Re: [Freesurfer] T2pial correction options

[Adam Martersteck]

External Email - Use Caution

Re-posting to see if anyone has had this problem before and solutions
they've implemented.


> Hi Freesurfer team,
>
> We’re having some trouble with the T2pial option. We are currently getting
> the Martinos Center ABCD project Tisdall/van der Kouwe vNav MPRAGE and
> T2SPACE at 0.8mm^3, bandwidth matched for distortion.
>
> Linked below are 2 gifs were we have found areas we thought the T2 and
> –T2pial option would help differentiate brain from non-brain:
> https://goo.gl/dc9pjj
> https://goo.gl/AsCCbA
>
> I’ve read the discussion by Bruce, Matt, and Antonin about altering the
> final lh/rh mris_make_surface command with the T2. Has anyone found more
> optimal numbers for the nsigma_above and nsigma_below arguments?
>
> Is there anything else I could try to get this working better?
>
> Thanks!
> -Adam
>
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Re: [Freesurfer] Troubles to determine the type of recon editing needed

[Matthieu Vanhoutte]

External Email - Use Caution

Ok I will test it on normal subjects.

Do I have to put this -bigventricles flag on all recon-all commands
following manual editing of brainmask, white matter,...etc or just once at
the first recon-all -all command ?

Best,
Matthieu

Le mar. 18 sept. 2018 à 18:03, Bruce Fischl  a
écrit :

> I think it should be ok. It will be a bit slower, but shouldn't reduce
> accuracy I don't think. Try it and see
> Bruce
> On Tue, 18 Sep 2018, Matthieu
> Vanhoutte wrote:
>
> >
> > External Email - Use Caution
> >
> > Hi Bruce,
> >
> > Thanks, but in this case will recon-all with -bigventricles flag work
> well on normal patients
> > without big ventricles ?
> >
> > Best,
> > Matthieu
> >
> > 2018-09-18 15:56 GMT+00:00 Bruce Fischl :
> >   Hi Matthieu
> >
> >   yes, you will want to run all of your subjects with it
> >
> >   cheers
> >   Bruce
> >   On Tue, 18 Sep 2018, Matthieu Vanhoutte wrote:
> >
> >
> > External Email - Use Caution
> >
> > Dear Bram,
> >
> > It looks like the -bigventricles flag fixed my problem with
> my specific
> > subject. Not only, this took
> > into account large ventricles but also corrected grey matter
> segmentation
> > from extra Dura tissue
> > that was erroneously segmented in GM.
> >
> > I understand the first point of amelioration allowed by the
> flag but don't
> > understand where the
> > second point come from ?
> >
> > If I used the -bigventricles flag for all my atrophied and
> large ventricles
> > patients and not for my
> > healthy patients, wouldn't it introduce a bias when further
> statistically
> > comparing groups between
> > them ?
> >
> > Best,
> > Matthieu
> >
> > 2018-09-14 15:35 GMT+00:00 Diamond, Bram Ryder <
> brdiam...@mgh.harvard.edu>:
> >   If you haven't already, you may want to run the
> subject through
> > recon-all with the
> >   -bigventricles flag since it looks like the
> lateral ventricle was
> > significantly
> >   mislabeled in the aseg. If using the -bigventricles
> flag doesn't fix
> > your problem, you
> >   can edit the aseg.mgz manually by following the
> directions in this
> > tutorial. Then run
> >   the following command (again, substituting 
> for your
> > subject's id):
> > recon-all -autorecon2-noaseg -autorecon3 -subjid 
> >
> > I would try this before doing the wm.mgz edits I suggested
> in my previous
> > email.
> >
> > Best,
> > Bram
> >
> >
> ___
> > _
> > From: freesurfer-boun...@nmr.mgh.harvard.edu
> >  on
> > behalf of Diamond, Bram Ryder 
> > Sent: Friday, September 14, 2018 11:07:42 AM
> > To: matthieuvanhou...@gmail.com
> > Cc: freesurfer@nmr.mgh.harvard.edu;
> astev...@nmr.mgh.harvard.edu
> > Subject: [Freesurfer] Troubles to determine the type of
> recon editing needed
> >
> >
> > Hi Matthieu,
> >
> >
> > I've taken a look through the files you shared with us and I
> see the poor
> > surfaces in the
> > posterior right hemisphere you were referring to in your
> message. It looks
> > like your subject
> > has a combination of abnormally large ventricles and
> significant wm
> > abnormalities, so I'm
> > surprised FreeSurfer did as well as it did.
> >
> >
> > As for the recon editing - I would recommend editing the
> wm.mgz to more
> > accurately represent
> > the wm from slice 84 to 39. You can take a look at the white
> matter edits
> > tutorial for details
> > on how to do that. Then run the following command
> (substituting 
> > for your
> > subject's id):
> >
> >
> > recon-all -autorecon2-wm -autorecon3 -subjid 
> >
> >
> > The surface reconstruction may also benefit from labeling
> the right lateral
> > ventricle in the
> > wm.mgz (as an intensity of 250) - but I'm not certain since
> you didn't send
> > us the surfaces
> > for the left hemisphere. Before you do that, edit the wm.mgz
> as explained in
> > the tutorial and
> > tell us how that goes.
> >
> >
> > All the best,
> >
> > Bram
> >
> >
> > Bram R. Diamond, BSc
> > Research Technician II
> > Laboratory for Computational Neuroimaging
> > Martinos 

Re: [Freesurfer] Troubles to determine the type of recon editing needed

[Bruce Fischl]

I think it should be ok. It will be a bit slower, but shouldn't reduce 
accuracy I don't think. Try it and see

Bruce
On Tue, 18 Sep 2018, Matthieu 
Vanhoutte wrote:




External Email - Use Caution

Hi Bruce,

Thanks, but in this case will recon-all with -bigventricles flag work well on 
normal patients
without big ventricles ?

Best,
Matthieu

2018-09-18 15:56 GMT+00:00 Bruce Fischl :
  Hi Matthieu

  yes, you will want to run all of your subjects with it

  cheers
  Bruce
  On Tue, 18 Sep 2018, Matthieu Vanhoutte wrote:


External Email - Use Caution

Dear Bram,

It looks like the -bigventricles flag fixed my problem with my 
specific
subject. Not only, this took
into account large ventricles but also corrected grey matter 
segmentation
from extra Dura tissue
that was erroneously segmented in GM.

I understand the first point of amelioration allowed by the flag 
but don't
understand where the
second point come from ?

If I used the -bigventricles flag for all my atrophied and large 
ventricles
patients and not for my
healthy patients, wouldn't it introduce a bias when further 
statistically
comparing groups between
them ?

Best,
Matthieu

2018-09-14 15:35 GMT+00:00 Diamond, Bram Ryder 
:
      If you haven't already, you may want to run the subject 
through
recon-all with the
      -bigventricles flag since it looks like the lateral ventricle 
was
significantly
      mislabeled in the aseg. If using the -bigventricles flag 
doesn't fix
your problem, you
      can edit the aseg.mgz manually by following the directions in 
this
tutorial. Then run
      the following command (again, substituting  for your
subject's id):
recon-all -autorecon2-noaseg -autorecon3 -subjid 

I would try this before doing the wm.mgz edits I suggested in my 
previous
email.

Best,
Bram

___
_
From: freesurfer-boun...@nmr.mgh.harvard.edu
 on
behalf of Diamond, Bram Ryder 
Sent: Friday, September 14, 2018 11:07:42 AM
To: matthieuvanhou...@gmail.com
Cc: freesurfer@nmr.mgh.harvard.edu; astev...@nmr.mgh.harvard.edu
Subject: [Freesurfer] Troubles to determine the type of recon 
editing needed
 

Hi Matthieu,


I've taken a look through the files you shared with us and I see 
the poor
surfaces in the
posterior right hemisphere you were referring to in your message. 
It looks
like your subject
has a combination of abnormally large ventricles and significant wm
abnormalities, so I'm
surprised FreeSurfer did as well as it did.


As for the recon editing - I would recommend editing the wm.mgz to 
more
accurately represent
the wm from slice 84 to 39. You can take a look at the white matter 
edits
tutorial for details
on how to do that. Then run the following command (substituting 

for your
subject's id):


recon-all -autorecon2-wm -autorecon3 -subjid 


The surface reconstruction may also benefit from labeling the right 
lateral
ventricle in the
wm.mgz (as an intensity of 250) - but I'm not certain since you 
didn't send
us the surfaces
for the left hemisphere. Before you do that, edit the wm.mgz as 
explained in
the tutorial and
tell us how that goes.


All the best,

Bram


Bram R. Diamond, BSc
Research Technician II
Laboratory for Computational Neuroimaging
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street 
Charlestown, MA 02129
(p): 617-726-6598

The information in this e-mail is intended only for the person to 
whom it is
addressed. If you believe this e-mail was sent to you in error and 
the
e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to 
you in
error
but does not contain patient information, please contact the sender 
and
properly
dispose of the e-mail.




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Re: [Freesurfer] Troubles to determine the type of recon editing needed

[Matthieu Vanhoutte]

External Email - Use Caution

Hi Bruce,

Thanks, but in this case will recon-all with -bigventricles flag work well
on normal patients without big ventricles ?

Best,
Matthieu

2018-09-18 15:56 GMT+00:00 Bruce Fischl :

> Hi Matthieu
>
> yes, you will want to run all of your subjects with it
>
> cheers
> Bruce
> On Tue, 18 Sep 2018, Matthieu Vanhoutte wrote:
>
>
>> External Email - Use Caution
>>
>> Dear Bram,
>>
>> It looks like the -bigventricles flag fixed my problem with my specific
>> subject. Not only, this took
>> into account large ventricles but also corrected grey matter segmentation
>> from extra Dura tissue
>> that was erroneously segmented in GM.
>>
>> I understand the first point of amelioration allowed by the flag but
>> don't understand where the
>> second point come from ?
>>
>> If I used the -bigventricles flag for all my atrophied and large
>> ventricles patients and not for my
>> healthy patients, wouldn't it introduce a bias when further statistically
>> comparing groups between
>> them ?
>>
>> Best,
>> Matthieu
>>
>> 2018-09-14 15:35 GMT+00:00 Diamond, Bram Ryder > >:
>>   If you haven't already, you may want to run the subject through
>> recon-all with the
>>   -bigventricles flag since it looks like the lateral ventricle was
>> significantly
>>   mislabeled in the aseg. If using the -bigventricles flag doesn't
>> fix your problem, you
>>   can edit the aseg.mgz manually by following the directions in this
>> tutorial. Then run
>>   the following command (again, substituting  for your
>> subject's id):
>> recon-all -autorecon2-noaseg -autorecon3 -subjid 
>>
>> I would try this before doing the wm.mgz edits I suggested in my previous
>> email.
>>
>> Best,
>> Bram
>>
>> 
>> 
>>
>> From: freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> on
>> behalf of Diamond, Bram Ryder 
>> Sent: Friday, September 14, 2018 11:07:42 AM
>> To: matthieuvanhou...@gmail.com
>> Cc: freesurfer@nmr.mgh.harvard.edu; astev...@nmr.mgh.harvard.edu
>> Subject: [Freesurfer] Troubles to determine the type of recon editing
>> needed
>>
>> Hi Matthieu,
>>
>>
>> I've taken a look through the files you shared with us and I see the poor
>> surfaces in the
>> posterior right hemisphere you were referring to in your message. It
>> looks like your subject
>> has a combination of abnormally large ventricles and significant wm
>> abnormalities, so I'm
>> surprised FreeSurfer did as well as it did.
>>
>>
>> As for the recon editing - I would recommend editing the wm.mgz to more
>> accurately represent
>> the wm from slice 84 to 39. You can take a look at the white matter edits
>> tutorial for details
>> on how to do that. Then run the following command (substituting 
>> for your
>> subject's id):
>>
>>
>> recon-all -autorecon2-wm -autorecon3 -subjid 
>>
>>
>> The surface reconstruction may also benefit from labeling the right
>> lateral ventricle in the
>> wm.mgz (as an intensity of 250) - but I'm not certain since you didn't
>> send us the surfaces
>> for the left hemisphere. Before you do that, edit the wm.mgz as explained
>> in the tutorial and
>> tell us how that goes.
>>
>>
>> All the best,
>>
>> Bram
>>
>>
>> Bram R. Diamond, BSc
>> Research Technician II
>> Laboratory for Computational Neuroimaging
>> Martinos Center for Biomedical Imaging
>> Massachusetts General Hospital
>> 149 13th Street
>> Charlestown, MA 02129
>> (p): 617-726-6598
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>>
>>
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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Re: [Freesurfer] Troubles to determine the type of recon editing needed

[Bruce Fischl]

Hi Matthieu

yes, you will want to run all of your subjects with it

cheers
Bruce
On Tue, 18 Sep 2018, 
Matthieu Vanhoutte wrote:




External Email - Use Caution

Dear Bram,

It looks like the -bigventricles flag fixed my problem with my specific 
subject. Not only, this took
into account large ventricles but also corrected grey matter segmentation from 
extra Dura tissue
that was erroneously segmented in GM.

I understand the first point of amelioration allowed by the flag but don't 
understand where the
second point come from ?

If I used the -bigventricles flag for all my atrophied and large ventricles 
patients and not for my
healthy patients, wouldn't it introduce a bias when further statistically 
comparing groups between
them ?

Best,
Matthieu

2018-09-14 15:35 GMT+00:00 Diamond, Bram Ryder :
  If you haven't already, you may want to run the subject through recon-all 
with the
  -bigventricles flag since it looks like the lateral ventricle was 
significantly
  mislabeled in the aseg. If using the -bigventricles flag doesn't fix your 
problem, you
  can edit the aseg.mgz manually by following the directions in this 
tutorial. Then run
  the following command (again, substituting  for your subject's 
id):
recon-all -autorecon2-noaseg -autorecon3 -subjid 

I would try this before doing the wm.mgz edits I suggested in my previous email.

Best,
Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on
behalf of Diamond, Bram Ryder 
Sent: Friday, September 14, 2018 11:07:42 AM
To: matthieuvanhou...@gmail.com
Cc: freesurfer@nmr.mgh.harvard.edu; astev...@nmr.mgh.harvard.edu
Subject: [Freesurfer] Troubles to determine the type of recon editing needed  

Hi Matthieu,


I've taken a look through the files you shared with us and I see the poor 
surfaces in the
posterior right hemisphere you were referring to in your message. It looks like 
your subject
has a combination of abnormally large ventricles and significant wm 
abnormalities, so I'm
surprised FreeSurfer did as well as it did.


As for the recon editing - I would recommend editing the wm.mgz to more 
accurately represent
the wm from slice 84 to 39. You can take a look at the white matter edits 
tutorial for details
on how to do that. Then run the following command (substituting  for 
your
subject's id):


recon-all -autorecon2-wm -autorecon3 -subjid 


The surface reconstruction may also benefit from labeling the right lateral 
ventricle in the
wm.mgz (as an intensity of 250) - but I'm not certain since you didn't send us 
the surfaces
for the left hemisphere. Before you do that, edit the wm.mgz as explained in 
the tutorial and
tell us how that goes.


All the best,

Bram


Bram R. Diamond, BSc
Research Technician II
Laboratory for Computational Neuroimaging
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street 
Charlestown, MA 02129
(p): 617-726-6598

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.



___
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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] Troubles to determine the type of recon editing needed

[Matthieu Vanhoutte]

External Email - Use Caution

Dear Bram,

It looks like the -bigventricles flag fixed my problem with my specific
subject. Not only, this took into account large ventricles but also
corrected grey matter segmentation from extra Dura tissue that was
erroneously segmented in GM.

I understand the first point of amelioration allowed by the flag but don't
understand where the second point come from ?

If I used the -bigventricles flag for all my atrophied and large ventricles
patients and not for my healthy patients, wouldn't it introduce a bias when
further statistically comparing groups between them ?

Best,
Matthieu

2018-09-14 15:35 GMT+00:00 Diamond, Bram Ryder :

> If you haven't already, you may want to run the subject through recon-all
> with the -bigventricles flag since it looks like the lateral ventricle was
> significantly mislabeled in the aseg. If using the -bigventricles flag
> doesn't fix your problem, you can edit the aseg.mgz manually by following
> the directions in this tutorial
> .
> Then run the following command (again, substituting  for your
> subject's id):
>
> recon-all -autorecon2-noaseg -autorecon3 -subjid 
>
> I would try this before doing the wm.mgz edits I suggested in my previous
> email.
>
> Best,
> Bram
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Diamond, Bram Ryder <
> brdiam...@mgh.harvard.edu>
> *Sent:* Friday, September 14, 2018 11:07:42 AM
> *To:* matthieuvanhou...@gmail.com
> *Cc:* freesurfer@nmr.mgh.harvard.edu; astev...@nmr.mgh.harvard.edu
> *Subject:* [Freesurfer] Troubles to determine the type of recon editing
> needed
>
>
> Hi Matthieu,
>
>
> I've taken a look through the files you shared with us and I see the poor
> surfaces in the posterior right hemisphere you were referring to in your
> message. It looks like your subject has a combination of abnormally large
> ventricles and significant wm abnormalities, so I'm surprised FreeSurfer
> did as well as it did.
>
>
> As for the recon editing - I would recommend editing the wm.mgz to more
> accurately represent the wm from slice 84 to 39. You can take a look at the 
> white
> matter edits tutorial
> 
> for details on how to do that. Then run the following command (substituting
>  for your subject's id):
>
>
> recon-all -autorecon2-wm -autorecon3 -subjid 
>
>
> The surface reconstruction may also benefit from labeling the right
> lateral ventricle in the wm.mgz (as an intensity of 250) - but I'm not
> certain since you didn't send us the surfaces for the left hemisphere.
> Before you do that, edit the wm.mgz as explained in the tutorial and tell
> us how that goes.
>
>
> All the best,
>
> Bram
>
>
> *Bram R. Diamond, BSc*
> Research Technician II
> Laboratory for Computational Neuroimaging
> Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
> 149 13th Street
> 
>
> Charlestown, MA 02129
> 
> (p): 617-726-6598
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] mris_register problem

[Bruce Fischl]

how much? Maybe we should expand the default range? I thought it was 
already pretty broad, but I haven't looked at it in a long time

Glad to hear it worked out
cheers
Bruce
On Tue, 18 
Sep 2018, Chris Adamson wrote:




External Email - Use Caution

Thanks Bruce.

 

I had to increase the angular search range in the affine part to get it to work.

 

Cheers,

 

Chris.

 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of
Bruce Fischl
Sent: Monday, 17 September 2018 11:49 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] mris_register problem

 

Hi Chris

you need to give us more information. What commands did you run? What was
their output? Also, if you can send images of what you think is incorrect
that might also be helpful

cheers
Bruce
On Mon, 17 Sep 2018, Chris Adamson wrote:

>
> External Email - Use Caution
>
> Freesurfer experts,
>
>  
>
> I’m having an issue with projecting labels from an atlas to a subject. I have 
a static annot file
on
> the atlas that I want to paint onto my subject. The pipeline I have performed 
is to mris_register
my
> subject to the atlas and then mri_surf2surf on the annot file using the 
registered spherical
> surfaces.
>
>  
>
> The labels, when painted, are incorrectly oriented. How can I debug the 
output of the registration
> to check if the registration is working? I assume the registration works in 
the 2D parameterised
> space, can I extract parameterised versions of the curvature maps at each 
iteration of the
> registration.
>
>  
>
> The strange thing is that when I view the spherical surfaces in freeview with 
the overlaid
curvature
> maps they look in alignment prior to registration, but using this 
unregistered sphere still puts
the
> labels in an incorrect orientation. So it appears as if there is some 
rotation that is being done
> internally that isn’t shown in freeview.
>
>  
>
> Please advise,
>
>  
>
> Chris.
>
>  
>
> Dr Chris Adamson
>
> Senior Research Officer
>
> Developmental Imaging, Clinical Sciences
>
>  
>
> Murdoch Childrens Research Institute
>
> The Royal Children’s Hospital
>
> Flemington Road, Parkville, VIC 3052 Australia
>
> E chris.adam...@mcri.edu.au 
>
> www.mcri.edu.au
>
>  
>
>  
>
> This e-mail and any attachments to it (the "Communication") are, unless 
otherwise stated,
> confidential, may contain copyright material and is for the use only of the 
intended recipient. If
> you receive the Communication in error, please notify the sender immediately 
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> delete the Communication and the return e-mail, and do not read, copy, 
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Re: [Freesurfer] How the resolution requirement was determined

[Bruce Fischl]

Hi Jo

the resolution requiirement is determined by cortical geometry. Once you 
get to about 2mm, you can no longer resolve the cortex in many places, 
and even worse you start losing the ability to resolve adjacent banks of 
a sulcus, resulting in topological catastrophes in the resulting models. 
The aseg probably works ok if that is all you are interested in, but you 
won't get good surfaces out of 7mm data


cheers
Bruce

On Tue, 18 
Sep 2018, 조성현 wrote:




External Email - Use Caution

Hello Freesurfer developers and subscribers,
I'm attempting to run brain segmentation with low resolution mri(thickness ~= 
7mm) for EEG analysis.
I know that this is very low resolution to get good quality results. However, I 
think the low
quality result is not meaningless in specific cases.

Therefore, I wonder if there is a tool to evaluate how low quality results are. 
In the 'freesurfer
beginners guide', it says 'Thickness should not exceed 1.5mm'.  How the 
resolution requirement was
determined? How did you know that the input of 1mm ^ 3 resolution is sufficient 
requirement? If I
use 2mm^3 resolution input, what kind of result will I get?

It may be a little dumb, but I do not have an answer of this question. I would 
appreciate your
reply.

Thanks,
Jo

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Re: [Freesurfer] Questions on multiple inputs

[Greve, Douglas N.,Ph.D.]

Most of FS/recon-all will run using the T1 only. The T2 can be used to refine 
the pial surface (-T2  T2file.mgz -T2pial)


On 9/18/18 4:56 AM, limiyu wrote:

External Email - Use Caution

Dear developers

I have a question on how could I segment two registered MRI images and 
get only one segmentation result, by command recon-all ?

In details, I have two MRI images which are T1-weighted and 
T2-weighted. They are the photos of one brain. How could I input both of them 
into Freesufer and output one segmentation result, which takes both of the 
input into consideration.
I know that command "recon-all -all" could output the segmentation but 
do not know what to do when there are multiple inputs.

Looking forward to your reply
Thank you
Mingyuan Liu








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[Freesurfer] 1-year position for an engineer to work in Parkinson, in the frontiers of imaging and machine learning (Bilbao, Spain)

[Iñigo Gabilondo]

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We are looking for an Engineer with skills in computer vision, programming
and machine learning to collaborate in the research project entitled:
"Study of the retina and the visual pathway by neuroimaging in genetic and
aggressive idiopathic synucleinopathies as a model to identify phenotypes
and prognostic biomarkers in idiopathic Parkinson's disease" (Principal
Investigator: Iñigo Gabilondo, MD, PhD) led by the Neurodegenerative
Diseases Group.The data to analyse are multimodal and longitudinal,
with a sample size bigger than N=100 and consisting in retina OCT, magnetic
resonance imaging (structural, functional, tensor  tensor and
spectroscopy), neuropsychology and clinical scales.

The engineer also will work in close collaboration with the Computational
Neuroimaging Group, led by Prof. Jesus M Cortes.

For further information about the groups, visit:
https://biocrucesbizkaia.org/web/biocruces/bc5.01 and
https://biocrucesbizkaia.org/bc5.08

Requirements:
- Bachelor of Engineering
- Good academic marks (average score higher than 7 over 10)
- Experience in computer vision, programming (Matlab, Python and / or R),
machine learning and other artificial intelligence techniques
- Experience with the magnetic resonance imaging analysis packages SPM, FSL
and Freesurfer
- Advanced English level (demonstrable with official degree - C1)
- Intention to develop a PhD in Biomedicine. The contract is for 1 year,
but exists the possibility to extend it to finalize the PhD

  Working conditions:
- Duration: 12 months (extendable)
- Full working day (100%) (1592 annual hours)
- Estimated annual gross salary: 23,004 euros per year
- Expected start date: As soon as possible

 Interested candidates send 2 reference letters and updated CV to
igabi...@gmail.com and/or jesus.m.cor...@gmail.com

*Gurutzetako Unibertsitate Ospitalea /*

*Hospital Universitario Cruces*

*Plaza de Cruces 12 *

*48903 – Barakaldo (Bizkaia)*


*Iñigo Gabilondo Cuellar, MD PhD*
Neurodegenerative Diseases Group


*+34 946006000 <%2B34%20946006000> ext. 7970*


igabi...@gmail.com

inigo.gabilondocuel...@osakidetza.eus
*biocrucesbizkaia.org/web/biocruces/bc5.01
*
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[Freesurfer] Questions on multiple inputs

[limiyu]

External Email - Use Caution

Dear developers

I have a question on how could I segment two registered MRI images and 
get only one segmentation result, by command recon-all ? 


In details, I have two MRI images which are T1-weighted and 
T2-weighted. They are the photos of one brain. How could I input both of them 
into Freesufer and output one segmentation result, which takes both of the 
input into consideration.
I know that command "recon-all -all" could output the segmentation but 
do not know what to do when there are multiple inputs.


Looking forward to your reply 
Thank you
Mingyuan Liu

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Re: [Freesurfer] trac-all using nifti

[Yendiki, Anastasia]

Hi Heidi - The config file that you sent looked fine to me. What is the 
trac-all command line that you run, and do you get any other output (like a 
trac-all.log file)?


Best,

a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Heidi Emmanuel Foo 

Sent: Monday, September 17, 2018 11:03:47 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] trac-all using nifti


External Email - Use Caution

Hi Anastasia,

It seems like I do. Could the problem be the config.txt?

Thanks!

Best Regards,
Heidi Foo

On Tue, Sep 18, 2018 at 12:47 AM Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Heidi – Do you have write permission to create the output directory 
/data_int/heidi/forHeidi/Preprocessed?

a.y

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Heidi Emmanuel Foo 
mailto:heidifo...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Monday, September 17, 2018 at 12:55 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] trac-all using nifti


External Email - Use Caution

Hi Anastasia,

I am currently trying to run trac-all with my DWI data. I do not have the DICOM 
but only the Nifti files and I would like to use the same bval and bvec 
template for every subject. I created a configiration file as attached. 
However, I have the following error message:

: Command not found.
: Command not found.
set: Variable name must begin with a letter.
does not exist.DIR /data_int/heidi/forHeidi/Preprocessed

It would be great if you could advise me on what to do.

Thank you!

Best Regards,
Heidi Foo


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