Re: [Freesurfer] errors on the WM and Gray inflated surfaces

[pablo najt]

Dear FS expert and users,We are coming across errors on the WM and Gray 
inflated surfaces.When trying to open the surfaces with tksurfer as follows 
(tksurfer subid lh inflated -gray) We get only a small part of the cortex 
displaying.  Also when we try file-label-import 
annotation  the following error occurs:colortable with 13 entries read 
(originally /usr/local/apps/freesurfer/5.1.0/average/colortable_BA.txt)Found 
embedded color table in annotation.
There seem to be no hard failures as recon-all log said "finished without 
errors". Also WM and pial surfaces look accurate.Now we are trying to figure 
what is that could have caused this for all subjects.We have an old 
instructions for freesurfer saying to to run recon-all as follows.run recon 
-all -s subjID /autorecon -all As I am not familiar with this way of running 
recon-all I wanted to ask if this could have caused the problem consistently 
across 70~ subjects.Any advise on this would be greatly appreciated.Cheers.Pablo


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Re: [Freesurfer] Regarding: oblique view

[Dr Sampada Sinha]

Hello Bruce,

Thanks for your reply. Brief history of my problem so far is that: as you
noticed before, my images have very low resolution and very less contrast.
My images slice thickness is also about 5mm, voxel size: 0.46x0.46x6.5;
dimension 512x512x20. I do run mri_convert to conform it to 1x1x1 mm voxel
dimension. But I am getting huge topological defect and in 3-4 patients,
and, brain areas are missing as well after running recon-all command. I
tried to manually edit those missing brain voxels. But, apart from getting
topological error, even after the process is complete, lGI stops running
because of high Euler number.

I am trying not to discard those sMRI images. Want to glean at least some
data out of it. Will greatly appreciate if I can be guided on this.

Thanks and regards,

Sampada

On Wed, Mar 30, 2016 at 6:53 PM, Bruce Fischl 
wrote:

> Hi Sampada
>
> could you include our previous corresponance in your emails so I can keep
> track of what we were talking about? If your slice thickness is really
> 6.5mm (or slice thickness + gap) then that is probably the source of your
> problems. You need something much closer to isotropic
>
> cheers
> Bruce
>
> On Wed, 30 Mar 2016, Dr Sampada Sinha wrote:
>
> Hello Bruce,
>>
>> Thanks for following it up. ​Sorry for tardy response. I am at the mercy
>> of
>> power supply and Internet connectivity here. ​The details of scans are
>> enclosed as a snapshots. Peculiar thing is that we have processed about
>> 23-24 participants' sMRI having similar scanning parameters and their
>> surface reconstruction is okay. One thing I would like to ask, if I may
>> (?)
>> is that:​
>> why am I seeing this problem in this particular participant and why not in
>> other ones that have been processed?​ All participants so far
>> pre-processed
>> with recon-all have similar sMRI image protocol.​
>>
>> Appreciate all your help!
>>
>> Thanks and kind regards,
>>
>> Sampada
>>
>>
>>
>>
>> --
>> Sampada
>> Pre-doctoral student
>> Department of Geriatric Mental Health (DGMH)
>> King George Medical University
>> Lucknow-226003
>> India
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
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>
>
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> is
> addressed. If you believe this e-mail was sent to you in error and the
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> HelpLine at
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> error
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> properly
> dispose of the e-mail.
>
>


-- 
Sampada
Pre-doctoral student
Department of Geriatric Mental Health (DGMH)
King George Medical University
Lucknow-226003
India
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[Freesurfer] Regarding: Group analysis of WMHs

[Dr Sampada Sinha]

Dear freeesurfer experts,

I am trying to calculate WMHs of MDD patient populations. I ran the T2FLAIR
separately after processing T1 with recon-all. Presently, I don't have any
dwi data where I can project the WMHs onto the WM tracts. Will you please
tell me how do I project the WMHs of 29 MDD patients on a template (?)
showing the WMH abnormalities? Or if you can please recommend a paper or
freesurfer page from where I can get a step by step directions of showing
WMHs of 29 cumulative MDD patients on subcortical surface.

Thanks and regards,

Sampada

-- 
Sampada
Pre-doctoral student
Department of Geriatric Mental Health (DGMH)
King George Medical University
Lucknow-226003
India
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Re: [Freesurfer] Regarding: oblique view

[Bruce Fischl]

sure. I wish I had a better answer for you
On Fri, 8 Apr 2016, Dr Sampada 
Sinha wrote:



Thanks Bruce. Appreciate all your help.
Kind regards,

Sampada

On Friday, April 8, 2016, Bruce Fischl  wrote:
  Hi Sampada

  I don't think it is possible to get reasonable surfaces out of 5
  or 6.5mm slice data. You might get ok asegs.

  sorry
  Bruce

  On Fri, 8 Apr 2016, Dr Sampada Sinha wrote:

Hello Bruce,

Thanks for your reply. Brief history of my problem
so far is that: as you noticed before, my images
have very low resolution and very less contrast.
My images slice thickness is also about 5mm, voxel
size: 0.46x0.46x6.5; dimension 512x512x20. I do run
mri_convert to conform it to 1x1x1 mm voxel
dimension. But I am getting huge topological defect
and in 3-4 patients, and, brain areas are missing as
well after running recon-all command. I
tried to manually edit those missing brain voxels.
But, apart from getting topological error, even
after the process is complete, lGI stops running
because of high Euler number.

I am trying not to discard those sMRI images. Want
to glean at least some data out of it. Will greatly
appreciate if I can be guided on this.

Thanks and regards,

Sampada

On Wed, Mar 30, 2016 at 6:53 PM, Bruce Fischl
 wrote:
      Hi Sampada

      could you include our previous corresponance
in your emails so I can keep track of what we were
talking about? If your slice thickness
      is really 6.5mm (or slice thickness + gap)
then that is probably the source of your problems.
You need something much closer to
      isotropic

      cheers
      Bruce
      On Wed, 30 Mar 2016, Dr Sampada Sinha wrote:

            Hello Bruce,

            Thanks for following it up. ​Sorry for
tardy response. I am at the mercy of
            power supply and Internet connectivity
here. ​The details of scans are
            enclosed as a snapshots. Peculiar thing
is that we have processed about
            23-24 participants' sMRI having similar
scanning parameters and their
            surface reconstruction is okay. One
thing I would like to ask, if I may (?)
            is that:​
            why am I seeing this problem in this
particular participant and why not in
            other ones that have been processed?​ All
participants so far pre-processed
            with recon-all have similar sMRI image
protocol.​

            Appreciate all your help!

            Thanks and kind regards,

            Sampada




            --
            Sampada
            Pre-doctoral student
            Department of Geriatric Mental Health
(DGMH)
            King George Medical University
            Lucknow-226003
            India










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dispose of the e-mail.




--
Sampada
Pre-doctoral student
Department of Geriatric Mental Health (DGMH)
King George Medical University
Lucknow-226003
India











--
Sampada
Pre-doctoral student
Department of Geriatric Mental Health (DGMH)
King George Medical University
Lucknow-226003
India










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[Freesurfer] REPOST: QDEC analysis

[Clara Kühn]

Dear FreeSurfer experts,

I am trying to analyze some single time points of my longitudinal data in QDEC. 
I have 3 groups and created a file for the discrete factor "group" with three 
levels (1,2 and 3). I have done the same for gender (with 2 levels). The 
analysis with gender works just fine but when I try to use group as a factor I 
get an error message that factor 1 must have 2 levels:

SUBJECTS_DIR is '/scr/etsch2/kids/ct'
ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels
ninputs = 72
Checking inputs
nframestot = 72
Allocing output
Done allocing
nframes = 72
Writing to /scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/y.mgh
gdfReadHeader: reading 
/scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/qdec.fsgd
INFO: gd2mtx_method is dods
Reading source surface /scr/etsch2/kids/ct/87kids_template/surf/lh.white
ERROR: no contrasts specified.
Error in Analyze: command failed: mri_glmfit --y 
/scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/y.mgh --fsgd 
/scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/qdec.fsgd dods --glmdir 
/scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1 --surf 87kids_template lh

In the tutorial it doesn't state that QDEC has to have discrete factors with 2 
levels only.
Am I doing something wrong or is there a work-around for that?

Cheers, Clara
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Re: [Freesurfer] Regarding: oblique view

[Bruce Fischl]

Hi Sampada

I don't think it is possible to get reasonable surfaces out of 5 or 6.5mm 
slice data. You might get ok asegs.


sorry
Bruce

On Fri, 8 Apr 2016, Dr Sampada Sinha 
wrote:



Hello Bruce,

Thanks for your reply. Brief history of my problem so far is that: as you 
noticed before, my images have very low resolution and very less contrast.
My images slice thickness is also about 5mm, voxel size: 0.46x0.46x6.5; 
dimension 512x512x20. I do run mri_convert to conform it to 1x1x1 mm voxel
dimension. But I am getting huge topological defect and in 3-4 patients, and, 
brain areas are missing as well after running recon-all command. I
tried to manually edit those missing brain voxels. But, apart from getting 
topological error, even after the process is complete, lGI stops running
because of high Euler number.

I am trying not to discard those sMRI images. Want to glean at least some data 
out of it. Will greatly appreciate if I can be guided on this.

Thanks and regards,

Sampada

On Wed, Mar 30, 2016 at 6:53 PM, Bruce Fischl  
wrote:
  Hi Sampada

  could you include our previous corresponance in your emails so I can keep 
track of what we were talking about? If your slice thickness
  is really 6.5mm (or slice thickness + gap) then that is probably the 
source of your problems. You need something much closer to
  isotropic

  cheers
  Bruce
  On Wed, 30 Mar 2016, Dr Sampada Sinha wrote:

Hello Bruce,

Thanks for following it up. ​Sorry for tardy response. I am at the 
mercy of
power supply and Internet connectivity here. ​The details of scans 
are
enclosed as a snapshots. Peculiar thing is that we have processed 
about
23-24 participants' sMRI having similar scanning parameters and 
their
surface reconstruction is okay. One thing I would like to ask, if I 
may (?)
is that:​
why am I seeing this problem in this particular participant and why 
not in
other ones that have been processed?​ All participants so far 
pre-processed
with recon-all have similar sMRI image protocol.​

Appreciate all your help!

Thanks and kind regards,

Sampada




--
Sampada
Pre-doctoral student
Department of Geriatric Mental Health (DGMH)
King George Medical University
Lucknow-226003
India










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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.




--
Sampada
Pre-doctoral student
Department of Geriatric Mental Health (DGMH)
King George Medical University
Lucknow-226003
India









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[Freesurfer] Freesurfer install on Debian 7.x

[Robert Welsh]

hi zeke,

i’m following your instructions for getting freesurfer 5.3.0 installed on 
debian, though i’m at 7.x as that is what came from ThinkMate on some recently 
delivered supermicro machines for our lab. 

i’m not successful, and have paused at an error.

1)  libtool-bin does not exist for debian/wheezy

but i decided to just plow ahead

2)  in doing the “git annex get .”

i get the following error (it worked for some time as grabbing things)

thoughts? 

#———error below this line 

2016-03-29 18:12:07 (6.58 MB/s) - 
`/home/Software/git/freesurfer/.git/annex/tmp/SHA256-s9167701--75de544880a3d0621958725eb3e89d31c78d13fe60276820123ad96541535099'
 saved [9167701/9167701]

ok
get vtkutils/vtkKWRGBATransferFunctionEditorTester-scalars.mgh (from origin...) 
--2016-03-29 18:12:07--  
http://freesurfer.net/anonftp/pub/dist/freesurfer/repo/freesurfer.git/annex/objects/d4f/53f/SHA256-s655672--85f9b50e8fb8a72a8783152c7ad098c0
60056a7244ccd595cbe67b9ea949/SHA256-s655672--85f9b50e8fb8a72a8783152c7ad098c060056a7244ccd595cbe67b9ea949
Resolving freesurfer.net(freesurfer.net)... 132.183.202.158
Connecting to freesurfer.net(freesurfer.net)|132.183.202.158|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 655672 (640K) [text/plain]
Saving to: 
`/home/Software/git/freesurfer/.git/annex/tmp/SHA256-s655672--85f9b50e8fb8a72a8783152c7ad098c060056a7244ccd595cbe67b9ea949'

100%[===>]
 655,672 1.36M/s   in 0.5s

2016-03-29 18:12:08 (1.36 MB/s) - 
`/home/Software/git/freesurfer/.git/annex/tmp/SHA256-s655672--85f9b50e8fb8a72a8783152c7ad098c060056a7244ccd595cbe67b9ea949'
 saved [655672/655672]

ok
(Recording state in git...)
git-annex: get: 5 failed


Robert C. Welsh, Ph.D.
Associate Professor
Department of Radiology
Department of Psychiatry
University of Michigan
rcwe...@umich.edu

Associate Director, VA-fMRI Research, VA Ann Arbor



-- 
typos due to iPhone 4S

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Re: [Freesurfer] REPOST: QDEC analysis

[Martin Reuter]

Hi Clara,

I think the message is correct and Qdec can only do 2 levels. Qdec is 
rather limited. You need to use mri_glmfit for that.

Best, Martin

On 04/08/2016 08:14 AM, Clara Kühn wrote:
> Dear FreeSurfer experts,
>
> I am trying to analyze some single time points of my longitudinal data in 
> QDEC. I have 3 groups and created a file for the discrete factor "group" with 
> three levels (1,2 and 3). I have done the same for gender (with 2 levels). 
> The analysis with gender works just fine but when I try to use group as a 
> factor I get an error message that factor 1 must have 2 levels:
>
> SUBJECTS_DIR is '/scr/etsch2/kids/ct'
> ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels
> ninputs = 72
> Checking inputs
> nframestot = 72
> Allocing output
> Done allocing
> nframes = 72
> Writing to /scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/y.mgh
> gdfReadHeader: reading 
> /scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/qdec.fsgd
> INFO: gd2mtx_method is dods
> Reading source surface /scr/etsch2/kids/ct/87kids_template/surf/lh.white
> ERROR: no contrasts specified.
> Error in Analyze: command failed: mri_glmfit --y 
> /scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/y.mgh --fsgd 
> /scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/qdec.fsgd dods --glmdir 
> /scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1 --surf 87kids_template lh
>
> In the tutorial it doesn't state that QDEC has to have discrete factors with 
> 2 levels only.
> Am I doing something wrong or is there a work-around for that?
>
> Cheers, Clara
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu

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Re: [Freesurfer] REPOST: QDEC analysis

[Clara Kühn]

That's what I feared. But ok, I'll try that.
Thank you!

- Ursprüngliche Mail -
Von: "mreuter" 
An: "Freesurfer support list" 
Gesendet: Freitag, 8. April 2016 14:55:42
Betreff: Re: [Freesurfer] REPOST: QDEC analysis

Hi Clara,

I think the message is correct and Qdec can only do 2 levels. Qdec is 
rather limited. You need to use mri_glmfit for that.

Best, Martin

On 04/08/2016 08:14 AM, Clara Kühn wrote:
> Dear FreeSurfer experts,
>
> I am trying to analyze some single time points of my longitudinal data in 
> QDEC. I have 3 groups and created a file for the discrete factor "group" with 
> three levels (1,2 and 3). I have done the same for gender (with 2 levels). 
> The analysis with gender works just fine but when I try to use group as a 
> factor I get an error message that factor 1 must have 2 levels:
>
> SUBJECTS_DIR is '/scr/etsch2/kids/ct'
> ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels
> ninputs = 72
> Checking inputs
> nframestot = 72
> Allocing output
> Done allocing
> nframes = 72
> Writing to /scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/y.mgh
> gdfReadHeader: reading 
> /scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/qdec.fsgd
> INFO: gd2mtx_method is dods
> Reading source surface /scr/etsch2/kids/ct/87kids_template/surf/lh.white
> ERROR: no contrasts specified.
> Error in Analyze: command failed: mri_glmfit --y 
> /scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/y.mgh --fsgd 
> /scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/qdec.fsgd dods --glmdir 
> /scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1 --surf 87kids_template lh
>
> In the tutorial it doesn't state that QDEC has to have discrete factors with 
> 2 levels only.
> Am I doing something wrong or is there a work-around for that?
>
> Cheers, Clara
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu

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Re: [Freesurfer] Regarding: oblique view

[Dr Sampada Sinha]

Thanks Bruce. Appreciate all your help.

Kind regards,

Sampada

On Friday, April 8, 2016, Bruce Fischl  wrote:

> Hi Sampada
>
> I don't think it is possible to get reasonable surfaces out of 5 or 6.5mm
> slice data. You might get ok asegs.
>
> sorry
> Bruce
>
> On Fri, 8 Apr 2016, Dr Sampada Sinha wrote:
>
> Hello Bruce,
>>
>> Thanks for your reply. Brief history of my problem so far is that: as you
>> noticed before, my images have very low resolution and very less contrast.
>> My images slice thickness is also about 5mm, voxel size: 0.46x0.46x6.5;
>> dimension 512x512x20. I do run mri_convert to conform it to 1x1x1 mm voxel
>> dimension. But I am getting huge topological defect and in 3-4 patients,
>> and, brain areas are missing as well after running recon-all command. I
>> tried to manually edit those missing brain voxels. But, apart from
>> getting topological error, even after the process is complete, lGI stops
>> running
>> because of high Euler number.
>>
>> I am trying not to discard those sMRI images. Want to glean at least some
>> data out of it. Will greatly appreciate if I can be guided on this.
>>
>> Thanks and regards,
>>
>> Sampada
>>
>> On Wed, Mar 30, 2016 at 6:53 PM, Bruce Fischl 
>> wrote:
>>   Hi Sampada
>>
>>   could you include our previous corresponance in your emails so I
>> can keep track of what we were talking about? If your slice thickness
>>   is really 6.5mm (or slice thickness + gap) then that is probably
>> the source of your problems. You need something much closer to
>>   isotropic
>>
>>   cheers
>>   Bruce
>>   On Wed, 30 Mar 2016, Dr Sampada Sinha wrote:
>>
>> Hello Bruce,
>>
>> Thanks for following it up. ​Sorry for tardy response. I am
>> at the mercy of
>> power supply and Internet connectivity here. ​The details of
>> scans are
>> enclosed as a snapshots. Peculiar thing is that we have
>> processed about
>> 23-24 participants' sMRI having similar scanning parameters
>> and their
>> surface reconstruction is okay. One thing I would like to
>> ask, if I may (?)
>> is that:​
>> why am I seeing this problem in this particular participant
>> and why not in
>> other ones that have been processed?​ All participants so far
>> pre-processed
>> with recon-all have similar sMRI image protocol.​
>>
>> Appreciate all your help!
>>
>> Thanks and kind regards,
>>
>> Sampada
>>
>>
>>
>>
>> --
>> Sampada
>> Pre-doctoral student
>> Department of Geriatric Mental Health (DGMH)
>> King George Medical University
>> Lucknow-226003
>> India
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> ___
>> 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.
>>
>>
>>
>>
>> --
>> Sampada
>> Pre-doctoral student
>> Department of Geriatric Mental Health (DGMH)
>> King George Medical University
>> Lucknow-226003
>> India
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>

-- 
Sampada
Pre-doctoral student
Department of Geriatric Mental Health (DGMH)
King George Medical University
Lucknow-226003
India
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Re: [Freesurfer] Group level analysis: Specifying contrasts

[Douglas N Greve]

I don't know what you mean, can you just send the header of the fsgd 
file and the contrast matrix?

On 04/04/2016 11:20 AM, Afzal, Afsana wrote:
> Hi,
>
> I want to perform a linear regression for a task with 3 different risk 
> conditions (low, medium, high) with the following linear trend: low = 
> 1, medium = 2, high = 3.
>
> Right now I'm specifying the above weighted under each risk condition 
> in my contrast matrix. Is this the correct approach? I want to make 
> sure I am calculating a regression and not a weighted average.
>
> Thank you for your help,
>
> Afsana
>
>
> __
> *Afsana Afzal*
> Clinical Research Coordinator
> Massachusetts General Hospital
> Division of Neurotherapeutics
> Department of Psychiatry: Neurosciences
> 149 13th St, Room 2612
> Charlestown, MA 02129
> Phone: 617-643-5129
> Fax: 617-726-4078
>
>
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Re: [Freesurfer] Regarding: Group analysis of WMHs

[Douglas N Greve]

ps, you may want to smooth the wmh volumes, eg,
mri_fwhm --smooth-only --i all.wmh.mgh --fwhm 5 --o all.wmh.sm05.mgh
then use all.wmh.sm05.mgh as input to glmfit

On 04/08/2016 12:27 PM, Douglas N Greve wrote:
> You can binarize each WMH volume, ie,
> mri_binarize --i aseg.mgz --match 77 --o wmh.mgz
> Convert to mni305 space with
> mri_convert wmh.mgz wmh.mni305.mgz --apply_transform
> transforms/talairach.xfm -oc 0 0 0
>
> View to check (only need to do for one subject):
> tkmedit fsaverage orig.mgz -ov wmh.mni305.mgz
>
> Concatenate all subjects together
> mri_concat subject1/mri/wmh.mgz subject2/mri/wmh.mgz ... --o all.wmh.mgz
>
> After that you can do some simple statitics (eg, presence or abscence of
> WMH)
> mri_glmfit --i all.wmgh.mgz --no-prune --osgm --o glmfit
>
> tkmedit fsaverage orig.mgz -of glmfit/osgm/sig.mgh
>
> Not sure what you mean by subcortical surface
>
>
> On 04/08/2016 08:07 AM, Dr Sampada Sinha wrote:
>> Dear freeesurfer experts,
>>
>> I am trying to calculate WMHs of MDD patient populations. I ran the
>> T2FLAIR separately after processing T1 with recon-all. Presently, I
>> don't have any dwi data where I can project the WMHs onto the WM
>> tracts. Will you please tell me how do I project the WMHs of 29 MDD
>> patients on a template (?) showing the WMH abnormalities? Or if you
>> can please recommend a paper or freesurfer page from where I can get a
>> step by step directions of showing WMHs of 29 cumulative MDD patients
>> on subcortical surface.
>>
>> Thanks and regards,
>>
>> Sampada
>>
>> -- 
>> Sampada
>> Pre-doctoral student
>> Department of Geriatric Mental Health (DGMH)
>> King George Medical University
>> Lucknow-226003
>> India
>>
>>
>>
>>
>>
>>
>> */
>> /*
>>
>>
>>
>> ___
>> 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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Regarding: Group analysis of WMHs

[Douglas N Greve]

You can binarize each WMH volume, ie,
mri_binarize --i aseg.mgz --match 77 --o wmh.mgz
Convert to mni305 space with
mri_convert wmh.mgz wmh.mni305.mgz --apply_transform 
transforms/talairach.xfm -oc 0 0 0

View to check (only need to do for one subject):
tkmedit fsaverage orig.mgz -ov wmh.mni305.mgz

Concatenate all subjects together
mri_concat subject1/mri/wmh.mgz subject2/mri/wmh.mgz ... --o all.wmh.mgz

After that you can do some simple statitics (eg, presence or abscence of 
WMH)
mri_glmfit --i all.wmgh.mgz --no-prune --osgm --o glmfit

tkmedit fsaverage orig.mgz -of glmfit/osgm/sig.mgh

Not sure what you mean by subcortical surface


On 04/08/2016 08:07 AM, Dr Sampada Sinha wrote:
> Dear freeesurfer experts,
>
> I am trying to calculate WMHs of MDD patient populations. I ran the 
> T2FLAIR separately after processing T1 with recon-all. Presently, I 
> don't have any dwi data where I can project the WMHs onto the WM 
> tracts. Will you please tell me how do I project the WMHs of 29 MDD 
> patients on a template (?) showing the WMH abnormalities? Or if you 
> can please recommend a paper or freesurfer page from where I can get a 
> step by step directions of showing WMHs of 29 cumulative MDD patients 
> on subcortical surface.
>
> Thanks and regards,
>
> Sampada
>
> -- 
> Sampada
> Pre-doctoral student
> Department of Geriatric Mental Health (DGMH)
> King George Medical University
> Lucknow-226003
> India
>
>
>
>
>
>
> */
> /*
>
>
>
> ___
> 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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] How to view entire brain results in Freeview for LME data

[Douglas N Greve]

This is what I don't understand: "done the cluster-thresholding for the aparc 
data"

The aparc data is an ROI and so you should not have (could not have) 
done clusterwise thresholding (?)

On 04/08/2016 12:57 PM, Jennifer Legault wrote:
> Hi Doug,
>
> I'm currently running the LME mass-univariate analysis (I've
> previously conducted the LME univariate analyses with ROIs with little
> to no problems) and, thanks to your help, have run my data through
> this analysis and done the cluster-thresholding for the aparc data but
> not the aseg data (since I'm not sure how to cluster-threshold the
> segmented data--any advice you have would be greatly appreciated).  Is
> there a way to view the significant voxels overlaid on the
> aseg+aparc.mgz in fsaverage for the whole brain?
>
> Best,
>
> Jen
>
> On Fri, Apr 8, 2016 at 12:36 PM, Douglas N Greve
>  wrote:
>>
>> On 04/01/2016 04:44 PM, Jennifer Legault wrote:
>>> Hi Doug,
>>>
>>> Thanks for your quick response!  When running the LME mass univariate
>>> analysis, I am assuming this also includes subcortical structures,
>>> correct?
>> Which processing are you doing? It should be obvious if you are doing
>> surface-based or ROI-based analysis.
>>>  From my understanding, subcortical areas are segmented as opposed to
>>> parcellated.  The main thing I want to examine all the regions of the
>>> brain that might change over time (as a function of the training task
>>> I've given my participants), so I would look at both the aparc and the
>>> aseg data, right?
>> Yes, you can.
>>> Apologies if I've misunderstood your question.  For the aseg data, I
>>> am currently having trouble with figuring out how to cluster threshold
>>> the data (do i use mri_surfcluster with an argument to call the aseg
>>> annotation or do I use mri_volcluster?) I would then want to visualize
>>> the cluster thresholded data for subcortical structures in freeview.
>> If you are doing an ROI analysis then there is no clustering.
>>> Optimally, I would like to find some way to look at the whole brain in
>>> Freeview to see these regions that have changed as a function of my
>>> training task.
>> If you have a value for each ROI (segmentation and/or parcellation),
>> then you can read in aseg+aparc.mgz in fsaverage (apas =
>> MRIread('aparc+aseg.mgz')), then find all the voxels that belong to a
>> given ROI and assign them the value for the ROI, then write it out, then
>> view the output as an overlay on orig.mgz
>>
>>> Best,
>>>
>>> Jen
>>>
>>> On Fri, Apr 1, 2016 at 11:23 AM, Douglas N Greve
>>> > wrote:
>>>
>>>  You can put surface data back into the volume with mri_surf2vol (which
>>>  will also merge left and right into one volume). What do you do
>>>  with the
>>>  aseg data?
>>>
>>>  On 04/01/2016 10:46 AM, Jennifer Legault wrote:
>>>  > Dear Freesurfer Experts,
>>>  >
>>>  > I have run my participants' longitudinal sMRI data through the
>>>  > preprocessing longitudinal pipeline, ran the LME multivariate
>>>  > analysis, cluster-thresholded the data, and am now trying to
>>>  visualize
>>>  > those results in Freeview (for some reason tksurfer is very,
>>>  very slow
>>>  > to run on my computer).  I am interested in the Fs volume
>>>  > (thickness*area) measure.
>>>  >
>>>  > I noticed in the FsFast Tutorial
>>>  >
>>>  
>>> ,
>>>  > that all the corrected results were able to be merged into one file
>>>  > using the vlrmerge command.  In the beginning of the tutorial, it
>>>  > states that fMRI and structuraI group analyses run similarly. /
>>>  I was
>>>  > therefore wondering if I can use the vlrmerge command (or some 
>>> similar
>>>  > command) for my LME data, such that I can view the following
>>>  > information all in one file: both hemispheres, aparc and aseg.
>>>  > / Currently I can only view the aparc results for each of the
>>>  > hemispheres separately (and I haven't found a way to visualize the
>>>  > aseg data).
>>>  >
>>>  > Thank you for taking the time to read this email.
>>>  >
>>>  > Best,
>>>  >
>>>  > Jennifer Legault
>>>  > Ph.D candidate, Neuroscience
>>>  > Brain, Language, and Computation Lab
>>>  > The Pennsylvania State University
>>>  >
>>>  >
>>>  > ___
>>>  > Freesurfer mailing list
>>>  > Freesurfer@nmr.mgh.harvard.edu
>>>  
>>>  > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>  --
>>>  Douglas N. Greve, Ph.D.
>>>  MGH-NMR Center
>>>  gr...@nmr.mgh.harvard.edu 
>>>  Phone Number: 617-724-2358 
>>>  Fax: 617-726-7422 
>>>
>>>  Bugs: 

Re: [Freesurfer] How to view entire brain results in Freeview for LME data

[Jennifer Legault]

Apologies for likely using the wrong term.  I meant to say that I've
done the cluster-thresholding for the surface data, using the
mri_surfcluster command with annot -aparc as an argument.

On Fri, Apr 8, 2016 at 1:03 PM, Douglas N Greve
 wrote:
> This is what I don't understand: "done the cluster-thresholding for the aparc 
> data"
>
> The aparc data is an ROI and so you should not have (could not have)
> done clusterwise thresholding (?)
>
> On 04/08/2016 12:57 PM, Jennifer Legault wrote:
>> Hi Doug,
>>
>> I'm currently running the LME mass-univariate analysis (I've
>> previously conducted the LME univariate analyses with ROIs with little
>> to no problems) and, thanks to your help, have run my data through
>> this analysis and done the cluster-thresholding for the aparc data but
>> not the aseg data (since I'm not sure how to cluster-threshold the
>> segmented data--any advice you have would be greatly appreciated).  Is
>> there a way to view the significant voxels overlaid on the
>> aseg+aparc.mgz in fsaverage for the whole brain?
>>
>> Best,
>>
>> Jen
>>
>> On Fri, Apr 8, 2016 at 12:36 PM, Douglas N Greve
>>  wrote:
>>>
>>> On 04/01/2016 04:44 PM, Jennifer Legault wrote:
 Hi Doug,

 Thanks for your quick response!  When running the LME mass univariate
 analysis, I am assuming this also includes subcortical structures,
 correct?
>>> Which processing are you doing? It should be obvious if you are doing
>>> surface-based or ROI-based analysis.
  From my understanding, subcortical areas are segmented as opposed to
 parcellated.  The main thing I want to examine all the regions of the
 brain that might change over time (as a function of the training task
 I've given my participants), so I would look at both the aparc and the
 aseg data, right?
>>> Yes, you can.
 Apologies if I've misunderstood your question.  For the aseg data, I
 am currently having trouble with figuring out how to cluster threshold
 the data (do i use mri_surfcluster with an argument to call the aseg
 annotation or do I use mri_volcluster?) I would then want to visualize
 the cluster thresholded data for subcortical structures in freeview.
>>> If you are doing an ROI analysis then there is no clustering.
 Optimally, I would like to find some way to look at the whole brain in
 Freeview to see these regions that have changed as a function of my
 training task.
>>> If you have a value for each ROI (segmentation and/or parcellation),
>>> then you can read in aseg+aparc.mgz in fsaverage (apas =
>>> MRIread('aparc+aseg.mgz')), then find all the voxels that belong to a
>>> given ROI and assign them the value for the ROI, then write it out, then
>>> view the output as an overlay on orig.mgz
>>>
 Best,

 Jen

 On Fri, Apr 1, 2016 at 11:23 AM, Douglas N Greve
 > wrote:

  You can put surface data back into the volume with mri_surf2vol (which
  will also merge left and right into one volume). What do you do
  with the
  aseg data?

  On 04/01/2016 10:46 AM, Jennifer Legault wrote:
  > Dear Freesurfer Experts,
  >
  > I have run my participants' longitudinal sMRI data through the
  > preprocessing longitudinal pipeline, ran the LME multivariate
  > analysis, cluster-thresholded the data, and am now trying to
  visualize
  > those results in Freeview (for some reason tksurfer is very,
  very slow
  > to run on my computer).  I am interested in the Fs volume
  > (thickness*area) measure.
  >
  > I noticed in the FsFast Tutorial
  >
  
 ,
  > that all the corrected results were able to be merged into one file
  > using the vlrmerge command.  In the beginning of the tutorial, it
  > states that fMRI and structuraI group analyses run similarly. /
  I was
  > therefore wondering if I can use the vlrmerge command (or some 
 similar
  > command) for my LME data, such that I can view the following
  > information all in one file: both hemispheres, aparc and aseg.
  > / Currently I can only view the aparc results for each of the
  > hemispheres separately (and I haven't found a way to visualize the
  > aseg data).
  >
  > Thank you for taking the time to read this email.
  >
  > Best,
  >
  > Jennifer Legault
  > Ph.D candidate, Neuroscience
  > Brain, Language, and Computation Lab
  > The Pennsylvania State University
  >
  >
  > ___
  > Freesurfer mailing list
  > 

Re: [Freesurfer] Qdec DOSS

[Douglas N Greve]

Yes, if the contrast matrix is correct, then everything should be fine. 
Also check the design matrix (but I'm pretty sure that will be correct).

On 04/05/2016 04:07 AM, tom parker wrote:
> Hi Freesurfers,
>
> I posted this question a few days ago but didn't get any replies.
> Would you mind answering this for me?
>
> I compared 2 groups, while controlling for 1 covariate in qdec using 
> freesurfer 5.1.
>
> There were no significant interactions with the covariate so I need to 
> use DOSS.
>
> I read on several post that DOSS has some bugs related to the 
> generation of contrasts in qdec and that mri_glmfit should be used to 
> run a DOSS analysis.
>
> However, when I ran my analysis with DOSS in qdec I saw that the C.mat 
> file looked like this: 1 -1 0, which seems correct to me.
>
> My question is can I use DOSS in qdec in this case? Or are there other 
> bugs related to using it in qdec?
>
> Thank you so much!
>
>
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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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Left right flip surfaces

[Douglas N Greve]

Look at http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
if you want to compare all subjects, then you'll need to do this for all 
subjects not just the ones you want to flip

On 03/28/2016 02:30 PM, Ajay Kurani wrote:
> Hello Freesurfer Experts,
>
>I processed all of my brains through freesurfer 6.0 dev for 
> Linux and warped the surfaces to standardized space.  For a handful of 
> subjects I want to perform a left right flip of the cortical thickness 
> files (standardized space) for a group analysis.  What is the best way 
> to perform this in freesurfer? I have found a previous post 
> referencing mris_reverse but there was a mention of it being off by a 
> voxel when flipped.  I wanted to see if this is still a concern with 
> the latest version?
>
> Is there a better way to achieve this goal without rerunning all of 
> freesurfer such as a newer took, or is this the preferred method?
>
>
>
> Thanks,
> Ajay
>
>
> ___
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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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Preprocessing task data with multiple B0-corrected runs

[Douglas N Greve]

Unfortunately, I only programmed it assuming that you would have only 
one B0 map per session. There are a couple of work-arounds. One is to 
create a different session for each run. This is probably easiest but 
makes the group analysis a little trickier.

On 04/05/2016 04:48 PM, Shea, Conor wrote:
> Dear Doug,
>
> I'm trying to use FSFAST to analyze task data with multiple runs.  Before 
> using the preproc-sess pipeline, I ran B0 correction on each of the runs, so 
> I have 3 different b0dcmap files.  I'm trying to figure out the best way to 
> run preprocessing on the three runs simultaneously using preproc-sess, but I 
> don't know how to get FSFAST to use each run's specific b0dcmap in the 
> preprocessing of each run's data.  FSFAST wants the b0dcmap files to be in 
> the task folder, but how can it differentiate between the three b0dcmap files 
> if they're not in the run folders?
>
> Thanks,
> Conor
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
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: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] mri_vol2surf misaligment

[Douglas N Greve]

can you show a pic? What were your matlab commands to read in and write 
out the volume?

On 04/04/2016 07:36 AM, Francesca Strappini wrote:
> Dear Freesurfers,
>
> I run the preprocessing step of some functional data with 
> preproc-sess, then the Fourier analysis with matlab. Now, I'm trying 
> to plot this data on the surface:
>
> mri_vol2surf --mov Katkov_OT_45.nii.gz --trgsubject MishaK --hemi lh 
> --reg register.dof6.dat --o Katkov_OT_45_LH.nii.gz
>
> I used as registration matrix the one produced by the preprocessing 
> step but when I try to visualize the map on the surface it looks like 
> completely misaligned.
>
> Thank you
> Best
> Francesca
>
>
>
> -- 
> Francesca Strappini, Ph.D.
> Neurobiology Department
> Weizmann Institute of Science
> 234 Herzl Street, Rehovot 7610001 Israel
> Tel.: +972 58 444 2584
> E-mail: francesca.strapp...@weizmann.ac.il 
> 
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
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: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] How to view entire brain results in Freeview for LME data

[Douglas N Greve]

On 04/01/2016 04:44 PM, Jennifer Legault wrote:
> Hi Doug,
>
> Thanks for your quick response!  When running the LME mass univariate 
> analysis, I am assuming this also includes subcortical structures, 
> correct?
Which processing are you doing? It should be obvious if you are doing 
surface-based or ROI-based analysis.
> From my understanding, subcortical areas are segmented as opposed to 
> parcellated.  The main thing I want to examine all the regions of the 
> brain that might change over time (as a function of the training task 
> I've given my participants), so I would look at both the aparc and the 
> aseg data, right?
Yes, you can.
> Apologies if I've misunderstood your question.  For the aseg data, I 
> am currently having trouble with figuring out how to cluster threshold 
> the data (do i use mri_surfcluster with an argument to call the aseg 
> annotation or do I use mri_volcluster?) I would then want to visualize 
> the cluster thresholded data for subcortical structures in freeview.
If you are doing an ROI analysis then there is no clustering.
> Optimally, I would like to find some way to look at the whole brain in 
> Freeview to see these regions that have changed as a function of my 
> training task.
If you have a value for each ROI (segmentation and/or parcellation), 
then you can read in aseg+aparc.mgz in fsaverage (apas = 
MRIread('aparc+aseg.mgz')), then find all the voxels that belong to a 
given ROI and assign them the value for the ROI, then write it out, then 
view the output as an overlay on orig.mgz

>
> Best,
>
> Jen
>
> On Fri, Apr 1, 2016 at 11:23 AM, Douglas N Greve 
> > wrote:
>
> You can put surface data back into the volume with mri_surf2vol (which
> will also merge left and right into one volume). What do you do
> with the
> aseg data?
>
> On 04/01/2016 10:46 AM, Jennifer Legault wrote:
> > Dear Freesurfer Experts,
> >
> > I have run my participants' longitudinal sMRI data through the
> > preprocessing longitudinal pipeline, ran the LME multivariate
> > analysis, cluster-thresholded the data, and am now trying to
> visualize
> > those results in Freeview (for some reason tksurfer is very,
> very slow
> > to run on my computer).  I am interested in the Fs volume
> > (thickness*area) measure.
> >
> > I noticed in the FsFast Tutorial
> >
> 
> ,
> > that all the corrected results were able to be merged into one file
> > using the vlrmerge command.  In the beginning of the tutorial, it
> > states that fMRI and structuraI group analyses run similarly. /
> I was
> > therefore wondering if I can use the vlrmerge command (or some similar
> > command) for my LME data, such that I can view the following
> > information all in one file: both hemispheres, aparc and aseg.
> > / Currently I can only view the aparc results for each of the
> > hemispheres separately (and I haven't found a way to visualize the
> > aseg data).
> >
> > Thank you for taking the time to read this email.
> >
> > Best,
> >
> > Jennifer Legault
> > Ph.D candidate, Neuroscience
> > Brain, Language, and Computation Lab
> > The Pennsylvania State University
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> 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: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> 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.
>
>
>
>
> -- 
> Jennifer Legault
> Ph.D 

Re: [Freesurfer] mri_vol2surf after recon-all

[Douglas N Greve]

On 04/07/2016 03:50 PM, Trisanna Sprung-Much wrote:
> thanks, Doug. I am still extremely confused, however. *Am I meant to 
> run recon-all first? *I was told in a previous email that I should do 
> this first, however, I thought that Freesurfer takes the volumes and 
> does a linear registration to MNI305 template, which would not work 
> for my scans that are linearly registered to ICBM152 nonlinear 2006 
> template...
run recon-all first, otherwise you won't have surfaces. recon-all 
computes the transform matrix to the mni305 but keeps all the data in 
the native anatomical space. I think the ICBM152 is the same as the 
MNI152. Is that right? If so, you can use mni152reg to compute the 
registration to 152 space. If not, then we'll have to workout something 
else.
>
> When you have a moment, could you please outline in a step by step 
> manner the steps I should run to take my labels.mnc and my volumes 
> such that I can generate surfaces for those 50 volumes, overlay the 
> labels (for which I thought I was using mri_vol2surf) and then edit 
> those labels to make them more accurate?
so you want to transfer the labels from labels.mnc to the surfaces of 
your individual 50 subjects? Start by running recon-all on the 50.
> *The idea is that I want to generate some sulcal probability maps 
> using surface-based registration, as I can already generate 
> probability maps using volumetric registration quite easily.*
>
> many thanks
>
> Trisanna
>
>
>
>
>
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Wed, Apr 6, 2016 at 2:43 PM, Douglas Greve 
> > wrote:
>
> For the 152, you can run mni152reg --s subject, then specify
> $SUBJECTS_DIR/subject/mri/transform/mni152reg.dat (or .lta) for
> the argument to --reg. I'll need to figure out how to generate a
> .dat/.lta for the 305.
>
>
>
> On 4/6/16 12:50 PM, Trisanna Sprung-Much wrote:
>> Any ideas?
>>
>> Trisanna
>>
>> --
>> Ph.D. Candidate
>> McGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Tue, Apr 5, 2016 at 9:37 PM, Trisanna Sprung-Much
>> > > wrote:
>>
>> Hi Dr. Fischl
>>
>> I have a mixture - some of the labels were painted in the
>> MNI305 space (older ones) and the more recent ones are
>> registered to the ICBM152 nonlinear symmetric VI (2006) template.
>>
>> Best
>>
>> Trisanna
>>
>> --
>> Ph.D. Candidate
>> McGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Tue, Apr 5, 2016 at 6:34 PM, Bruce Fischl
>> > > wrote:
>>
>> Hi Trisanna
>>
>> what space are your labels in?
>>
>> cheers
>> Bruce
>> On Tue, 5 Apr 2016, Trisanna Sprung-Much
>> wrote:
>>
>> > Hi Freesurfer
>> >
>> > I have some labels (.mnc) that are painted voxels
>> generated from a Montreal
>> > Neurological Institute software. I am trying to project
>> the labels onto the
>> > surfaces generated from recon-all that I applied to the
>> corresponding MRI
>> > volumes.
>> >
>> > I used mri_vol2surf:
>> >
>> > mri_vol2surf --src labels.mnc --out test.mgz --srcreg
>> talairach.auto.xfm
>> > --hemi lh
>> >
>> > and got the following error:
>> >
>> > Error reading inplaneres from talairach.auto.xfm
>> >
>> >
>> > Do I need a .dat file? If so, how can I attain it?
>> Essentially, what is the
>> > registration file that I am supposed to be using?
>> >
>> > Many thanks!
>> >
>> > Trisanna
>> >
>> > --
>> > Ph.D. CandidateMcGill University
>> > Integrated Program in Neuroscience
>> > Psychology
>> >
>> >
>> >
>> >
>> ___
>> 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 

Re: [Freesurfer] How to view entire brain results in Freeview for LME data

[Jennifer Legault]

Hi Doug,

I'm currently running the LME mass-univariate analysis (I've
previously conducted the LME univariate analyses with ROIs with little
to no problems) and, thanks to your help, have run my data through
this analysis and done the cluster-thresholding for the aparc data but
not the aseg data (since I'm not sure how to cluster-threshold the
segmented data--any advice you have would be greatly appreciated).  Is
there a way to view the significant voxels overlaid on the
aseg+aparc.mgz in fsaverage for the whole brain?

Best,

Jen

On Fri, Apr 8, 2016 at 12:36 PM, Douglas N Greve
 wrote:
>
>
> On 04/01/2016 04:44 PM, Jennifer Legault wrote:
>> Hi Doug,
>>
>> Thanks for your quick response!  When running the LME mass univariate
>> analysis, I am assuming this also includes subcortical structures,
>> correct?
> Which processing are you doing? It should be obvious if you are doing
> surface-based or ROI-based analysis.
>> From my understanding, subcortical areas are segmented as opposed to
>> parcellated.  The main thing I want to examine all the regions of the
>> brain that might change over time (as a function of the training task
>> I've given my participants), so I would look at both the aparc and the
>> aseg data, right?
> Yes, you can.
>> Apologies if I've misunderstood your question.  For the aseg data, I
>> am currently having trouble with figuring out how to cluster threshold
>> the data (do i use mri_surfcluster with an argument to call the aseg
>> annotation or do I use mri_volcluster?) I would then want to visualize
>> the cluster thresholded data for subcortical structures in freeview.
> If you are doing an ROI analysis then there is no clustering.
>> Optimally, I would like to find some way to look at the whole brain in
>> Freeview to see these regions that have changed as a function of my
>> training task.
> If you have a value for each ROI (segmentation and/or parcellation),
> then you can read in aseg+aparc.mgz in fsaverage (apas =
> MRIread('aparc+aseg.mgz')), then find all the voxels that belong to a
> given ROI and assign them the value for the ROI, then write it out, then
> view the output as an overlay on orig.mgz
>
>>
>> Best,
>>
>> Jen
>>
>> On Fri, Apr 1, 2016 at 11:23 AM, Douglas N Greve
>> > wrote:
>>
>> You can put surface data back into the volume with mri_surf2vol (which
>> will also merge left and right into one volume). What do you do
>> with the
>> aseg data?
>>
>> On 04/01/2016 10:46 AM, Jennifer Legault wrote:
>> > Dear Freesurfer Experts,
>> >
>> > I have run my participants' longitudinal sMRI data through the
>> > preprocessing longitudinal pipeline, ran the LME multivariate
>> > analysis, cluster-thresholded the data, and am now trying to
>> visualize
>> > those results in Freeview (for some reason tksurfer is very,
>> very slow
>> > to run on my computer).  I am interested in the Fs volume
>> > (thickness*area) measure.
>> >
>> > I noticed in the FsFast Tutorial
>> >
>> 
>> ,
>> > that all the corrected results were able to be merged into one file
>> > using the vlrmerge command.  In the beginning of the tutorial, it
>> > states that fMRI and structuraI group analyses run similarly. /
>> I was
>> > therefore wondering if I can use the vlrmerge command (or some similar
>> > command) for my LME data, such that I can view the following
>> > information all in one file: both hemispheres, aparc and aseg.
>> > / Currently I can only view the aparc results for each of the
>> > hemispheres separately (and I haven't found a way to visualize the
>> > aseg data).
>> >
>> > Thank you for taking the time to read this email.
>> >
>> > Best,
>> >
>> > Jennifer Legault
>> > Ph.D candidate, Neuroscience
>> > Brain, Language, and Computation Lab
>> > The Pennsylvania State University
>> >
>> >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> 
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> --
>> 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: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> 
>> Outgoing:
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> 

Re: [Freesurfer] How to view entire brain results in Freeview for LME data

[Douglas N Greve]

And now you want to do an ROI analysis or a map-based analysis of the 
subcortical structures? We don't do the latter as that is a VBM analysis.

On 04/08/2016 01:07 PM, Jennifer Legault wrote:
> Apologies for likely using the wrong term.  I meant to say that I've
> done the cluster-thresholding for the surface data, using the
> mri_surfcluster command with annot -aparc as an argument.
>
> On Fri, Apr 8, 2016 at 1:03 PM, Douglas N Greve
>  wrote:
>> This is what I don't understand: "done the cluster-thresholding for the 
>> aparc data"
>>
>> The aparc data is an ROI and so you should not have (could not have)
>> done clusterwise thresholding (?)
>>
>> On 04/08/2016 12:57 PM, Jennifer Legault wrote:
>>> Hi Doug,
>>>
>>> I'm currently running the LME mass-univariate analysis (I've
>>> previously conducted the LME univariate analyses with ROIs with little
>>> to no problems) and, thanks to your help, have run my data through
>>> this analysis and done the cluster-thresholding for the aparc data but
>>> not the aseg data (since I'm not sure how to cluster-threshold the
>>> segmented data--any advice you have would be greatly appreciated).  Is
>>> there a way to view the significant voxels overlaid on the
>>> aseg+aparc.mgz in fsaverage for the whole brain?
>>>
>>> Best,
>>>
>>> Jen
>>>
>>> On Fri, Apr 8, 2016 at 12:36 PM, Douglas N Greve
>>>  wrote:
 On 04/01/2016 04:44 PM, Jennifer Legault wrote:
> Hi Doug,
>
> Thanks for your quick response!  When running the LME mass univariate
> analysis, I am assuming this also includes subcortical structures,
> correct?
 Which processing are you doing? It should be obvious if you are doing
 surface-based or ROI-based analysis.
>   From my understanding, subcortical areas are segmented as opposed to
> parcellated.  The main thing I want to examine all the regions of the
> brain that might change over time (as a function of the training task
> I've given my participants), so I would look at both the aparc and the
> aseg data, right?
 Yes, you can.
> Apologies if I've misunderstood your question.  For the aseg data, I
> am currently having trouble with figuring out how to cluster threshold
> the data (do i use mri_surfcluster with an argument to call the aseg
> annotation or do I use mri_volcluster?) I would then want to visualize
> the cluster thresholded data for subcortical structures in freeview.
 If you are doing an ROI analysis then there is no clustering.
> Optimally, I would like to find some way to look at the whole brain in
> Freeview to see these regions that have changed as a function of my
> training task.
 If you have a value for each ROI (segmentation and/or parcellation),
 then you can read in aseg+aparc.mgz in fsaverage (apas =
 MRIread('aparc+aseg.mgz')), then find all the voxels that belong to a
 given ROI and assign them the value for the ROI, then write it out, then
 view the output as an overlay on orig.mgz

> Best,
>
> Jen
>
> On Fri, Apr 1, 2016 at 11:23 AM, Douglas N Greve
> > wrote:
>
>   You can put surface data back into the volume with mri_surf2vol 
> (which
>   will also merge left and right into one volume). What do you do
>   with the
>   aseg data?
>
>   On 04/01/2016 10:46 AM, Jennifer Legault wrote:
>   > Dear Freesurfer Experts,
>   >
>   > I have run my participants' longitudinal sMRI data through the
>   > preprocessing longitudinal pipeline, ran the LME multivariate
>   > analysis, cluster-thresholded the data, and am now trying to
>   visualize
>   > those results in Freeview (for some reason tksurfer is very,
>   very slow
>   > to run on my computer).  I am interested in the Fs volume
>   > (thickness*area) measure.
>   >
>   > I noticed in the FsFast Tutorial
>   >
>   
> ,
>   > that all the corrected results were able to be merged into one 
> file
>   > using the vlrmerge command.  In the beginning of the tutorial, it
>   > states that fMRI and structuraI group analyses run similarly. /
>   I was
>   > therefore wondering if I can use the vlrmerge command (or some 
> similar
>   > command) for my LME data, such that I can view the following
>   > information all in one file: both hemispheres, aparc and aseg.
>   > / Currently I can only view the aparc results for each of the
>   > hemispheres separately (and I haven't found a way to visualize the
>   > aseg data).
>   >
>   > Thank you for taking the time to read this email.
> 

Re: [Freesurfer] errors on the WM and Gray inflated surfaces

[Bruce Fischl]

Can you check and see if they look ok with freeview? It might just be a display 
problem

> On Apr 8, 2016, at 9:26 AM, pablo najt  wrote:
> 
> Dear FS expert and users,
> We are coming across errors on the WM and Gray inflated surfaces.
> When trying to open the surfaces with tksurfer as follows (tksurfer subid lh 
> inflated -gray) 
> We get only a small part of the cortex displaying.  
> 
> Also when we try file-label-import annotation  the following error occurs:
> colortable with 13 entries read (originally 
> /usr/local/apps/freesurfer/5.1.0/average/colortable_BA.txt)
> Found embedded color table in annotation.
> 
> There seem to be no hard failures as recon-all log said "finished without 
> errors". Also WM and pial surfaces look accurate.
> Now we are trying to figure what is that could have caused this for all 
> subjects.
> We have an old instructions for freesurfer saying to to run recon-all as 
> follows.
> run recon -all -s subjID /autorecon -all 
> As I am not familiar with this way of running recon-all I wanted to ask if 
> this could have caused the problem consistently across 70~ subjects.
> Any advise on this would be greatly appreciated.
> Cheers.
> Pablo
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] errors on the WM and Gray inflated surfaces

[pablo najt]

Thank you Bruce for the response.Actually the surface works in freeview just 
fine. However my second issue about  loading annotation continues.In freeview I 
clicked on "Annotations" selected inside "label" folder BA1 and everything 
Freezes.Terminal shows endless column of the text below. Could there be that 
anything went wrong with the annotations? Any way to check for this and ideally 
correct without running entire recon-all again?Thanks a lotPablo








MRISreadAnnotationIntoArray: vertex index out of range: 1667852576 i=6C616265, 
in_array_size=181405
annot file: 
/Volumes/NEW_VOLUME/Maudsley_study/subjects/217NJ/label/lh.BA1.label
MRISreadAnnotationIntoArray: vertex index out of range: 1814044716 i=2066726F, 
in_array_size=181405
annot file: 
/Volumes/NEW_VOLUME/Maudsley_study/subjects/217NJ/label/lh.BA1.label
MRISreadAnnotationIntoArray: vertex index out of range: 1830843253 i=626A6563, 
in_array_size=181405
annot file: /Vo
From: fis...@nmr.mgh.harvard.edu
Date: Fri, 8 Apr 2016 09:56:46 -0400
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] errors on the WM and Gray inflated surfaces

Can you check and see if they look ok with freeview? It might just be a display 
problem
On Apr 8, 2016, at 9:26 AM, pablo najt  wrote:




Dear FS expert and users,We are coming across errors on the WM and Gray 
inflated surfaces.When trying to open the surfaces with tksurfer as follows 
(tksurfer subid lh inflated -gray) We get only a small part of the cortex 
displaying.  Also 
when we try file-label-import annotation  the following error occurs:colortable 
with 13 entries read (originally 
/usr/local/apps/freesurfer/5.1.0/average/colortable_BA.txt)Found embedded color 
table in annotation.
There seem to be no hard failures as recon-all log said "finished without 
errors". Also WM and pial surfaces look accurate.Now we are trying to figure 
what is that could have caused this for all subjects.We have an old 
instructions for freesurfer saying to to run recon-all as follows.run recon 
-all -s subjID /autorecon -all As I am not familiar with this way of running 
recon-all I wanted to ask if this could have caused the problem consistently 
across 70~ subjects.Any advise on this would be greatly appreciated.Cheers.Pablo


  
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Re: [Freesurfer] errors on the WM and Gray inflated surfaces

[pablo najt]

Thank you.I confirm, Annotation works fine. However when trying to load label 
and select .label file.I get the following message:







reading colortable from annotation file...


colortable with 76 entries read (originally 
/autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt)colortable
 with 76 entries read (originally 
/autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt)ERROR:
 LabelMarkSurface: label point 181451 exceeds nvertices 181405[0]PETSC ERROR: 
[0]PETSC
 ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory 
access out of range[0]PETSC ERROR: Try option -start_in_debugger or 
-on_error_attach_debugger[0]PETSC ERROR: or see 
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
 ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find 
memory corruption errors[0]PETSC ERROR: configure using --with-debugging=yes, 
recompile, link, and run [0]PETSC ERROR: to get more information on the 
crash.[0]PETSC ERROR: - Error Message 
[0]PETSC ERROR: Signal received![0]PETSC 
ERROR: 
[0]PETSC
 ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG 
revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124[0]PETSC ERROR: See 
docs/changes/index.html for recent updates.[0]PETSC ERROR: See docs/faq.html 
for hints about trouble shooting.[0]PETSC ERROR: See docs/index.html for manual 
pages.[0]PETSC ERROR: 
[0]PETSC
 ERROR: Unknown Name on a darwin12. named  by Fri Apr  8 16:47:36 2016[0]PETSC 
ERROR: Libraries linked from 
/usr/pubsw/packages/petsc/2.3.3-p13-64b/src/petsc-2.3.3-p13/lib/darwin12.2.0-c-opt[0]PETSC
 ERROR: Configure run at Mon Dec 17 15:29:35 2012[0]PETSC ERROR: Configure 
options --with-debugging=no --with-cc=gcc --with-fc=0 
--download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 
--with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 
FOPTFLAGS=-O3[0]PETSC ERROR: 
[0]PETSC
 ERROR: User provided function() line 0 in unknown directory unknown 
file[unset]: aborting job:application called MPI_Abort(MPI_COMM_WORLD, 59) - 
process 0



























Date: Fri, 8 Apr 2016 11:37:29 -0400
From: fis...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] errors on the WM and Gray inflated surfaces

Hi Pablo
 
if it has the extension .label then it is a label not an annotation, and 
you should load it as such
 
cheers
Bruce
 
On Fri, 8 Apr 2016, pablo najt wrote:
 
> Thank you Bruce for the response.Actually the surface works in freeview just
> fine. However my second issue about  loading annotation continues.
> In freeview I clicked on "Annotations" selected inside "label" folder BA1
> and everything Freezes.
> Terminal shows endless column of the text below. 
> Could there be that anything went wrong with the annotations? Any way to
> check for this and ideally correct without running entire recon-all again?
> Thanks a lot
> Pablo
> 
> MRISreadAnnotationIntoArray: vertex index out of range: 1667852576
> i=6C616265, in_array_size=181405
> 
> annot file:
> /Volumes/NEW_VOLUME/Maudsley_study/subjects/217NJ/label/lh.BA1.label
> 
> MRISreadAnnotationIntoArray: vertex index out of range: 1814044716
> i=2066726F, in_array_size=181405
> 
> annot file:
> /Volumes/NEW_VOLUME/Maudsley_study/subjects/217NJ/label/lh.BA1.label
> 
> MRISreadAnnotationIntoArray: vertex index out of range: 1830843253
> i=626A6563, in_array_size=181405
> 
> annot file: /Vo
> 
> 
> 
> From: fis...@nmr.mgh.harvard.edu
> Date: Fri, 8 Apr 2016 09:56:46 -0400
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] errors on the WM and Gray inflated surfaces
> 
> Can you check and see if they look ok with freeview? It might just be a
> display problem
> 
> On Apr 8, 2016, at 9:26 AM, pablo najt  wrote:
>
>   Dear FS expert and users,
> We are coming across errors on the WM and Gray inflated surfaces.
> When trying to open the surfaces with tksurfer as follows (tksurfer
> subid lh inflated -gray) 
> We get only a small part of the cortex displaying.  
>   
>  
>   
>  
> Also when we try file-label-import annotation  the following error
> occurs:
>   colortable with 13 entries read (originally
>   /usr/local/apps/freesurfer/5.1.0/average/colortable_BA.txt)
> Found embedded color table in annotation.
> 
> 
> There seem to be no hard failures as recon-all log said "finished
> without errors". Also WM and pial surfaces 

Re: [Freesurfer] axial or sagittal?

[Gamaliel Huerta Urrea]

2016-04-08 12:09 GMT-03:00 Gamaliel Huerta Urrea :

> Hello Freesurfers
>
> I'm trying to do volumetric reconstruction, i already have done this but.
> i wanted to see if for the same subject, with different directions of
> slices i have the same result, and obviously i had different results of
> volumetric measures. i have used the sequence FSPGR T1 ponderation, with
> the same parameters for both data acquisition; with voxel 1 mm3, but the
> direction is changed in both studies axial and sagittal. Both studies are
> in *.dcm format, and i used the next command for convert dicom to .mgz and
> after to apply recon-all process:
>
>
>1.
>
>mri_convert firstdicom.dcm 001.mgz
>
> I would like to know why would i have this problem?
>
> There is some specific slice direction for this kind of study which is
> suitable ?
>
> I'm interested in cerebellum volumetric information. I attached my results
> for volumetry.
>
> Cheers
>
> --
> *Gamaliel Huerta*
> *Ingeniero Civil Biomédico*
> *HealthCare Analytics*
> *Centro Interdisciplinario de Innovación en Salud*
> *Universidad de Valparaíso*
>
>


-- 
*Gamaliel Huerta*
*Ingeniero Civil Biomédico*
*HealthCare Analytics*
*Centro Interdisciplinario de Innovación en Salud*
*Universidad de Valparaíso*
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[Freesurfer] Monte Carlo correction in QDEC

[Clara Kühn]

Dear FreeSurfer experts,

for the analysis in QDEC I created my own Monte Carlo correction.
My questions relate to the threshold option.

1. Would I use neg if I have mostly blue clusters in the QDEC display and pos 
if I have mostly red clusters?

2. When do I use abs?

3. I compared the neg option at different thresholds (1.3, 2 and 2.3) and I get 
different clusters:
1.3 (=.05)
# ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZCWPCWPLow
CWPHi   NVtxs   Annot
   1   -2.669   76591   1148.00 -6.7   14.5   62.7  0.00880  0.00760  
0.01000  1600  superiorfrontal
   2   -2.443   91912   2128.78-10.3   55.3  -23.5  0.00010  0.0  
0.00020  2971  medialorbitofrontal

2.0 (=.01)
# ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZCWPCWPLow
CWPHi   NVtxs   Annot
   1   -3.289   92754420.03-36.5   57.0  -21.0  0.02140  0.01960  
0.02330   571  parsorbitalis
   2   -2.669   76591428.11 -6.7   14.5   62.7  0.01940  0.01760  
0.02120   604  superiorfrontal

2.3 (=.005)
# ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZCWPCWPLow
CWPHi   NVtxs   Annot
   1   -3.289   92754314.80-36.5   57.0  -21.0  0.01900  0.01730  
0.02080   410  parsorbitalis

Technically, if parsorbitalis is significant at .01 and .005, shouldn't it also 
be significant at .05? I've compared the clusters in freeview and the 
superiorfrontal is the same cluster in both 1.3 and 2.0. The parsorbitalis and 
the medialorbitofrontal clusters are completely different, not even closely 
overlapping.

Do you have any idea why that is and what it does differently?
Thank you!
Cheers, Clara
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Re: [Freesurfer] errors on the WM and Gray inflated surfaces

[Bruce Fischl]

Hi Pablo

if it has the extension .label then it is a label not an annotation, and 
you should load it as such


cheers
Bruce

On Fri, 8 Apr 2016, pablo najt wrote:


Thank you Bruce for the response.Actually the surface works in freeview just
fine. However my second issue about  loading annotation continues.
In freeview I clicked on "Annotations" selected inside "label" folder BA1
and everything Freezes.
Terminal shows endless column of the text below. 
Could there be that anything went wrong with the annotations? Any way to
check for this and ideally correct without running entire recon-all again?
Thanks a lot
Pablo

MRISreadAnnotationIntoArray: vertex index out of range: 1667852576
i=6C616265, in_array_size=181405

    annot file:
/Volumes/NEW_VOLUME/Maudsley_study/subjects/217NJ/label/lh.BA1.label

MRISreadAnnotationIntoArray: vertex index out of range: 1814044716
i=2066726F, in_array_size=181405

    annot file:
/Volumes/NEW_VOLUME/Maudsley_study/subjects/217NJ/label/lh.BA1.label

MRISreadAnnotationIntoArray: vertex index out of range: 1830843253
i=626A6563, in_array_size=181405

    annot file: /Vo



From: fis...@nmr.mgh.harvard.edu
Date: Fri, 8 Apr 2016 09:56:46 -0400
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] errors on the WM and Gray inflated surfaces

Can you check and see if they look ok with freeview? It might just be a
display problem

On Apr 8, 2016, at 9:26 AM, pablo najt  wrote:

  Dear FS expert and users,
We are coming across errors on the WM and Gray inflated surfaces.
When trying to open the surfaces with tksurfer as follows (tksurfer
subid lh inflated -gray) 
We get only a small part of the cortex displaying.  
  
 
  
 
Also when we try file-label-import annotation  the following error
occurs:
  colortable with 13 entries read (originally
  /usr/local/apps/freesurfer/5.1.0/average/colortable_BA.txt)
Found embedded color table in annotation.


There seem to be no hard failures as recon-all log said "finished
without errors". Also WM and pial surfaces look accurate.
Now we are trying to figure what is that could have caused this for
all subjects.
We have an old instructions for freesurfer saying to to run recon-all
as follows.
run recon -all -s subjID /autorecon -all 
As I am not familiar with this way of running recon-all I wanted to
ask if this could have caused the problem consistently across 70~
subjects.
Any advise on this would be greatly appreciated.
Cheers.
Pablo

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Re: [Freesurfer] axial or sagittal?

[Bruce Fischl]

Hi Gamaliel

many things will change when you change the slice direction - amount of 
wrap, possibly your FOV, slab-selection profile if your protocol is 
slab-selective, and some types of distortion. These will all change the 
image which will change our results. Of course even if you don't change 
anything you won't get identical results if you scan twice, but our 
longitudinal stream is pretty reliable. Andre van der Kouwe has 
acquitisiton recommendations here:


http://www.nmr.mgh.harvard.edu/~andre/FreeSurfer_recommended_morphometry_protocols.pdf

cheers
Bruce

On Fri, 8 Apr 2016, Gamaliel 
Huerta Urrea wrote:





2016-04-08 12:09 GMT-03:00 Gamaliel Huerta Urrea :
  Hello Freesurfers
I'm trying to do volumetric reconstruction, i already have done this
but. i wanted to see if for the same subject, with different
directions of slices i have the same result, and obviously i had
different results of volumetric measures. i have used the sequence
FSPGR T1 ponderation, with the same parameters for both data
acquisition; with voxel 1 mm3, but the direction is changed in both
studies axial and sagittal. Both studies are in *.dcm format, and i
used the next command for convert dicom to .mgz and after to apply
recon-all process:

 1.

mri_convert firstdicom.dcm 001.mgz 

I would like to know why would i have this problem?

There is some specific slice direction for this kind of study which is
suitable ?

I'm interested in cerebellum volumetric information. I attached my
results for volumetry.

Cheers

--
Gamaliel Huerta
Ingeniero Civil Biomédico
HealthCare Analytics
Centro Interdisciplinario de Innovación en Salud
Universidad de Valparaíso




--
Gamaliel Huerta
Ingeniero Civil Biomédico
HealthCare Analytics
Centro Interdisciplinario de Innovación en Salud
Universidad de Valparaíso


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Re: [Freesurfer] R-Map

[Douglas N Greve]

Use this version of mri_glmfit. For t-tests is will automatically 
compute a partial correlation coefficient (pcc.mgh)
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit


On 04/04/2016 12:12 PM, Morenikeji Adebayo wrote:
> Hello Freesurfers,
>
> I'm interested in creating a group map where each vertex/voxel 
> represents the correlation (as a correlation coefficient) between a 
> task-related BOLD contrast values (ces.nii.gz) and a single covariate. 
> This is analogous to a cortical thickness GLM with one group and one 
> covariate, but I'd want an r-map instead of a log10p-map.
>
> How exactly might I do this? I’m trying to accomplish this 
> using mri_glmfit, but I’m having generating output that is 
> interpretable in terms of  a correlation coefficient and in 
> particular, the direction of the effect.
>
> Thanks,
> Keji
> ---
> Morenikeji Adebayo
> Clinical Research Coordinator
> Department of Psychiatric Neuroscience
> Massachusetts General Hospital
> (p) 617.643.6347
> k...@nmr.mgh.harvard.edu 
>
>
>
> ___
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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: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] mri_vol2surf after recon-all

[Trisanna Sprung-Much]

thanks, Doug. I'll get started on running all brains using recon-all.

The MNI has several ICBM templates now:

ICBM152 linear
ICBM152 nonlinear symmetric VI
ICBM152 nonlinear 2009

Do you know which one mni152reg is using?

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Apr 8, 2016 at 12:47 PM, Douglas N Greve 
wrote:

>
>
> On 04/07/2016 03:50 PM, Trisanna Sprung-Much wrote:
> > thanks, Doug. I am still extremely confused, however. *Am I meant to
> > run recon-all first? *I was told in a previous email that I should do
> > this first, however, I thought that Freesurfer takes the volumes and
> > does a linear registration to MNI305 template, which would not work
> > for my scans that are linearly registered to ICBM152 nonlinear 2006
> > template...
> run recon-all first, otherwise you won't have surfaces. recon-all
> computes the transform matrix to the mni305 but keeps all the data in
> the native anatomical space. I think the ICBM152 is the same as the
> MNI152. Is that right? If so, you can use mni152reg to compute the
> registration to 152 space. If not, then we'll have to workout something
> else.
> >
> > When you have a moment, could you please outline in a step by step
> > manner the steps I should run to take my labels.mnc and my volumes
> > such that I can generate surfaces for those 50 volumes, overlay the
> > labels (for which I thought I was using mri_vol2surf) and then edit
> > those labels to make them more accurate?
> so you want to transfer the labels from labels.mnc to the surfaces of
> your individual 50 subjects? Start by running recon-all on the 50.
> > *The idea is that I want to generate some sulcal probability maps
> > using surface-based registration, as I can already generate
> > probability maps using volumetric registration quite easily.*
> >
> > many thanks
> >
> > Trisanna
> >
> >
> >
> >
> >
> >
> > --
> > Ph.D. Candidate
> > McGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> > On Wed, Apr 6, 2016 at 2:43 PM, Douglas Greve
> > > wrote:
> >
> > For the 152, you can run mni152reg --s subject, then specify
> > $SUBJECTS_DIR/subject/mri/transform/mni152reg.dat (or .lta) for
> > the argument to --reg. I'll need to figure out how to generate a
> > .dat/.lta for the 305.
> >
> >
> >
> > On 4/6/16 12:50 PM, Trisanna Sprung-Much wrote:
> >> Any ideas?
> >>
> >> Trisanna
> >>
> >> --
> >> Ph.D. Candidate
> >> McGill University
> >> Integrated Program in Neuroscience
> >> Psychology
> >>
> >>
> >> On Tue, Apr 5, 2016 at 9:37 PM, Trisanna Sprung-Much
> >>  >> > wrote:
> >>
> >> Hi Dr. Fischl
> >>
> >> I have a mixture - some of the labels were painted in the
> >> MNI305 space (older ones) and the more recent ones are
> >> registered to the ICBM152 nonlinear symmetric VI (2006)
> template.
> >>
> >> Best
> >>
> >> Trisanna
> >>
> >> --
> >> Ph.D. Candidate
> >> McGill University
> >> Integrated Program in Neuroscience
> >> Psychology
> >>
> >>
> >> On Tue, Apr 5, 2016 at 6:34 PM, Bruce Fischl
> >>  >> > wrote:
> >>
> >> Hi Trisanna
> >>
> >> what space are your labels in?
> >>
> >> cheers
> >> Bruce
> >> On Tue, 5 Apr 2016, Trisanna Sprung-Much
> >> wrote:
> >>
> >> > Hi Freesurfer
> >> >
> >> > I have some labels (.mnc) that are painted voxels
> >> generated from a Montreal
> >> > Neurological Institute software. I am trying to project
> >> the labels onto the
> >> > surfaces generated from recon-all that I applied to the
> >> corresponding MRI
> >> > volumes.
> >> >
> >> > I used mri_vol2surf:
> >> >
> >> > mri_vol2surf --src labels.mnc --out test.mgz --srcreg
> >> talairach.auto.xfm
> >> > --hemi lh
> >> >
> >> > and got the following error:
> >> >
> >> > Error reading inplaneres from talairach.auto.xfm
> >> >
> >> >
> >> > Do I need a .dat file? If so, how can I attain it?
> >> Essentially, what is the
> >> > registration file that I am supposed to be using?
> >> >
> >> > Many thanks!
> >> >
> >> > Trisanna
> >> >
> >> > --
> >> > Ph.D. CandidateMcGill University
> >> > Integrated Program in Neuroscience
> >> > Psychology
> >> >

Re: [Freesurfer] mri_vol2surf after recon-all

[Douglas N Greve]

not sure, mni152reg uses $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz

You can always just run the following command directly

fslregister --mov icbm.nii.gz --s $subject --reg 
$SUBJECTS_DIR/subject/transforms/icbm.reg.dat --dof 12
  --lta $SUBJECTS_DIR/subject/transforms/icbm.reg.lta

This will use a linear (12 dof) registration which might not be 
particularly accurate


On 04/08/2016 01:27 PM, Trisanna Sprung-Much wrote:
> thanks, Doug. I'll get started on running all brains using recon-all.
>
> The MNI has several ICBM templates now:
>
> ICBM152 linear
> ICBM152 nonlinear symmetric VI
> ICBM152 nonlinear 2009
>
> Do you know which one mni152reg is using?
>
> Trisanna
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Fri, Apr 8, 2016 at 12:47 PM, Douglas N Greve 
> > wrote:
>
>
>
> On 04/07/2016 03:50 PM, Trisanna Sprung-Much wrote:
> > thanks, Doug. I am still extremely confused, however. *Am I meant to
> > run recon-all first? *I was told in a previous email that I
> should do
> > this first, however, I thought that Freesurfer takes the volumes and
> > does a linear registration to MNI305 template, which would not work
> > for my scans that are linearly registered to ICBM152 nonlinear 2006
> > template...
> run recon-all first, otherwise you won't have surfaces. recon-all
> computes the transform matrix to the mni305 but keeps all the data in
> the native anatomical space. I think the ICBM152 is the same as the
> MNI152. Is that right? If so, you can use mni152reg to compute the
> registration to 152 space. If not, then we'll have to workout
> something
> else.
> >
> > When you have a moment, could you please outline in a step by step
> > manner the steps I should run to take my labels.mnc and my volumes
> > such that I can generate surfaces for those 50 volumes, overlay the
> > labels (for which I thought I was using mri_vol2surf) and then edit
> > those labels to make them more accurate?
> so you want to transfer the labels from labels.mnc to the surfaces of
> your individual 50 subjects? Start by running recon-all on the 50.
> > *The idea is that I want to generate some sulcal probability maps
> > using surface-based registration, as I can already generate
> > probability maps using volumetric registration quite easily.*
> >
> > many thanks
> >
> > Trisanna
> >
> >
> >
> >
> >
> >
> > --
> > Ph.D. Candidate
> > McGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> > On Wed, Apr 6, 2016 at 2:43 PM, Douglas Greve
> > 
>  >> wrote:
> >
> > For the 152, you can run mni152reg --s subject, then specify
> > $SUBJECTS_DIR/subject/mri/transform/mni152reg.dat (or .lta) for
> > the argument to --reg. I'll need to figure out how to generate a
> > .dat/.lta for the 305.
> >
> >
> >
> > On 4/6/16 12:50 PM, Trisanna Sprung-Much wrote:
> >> Any ideas?
> >>
> >> Trisanna
> >>
> >> --
> >> Ph.D. Candidate
> >> McGill University
> >> Integrated Program in Neuroscience
> >> Psychology
> >>
> >>
> >> On Tue, Apr 5, 2016 at 9:37 PM, Trisanna Sprung-Much
> >>  
> >>  >> wrote:
> >>
> >> Hi Dr. Fischl
> >>
> >> I have a mixture - some of the labels were painted in the
> >> MNI305 space (older ones) and the more recent ones are
> >> registered to the ICBM152 nonlinear symmetric VI (2006)
> template.
> >>
> >> Best
> >>
> >> Trisanna
> >>
> >> --
> >> Ph.D. Candidate
> >> McGill University
> >> Integrated Program in Neuroscience
> >> Psychology
> >>
> >>
> >> On Tue, Apr 5, 2016 at 6:34 PM, Bruce Fischl
> >>  
> >>  >> wrote:
> >>
> >> Hi Trisanna
> >>
> >> what space are your labels in?
> >>
> >> cheers
> >> Bruce
> >> On Tue, 5 Apr 2016, Trisanna Sprung-Much
> >> wrote:
> >>
> >> > Hi Freesurfer
> >> >
> >> > I have some labels (.mnc) that are painted 

Re: [Freesurfer] axial or sagittal?

[Matt Glasser]

I¹d add that SNR may also change if you don¹t acquire as much data axially
as you did sagittally.  Really it¹s better to acquire your 3D
T1w/T2w/FLAIR scans sagittally as this is most efficient.

Peace,

Matt.

On 4/8/16, 10:23 AM, "Bruce Fischl"
 wrote:

>Hi Gamaliel
>
>many things will change when you change the slice direction - amount of
>wrap, possibly your FOV, slab-selection profile if your protocol is
>slab-selective, and some types of distortion. These will all change the
>image which will change our results. Of course even if you don't change
>anything you won't get identical results if you scan twice, but our
>longitudinal stream is pretty reliable. Andre van der Kouwe has
>acquitisiton recommendations here:
>
>http://www.nmr.mgh.harvard.edu/~andre/FreeSurfer_recommended_morphometry_p
>rotocols.pdf
>
>cheers
>Bruce
>
>On Fri, 8 Apr 2016, Gamaliel
>Huerta Urrea wrote:
>
>> 
>> 
>> 2016-04-08 12:09 GMT-03:00 Gamaliel Huerta Urrea
>>:
>>   Hello Freesurfers
>> I'm trying to do volumetric reconstruction, i already have done this
>> but. i wanted to see if for the same subject, with different
>> directions of slices i have the same result, and obviously i had
>> different results of volumetric measures. i have used the sequence
>> FSPGR T1 ponderation, with the same parameters for both data
>> acquisition; with voxel 1 mm3, but the direction is changed in both
>> studies axial and sagittal. Both studies are in *.dcm format, and i
>> used the next command for convert dicom to .mgz and after to apply
>> recon-all process:
>>
>>  1.
>>
>> mri_convert firstdicom.dcm 001.mgz
>> 
>> I would like to know why would i have this problem?
>> 
>> There is some specific slice direction for this kind of study which is
>> suitable ?
>> 
>> I'm interested in cerebellum volumetric information. I attached my
>> results for volumetry.
>> 
>> Cheers
>> 
>> --
>> Gamaliel Huerta
>> Ingeniero Civil Biomédico
>> HealthCare Analytics
>> Centro Interdisciplinario de Innovación en Salud
>> Universidad de Valparaíso
>> 
>> 
>> 
>> 
>> --
>> Gamaliel Huerta
>> Ingeniero Civil Biomédico
>> HealthCare Analytics
>> Centro Interdisciplinario de Innovación en Salud
>> Universidad de Valparaíso
>> 
>> 
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