Re: [Freesurfer] Retinotopy-polar angle

[Michelle Umali]

Hi Doug,
I'm trying to analyze my retinotopy data and visualizing in tksurfer.

I've been able to view the significance maps through:
  tksurfer-sess -a rtopy.self.lh -s sessid

But I've had issues displaying the polar angle data using the  
Configure Overlay tool.  Specifically, I want to use the color wheel  
to assign colors to angles in order to help define boundaries between  
regions:

1) Do the angles range from -pi to +pi?

2)In the Configure overlay window, after I've clicked the 'Color  
wheel' radio button, I can't find the 'Apply' button that is supposed  
to be at the bottom of the window.  Resizing the window doesn't work.

  tksurfer-sess -a rtopy.self.lh -s sessid -map angle

  tksurfer-sess -a rtopy.self.lh -s sessid -map angle.masked



Also, is there a guide on how to draw region boundaries using angle,  
polar, and fieldsign info?

Thanks very much.
Michelle


Quoting Douglas N Greve :

> Michelle,
> Can you give more details of what you are doing? How did you generate
> the files you are trying to load?
> doug
>
> Michelle Umali wrote:
>> Dear Freesurfers,
>> I'm having issues trying to display the polar angle data using the   
>>  color wheel. Unfortunately, I can't resizing the Configure Overlay  
>>   Display window.  No matter what I try, I can't actually see the   
>> Apply  button.
>>
>> Any suggestions?
>> Also, is there a quickie guide on defining the boundaries of visual areas?
>>
>> Thanks.
>> Michelle
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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
>
>
>
> 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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Re: [Freesurfer] Fedora 14

[Pedro Paulo de Magalhães Oliveira Junior]

Yes. It works.

-- iOS 4.3

Em 18/04/2011, às 21:13, "roger@yale.edu"  escreveu:

> Hi all,
> Quick question: will the latest Linux 32-bit install work with Fedora 14?
> Please let me know if there are known issues.
> Thanks,
> Roger
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[Freesurfer] Fedora 14

[roger . jou]

Hi all,
Quick question: will the latest Linux 32-bit install work with Fedora 14? 
Please let me know if there are known issues.
Thanks,
Roger
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Re: [Freesurfer] Pial surface error

[Allie Rosen]

Hi Bruce,

I am running recon-all tonight using wm voxels that I manually added (I also
edited brainmask.mgz to add missing grey matter). To me it doesn't really
look like a case of the white matter not having a high enough intensity. It
simply looks like the whole lobe was ignored, regardless of intensity. But
I'll check tomorrow to see if the intensity is low.

Thanks,
Allie


On Mon, Apr 18, 2011 at 7:38 PM, Bruce Fischl wrote:

> What is the intensity of the white matter in the regions you drew in? A
> couple of control points might help if it is less than 110
>
>
>
> On Apr 18, 2011, at 12:36 PM, Allie Rosen  wrote:
>
> Hi Sita,
>
> Thanks for all the responses! I've actually had the same problem for
> multiple subjects. I'm using version 5.0.0. I'll try fixing the cerebellum
> as well. I've attached pictures of where I am adding wm voxels. They aren't
> really in the same places as in the online tutorials. Could you take a quick
> look to see if they're in the right place?
>
> Thanks,
> Allie
>
>
>
>
> On Mon, Apr 18, 2011 at 12:31 PM, Sita Kakunoori <
> s...@nmr.mgh.harvard.edu> wrote:
>
>>
>> Hi Allie,
>>
>> pial surface which looks like this can only be corrected by correcting the
>> wm.mgz. Also I would suggest to try and fix the cerebellum and see if it
>> corrects the surfaces as well. Since part of the cerebellum is stripped off,
>> it's probably affecting the segmentation as well but I could be wrong. what
>> version of freesurfer are you using.
>>
>>
>> Sita.
>>
>>
>>
>> On Mon, 18 Apr 2011, Allie Rosen wrote:
>>
>>  Hi Sita,
>>>
>>> Can I still add voxels to wm.mgz even though the points would be outside
>>> even the pial boundary?
>>>
>>> Thanks
>>> Allie
>>>
>>>
>>>
>>> On Mon, Apr 18, 2011 at 12:18 PM, Sita Kakunoori
>>> < s...@nmr.mgh.harvard.edu>wrote:
>>>
>>>
 Hi Allie,

 This probably needs white matter edits but it's hard to tell from one
 slice. Please refer to our white matter edits wiki and toplogical
 defects
 wiki and see if it helps in fixing the errors in your datasets. Also it
 looks like part of the Cerebellum is stripped off. You might want to
 correct
 that as well.

  
 https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits

 
 https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect


 Sita.




 On Mon, 18 Apr 2011, Allie Rosen wrote:

  Hi,

>
> Once processed, several of my subjects have had errors around the
> occipital
> lobe. Attached is an example. I've already tried editing brainmask.mgz
> and
> running recon-all, but as you can see, this didn't change the pial or
> wm
> borders. What can I do to fix this?
>
> Thank you,
> Allie Rosen, MSc Candidate
> Graduate Student, Department of Neurosurgery
> Toronto Western Hospital 14-327
> 399 Bathurst St.
> University of Toronto
>
>
>
 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.



>>>
> <2.png>
>
> <3.png>
>
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Re: [Freesurfer] Grey Matter Not Included In Pial Surface

[Bruce Fischl]

You shouldn't ever add any that are not in white matter. Feel free to upload 
the subject and we will take a look



On Apr 18, 2011, at 7:35 PM, andrewmain...@berkeley.edu wrote:

> Hi all,
> 
> I have several subjects whose cortical grey matter continues to not be
> included in the pial surface even after adding numerous control points to
> the white matter as suggested in
> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2007-July/005649.html
> . Some of the control points I added were outside of the pial surface
> boundary--does this cause them to be ignored? I have white matter areas
> with multiple control points that are still not included in either the
> pial or white matter boundaries.
> 
> I can supply images if it would be helpful.
> 
> Thanks for any help!
> 
> Andrew
> 
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> 

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Re: [Freesurfer] Pial surface error

[Bruce Fischl]

What is the intensity of the white matter in the regions you drew in? A couple 
of control points might help if it is less than 110



On Apr 18, 2011, at 12:36 PM, Allie Rosen  wrote:

> Hi Sita,
> 
> Thanks for all the responses! I've actually had the same problem for multiple 
> subjects. I'm using version 5.0.0. I'll try fixing the cerebellum as well. 
> I've attached pictures of where I am adding wm voxels. They aren't really in 
> the same places as in the online tutorials. Could you take a quick look to 
> see if they're in the right place?
> 
> Thanks,
> Allie
> 
> 
> 
> 
> On Mon, Apr 18, 2011 at 12:31 PM, Sita Kakunoori  
> wrote:
> 
> Hi Allie,
> 
> pial surface which looks like this can only be corrected by correcting the 
> wm.mgz. Also I would suggest to try and fix the cerebellum and see if it 
> corrects the surfaces as well. Since part of the cerebellum is stripped off, 
> it's probably affecting the segmentation as well but I could be wrong. what 
> version of freesurfer are you using.
> 
> 
> Sita.
> 
> 
> 
> On Mon, 18 Apr 2011, Allie Rosen wrote:
> 
> Hi Sita,
> 
> Can I still add voxels to wm.mgz even though the points would be outside
> even the pial boundary?
> 
> Thanks
> Allie
> 
> 
> 
> On Mon, Apr 18, 2011 at 12:18 PM, Sita Kakunoori
> wrote:
> 
> 
> Hi Allie,
> 
> This probably needs white matter edits but it's hard to tell from one
> slice. Please refer to our white matter edits wiki and toplogical defects
> wiki and see if it helps in fixing the errors in your datasets. Also it
> looks like part of the Cerebellum is stripped off. You might want to correct
> that as well.
> 
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits
> 
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect
> 
> 
> Sita.
> 
> 
> 
> 
> On Mon, 18 Apr 2011, Allie Rosen wrote:
> 
>  Hi,
> 
> Once processed, several of my subjects have had errors around the
> occipital
> lobe. Attached is an example. I've already tried editing brainmask.mgz and
> running recon-all, but as you can see, this didn't change the pial or wm
> borders. What can I do to fix this?
> 
> Thank you,
> Allie Rosen, MSc Candidate
> Graduate Student, Department of Neurosurgery
> Toronto Western Hospital 14-327
> 399 Bathurst St.
> University of Toronto
> 
> 
> 
> 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.
> 
> 
> 
> 
> <2.png>
> <3.png>
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[Freesurfer] Grey Matter Not Included In Pial Surface

[andrewmains12]

Hi all,

I have several subjects whose cortical grey matter continues to not be
included in the pial surface even after adding numerous control points to
the white matter as suggested in
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2007-July/005649.html
. Some of the control points I added were outside of the pial surface
boundary--does this cause them to be ignored? I have white matter areas
with multiple control points that are still not included in either the
pial or white matter boundaries.

I can supply images if it would be helpful.

Thanks for any help!

Andrew

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[Freesurfer] question regarding clusterwise correction for multiple comparisons

[Ilana Hairston]

Hi there,
After running mri_glmfit with several different contrasts, all stored in the
same folder  (e.g., gender controlling for age: 1 -1 0 0; interaction of
gender with age: 0 0 1 -1, etc.), i am interested in correcting for only one
of the effects (e.g., gender).  However, the mri_glmfit-sim doesn't seem to
specify which contrast.
I guess i'm not clear as to what information is used for the montecarlo
thanks
ilana

-- 
***
peligro! flaca pero mala!
**
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Re: [Freesurfer] Question about "bbregister"

[Douglas N Greve]

Hi Xiaojian, you can use mri_vol2surf or mri_vol2vol.
doug

ps. Please send these types of questions to the freesurfer list and not 
to me directly. Thanks!

XJ Kang wrote:
>  Hi Dr Greve,
>
> Thank you for your prompt reply.
>
> By "registration matrix", do you mean the matrix in "register.dat"? 
> Could you please remind me how to apply it in all the frames? I am 
> using spm to process all the data. Maybe there are some freesurfer 
> functions to apply the matrix for all the frames. Or any help page in 
> FreeSurferWiki?
>
> Again, thank you for your time.
>
> Xiaojian
>
>
>
> On 4/18/2011 11:23 AM, Douglas N Greve wrote:
>> Hi Xiaojian, what is usually done is to run motion correction on your 
>> fMRI time series picking the middle time point as a reference. Then 
>> registration matrix for the middle time point will be appropriate for 
>> all the frames in the time series.
>>
>> doug
>>
>
>

-- 
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
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Re: [Freesurfer] Question about "bbregister"

[Douglas N Greve]

Hi Xiaojian, what is usually done is to run motion correction on your 
fMRI time series picking the middle time point as a reference. Then 
registration matrix for the middle time point will be appropriate for 
all the frames in the time series.

doug





XJ Kang wrote:
>  Dear Dr. Greve,
>
> I am trying to apply "bbregister" to our EPI data after I read your 
> 2009 Neuroimage paper "Accurate and robust brain image alignment using 
> boundary-based registration".
>
> One thing I found that bbregister will not save the coregistered 
> information to the original --mov frame. Instread, it incorporated the 
> info into "register.dat" or in the resampled "--o " image.  Then I 
> have to register all the EPI frames one by one and resampled them into 
> the orig.mgz (256^3) space to compare them.
>
> Is there any way or option that I can save the bbregistered frame (in 
> low resolution EPI) in its own space? Then I can realign all other 
> EPIs to this coregistered frame in the EPI resolution space.
>
> Thank you for your time.
>
> Sincerely,
> Xiaojian Kang
>
>

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

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Re: [Freesurfer] to paint functional on surface, use mri_vol2surf or tksurfer?

[Douglas N Greve]

yes, that works. You'll probably want to fill the ribbon using the 
--proj option (something like --proj frac 0 1 .1)

doug

Yang Liu wrote:
> Hi Doug,
>
> Thanks for the quick reply.
> What the standard procedure to get a volume ROI from a surfaced 
> defined ROI?  
>
> My solution is to create a label by filling a region in a closed 
> path.  Then is the next step to use mri_label2vol?
>
>
> Yang
>
>
> On Mon, Apr 18, 2011 at 1:15 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> Hi Yang, using mri_vol2surf is more accurate than tksurfer by
> itself. You can also control the depth of projection with
> mri_vol2surf (eg, sample half way between the white and pial
> surfaces).
>
> doug
>
> Yang Liu wrote:
>
> Hi,
>
> I am trying to paint the functional significance map onto the
> surface generated from the antomical (monkey brain).  What I
> am doing now is using the following command:
>
> " tksurfer ${tmp_subj} ${hemi} ${cut_surface}  -overlay
> 
> /space/data/stan/cooked/2010/100131CastorTEST2/MION/fmc_reg/H-vs-V/sig.256.reg.nii
> -overlay-reg ${reg_dir}/register.dat "
>
> the "sig.256.reg.nii" is the significance map and
> "register.dat" is the transformation matrix.
>
> It looks like that the commands are doing fine, I see the
> signicance map on inflated surfaces.  However, I also see
> other tutorial that used mri_vol2surf to display the
> significance map.
> I wonder whether or not our method is not as good as mri_vol2surf.
>
> I am asking this question also because we are creating ROIs
> from the surfaces. Now our ROIs (labels)  are only
> corresponding to a very tight layer of voxels surrounding the
> white matter. Shall I use mri_label2vol to include all the
> graymatter voxels surrounding the label?
>
> Any suggestions would be very helpful.
>
>
> Yang
> 
> 
>
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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
> 
>
>
>
> 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.
>
>

-- 
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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
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Re: [Freesurfer] to paint functional on surface, use mri_vol2surf or tksurfer?

[Yang Liu]

Hi Doug,

Thanks for the quick reply.
What the standard procedure to get a volume ROI from a surfaced defined ROI?


My solution is to create a label by filling a region in a closed path.  Then
is the next step to use mri_label2vol?


Yang


On Mon, Apr 18, 2011 at 1:15 PM, Douglas N Greve
wrote:

> Hi Yang, using mri_vol2surf is more accurate than tksurfer by itself. You
> can also control the depth of projection with mri_vol2surf (eg, sample half
> way between the white and pial surfaces).
>
> doug
>
> Yang Liu wrote:
>
>> Hi,
>>
>> I am trying to paint the functional significance map onto the surface
>> generated from the antomical (monkey brain).  What I am doing now is using
>> the following command:
>>
>> " tksurfer ${tmp_subj} ${hemi} ${cut_surface}  -overlay
>> /space/data/stan/cooked/2010/100131CastorTEST2/MION/fmc_reg/H-vs-V/sig.256.reg.nii
>> -overlay-reg ${reg_dir}/register.dat "
>>
>> the "sig.256.reg.nii" is the significance map and "register.dat" is the
>> transformation matrix.
>>
>> It looks like that the commands are doing fine, I see the signicance map
>> on inflated surfaces.  However, I also see other tutorial that used
>> mri_vol2surf to display the significance map.
>> I wonder whether or not our method is not as good as mri_vol2surf.
>>
>> I am asking this question also because we are creating ROIs from the
>> surfaces. Now our ROIs (labels)  are only corresponding to a very tight
>> layer of voxels surrounding the white matter. Shall I use mri_label2vol to
>> include all the graymatter voxels surrounding the label?
>>
>> Any suggestions would be very helpful.
>>
>>
>> Yang
>> 
>>
>> ___
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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
>
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Re: [Freesurfer] to paint functional on surface, use mri_vol2surf or tksurfer?

[Douglas N Greve]

Hi Yang, using mri_vol2surf is more accurate than tksurfer by itself. 
You can also control the depth of projection with mri_vol2surf (eg, 
sample half way between the white and pial surfaces).

doug

Yang Liu wrote:
> Hi,
>
> I am trying to paint the functional significance map onto the surface 
> generated from the antomical (monkey brain).  What I am doing now is 
> using the following command:
>
> " tksurfer ${tmp_subj} ${hemi} ${cut_surface}  -overlay 
> /space/data/stan/cooked/2010/100131CastorTEST2/MION/fmc_reg/H-vs-V/sig.256.reg.nii
>  
> -overlay-reg ${reg_dir}/register.dat "
>
> the "sig.256.reg.nii" is the significance map and "register.dat" is 
> the transformation matrix.
>
> It looks like that the commands are doing fine, I see the signicance 
> map on inflated surfaces.  However, I also see other tutorial that 
> used mri_vol2surf to display the significance map.
> I wonder whether or not our method is not as good as mri_vol2surf.
>
> I am asking this question also because we are creating ROIs from the 
> surfaces. Now our ROIs (labels)  are only corresponding to a very 
> tight layer of voxels surrounding the white matter. Shall I use 
> mri_label2vol to include all the graymatter voxels surrounding the label?
>
> Any suggestions would be very helpful.
>
>
> Yang
> 
>
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[Freesurfer] to paint functional on surface, use mri_vol2surf or tksurfer?

[Yang Liu]

Hi,

I am trying to paint the functional significance map onto the surface
generated from the antomical (monkey brain).  What I am doing now is using
the following command:

" tksurfer ${tmp_subj} ${hemi} ${cut_surface}  -overlay
/space/data/stan/cooked/2010/100131CastorTEST2/MION/fmc_reg/H-vs-V/sig.256.reg.nii
-overlay-reg ${reg_dir}/register.dat "

the "sig.256.reg.nii" is the significance map and "register.dat" is the
transformation matrix.

It looks like that the commands are doing fine, I see the signicance map on
inflated surfaces.  However, I also see other tutorial that used
mri_vol2surf to display the significance map.
I wonder whether or not our method is not as good as mri_vol2surf.

I am asking this question also because we are creating ROIs from the
surfaces. Now our ROIs (labels)  are only corresponding to a very tight
layer of voxels surrounding the white matter. Shall I use mri_label2vol to
include all the graymatter voxels surrounding the label?

Any suggestions would be very helpful.


Yang
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Re: [Freesurfer] error when running funcroi-table-sess

[Douglas N Greve]

The problem is that three of the subjects have no voxels in the ROI (14, 
17, and 26). I need to have a better error message, but the issue as to 
what to do with them will remain. How do you intend to handle such subjects?

doug

Douglas N Greve wrote:
> What directory are you running it from and what is your $SUBJECTS_DIR?
> doug
>
> suzanne oosterwijk wrote:
>> Hi Freesurfers,
>>
>> I am trying to run an ROI analysis with a structural and functional 
>> constraint in Freesurfer 5 and after I run funcroi-table-sess I get 
>> the following error:
>>
>> Parsing the .stats files
>> Building the table..
>> ERROR: All stat files should have the same segmentations
>>
>> There is also no .dat file created.
>>
>> I am using the following commands:
>>
>> foreach s ( `more sessid` )
>> mri_cor2label --c $s/mri/aparc+aseg.mgz --id 1035 --l 
>> $s/label/lh_insula_aseg.label
>> mri_cor2label --c $s/mri/aparc+aseg.mgz --id 2035 --l 
>> $s/label/rh_insula_aseg.label
>> end
>>
>> funcroi-config -roi R_insula_g_mni.roicfg -label rh_insula_aseg -a 
>> constr_sm5_mni_gamma_nopace_cor -contrast allvsfix -thresh 2 -sign 
>> pos -map sig -fillthresh .5
>> funcroi-sess -roi R_insula_g_mni.roicfg -sf sessid
>> funcroi-table-sess -roi R_insula_g_mni.roicfg -a 
>> constr_sm5_mni_gamma_nopace_cor_extra -c bfvsfix_script -o 
>> R_insula_g_mni.bfvsfix_script.dat -sf sessid
>>
>> I have tried many things to see what I am doing wrong, but I can't 
>> figure it out.
>>
>> Thanks for any help!
>> Suzanne
>>
>> -- 
>>
>> Suzanne Oosterwijk, Ph.D.
>>
>> Postdoctoral Researcher
>>
>> Interdisciplinary Affective Science Lab
>>
>> Department of Psychology
>>
>> Northeastern University
>>
>> 114 Lake Hall
>>
>> s.oosterw...@neu.edu 
>>
>>
>> 
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>

-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

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Re: [Freesurfer] Frontal lobes excluded

[Allison Stevens]

Hi Sean,
Yes, we can help. Best would be to upload the subject and Khoa can take a 
look. She can give you additional instructions if needed. 
Allison


On Mon, 18 Apr 2011, Seán Froudist Walsh wrote:


Dear FreeSurfer gurus,

I have T1 scans of a patient at three different time-points (one run at each
time-point). The cortical reconstructions of the first and third time-points
seem to have worked reasonably well, but the reconstruction of the second
time-point was a disaster. A massive part of the frontal lobe (bilaterally)
is cut out from the wm and gm  surfaces. I tried fixing this with wm edits,
but that exited with errors, then I tried to add control points to the new
wm.mgz and recon-all again exited with errors. Is there any possibility of
saving this scan? Would I be able to upload some screenshots to help you see
what is going on?

Many thanks in advance,

Sean
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Re: [Freesurfer] Pial surface error

[Sita Kakunoori]

Hi Allie,

This probably needs white matter edits but it's hard to tell 
from one slice. Please refer to our white 
matter edits wiki and toplogical defects wiki and see if it helps in 
fixing the errors in your datasets. Also it looks like part of the 
Cerebellum is stripped off. You might want to correct that as well.

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect


Sita.



On Mon, 18 Apr 2011, Allie Rosen wrote:

> Hi,
>
> Once processed, several of my subjects have had errors around the occipital
> lobe. Attached is an example. I've already tried editing brainmask.mgz and
> running recon-all, but as you can see, this didn't change the pial or wm
> borders. What can I do to fix this?
>
> Thank you,
> Allie Rosen, MSc Candidate
> Graduate Student, Department of Neurosurgery
> Toronto Western Hospital 14-327
> 399 Bathurst St.
> University of Toronto
>
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Re: [Freesurfer] gray/white/other with mri_segstats with version 5stable

[Douglas N Greve]

Hi Saad, the default color table 
($FREESURFER_HOME/FreeSurferColorLUT.txt) does have a huge number of 
segmentations in there (much more than what is in the aparc+aseg). To 
get just the cortical white matter, you can look in the aseg.stats file. 
This has a n entry in the header for the total cortical WM (better to 
use this as it is surface-based not voxel based). The aseg.stats file 
also has info about total cortical gray and total gray (also in the 
header, also surface-based). We don't have a total CSF measure, but you 
can add them up from the individual measures in the aseg.stats (this is 
ventricular only, not sulcal). Is this what you want or do you need to 
average your svs file over all of GM, WM, and CSF?

doug

Saad Ramadan wrote:
> Hi ,
>  
> When I do mri_segstats, about 1200 "segmentation ids" are produced 
> with some of them having vague names (at least for me).
> Pls find below a typical output (around 1200 lines) or mri_segstats.
>  
> The commad I use is:
> mri_segstats --seg $SUBJECTS_DIR/subject/mri/aparc+aseg.mgz  
> --ctab-default --i svs.anat.nii --mask svs.anat.nii --sum 
> svs.summary.dat  
>  
> My desired output would contain (1) how many voxels of gray matter I 
> have, (2) white matter and (3) other of CSF.
> Presently, I have to go through the output line by line, and classify 
> each item as gray. white. or csf and then do the sums in the end.
>  
> Is there a way to obtain a simplified output like the one I described 
> above?
>  
> Thank you
>  
>  
>  0 0  Unknown 16769446  1.67694e+07
>   1 1  Left-Cerebral-Exterior  0
>   2 2  Left-Cerebral-White-Matter 5867  5867
>   3 3  Left-Cerebral-Cortex  0
>   4 4  Left-Lateral-Ventricle   30  30
>   5 5  Left-Inf-Lat-Vent  0
>   6 6  Left-Cerebellum-Exterior  0
>   7 7  Left-Cerebellum-White-Matter  0
>   8 8  Left-Cerebellum-Cortex  0
>   9 9  Left-Thalamus  0
>  1010  Left-Thalamus-Proper  0
>  1111  Left-Caudate  196  196
>  1212  Left-Putamen  0
>  1313  Left-Pallidum  0
>  1414  3rd-Ventricle  0
>  1515  4th-Ventricle  0
>  1616  Brain-Stem  0
>  1717  Left-Hippocampus  0
>  1818  Left-Amygdala  0
>  1919  Left-Insula  0
>  2020  Left-Operculum  0
>  2121  Line-1  0
>  2222  Line-2  0
>  2323  Line-3  0
>  2424  CSF  0
>  2525  Left-Lesion  0
>  2626  Left-Accumbens-area  0
>  2727  Left-Substancia-Nigra  0
>  2828  Left-VentralDC  0
>  2929  Left-undetermined  0
>  3030  Left-vessel  0
>  3131  Left-choroid-plexus2  2
>  3232  Left-F3orb  0
>  3333  Left-lOg  0
>  3434  Left-aOg  0
>  3535  Left-mOg  0
>  3636  Left-pOg  0
>  3737  Left-Stellate  0
>  3838  Left-Porg  0
>  3939  Left-Aorg  0
>  4040  Right-Cerebral-Exterior  0
>  4141  Right-Cerebral-White-Matter  0
>  4242  Right-Cerebral-Cortex  0
>  4343  Right-Lateral-Ventricle  0
>  4444  Right-Inf-Lat-Vent  0
>  4545  Right-Cerebellum-Exterior  0
>  4646  Right-Cerebellum-White-Matter  0
>  4747  Right-Cerebellum-Cortex  0
>  4848  Right-Thalamus  0
>  4949  Right-Thalamus-Proper  0
>  5050  Right-Caudate  0
>  5151  Right-Putamen  0
>  5252  Right-Pallidum  0
>  5353  Right-Hippocampus  0
>  5454  Right-Amygdala  0
>  5555  Right-Insula  0
>  5656  Right-Operculum  0
>  5757  Right-Lesion  0
>  5858  Right-Accumbens-area  0
>  5959  Right-Substancia-Nigra  0
>  6060  Right-VentralDC  0
>  6161  Right-undetermined  0
>  6262  Right-vessel  0
>  6363  Right-choroid-plexus  0
>  6464  Right-F3orb  0
>  6565  Right-lOg  0
>  6666  Right-aOg  0
>  6767  Right-mOg  0
>  6868  Right-pOg  0
>  6969  Right-Stellate  0
>  7070  Right-Porg  0
>  7171  Right-Aorg  0
>  7272  5th-Ventricle  0
>  7373  Left-Interior  0
>  7474  Right-Interior  0
>  7575  Left-Lateral-Ventricles  0
>  7676  Right-Lateral-Ventricles  0
>  7777  WM-hypointensities   87  87
>  7878  Left-WM-hypointensities  0
>  7979  Right-WM-hypointensities  0
>  8080  non-WM-hypointensities  0
>  8181  Left-non-WM-hypointensities  0
>  8282  Right-non-WM-hypointensities  0
>  8383  Left-F1  0
>  8484  Right-F1  0
>  8585  Optic-Chiasm  0
>  8686  Corpus_Callosum  0
>  8796  Left-Amygdala-Anterior  0
>  8897  Right-Amygdala-Anterior  0
>  8998  Dura  0
>  90   100  Left-wm-intensity-abnormality  0
>  91   101  Left-caudate-intensity-abnormality  0
>  92   102  Left-putamen-intensity-abnormality  0
>  93   103  Left-accumbens-intensity-abnormality  0
>  94   104  Left-pallidum-intensity-abnormality  0
>  95   105  Left-amygdala-intensity-abnormality  0
>  96   106  Left-hippocampus-intensity-abnormality  0
>  97   107  Left-thalamus-intensity-abnormality  0
>  98   108  Left-VDC-intensity-abnormality  0
>  99   109  Right-wm-intensity-abnormality  0
> 100

Re: [Freesurfer] Retinotopy-polar angle

[Douglas N Greve]

Michelle,
Can you give more details of what you are doing? How did you generate 
the files you are trying to load?
doug

Michelle Umali wrote:
> Dear Freesurfers,
> I'm having issues trying to display the polar angle data using the  
> color wheel. Unfortunately, I can't resizing the Configure Overlay  
> Display window.  No matter what I try, I can't actually see the Apply  
> button.
>
> Any suggestions?
> Also, is there a quickie guide on defining the boundaries of visual areas?
>
> Thanks.
> Michelle
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>
>
>   

-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

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Re: [Freesurfer] error when running funcroi-table-sess

[Douglas N Greve]

What directory are you running it from and what is your $SUBJECTS_DIR?
doug

suzanne oosterwijk wrote:
> Hi Freesurfers,
>
> I am trying to run an ROI analysis with a structural and functional 
> constraint in Freesurfer 5 and after I run funcroi-table-sess I get 
> the following error:
>
> Parsing the .stats files
> Building the table..
> ERROR: All stat files should have the same segmentations
>
> There is also no .dat file created.
>
> I am using the following commands:
>
> foreach s ( `more sessid` )
> mri_cor2label --c $s/mri/aparc+aseg.mgz --id 1035 --l 
> $s/label/lh_insula_aseg.label
> mri_cor2label --c $s/mri/aparc+aseg.mgz --id 2035 --l 
> $s/label/rh_insula_aseg.label
> end
>
> funcroi-config -roi R_insula_g_mni.roicfg -label rh_insula_aseg -a 
> constr_sm5_mni_gamma_nopace_cor -contrast allvsfix -thresh 2 -sign pos 
> -map sig -fillthresh .5
> funcroi-sess -roi R_insula_g_mni.roicfg -sf sessid
> funcroi-table-sess -roi R_insula_g_mni.roicfg -a 
> constr_sm5_mni_gamma_nopace_cor_extra -c bfvsfix_script -o 
> R_insula_g_mni.bfvsfix_script.dat -sf sessid
>
> I have tried many things to see what I am doing wrong, but I can't 
> figure it out.
>
> Thanks for any help!
> Suzanne
>
> -- 
>
> Suzanne Oosterwijk, Ph.D.
>
> Postdoctoral Researcher
>
> Interdisciplinary Affective Science Lab
>
> Department of Psychology
>
> Northeastern University
>
> 114 Lake Hall
>
> s.oosterw...@neu.edu 
>
>
> 
>
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-- 
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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

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[Freesurfer] high-resolution cerebellar surface map

[Judy Kipping]

Dear freesurfer community, 

I have started using freesurfer in order to visualize functional data of the 
cerebellum on a surface map. I was reading a lot in the freesurfer archives, 
and have found entries discussing or asking about a progress in order to 
properly segment and map highly resolved anatomical data (in my case 
0.5x0.5x0.6). 
After some time now I managed to create surface maps, going stepwise through 
the recon-all scripts to improve cerebellar segmentation. But still, I struggle 
with parameter settings in autorecon-2. Do you have any suggestions on 
parameters which might have a crucial benefit in order to keep the folia of 
cerebellar cortex maintained? 

However, I was also wondering, whether the experts can report something new at 
the 'automatic cerebellar segmentation' front. 

I highly appreciate any advice! 

Thanks, 
Judy Kipping 
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Re: [Freesurfer] High resolution segmentation

[Bruce Fischl]

Hi Sara

mri_aparc2aseg should do the trick. I don't think there's an easy way to do 
#2 though. The make_face_parcellation stuff samples relatively uniformly 
over the cortex so the parcels in it won't correspond to the aparc.annot 
labels in any real way.

cheers
Bruce


On Mon, 18 Apr 2011, Jahfari, Sara wrote:

> Dear Freesurfer crew,
>
> We would like to use freesurfer to do the high resolution parcellation of 
> gray matter reported in Hagmann et all. 2008.
>
> This far I have used (looking also at previous postings on this matter)
>
> mris_divide_parcellation pp0672 rh aparc.annot 150 rh.split150.annot (but 
> this creates a parcellation of long strips per region, that is not fully 
> suited for what we want).
>
> mris_make_face_parcellation lh.inflated $FREESURFER_HOME/lib/bem/ic3.tri 
> ./lh.ic3.annot
>
>
> The make_face_parcellation looks very nice, but I have the following 
> questions:
>
>
>  1.  How can I convert the .annot file to an actual .mgz volume segmentation. 
> ( I have tried mri_annotation2label but I am not sure how the ? segbase 
> should be specified)
>  2.  Is there a way to match the aparc.annot labels to the ic3.annot  
> parcellation (in the way that is done with mris_divide_parcellation)
>
>  ( I have converted the both annot files to labels to look at the vertex 
> numbers, but preferably I would like the eventual segmentation to contain 
> label info?s per volume such as in aparc+aseg.mgz)
>
>
> Any help would be appreciated a lot.
>
> Thanks,
>
>
> Sara
>
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Re: [Freesurfer] install tracula

[John Fredy]

Thanks, I will wait the 5.1 release

John Ochoa

On Fri, Apr 15, 2011 at 5:29 PM, Allison Stevens <
astev...@nmr.mgh.harvard.edu> wrote:

> John,
> Tracula is available in the soon to be released 5.1 but not in 5.1.
> Allison
>
>
> On Fri, 15 Apr 2011, John Fredy wrote:
>
>  Hello all
>>
>> I am doing the tutorial about tracula (
>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula), but I can`t
>> find the trac-all command in my system. I was running freesurfer 4.5, and
>> now I am running
>> freesurfer 5, but I can´t see the executable in any folder
>>
>> Thanks in advance
>>
>> John Ochoa
>>
>>
>
> 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
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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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[Freesurfer] High resolution segmentation

[Jahfari, Sara]

Dear Freesurfer crew,

We would like to use freesurfer to do the high resolution parcellation of gray 
matter reported in Hagmann et all. 2008.

This far I have used (looking also at previous postings on this matter)

mris_divide_parcellation pp0672 rh aparc.annot 150 rh.split150.annot (but this 
creates a parcellation of long strips per region, that is not fully suited for 
what we want).

mris_make_face_parcellation lh.inflated $FREESURFER_HOME/lib/bem/ic3.tri 
./lh.ic3.annot


The make_face_parcellation looks very nice, but I have the following questions:


  1.  How can I convert the .annot file to an actual .mgz volume segmentation. 
( I have tried mri_annotation2label but I am not sure how the — segbase should 
be specified)
  2.  Is there a way to match the aparc.annot labels to the ic3.annot  
parcellation (in the way that is done with mris_divide_parcellation)

  ( I have converted the both annot files to labels to look at the vertex 
numbers, but preferably I would like the eventual segmentation to contain label 
info’s per volume such as in aparc+aseg.mgz)


Any help would be appreciated a lot.

Thanks,


Sara
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[Freesurfer] Frontal lobes excluded

[Seán Froudist Walsh]

Dear FreeSurfer gurus,

I have T1 scans of a patient at three different time-points (one run at each
time-point). The cortical reconstructions of the first and third time-points
seem to have worked reasonably well, but the reconstruction of the second
time-point was a disaster. A massive part of the frontal lobe (bilaterally)
is cut out from the wm and gm  surfaces. I tried fixing this with wm edits,
but that exited with errors, then I tried to add control points to the new
wm.mgz and recon-all again exited with errors. Is there any possibility of
saving this scan? Would I be able to upload some screenshots to help you see
what is going on?

Many thanks in advance,

Sean
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[Freesurfer] Retinotopy-polar angle

[Michelle Umali]

Dear Freesurfers,
I'm having issues trying to display the polar angle data using the  
color wheel. Unfortunately, I can't resizing the Configure Overlay  
Display window.  No matter what I try, I can't actually see the Apply  
button.

Any suggestions?
Also, is there a quickie guide on defining the boundaries of visual areas?

Thanks.
Michelle
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