> 
> >>
> 
> 
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Re: [Freesurfer] WM & Pial Segmentation Errors

[Bruce Fischl]

glad to hear it
Bruce
On Fri, 10 Oct 2014, Smith, Michael wrote:


We re-ran that subject and it seemed to fix the problem, thanks! We will test 
it out on the other subjects with the same issue and see how that goes, but it 
looks like everything is good.  Thanks again!

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Varjabedian, Ani
Sent: Thursday, October 09, 2014 10:02 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] WM & Pial Segmentation Errors

Hi Michael,

I took a look at your data and it seems that you paired a T2 image with a T1 
image when you submitted to recon all. Recon-all will try to average these 
together, and since they have such different contrasts, you will end up with a 
poor template for surfaces later on.

Try running recon-all again without the T2 and see if that helps.


-Ani


On Wed, 2014-10-08 at 17:21 +, Smith, Michael wrote:

Ah, sorry for some reason it just wasn’t clicking before.  I was able
to upload a dataset.  Thanks!

On 10/8/14, 10:59 AM, "Bruce Fischl"  wrote:


Hi Michael

you need to follow the directions on this page:

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

in particular, make sure you change directories before trying to put

cheers
Bruce

On Wed,
8 Oct 2014,
Smith,
Michael wrote:


See attached

On 10/8/14, 10:46 AM, "Bruce Fischl"  wrote:


can you send us the details of your ftp command?
On Wed, 8 Oct 2014, Smith,
Michael wrote:


Hi Bruce,

Do I not have permission to transfer files to the remote machine?
I can  login fine as an anonymous user but when I attempt to use
the put  command  it says it could not create the file.

On 10/7/14, 7:33 PM, "Bruce Fischl" 
wrote:


Hi Michael

sure, the T2 can help if you have it (although you'll need to
download  some  updated binaries), but it is impossible to tell
from these images what  is  going on. Looks either the intensity
normalization, mri_segment or  mris_make_surfaces failed. You can
try the expert options for each one  to  prespecify the range of
allowable intensities for gray and white  matter.
If
you upload the subject to our ftp site (the whole subject
directory  tarred  and gzipped) we will take a look

cheers
Bruce

On Mon, 6 Oct 2014, Smith, Michael wrote:


Hi,

I¹ve been having trouble on a few of our subjects with getting
the  white  matter and pial surface files to ³line up² correctly
with the volume  files.
 I¹ve attached a screenshot of what is happening: the pial
surface is  in red  and the white matter surface file is in
yellow. I have also attached  an  example of a ³good² subject
for comparison.

I¹ve tried looking through the tutorials online but didn¹t see
anything  that  was really related to my issue and I was
wondering what the best way  to  correct this.  We have T2
weighted images for several subjects is well  if  that helps.
Not sure if Freesurfer can use T2 images instead of T1 in  the
­reconall script but I thought I would mention it.  Thank you
very  much  in  advance!

Best,

Michael S.





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Re: [Freesurfer] Image normalization and pial/wm error

[Bruce Fischl]

Hi Sneha

it looks like it is grabbing a bunch of dura. Do you happen to have a 
hires T2 or flair image? If so, you can use that in recon-all 
postprocessing to remove the dura. If not you can try using the graph 
cuts skull stripping to get rid of some of it. I can't tell the accuracy 
of the surfaces in other locations in the images. Other than dura is it 
reasonably acurate?
cheers
Bruce

On Fri, 10 Oct 2014, Sneha Pandya wrote:

> Dear all,
> 
> I am running recon-all on few SPGR T1s and few MPRAGE T1s. However most of
> my dataset, may it be SPGR or MPRAGE has some artifacts and poor wm/gm
> contrast. Have attached a screen shot of bad pial and wm error (going beyond
> dura). Even gcut did not do a good job of cutting of all the dura, and I had
> to manually edit voxels in all the slices. I feel even after that if I run
> recon-all, it will not give me any reliable cortical thickness measures.
> 
> Can anyone please suggest me if I should still manually edit all other
> subjects for all the slices throughout the volume or exclude them from
> analysis?
> 
> PS: attached image FOV is 260 and I used -cw256 flag to restrict FOV to 256.
> For other images FOV is within 256, but still there is lot of dura in the
> brainmask.
> 
> Thanks,
> Sneha
> 
> 
>
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Re: [Freesurfer] Image normalization and pial/wm error

[Sneha Pandya]

Hi Bruce,

Yes, there is a lot of dura. Unfortunately we do not have either flair or T2 as 
a reference to remove dura. I tried running gcut to cut off dura, it still 
won't help and I still had to manually edit whole volume to get rid of it. If 
it helps I can send you orig.mgz, nu.mgz and brainmask.mgz post graph cut to 
look at. However for other structures it is difficult to tell about the 
accuracy because I feel contrast is a little poor. Sequence of this subject is 
spgr with voxel size of 1.01mm*1.35mm*1.5mm(sl. thk), with 26FOV. I even used 
cw256 flag to restrict the field of view. So not really sure why is 
segmentation so poor. 

Other subjects in this dataset has between 20 to 25FOV, and varying voxel size 
from 0.93*1.25*1.5 to 1*1*2. 

Thanks,
Sneha
___
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Friday, October 10, 2014 1:58 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Image normalization and pial/wm error

Hi Sneha

it looks like it is grabbing a bunch of dura. Do you happen to have a
hires T2 or flair image? If so, you can use that in recon-all
postprocessing to remove the dura. If not you can try using the graph
cuts skull stripping to get rid of some of it. I can't tell the accuracy
of the surfaces in other locations in the images. Other than dura is it
reasonably acurate?
cheers
Bruce

On Fri, 10 Oct 2014, Sneha Pandya wrote:

> Dear all,
>
> I am running recon-all on few SPGR T1s and few MPRAGE T1s. However most of
> my dataset, may it be SPGR or MPRAGE has some artifacts and poor wm/gm
> contrast. Have attached a screen shot of bad pial and wm error (going beyond
> dura). Even gcut did not do a good job of cutting of all the dura, and I had
> to manually edit voxels in all the slices. I feel even after that if I run
> recon-all, it will not give me any reliable cortical thickness measures.
>
> Can anyone please suggest me if I should still manually edit all other
> subjects for all the slices throughout the volume or exclude them from
> analysis?
>
> PS: attached image FOV is 260 and I used -cw256 flag to restrict FOV to 256.
> For other images FOV is within 256, but still there is lot of dura in the
> brainmask.
>
> Thanks,
> Sneha
>
>
>
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Re: [Freesurfer] Image normalization and pial/wm error

[Bruce Fischl]

Hi Sneha

then I think manually editing is your best bet (sorry)
Bruce


On Fri, 10 Oct 2014, Sneha Pandya wrote:

> Hi Bruce,
>
> Yes, there is a lot of dura. Unfortunately we do not have either flair or 
> T2 as a reference to remove dura. I tried running gcut to cut off dura, 
> it still won't help and I still had to manually edit whole volume to get 
> rid of it. If it helps I can send you orig.mgz, nu.mgz and brainmask.mgz 
> post graph cut to look at. However for other structures it is difficult 
> to tell about the accuracy because I feel contrast is a little poor. 
> Sequence of this subject is spgr with voxel size of 
> 1.01mm*1.35mm*1.5mm(sl. thk), with 26FOV. I even used cw256 flag to 
> restrict the field of view. So not really sure why is segmentation so 
> poor.
>
> Other subjects in this dataset has between 20 to 25FOV, and varying voxel 
> size from 0.93*1.25*1.5 to 1*1*2.
>
> Thanks,
> Sneha
> ___
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Friday, October 10, 2014 1:58 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Image normalization and pial/wm error
>
> Hi Sneha
>
> it looks like it is grabbing a bunch of dura. Do you happen to have a
> hires T2 or flair image? If so, you can use that in recon-all
> postprocessing to remove the dura. If not you can try using the graph
> cuts skull stripping to get rid of some of it. I can't tell the accuracy
> of the surfaces in other locations in the images. Other than dura is it
> reasonably acurate?
> cheers
> Bruce
>
> On Fri, 10 Oct 2014, Sneha Pandya wrote:
>
>> Dear all,
>>
>> I am running recon-all on few SPGR T1s and few MPRAGE T1s. However most of
>> my dataset, may it be SPGR or MPRAGE has some artifacts and poor wm/gm
>> contrast. Have attached a screen shot of bad pial and wm error (going beyond
>> dura). Even gcut did not do a good job of cutting of all the dura, and I had
>> to manually edit voxels in all the slices. I feel even after that if I run
>> recon-all, it will not give me any reliable cortical thickness measures.
>>
>> Can anyone please suggest me if I should still manually edit all other
>> subjects for all the slices throughout the volume or exclude them from
>> analysis?
>>
>> PS: attached image FOV is 260 and I used -cw256 flag to restrict FOV to 256.
>> For other images FOV is within 256, but still there is lot of dura in the
>> brainmask.
>>
>> Thanks,
>> Sneha
>>
>>
>>
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>
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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
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
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> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.
>
>
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Re: [Freesurfer] Image normalization and pial/wm error

[Sneha Pandya]

Thanks again, yes that's what it looks like, but I just have one concern, if I 
have to manually edit dura and wm in all the slices and in most of the 
subjects, will it still give me reliable cortical thickness measure?

Thanks,
Sneha

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Friday, October 10, 2014 2:30 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Image normalization and pial/wm error

Hi Sneha

then I think manually editing is your best bet (sorry)
Bruce


On Fri, 10 Oct 2014, Sneha Pandya wrote:

> Hi Bruce,
>
> Yes, there is a lot of dura. Unfortunately we do not have either flair or
> T2 as a reference to remove dura. I tried running gcut to cut off dura,
> it still won't help and I still had to manually edit whole volume to get
> rid of it. If it helps I can send you orig.mgz, nu.mgz and brainmask.mgz
> post graph cut to look at. However for other structures it is difficult
> to tell about the accuracy because I feel contrast is a little poor.
> Sequence of this subject is spgr with voxel size of
> 1.01mm*1.35mm*1.5mm(sl. thk), with 26FOV. I even used cw256 flag to
> restrict the field of view. So not really sure why is segmentation so
> poor.
>
> Other subjects in this dataset has between 20 to 25FOV, and varying voxel
> size from 0.93*1.25*1.5 to 1*1*2.
>
> Thanks,
> Sneha
> ___
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Friday, October 10, 2014 1:58 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Image normalization and pial/wm error
>
> Hi Sneha
>
> it looks like it is grabbing a bunch of dura. Do you happen to have a
> hires T2 or flair image? If so, you can use that in recon-all
> postprocessing to remove the dura. If not you can try using the graph
> cuts skull stripping to get rid of some of it. I can't tell the accuracy
> of the surfaces in other locations in the images. Other than dura is it
> reasonably acurate?
> cheers
> Bruce
>
> On Fri, 10 Oct 2014, Sneha Pandya wrote:
>
>> Dear all,
>>
>> I am running recon-all on few SPGR T1s and few MPRAGE T1s. However most of
>> my dataset, may it be SPGR or MPRAGE has some artifacts and poor wm/gm
>> contrast. Have attached a screen shot of bad pial and wm error (going beyond
>> dura). Even gcut did not do a good job of cutting of all the dura, and I had
>> to manually edit voxels in all the slices. I feel even after that if I run
>> recon-all, it will not give me any reliable cortical thickness measures.
>>
>> Can anyone please suggest me if I should still manually edit all other
>> subjects for all the slices throughout the volume or exclude them from
>> analysis?
>>
>> PS: attached image FOV is 260 and I used -cw256 flag to restrict FOV to 256.
>> For other images FOV is within 256, but still there is lot of dura in the
>> brainmask.
>>
>> Thanks,
>> Sneha
>>
>>
>>
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Re: [Freesurfer] Image normalization and pial/wm error

[Bruce Fischl]

I don't really know, sorry. You could to an inter- and intra-rater test 
by editing some of the images twice
On Fri, 10 Oct 2014, Sneha Pandya wrote:

> Thanks again, yes that's what it looks like, but I just have one concern, if 
> I have to manually edit dura and wm in all the slices and in most of the 
> subjects, will it still give me reliable cortical thickness measure?
>
> Thanks,
> Sneha
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Friday, October 10, 2014 2:30 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Image normalization and pial/wm error
>
> Hi Sneha
>
> then I think manually editing is your best bet (sorry)
> Bruce
>
>
> On Fri, 10 Oct 2014, Sneha Pandya wrote:
>
>> Hi Bruce,
>>
>> Yes, there is a lot of dura. Unfortunately we do not have either flair or
>> T2 as a reference to remove dura. I tried running gcut to cut off dura,
>> it still won't help and I still had to manually edit whole volume to get
>> rid of it. If it helps I can send you orig.mgz, nu.mgz and brainmask.mgz
>> post graph cut to look at. However for other structures it is difficult
>> to tell about the accuracy because I feel contrast is a little poor.
>> Sequence of this subject is spgr with voxel size of
>> 1.01mm*1.35mm*1.5mm(sl. thk), with 26FOV. I even used cw256 flag to
>> restrict the field of view. So not really sure why is segmentation so
>> poor.
>>
>> Other subjects in this dataset has between 20 to 25FOV, and varying voxel
>> size from 0.93*1.25*1.5 to 1*1*2.
>>
>> Thanks,
>> Sneha
>> ___
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
>> [fis...@nmr.mgh.harvard.edu]
>> Sent: Friday, October 10, 2014 1:58 PM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] Image normalization and pial/wm error
>>
>> Hi Sneha
>>
>> it looks like it is grabbing a bunch of dura. Do you happen to have a
>> hires T2 or flair image? If so, you can use that in recon-all
>> postprocessing to remove the dura. If not you can try using the graph
>> cuts skull stripping to get rid of some of it. I can't tell the accuracy
>> of the surfaces in other locations in the images. Other than dura is it
>> reasonably acurate?
>> cheers
>> Bruce
>>
>> On Fri, 10 Oct 2014, Sneha Pandya wrote:
>>
>>> Dear all,
>>>
>>> I am running recon-all on few SPGR T1s and few MPRAGE T1s. However most of
>>> my dataset, may it be SPGR or MPRAGE has some artifacts and poor wm/gm
>>> contrast. Have attached a screen shot of bad pial and wm error (going beyond
>>> dura). Even gcut did not do a good job of cutting of all the dura, and I had
>>> to manually edit voxels in all the slices. I feel even after that if I run
>>> recon-all, it will not give me any reliable cortical thickness measures.
>>>
>>> Can anyone please suggest me if I should still manually edit all other
>>> subjects for all the slices throughout the volume or exclude them from
>>> analysis?
>>>
>>> PS: attached image FOV is 260 and I used -cw256 flag to restrict FOV to 256.
>>> For other images FOV is within 256, but still there is lot of dura in the
>>> brainmask.
>>>
>>> Thanks,
>>> Sneha
>>>
>>>
>>>
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[Freesurfer] cortical surface area measurement and vertex-wise analysis

[Emma Thompson]

Dear Freesurfers,
I recently heard that there are several disadvantages to using a measure of
cortical surface area in Freesurfer, specifically due to conducting a
vertex-wise analysis. Can someone help me understand why a measure of
surface area using this approach might be flawed? Thanks!
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Re: [Freesurfer] cortical surface area measurement and vertex-wise analysis

[Donna Dierker]

Hi Emma,

I might not be the only one who is unsure what you mean by a vertex-wise 
cortical surface area measure.  Do you mean something like what is illustrated 
in figures 2 and 3 here:

http://www.pnas.org/content/107/29/13135.figures-only

… which is similar, but not identical to the local gyrification index?

If so, would you use this measure on surfaces before or after registration to a 
target atlas?

Donna


On Oct 10, 2014, at 4:19 PM, Emma Thompson  wrote:

> Dear Freesurfers,
> I recently heard that there are several disadvantages to using a measure of 
> cortical surface area in Freesurfer, specifically due to conducting a 
> vertex-wise analysis. Can someone help me understand why a measure of surface 
> area using this approach might be flawed? Thanks!



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