Re: [Freesurfer] freeview: load multiple volumes with a single option

[Jang, Ikbeom]

Hi Ruopeng,

I agree that the options are treated as part of the file path in my command 
line.

Thank you for the support.

Best,

Ikbeom

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Ruopeng Wang 

Sent: Wednesday, October 16, 2019 4:27 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] freeview: load multiple volumes with a single option


Hi Ikbeom,


I think this is because the added options at the end of file path are treated 
as part of the path by the shell and thus returns no match. I will try to put a 
fix on that.


Best,

Ruopeng


On 10/16/19 4:09 PM, Jang, Ikbeom wrote:
Dear FreeSurfer community:

I am a beginner and tying to load multiple volumes in Freeview with a single 
option applied to all the volumes.

For example, I would like to set grayscale window as min=0 and max=100 for all 
volumes. Is there a simple command line which does that efficiently?

The command line below works if I provide the option for each volume:
freeview -v sitename/mri/subj0401/brainmask.mgz:grayscale=0,100 \
sitename/mri/subj0402/brainmask.mgz:grayscale=0,100 \
... \
sitename/mri/subj0425/brainmask.mgz:grayscale=0,100

However, the command line something like this does not:
freeview -v sitename/mri/subj*/brainmask.mgz:grayscale=0,100

Thanks in advance,

Ikbeom



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Re: [Freesurfer] freeview: load multiple volumes with a single option

[Ruopeng Wang]

Hi Ikbeom,


I think this is because the added options at the end of file path are 
treated as part of the path by the shell and thus returns no match. I 
will try to put a fix on that.



Best,

Ruopeng


On 10/16/19 4:09 PM, Jang, Ikbeom wrote:

Dear FreeSurfer community:

I am a beginner and tying to load multiple volumes in Freeview with a 
single option applied to all the volumes.


For example, I would like to set grayscale window as min=0 and max=100 
for all volumes. Is there a simple command line which does that 
efficiently?


The command line below works if I provide the option for each volume:

freeview -v sitename/mri/subj0401/brainmask.mgz:grayscale=0,100 \
sitename/mri/subj0402/brainmask.mgz:grayscale=0,100\
... \
sitename/mri/subj0425/brainmask.mgz:grayscale=0,100


However, the command line something like this does not:

freeview -v sitename/mri/subj*/brainmask.mgz:grayscale=0,100


Thanks in advance,

Ikbeom

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[Freesurfer] freeview: load multiple volumes with a single option

[Jang, Ikbeom]

Dear FreeSurfer community:

I am a beginner and tying to load multiple volumes in Freeview with a single 
option applied to all the volumes.

For example, I would like to set grayscale window as min=0 and max=100 for all 
volumes. Is there a simple command line which does that efficiently?

The command line below works if I provide the option for each volume:
freeview -v sitename/mri/subj0401/brainmask.mgz:grayscale=0,100 \
sitename/mri/subj0402/brainmask.mgz:grayscale=0,100 \
... \
sitename/mri/subj0425/brainmask.mgz:grayscale=0,100

However, the command line something like this does not:
freeview -v sitename/mri/subj*/brainmask.mgz:grayscale=0,100

Thanks in advance,

Ikbeom
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[Freesurfer] Question re: Longitudinal processing stream transforms.

[Jamie Hanson]

External Email - Use Caution

Dear FS List,

My group was trying to look at the overlap between cortical labels in the
longitudinal processing stream and I had a question re: use of transform
files. In brief, we followed the commands for the longitudinal
processing stream, creating a "subject-specific" template for each
participant (
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing#WorkflowSummary,
using FS v.6.0). We processed T1w images multiple times and now, we wanted
to transform the time 1 and time 2 (native space) scans to their
subject-specific template.

We used the following commands--
mri_vol2vol --mov
$INDIVIDUAL_SCAN_TIME1_DIR/sub-BNU_25864_001.long.sub-BNU_25864_template/mri/brain.mgz
--o $INDIVIDUAL_SCAN_TIME1/brain_001_to_temp.mgz --lta
$SUBJECT_SPECIFIC_TEMPLATE_DIR/mri/transforms/sub-BNU_25864_001_to_sub-BNU_25864_template.lta
--targ $SUBJECT_SPECIFIC_TEMPLATE_DIR/mri/brain.mgz

But when we did this for time 1 and time 2 scans, they were poorly aligned.
I also used the lta file for template to 001, but again things were poorly
aligned. Should we be using m3z files? Or combining different transforms?
Any guidance or suggestions are deeply appreciated.

Thanks much,
Jamie.


--
Jamie Hanson
Assistant Professor, Psychology
Research Scientist, Learning Research and Development Center
University of Pittsburgh
Personal website: jamiehanson.org
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Re: [Freesurfer] R: R: R: R: recon-all skull stripping

[Bruce Fischl]

it will figure out the input and output for you
On Wed, 16 Oct 2019, 
Inglese, Marianna wrote:




External Email - Use Caution

Hi Bruce,

shall I do that with my original T1 as input or the T1.mgz?

Thank you.

BW
Marianna


Da: freesurfer-boun...@nmr.mgh.harvard.edu
 per conto di Bruce Fischl

Inviato: mercoledì 16 ottobre 2019 17:58
A: Freesurfer support list 
Oggetto: Re: [Freesurfer] R: R: R: recon-all skull stripping  
Hi Marianna

I think you can just run recon-all -s  -skullstrip and it will
run it for you as it normally does

cheers
Bruce
On Wed, 16 Oct 2019, Inglese, Marianna
wrote:

>
> External Email - Use Caution
>
> Dear all,
>
> from this:
>
> (...) Removes the skull from mri/T1.mgz and stores the result in
> mri/brainmask.auto.mgz and mri/brainmask.mgz. Runs the mri_watershed
> program. If the strip fails, users can specify seed points (-wsseed) or
> change the threshold (-wsthresh, -wsmore, -wsless). The -autorecon1 stage
> ends here.
>
> i guess the function I need is mri_watershed. Now the question is: does
> recon-all add optional flagged arguments to this function while running
> recon-all? and which of them?
>
> Thank you.
>
> BW
> Marianna
>
>___
_
> Da: freesurfer-boun...@nmr.mgh.harvard.edu
>  per conto di Bruce Fischl
> 
> Inviato: mercoledì 16 ottobre 2019 17:52
> A: Freesurfer support list 
> Oggetto: Re: [Freesurfer] R: R: recon-all skull stripping  
> that will do a bit more than just the skullstripping
> On Wed, 16 Oct 2019,
> Krieger, Donald N. wrote:
>
> >    External Email - Use Caution
> >
> > Please pardon me for jumping in here.
> > I looks like recon-all -autorecon1 will do it, yes?
> >
> > Best - Don
> >
> > -Original Message-
> > From: freesurfer-boun...@nmr.mgh.harvard.edu
>  On Behalf Of Bruce Fischl
> > Sent: Wednesday, October 16, 2019 12:48 PM
> > To: Freesurfer support list 
> > Subject: Re: [Freesurfer] R: R: recon-all skull stripping
> >
> > oh, sure, you can just run that part of recon-all. You don't need to
rerun
> the whole thing cheers Bruce On Wed, 16 Oct 2019, Inglese, Marianna wrote:
> >
> >>
> >> External Email - Use Caution
> >>
> >> Hi Bruce,
> >>
> >> what I mean is that, two of the main outputs of recon-all are T1.mgz
> >> (which has the skull) and brain.mgz (which has been skull stripped).
> >> For a group of patients, I lost the brain.mgz file and I still have
> >> the T1.mgz. I was wondering if there was a way, given T1.mgz as input,
> >> to get brain.mgz (avoiding the whole segmentation procedure again).
> >>
> >> Thank you
> >>
> >> BW
> >> Marianna
> >>
> >> __
> >> __
> >> Da: freesurfer-boun...@nmr.mgh.harvard.edu
> >>  per conto di Bruce Fischl
> >> 
> >> Inviato: mercoledì 16 ottobre 2019 17:40
> >> A: Freesurfer support list 
> >> Oggetto: Re: [Freesurfer] R: recon-all skull stripping Hi Marianna
> >>
> >> I'm not sure what you mean by "replicate". The procedure should be the
> >> same for all inputs unless you change something explicitly
> >>
> >> cheers
> >> Bruce
> >>
> >> On Wed, 16 Oct 2019,
> >> Inglese, Marianna wrote:
> >>
> >>>
> >>> External Email - Use Caution
> >>>
> >>> Thank you Bruce.
> >>> I thought it was something similar to the FSL bet function, which
> >>> extracts the brain using a fractional intensity threshold (0.5 for
> example).
> >>> So I guess I won't be able to replicate the same exact skull
> >>> stripping of freesurfer's recon-all.
> >>>
> >>> BW
> >>> Marianna
> >>>
> >>> _
> >>> __
> >> _
> >>> Da: freesurfer-boun...@nmr.mgh.harvard.edu
> >>>  per conto di Bruce Fischl
> >>> 
> >>> Inviato: mercoledì 16 ottobre 2019 17:23
> >>> A: Freesurfer support list 
> >>> Oggetto: Re: [Freesurfer] recon-all skull stripping Hi Marianna
> >>>
> >>> the skull stripping is a hybrid procedure that uses both a watershed
> >>> algorithm and a deformable surface. There is no single intensity
> >>> threshold in it. Maybe I'm misunderstanding your question? There are
> >>> parameters you can change (for example the preflooding height), but
> >>> there is no intensity thresholding
> >>>
> >>> cheers
> >>> Bruce
> >>>
> >>>
> >>> On Wed, 16 Oct 2019, Inglese, Marianna
> >>> wrote:
> >>>
> 
>  External Email - Use Caution
> 
>  To whom it may concern,
> 
>  I am using recon-all to segment many T1s. As I can see, one of the
> >>> automatic
>  step performed by recon-all is the skull stripping. Would it be
>  possible
> >>> to
>  know the threshold used for the stripping? I guess it is the same
> >>> threshold
>  everytime. I would like to apply the skull stripping only on other
>  T1s
> >> and
>  need to get the same result.
> 

[Freesurfer] R: R: R: R: recon-all skull stripping

[Inglese, Marianna]

External Email - Use Caution

Hi Bruce,

shall I do that with my original T1 as input or the T1.mgz?

Thank you.

BW
Marianna

Da: freesurfer-boun...@nmr.mgh.harvard.edu 
 per conto di Bruce Fischl 

Inviato: mercoledì 16 ottobre 2019 17:58
A: Freesurfer support list 
Oggetto: Re: [Freesurfer] R: R: R: recon-all skull stripping

Hi Marianna

I think you can just run recon-all -s  -skullstrip and it will
run it for you as it normally does

cheers
Bruce
On Wed, 16 Oct 2019, Inglese, Marianna
wrote:

>
> External Email - Use Caution
>
> Dear all,
>
> from this:
>
> (...) Removes the skull from mri/T1.mgz and stores the result in
> mri/brainmask.auto.mgz and mri/brainmask.mgz. Runs the mri_watershed
> program. If the strip fails, users can specify seed points (-wsseed) or
> change the threshold (-wsthresh, -wsmore, -wsless). The -autorecon1 stage
> ends here.
>
> i guess the function I need is mri_watershed. Now the question is: does
> recon-all add optional flagged arguments to this function while running
> recon-all? and which of them?
>
> Thank you.
>
> BW
> Marianna
>
> 
> Da: freesurfer-boun...@nmr.mgh.harvard.edu
>  per conto di Bruce Fischl
> 
> Inviato: mercoledì 16 ottobre 2019 17:52
> A: Freesurfer support list 
> Oggetto: Re: [Freesurfer] R: R: recon-all skull stripping
> that will do a bit more than just the skullstripping
> On Wed, 16 Oct 2019,
> Krieger, Donald N. wrote:
>
> >External Email - Use Caution
> >
> > Please pardon me for jumping in here.
> > I looks like recon-all -autorecon1 will do it, yes?
> >
> > Best - Don
> >
> > -Original Message-
> > From: freesurfer-boun...@nmr.mgh.harvard.edu
>  On Behalf Of Bruce Fischl
> > Sent: Wednesday, October 16, 2019 12:48 PM
> > To: Freesurfer support list 
> > Subject: Re: [Freesurfer] R: R: recon-all skull stripping
> >
> > oh, sure, you can just run that part of recon-all. You don't need to rerun
> the whole thing cheers Bruce On Wed, 16 Oct 2019, Inglese, Marianna wrote:
> >
> >>
> >> External Email - Use Caution
> >>
> >> Hi Bruce,
> >>
> >> what I mean is that, two of the main outputs of recon-all are T1.mgz
> >> (which has the skull) and brain.mgz (which has been skull stripped).
> >> For a group of patients, I lost the brain.mgz file and I still have
> >> the T1.mgz. I was wondering if there was a way, given T1.mgz as input,
> >> to get brain.mgz (avoiding the whole segmentation procedure again).
> >>
> >> Thank you
> >>
> >> BW
> >> Marianna
> >>
> >> __
> >> __
> >> Da: freesurfer-boun...@nmr.mgh.harvard.edu
> >>  per conto di Bruce Fischl
> >> 
> >> Inviato: mercoledì 16 ottobre 2019 17:40
> >> A: Freesurfer support list 
> >> Oggetto: Re: [Freesurfer] R: recon-all skull stripping Hi Marianna
> >>
> >> I'm not sure what you mean by "replicate". The procedure should be the
> >> same for all inputs unless you change something explicitly
> >>
> >> cheers
> >> Bruce
> >>
> >> On Wed, 16 Oct 2019,
> >> Inglese, Marianna wrote:
> >>
> >>>
> >>> External Email - Use Caution
> >>>
> >>> Thank you Bruce.
> >>> I thought it was something similar to the FSL bet function, which
> >>> extracts the brain using a fractional intensity threshold (0.5 for
> example).
> >>> So I guess I won't be able to replicate the same exact skull
> >>> stripping of freesurfer's recon-all.
> >>>
> >>> BW
> >>> Marianna
> >>>
> >>> _
> >>> __
> >> _
> >>> Da: freesurfer-boun...@nmr.mgh.harvard.edu
> >>>  per conto di Bruce Fischl
> >>> 
> >>> Inviato: mercoledì 16 ottobre 2019 17:23
> >>> A: Freesurfer support list 
> >>> Oggetto: Re: [Freesurfer] recon-all skull stripping Hi Marianna
> >>>
> >>> the skull stripping is a hybrid procedure that uses both a watershed
> >>> algorithm and a deformable surface. There is no single intensity
> >>> threshold in it. Maybe I'm misunderstanding your question? There are
> >>> parameters you can change (for example the preflooding height), but
> >>> there is no intensity thresholding
> >>>
> >>> cheers
> >>> Bruce
> >>>
> >>>
> >>> On Wed, 16 Oct 2019, Inglese, Marianna
> >>> wrote:
> >>>
> 
>  External Email - Use Caution
> 
>  To whom it may concern,
> 
>  I am using recon-all to segment many T1s. As I can see, one of the
> >>> automatic
>  step performed by recon-all is the skull stripping. Would it be
>  possible
> >>> to
>  know the threshold used for the stripping? I guess it is the same
> >>> threshold
>  everytime. I would like to apply the skull stripping only on other
>  T1s
> >> and
>  need to get the same result.
> 
>  Thank you very much for the help.
> 
>  Yours faithfully,
> 
>  Marianna Inglese
> 
>  Research fellow, Imperial Colle

[Freesurfer] Postdoctoral Positions in Pediatric Neuroimaging at the Waisman Center, University of Wisconsin Madison

[Doug Dean III]

External Email - Use Caution

Postdoctoral Research Associate

Waisman Center, University of Wisconsin–Madison, Madison WI



The Waisman Laboratory for Brain Imaging & Behavior at the Waisman Center, 
University of Wisconsin–Madison, is seeking highly motivated postdoctoral 
researchers to work on neuroimaging research studies of young children and 
individuals with intellectual and developmental disorders (IDDs).



Areas of research include the development and evaluation of image acquisition 
and analyses for brain imaging studies of infants, young children, and 
individuals with autism, Down syndrome and fragile X syndrome. The Alexander 
and Dean labs at the Waisman Laboratory for Brain Imaging & Behavior have 
multiple projects using MRI and functional near infrared spectroscopy (fNIRS). 
Work is ongoing to develop rapid, quiet and motion-correction imaging methods 
to improve studies in these challenging populations. Studies are also under way 
to characterize brain structure, microstructure and function change during 
early brain development and how development is affected in IDDs. The 
postdoctoral research associates will have opportunities to participate in 
activities related to neuroimaging methods development and evaluation, study 
data collection and analyses, research publications, grant writing and are 
expected to make positive scholarly contributions to our interdisciplinary and 
highly collaborative research programs.


Desired Qualifications: Ph.D. in medical physics, neuroscience, engineering 
and/or a related field. Prior experience with imaging techniques (e.g. MRI, 
DTI, fMRI, PET, fNIRS) is preferred.  Experience with brain image analysis 
software tools, MATLAB, Python, C++ and/or other computer programming is highly 
desirable. Pulse sequence programming experience would be a plus but not 
required. The candidate is expected to have an emerging track record of 
publishing in academic journals, strong analytic skills, and capable of working 
within a collaborative environment.



Interested candidates should send: 1) curriculum vitae; 2) cover letter 
outlining research interests, experience, and career goals; and 3) a list of 
three references to either Dr. Andy Alexander at 
alalexand...@wisc.edu or Dr. Douglas Dean at 
dean...@wisc.edu.
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Re: [Freesurfer] R: R: R: recon-all skull stripping

[Bruce Fischl]

Hi Marianna

I think you can just run recon-all -s  -skullstrip and it will 
run it for you as it normally does


cheers
Bruce
On Wed, 16 Oct 2019, Inglese, Marianna 
wrote:




External Email - Use Caution

Dear all,

from this:

(...) Removes the skull from mri/T1.mgz and stores the result in
mri/brainmask.auto.mgz and mri/brainmask.mgz. Runs the mri_watershed
program. If the strip fails, users can specify seed points (-wsseed) or
change the threshold (-wsthresh, -wsmore, -wsless). The -autorecon1 stage
ends here.

i guess the function I need is mri_watershed. Now the question is: does
recon-all add optional flagged arguments to this function while running
recon-all? and which of them?

Thank you.

BW
Marianna


Da: freesurfer-boun...@nmr.mgh.harvard.edu
 per conto di Bruce Fischl

Inviato: mercoledì 16 ottobre 2019 17:52
A: Freesurfer support list 
Oggetto: Re: [Freesurfer] R: R: recon-all skull stripping  
that will do a bit more than just the skullstripping
On Wed, 16 Oct 2019,
Krieger, Donald N. wrote:

>    External Email - Use Caution
>
> Please pardon me for jumping in here.
> I looks like recon-all -autorecon1 will do it, yes?
>
> Best - Don
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu
 On Behalf Of Bruce Fischl
> Sent: Wednesday, October 16, 2019 12:48 PM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] R: R: recon-all skull stripping
>
> oh, sure, you can just run that part of recon-all. You don't need to rerun
the whole thing cheers Bruce On Wed, 16 Oct 2019, Inglese, Marianna wrote:
>
>>
>> External Email - Use Caution
>>
>> Hi Bruce,
>>
>> what I mean is that, two of the main outputs of recon-all are T1.mgz
>> (which has the skull) and brain.mgz (which has been skull stripped).
>> For a group of patients, I lost the brain.mgz file and I still have
>> the T1.mgz. I was wondering if there was a way, given T1.mgz as input,
>> to get brain.mgz (avoiding the whole segmentation procedure again).
>>
>> Thank you
>>
>> BW
>> Marianna
>>
>> __
>> __
>> Da: freesurfer-boun...@nmr.mgh.harvard.edu
>>  per conto di Bruce Fischl
>> 
>> Inviato: mercoledì 16 ottobre 2019 17:40
>> A: Freesurfer support list 
>> Oggetto: Re: [Freesurfer] R: recon-all skull stripping Hi Marianna
>>
>> I'm not sure what you mean by "replicate". The procedure should be the
>> same for all inputs unless you change something explicitly
>>
>> cheers
>> Bruce
>>
>> On Wed, 16 Oct 2019,
>> Inglese, Marianna wrote:
>>
>>>
>>> External Email - Use Caution
>>>
>>> Thank you Bruce.
>>> I thought it was something similar to the FSL bet function, which
>>> extracts the brain using a fractional intensity threshold (0.5 for
example).
>>> So I guess I won't be able to replicate the same exact skull
>>> stripping of freesurfer's recon-all.
>>>
>>> BW
>>> Marianna
>>>
>>> _
>>> __
>> _
>>> Da: freesurfer-boun...@nmr.mgh.harvard.edu
>>>  per conto di Bruce Fischl
>>> 
>>> Inviato: mercoledì 16 ottobre 2019 17:23
>>> A: Freesurfer support list 
>>> Oggetto: Re: [Freesurfer] recon-all skull stripping Hi Marianna
>>>
>>> the skull stripping is a hybrid procedure that uses both a watershed
>>> algorithm and a deformable surface. There is no single intensity
>>> threshold in it. Maybe I'm misunderstanding your question? There are
>>> parameters you can change (for example the preflooding height), but
>>> there is no intensity thresholding
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>> On Wed, 16 Oct 2019, Inglese, Marianna
>>> wrote:
>>>

 External Email - Use Caution

 To whom it may concern,

 I am using recon-all to segment many T1s. As I can see, one of the
>>> automatic
 step performed by recon-all is the skull stripping. Would it be
 possible
>>> to
 know the threshold used for the stripping? I guess it is the same
>>> threshold
 everytime. I would like to apply the skull stripping only on other
 T1s
>> and
 need to get the same result.

 Thank you very much for the help.

 Yours faithfully,

 Marianna Inglese

 Research fellow, Imperial College London Department of Surgery and
 Cancer



>>>
>>>
>>
>>
>
>
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>
>
>

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[Freesurfer] R: R: R: recon-all skull stripping

[Inglese, Marianna]

External Email - Use Caution

Dear all,

from this:

(...) Removes the skull from mri/T1.mgz and stores the result in 
mri/brainmask.auto.mgz and mri/brainmask.mgz. Runs the mri_watershed program. 
If the strip fails, users can specify seed points (-wsseed) or change the 
threshold (-wsthresh, -wsmore, -wsless). The -autorecon1 stage ends here.

i guess the function I need is mri_watershed. Now the question is: does 
recon-all add optional flagged arguments to this function while running 
recon-all? and which of them?

Thank you.

BW
Marianna

Da: freesurfer-boun...@nmr.mgh.harvard.edu 
 per conto di Bruce Fischl 

Inviato: mercoledì 16 ottobre 2019 17:52
A: Freesurfer support list 
Oggetto: Re: [Freesurfer] R: R: recon-all skull stripping

that will do a bit more than just the skullstripping
On Wed, 16 Oct 2019,
Krieger, Donald N. wrote:

>External Email - Use Caution
>
> Please pardon me for jumping in here.
> I looks like recon-all -autorecon1 will do it, yes?
>
> Best - Don
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  On Behalf Of Bruce Fischl
> Sent: Wednesday, October 16, 2019 12:48 PM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] R: R: recon-all skull stripping
>
> oh, sure, you can just run that part of recon-all. You don't need to rerun 
> the whole thing cheers Bruce On Wed, 16 Oct 2019, Inglese, Marianna wrote:
>
>>
>> External Email - Use Caution
>>
>> Hi Bruce,
>>
>> what I mean is that, two of the main outputs of recon-all are T1.mgz
>> (which has the skull) and brain.mgz (which has been skull stripped).
>> For a group of patients, I lost the brain.mgz file and I still have
>> the T1.mgz. I was wondering if there was a way, given T1.mgz as input,
>> to get brain.mgz (avoiding the whole segmentation procedure again).
>>
>> Thank you
>>
>> BW
>> Marianna
>>
>> __
>> __
>> Da: freesurfer-boun...@nmr.mgh.harvard.edu
>>  per conto di Bruce Fischl
>> 
>> Inviato: mercoledì 16 ottobre 2019 17:40
>> A: Freesurfer support list 
>> Oggetto: Re: [Freesurfer] R: recon-all skull stripping Hi Marianna
>>
>> I'm not sure what you mean by "replicate". The procedure should be the
>> same for all inputs unless you change something explicitly
>>
>> cheers
>> Bruce
>>
>> On Wed, 16 Oct 2019,
>> Inglese, Marianna wrote:
>>
>>>
>>> External Email - Use Caution
>>>
>>> Thank you Bruce.
>>> I thought it was something similar to the FSL bet function, which
>>> extracts the brain using a fractional intensity threshold (0.5 for example).
>>> So I guess I won't be able to replicate the same exact skull
>>> stripping of freesurfer's recon-all.
>>>
>>> BW
>>> Marianna
>>>
>>> _
>>> __
>> _
>>> Da: freesurfer-boun...@nmr.mgh.harvard.edu
>>>  per conto di Bruce Fischl
>>> 
>>> Inviato: mercoledì 16 ottobre 2019 17:23
>>> A: Freesurfer support list 
>>> Oggetto: Re: [Freesurfer] recon-all skull stripping Hi Marianna
>>>
>>> the skull stripping is a hybrid procedure that uses both a watershed
>>> algorithm and a deformable surface. There is no single intensity
>>> threshold in it. Maybe I'm misunderstanding your question? There are
>>> parameters you can change (for example the preflooding height), but
>>> there is no intensity thresholding
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>> On Wed, 16 Oct 2019, Inglese, Marianna
>>> wrote:
>>>

 External Email - Use Caution

 To whom it may concern,

 I am using recon-all to segment many T1s. As I can see, one of the
>>> automatic
 step performed by recon-all is the skull stripping. Would it be
 possible
>>> to
 know the threshold used for the stripping? I guess it is the same
>>> threshold
 everytime. I would like to apply the skull stripping only on other
 T1s
>> and
 need to get the same result.

 Thank you very much for the help.

 Yours faithfully,

 Marianna Inglese

 Research fellow, Imperial College London Department of Surgery and
 Cancer



>>>
>>>
>>
>>
>
>
> ___
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>
>
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Re: [Freesurfer] R: R: recon-all skull stripping

[Bruce Fischl]

that will do a bit more than just the skullstripping
On Wed, 16 Oct 2019, 
Krieger, Donald N. wrote:



   External Email - Use Caution

Please pardon me for jumping in here.
I looks like recon-all -autorecon1 will do it, yes?

Best - Don

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Bruce Fischl
Sent: Wednesday, October 16, 2019 12:48 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] R: R: recon-all skull stripping

oh, sure, you can just run that part of recon-all. You don't need to rerun the 
whole thing cheers Bruce On Wed, 16 Oct 2019, Inglese, Marianna wrote:



External Email - Use Caution

Hi Bruce,

what I mean is that, two of the main outputs of recon-all are T1.mgz
(which has the skull) and brain.mgz (which has been skull stripped).
For a group of patients, I lost the brain.mgz file and I still have
the T1.mgz. I was wondering if there was a way, given T1.mgz as input,
to get brain.mgz (avoiding the whole segmentation procedure again).

Thank you

BW
Marianna

__
__
Da: freesurfer-boun...@nmr.mgh.harvard.edu
 per conto di Bruce Fischl

Inviato: mercoledì 16 ottobre 2019 17:40
A: Freesurfer support list 
Oggetto: Re: [Freesurfer] R: recon-all skull stripping Hi Marianna

I'm not sure what you mean by "replicate". The procedure should be the
same for all inputs unless you change something explicitly

cheers
Bruce

On Wed, 16 Oct 2019,
Inglese, Marianna wrote:



External Email - Use Caution

Thank you Bruce.
I thought it was something similar to the FSL bet function, which
extracts the brain using a fractional intensity threshold (0.5 for example).
So I guess I won't be able to replicate the same exact skull
stripping of freesurfer's recon-all.

BW
Marianna

_
__

_

Da: freesurfer-boun...@nmr.mgh.harvard.edu
 per conto di Bruce Fischl

Inviato: mercoledì 16 ottobre 2019 17:23
A: Freesurfer support list 
Oggetto: Re: [Freesurfer] recon-all skull stripping Hi Marianna

the skull stripping is a hybrid procedure that uses both a watershed
algorithm and a deformable surface. There is no single intensity
threshold in it. Maybe I'm misunderstanding your question? There are
parameters you can change (for example the preflooding height), but
there is no intensity thresholding

cheers
Bruce


On Wed, 16 Oct 2019, Inglese, Marianna
wrote:



External Email - Use Caution

To whom it may concern,

I am using recon-all to segment many T1s. As I can see, one of the

automatic

step performed by recon-all is the skull stripping. Would it be
possible

to

know the threshold used for the stripping? I guess it is the same

threshold

everytime. I would like to apply the skull stripping only on other
T1s

and

need to get the same result.

Thank you very much for the help.

Yours faithfully,

Marianna Inglese

Research fellow, Imperial College London Department of Surgery and
Cancer












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Re: [Freesurfer] R: R: recon-all skull stripping

[Krieger, Donald N.]

External Email - Use Caution

Please pardon me for jumping in here.
I looks like recon-all -autorecon1 will do it, yes?

Best - Don 

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Bruce Fischl
Sent: Wednesday, October 16, 2019 12:48 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] R: R: recon-all skull stripping

oh, sure, you can just run that part of recon-all. You don't need to rerun the 
whole thing cheers Bruce On Wed, 16 Oct 2019, Inglese, Marianna wrote:

> 
> External Email - Use Caution
> 
> Hi Bruce,
> 
> what I mean is that, two of the main outputs of recon-all are T1.mgz 
> (which has the skull) and brain.mgz (which has been skull stripped). 
> For a group of patients, I lost the brain.mgz file and I still have 
> the T1.mgz. I was wondering if there was a way, given T1.mgz as input, 
> to get brain.mgz (avoiding the whole segmentation procedure again).
> 
> Thank you
> 
> BW
> Marianna
> 
> __
> __
> Da: freesurfer-boun...@nmr.mgh.harvard.edu
>  per conto di Bruce Fischl 
> 
> Inviato: mercoledì 16 ottobre 2019 17:40
> A: Freesurfer support list 
> Oggetto: Re: [Freesurfer] R: recon-all skull stripping Hi Marianna
> 
> I'm not sure what you mean by "replicate". The procedure should be the 
> same for all inputs unless you change something explicitly
> 
> cheers
> Bruce
> 
> On Wed, 16 Oct 2019,
> Inglese, Marianna wrote:
> 
> >
> > External Email - Use Caution
> >
> > Thank you Bruce.
> > I thought it was something similar to the FSL bet function, which 
> > extracts the brain using a fractional intensity threshold (0.5 for example).
> > So I guess I won't be able to replicate the same exact skull 
> > stripping of freesurfer's recon-all.
> >
> > BW
> > Marianna
> >
> >_
> >__
> _
> > Da: freesurfer-boun...@nmr.mgh.harvard.edu
> >  per conto di Bruce Fischl 
> > 
> > Inviato: mercoledì 16 ottobre 2019 17:23
> > A: Freesurfer support list 
> > Oggetto: Re: [Freesurfer] recon-all skull stripping Hi Marianna
> >
> > the skull stripping is a hybrid procedure that uses both a watershed 
> > algorithm and a deformable surface. There is no single intensity 
> > threshold in it. Maybe I'm misunderstanding your question? There are 
> > parameters you can change (for example the preflooding height), but 
> > there is no intensity thresholding
> >
> > cheers
> > Bruce
> >
> >
> > On Wed, 16 Oct 2019, Inglese, Marianna
> > wrote:
> >
> > >
> > > External Email - Use Caution
> > >
> > > To whom it may concern,
> > >
> > > I am using recon-all to segment many T1s. As I can see, one of the
> > automatic
> > > step performed by recon-all is the skull stripping. Would it be 
> > > possible
> > to
> > > know the threshold used for the stripping? I guess it is the same
> > threshold
> > > everytime. I would like to apply the skull stripping only on other 
> > > T1s
> and
> > > need to get the same result.
> > >
> > > Thank you very much for the help.
> > >
> > > Yours faithfully,
> > >
> > > Marianna Inglese
> > >
> > > Research fellow, Imperial College London Department of Surgery and 
> > > Cancer
> > >
> > >
> > >
> >
> >
> 
>


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Re: [Freesurfer] R: R: recon-all skull stripping

[Bruce Fischl]

oh, sure, you can just run that part of recon-all. You don't need to 
rerun the whole thing

cheers
Bruce
On Wed, 16 Oct 2019, Inglese, Marianna wrote:



External Email - Use Caution

Hi Bruce,

what I mean is that, two of the main outputs of recon-all are T1.mgz (which
has the skull) and brain.mgz (which has been skull stripped). For a group of
patients, I lost the brain.mgz file and I still have the T1.mgz. I was
wondering if there was a way, given T1.mgz as input, to get brain.mgz
(avoiding the whole segmentation procedure again). 

Thank you

BW
Marianna


Da: freesurfer-boun...@nmr.mgh.harvard.edu
 per conto di Bruce Fischl

Inviato: mercoledì 16 ottobre 2019 17:40
A: Freesurfer support list 
Oggetto: Re: [Freesurfer] R: recon-all skull stripping  
Hi Marianna

I'm not sure what you mean by "replicate". The procedure should be the
same for all inputs unless you change something explicitly

cheers
Bruce

On Wed, 16 Oct 2019,
Inglese, Marianna wrote:

>
> External Email - Use Caution
>
> Thank you Bruce. 
> I thought it was something similar to the FSL bet function, which extracts
> the brain using a fractional intensity threshold (0.5 for example). 
> So I guess I won't be able to replicate the same exact skull stripping of
> freesurfer's recon-all.
>
> BW
> Marianna
>
>___
_
> Da: freesurfer-boun...@nmr.mgh.harvard.edu
>  per conto di Bruce Fischl
> 
> Inviato: mercoledì 16 ottobre 2019 17:23
> A: Freesurfer support list 
> Oggetto: Re: [Freesurfer] recon-all skull stripping  
> Hi Marianna
>
> the skull stripping is a hybrid procedure that uses both a watershed
> algorithm and a deformable surface. There is no single intensity threshold
> in it. Maybe I'm misunderstanding your question? There are parameters you
> can change (for example the preflooding height), but there is no intensity
> thresholding
>
> cheers
> Bruce
>
>
> On Wed, 16 Oct 2019, Inglese, Marianna
> wrote:
>
> >
> > External Email - Use Caution
> >
> > To whom it may concern,
> >
> > I am using recon-all to segment many T1s. As I can see, one of the
> automatic
> > step performed by recon-all is the skull stripping. Would it be possible
> to
> > know the threshold used for the stripping? I guess it is the same
> threshold
> > everytime. I would like to apply the skull stripping only on other T1s
and
> > need to get the same result.
> >
> > Thank you very much for the help.
> >
> > Yours faithfully,
> >
> > Marianna Inglese
> >
> > Research fellow, Imperial College London
> > Department of Surgery and Cancer
> >
> >
> >
>
>

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[Freesurfer] R: R: recon-all skull stripping

[Inglese, Marianna]

External Email - Use Caution

Hi Bruce,

what I mean is that, two of the main outputs of recon-all are T1.mgz (which has 
the skull) and brain.mgz (which has been skull stripped). For a group of 
patients, I lost the brain.mgz file and I still have the T1.mgz. I was 
wondering if there was a way, given T1.mgz as input, to get brain.mgz (avoiding 
the whole segmentation procedure again).

Thank you

BW
Marianna

Da: freesurfer-boun...@nmr.mgh.harvard.edu 
 per conto di Bruce Fischl 

Inviato: mercoledì 16 ottobre 2019 17:40
A: Freesurfer support list 
Oggetto: Re: [Freesurfer] R: recon-all skull stripping

Hi Marianna

I'm not sure what you mean by "replicate". The procedure should be the
same for all inputs unless you change something explicitly

cheers
Bruce

On Wed, 16 Oct 2019,
Inglese, Marianna wrote:

>
> External Email - Use Caution
>
> Thank you Bruce.
> I thought it was something similar to the FSL bet function, which extracts
> the brain using a fractional intensity threshold (0.5 for example).
> So I guess I won't be able to replicate the same exact skull stripping of
> freesurfer's recon-all.
>
> BW
> Marianna
>
> 
> Da: freesurfer-boun...@nmr.mgh.harvard.edu
>  per conto di Bruce Fischl
> 
> Inviato: mercoledì 16 ottobre 2019 17:23
> A: Freesurfer support list 
> Oggetto: Re: [Freesurfer] recon-all skull stripping
> Hi Marianna
>
> the skull stripping is a hybrid procedure that uses both a watershed
> algorithm and a deformable surface. There is no single intensity threshold
> in it. Maybe I'm misunderstanding your question? There are parameters you
> can change (for example the preflooding height), but there is no intensity
> thresholding
>
> cheers
> Bruce
>
>
> On Wed, 16 Oct 2019, Inglese, Marianna
> wrote:
>
> >
> > External Email - Use Caution
> >
> > To whom it may concern,
> >
> > I am using recon-all to segment many T1s. As I can see, one of the
> automatic
> > step performed by recon-all is the skull stripping. Would it be possible
> to
> > know the threshold used for the stripping? I guess it is the same
> threshold
> > everytime. I would like to apply the skull stripping only on other T1s and
> > need to get the same result.
> >
> > Thank you very much for the help.
> >
> > Yours faithfully,
> >
> > Marianna Inglese
> >
> > Research fellow, Imperial College London
> > Department of Surgery and Cancer
> >
> >
> >
>
>
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Re: [Freesurfer] R: recon-all skull stripping

[Bruce Fischl]

Hi Marianna

I'm not sure what you mean by "replicate". The procedure should be the 
same for all inputs unless you change something explicitly


cheers
Bruce

On Wed, 16 Oct 2019, 
Inglese, Marianna wrote:




External Email - Use Caution

Thank you Bruce. 
I thought it was something similar to the FSL bet function, which extracts
the brain using a fractional intensity threshold (0.5 for example). 
So I guess I won't be able to replicate the same exact skull stripping of
freesurfer's recon-all.

BW
Marianna


Da: freesurfer-boun...@nmr.mgh.harvard.edu
 per conto di Bruce Fischl

Inviato: mercoledì 16 ottobre 2019 17:23
A: Freesurfer support list 
Oggetto: Re: [Freesurfer] recon-all skull stripping  
Hi Marianna

the skull stripping is a hybrid procedure that uses both a watershed
algorithm and a deformable surface. There is no single intensity threshold
in it. Maybe I'm misunderstanding your question? There are parameters you
can change (for example the preflooding height), but there is no intensity
thresholding

cheers
Bruce


On Wed, 16 Oct 2019, Inglese, Marianna
wrote:

>
> External Email - Use Caution
>
> To whom it may concern,
>
> I am using recon-all to segment many T1s. As I can see, one of the
automatic
> step performed by recon-all is the skull stripping. Would it be possible
to
> know the threshold used for the stripping? I guess it is the same
threshold
> everytime. I would like to apply the skull stripping only on other T1s and
> need to get the same result.
>
> Thank you very much for the help.
>
> Yours faithfully,
>
> Marianna Inglese
>
> Research fellow, Imperial College London
> Department of Surgery and Cancer
>
>
>

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[Freesurfer] R: recon-all skull stripping

[Inglese, Marianna]

External Email - Use Caution

Thank you Bruce.
I thought it was something similar to the FSL bet function, which extracts the 
brain using a fractional intensity threshold (0.5 for example).
So I guess I won't be able to replicate the same exact skull stripping of 
freesurfer's recon-all.

BW
Marianna

Da: freesurfer-boun...@nmr.mgh.harvard.edu 
 per conto di Bruce Fischl 

Inviato: mercoledì 16 ottobre 2019 17:23
A: Freesurfer support list 
Oggetto: Re: [Freesurfer] recon-all skull stripping

Hi Marianna

the skull stripping is a hybrid procedure that uses both a watershed
algorithm and a deformable surface. There is no single intensity threshold
in it. Maybe I'm misunderstanding your question? There are parameters you
can change (for example the preflooding height), but there is no intensity
thresholding

cheers
Bruce


On Wed, 16 Oct 2019, Inglese, Marianna
wrote:

>
> External Email - Use Caution
>
> To whom it may concern,
>
> I am using recon-all to segment many T1s. As I can see, one of the automatic
> step performed by recon-all is the skull stripping. Would it be possible to
> know the threshold used for the stripping? I guess it is the same threshold
> everytime. I would like to apply the skull stripping only on other T1s and
> need to get the same result.
>
> Thank you very much for the help.
>
> Yours faithfully,
>
> Marianna Inglese
>
> Research fellow, Imperial College London
> Department of Surgery and Cancer
>
>
>
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Re: [Freesurfer] recon-all skull stripping

[Bruce Fischl]

Hi Marianna

the skull stripping is a hybrid procedure that uses both a watershed 
algorithm and a deformable surface. There is no single intensity threshold 
in it. Maybe I'm misunderstanding your question? There are parameters you 
can change (for example the preflooding height), but there is no intensity 
thresholding


cheers
Bruce


On Wed, 16 Oct 2019, Inglese, Marianna 
wrote:




External Email - Use Caution

To whom it may concern,

I am using recon-all to segment many T1s. As I can see, one of the automatic
step performed by recon-all is the skull stripping. Would it be possible to
know the threshold used for the stripping? I guess it is the same threshold
everytime. I would like to apply the skull stripping only on other T1s and
need to get the same result.

Thank you very much for the help.

Yours faithfully,

Marianna Inglese

Research fellow, Imperial College London
Department of Surgery and Cancer


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[Freesurfer] recon-all skull stripping

[Inglese, Marianna]

External Email - Use Caution

To whom it may concern,

I am using recon-all to segment many T1s. As I can see, one of the automatic 
step performed by recon-all is the skull stripping. Would it be possible to 
know the threshold used for the stripping? I guess it is the same threshold 
everytime. I would like to apply the skull stripping only on other T1s and need 
to get the same result.

Thank you very much for the help.

Yours faithfully,

Marianna Inglese

Research fellow, Imperial College London
Department of Surgery and Cancer

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Re: [Freesurfer] imperfect segmentation in the occipital lobe in epilepsy patient

[Xiaoqian Yan]

External Email - Use Caution

Dear Bruce,

Thanks for the reply. I have uploaded my data through the Martinos Center
FileDrop, here is the link:
+ Data_Xiaoqian.zip (169.46 MiB) <
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=6wbctqzrzh1>

I explained my problems in that link, but still copy and past here:

'' I am having troubles doing a good segmentation in the right occipital
lobe in a patient's brain. There is a thermal lesion in that region, a
black whole, that could make the segmentations go wrong. I tried to edit
the wm, but the results were not ideal.

The thermal lesion can be clearly seen from the axial slices 108 - 115,
e.g. in RAS coordinate [40,-50,-4] on the axial slice 112. The bad
segmentation (wm and pial surface) can be seen from the coronal slices 54 -
62, e.g. in coordinate [42, -52, -10] on the coronal slice 57. The wrong
segmentation made it impossible to overlap the functional activations in
the OFA (occipital face area) region on the surface.

In my uploaded data directory, I already edited the wm and brainmask, and I
only reran 'recon-all -autorecon2-wm -subjid name' to save time. ''

Thanks in advance, and best wishes,

Xiaoqian





On Wed, 16 Oct 2019 at 15:07, Bruce Fischl 
wrote:

> Hi Xiaoqian
>
> it's pretty hard to tell what's going on from these images. If you
> tar/gzip
> your whole subject dir and upload it with an email telling us the specific
> voxel coords that you want us to examine
>
> cheers
> Bruce
>
>
> On Wed, 16 Oct 2019, Xiaoqian Yan wrote:
>
> >
> > External Email - Use Caution
> >
> > Dear Douglas,
> > Thanks for your reply. I double checked my results. It was true that the
> > rh.orig.nofix and rh.orig did not overlap over the region that I was
> > interested in. I re-edit the wm, and only ran 'recon-all -autorecon2-wm
> > -subjid patientname' to check the results, but the rh.orig.nofix and
> rh.orig
> > were still not overlapped. Do you mind helping me check my wm edits? For
> me,
> > the thermal lesion is a black hole that big enough to confuse the
> > segmentation. Maybe there is a way to mark that region or add a label,
> > before I run the recon-all?
> >
> > P.S. in the attached figures, pial is in green, rh.orig.nofix in red, and
> > rh.orig in yellow.
> >
> > Thanks and have a nice day,
> >
> > Xiaoqian
> >
> >
> >
> > On Fri, 11 Oct 2019 at 00:47, Greve, Douglas N.,Ph.D.
> >  wrote:
> >   I think that the wm edits should have worked. Can you load the
> >   rh.orig.nofix and rh.orig to see if they encompass your edits?
> >   If not, then maybe your did not re-run it properly.
> >
> >   On 10/8/2019 12:22 PM, Xiaoqian Yan wrote:
> >
> >   External Email - Use Caution
> >
> >   Dear Freesurfer experts,
> > I am trying to do the segmentation on a patient's T1 image. I
> > did not get error messages running the 'recon-all' (recon-all -i
> > T1.nii -subjid PatientName -all), but the segmentation over the
> > right occipital lobe was imperfect, which caused failures to map
> > the functional activations in this region onto the surface.
> >
> > I tried to manually edit the wm.mgz several times, but the
> > output did not change a lot (please see the attached image). The
> > patient had depth EEG electrodes implanted in this region
> > before, so there is a thermal lesion which I thought could have
> > caused the bad segmentation.  Do you have any ideas about what I
> > can do next, or it is possible for you to help me editing the
> > data?
> >
> > Thanks in advance, best wishes
> >
> > Xiaoqian
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >___
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[Freesurfer] Postdoc Position at UPenn

[Mackey, Allyson P]

External Email - Use Caution

Postdoctoral Fellowship in Pediatric Neuroimaging at the University of 
Pennsylvania

Drs. Allyson Mackey and Dylan Tisdall are seeking a postdoctoral fellow for an 
NIH-funded study on early childhood brain development. The goals of the study 
are to develop motion-resilient structural and functional MRI sequences, and to 
validate the new sequences in 100 children between the ages of 3 and 5. 
Children will be recruited from high-poverty, high-opioid use neighborhoods of 
Philadelphia. This study is part of the HEALthy Brain and Child Development 
(HBCD) 
planning initiative. Ultimately, HBCD will enroll pregnant mothers and follow 
children for at least 10 years, and will include data on children’s 
experiences, brain structure and function, and social, emotional, and cognitive 
development.

The postdoctoral fellow will join the Changing Brain 
Lab at the University of Pennsylvania, an 
interdisciplinary research group that studies how young children’s experiences 
change their brains. We are interested in the development of 
academically-relevant skills including reasoning, curiosity, creativity, and 
persistence. The CBL is part of a vibrant psychology and neuroscience community 
at Penn, and is affiliated with mindCORE, the 
Center for Neuroscience and Society, and the 
Positive Psychology Center. Imaging is conducted at 
the Center for Functional Neuroimaging, 
which includes research-dedicated 3T Siemens Prisma and 7T Siemens Terra 
scanners.

We welcome candidates with doctoral degrees in a wide variety of fields, 
including physics, engineering, statistics, neuroscience, and psychology. 
Applicants should have strong publication records, experience with pediatric 
neuroimaging, strong statistical training, and excellent computational skills.

To apply, please send a cover letter describing your doctoral research and your 
goals for postdoctoral training, as well as your CV to Allyson Mackey at 
mack...@upenn.edu. As the position involves 
collaborating with multiple advisors, graduate students, and research 
assistants, please provide contact information for someone who has mentored 
you, and for someone you have mentored.

Applications will be reviewed as they are received.The position is for one 
year, renewable for up to 3 years total. Ideal start date is on or before 
February 1st, 2020.

--
Allyson Mackey, Ph.D.
Assistant Professor
Department of Psychology
University of Pennsylvania
425 S. University Avenue
Levin Building, Room 354
Philadelphia, PA 19104
215-573-3074
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[Freesurfer] Group effect Contrast for 6 groups

[cody samth]

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Hi,

I'm designing an analysis that will have 6 groups (two factors/three
levels). I was wondering if I could get some input regarding my contrast
for the group effect. Based on the group effect contrast under the FSGD
examples for 3 groups I've written a five line contrast file that compares
group 1 against the other 5 groups.

1-1 0 0 0 0
1 0 -1 0 0 0
1 0 0 -1 0 0
1 0 0 0 -1 0
1 0 0 0 0 -1

Which from my understanding should cover the rest of the contrasts such as
2v5 3v6 and etc. Is my understanding of this correct?
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Re: [Freesurfer] imperfect segmentation in the occipital lobe in epilepsy patient

[Bruce Fischl]

Hi Xiaoqian

it's pretty hard to tell what's going on from these images. If you tar/gzip 
your whole subject dir and upload it with an email telling us the specific 
voxel coords that you want us to examine


cheers
Bruce


On Wed, 16 Oct 2019, Xiaoqian Yan wrote:



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Dear Douglas,
Thanks for your reply. I double checked my results. It was true that the
rh.orig.nofix and rh.orig did not overlap over the region that I was
interested in. I re-edit the wm, and only ran 'recon-all -autorecon2-wm
-subjid patientname' to check the results, but the rh.orig.nofix and rh.orig
were still not overlapped. Do you mind helping me check my wm edits? For me,
the thermal lesion is a black hole that big enough to confuse the
segmentation. Maybe there is a way to mark that region or add a label,
before I run the recon-all?

P.S. in the attached figures, pial is in green, rh.orig.nofix in red, and
rh.orig in yellow.

Thanks and have a nice day,

Xiaoqian



On Fri, 11 Oct 2019 at 00:47, Greve, Douglas N.,Ph.D.
 wrote:
  I think that the wm edits should have worked. Can you load the
  rh.orig.nofix and rh.orig to see if they encompass your edits?
  If not, then maybe your did not re-run it properly.

  On 10/8/2019 12:22 PM, Xiaoqian Yan wrote:

  External Email - Use Caution

  Dear Freesurfer experts,
I am trying to do the segmentation on a patient's T1 image. I
did not get error messages running the 'recon-all' (recon-all -i
T1.nii -subjid PatientName -all), but the segmentation over the
right occipital lobe was imperfect, which caused failures to map
the functional activations in this region onto the surface. 

I tried to manually edit the wm.mgz several times, but the
output did not change a lot (please see the attached image). The
patient had depth EEG electrodes implanted in this region
before, so there is a thermal lesion which I thought could have
caused the bad segmentation.  Do you have any ideas about what I
can do next, or it is possible for you to help me editing the
data?

Thanks in advance, best wishes

Xiaoqian

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Re: [Freesurfer] FS-FAST: cluster size from 1st level analysis

[Keri Woods]

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Thanks.

On Tue, Oct 15, 2019 at 5:00 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> Correct
>
> On 10/15/2019 9:38 AM, Keri Woods wrote:
>
> External Email - Use Caution
> Hi Doug
>
> Thank you very much for the very helpful reply! It worked perfectly and
> was exactly what I needed. I assume that these are the clusters after
> cluster-level correction for multiple comparison since --csd is used?
>
> Thanks,
> Keri
>
> On Tue, Oct 15, 2019 at 4:17 AM Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> Sorry for the delay ...
>>
>> First, run selxavg3-sess with -fwhm ( you might need to delete the
>> bold/analysis folder to get it to re-run).
>>
>> cd session/bold/analyis
>> There will be a filed called fwhm.dat. Look in that. Depending upon how
>> much you smoothed it might be something like 10.395. This is the FWHM in
>> mm. Next, you can run something like the following command
>>
>> mri_surfcluster --in contrast/sig.nii.gz --hemi lh --csd
>> $FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/cortex/fwhmXX/abs/thTT/mc-z.cdf
>> --mask mask.nii.gz --sum contrast.sum.dat --oannot ./lh.contrast.annot
>> --thmin T --sign abs --subject fsaverage --cwpvalthresh .05
>>
>> Note that the subject must be fsaverage because the tables were computed
>> with fsaverage. Above, fwhmXX would be fwhm11 (because the FWHM is 10.395,
>> but round up to 11). TT refers to the cluster forming threshold (eg, p<.001
>> would be 30), and so --thmin T would be 3. "abs" in the path to the CSD
>> file indicates that you want to use an unsigned (absolute) value; you can
>> also use pos and neg. --cwpvalthresh .05 means to filter out any clusters
>> that are not significant at p=0.05. The cluster table will be in
>> contrast.sum.dat
>>
>> doug
>>
>>
>> On 10/3/2019 7:52 AM, Keri Woods wrote:
>>
>> External Email - Use Caution
>> Hi
>>
>> From the 1st level analysis of an fMRI study I'm trying to extract the
>> size of the clusters of activation from each subject, but don't know how to
>> go about this. I know that for the group analysis you can get the cluster
>> sizes from the output from mri_glm-sim. Is there a way to run the multiple
>> comparison correction on the first level analysis in order to get this
>> table? Or is there another way of getting the cluster sizes?
>>
>> Any help would be much appreciated.
>>
>> Thank you,
>> Keri
>>
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