Re: [Freesurfer] registering to fsaverage

[Trisanna Sprung-Much]

Hi Doug

My apologies for the delay - I just returned from vacation.

Ok, so when I take a volumetric spam created using minc tools and create an
overlay from it using mri_vol2surf, the min and max seems to be between 1
and 255. I am wondering if there is any where to change this into a %? When
I open the spam using a minc software, for instance, it shows me the %.

best

Trisanna

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


On Wed, Jul 6, 2016 at 1:28 PM, Douglas N Greve 
wrote:

> Trisanna, has this issue been resolved?
> doug
>
> On 06/30/2016 01:26 PM, Trisanna Sprung-Much wrote:
> > Hi Bruce
> >
> > here is the output of my mri_vol2surf for a volumetric spam created in
> > minc tools. When I then overlay this result in Freeview, it displays a
> > Min of 127 and a Max of 255.
> >
> > trisanna@kaplan:~$ mri_vol2surf --mov
> >
> /data-01/trisanna/freesurfer/MNI_average_2009a_asymm/spam_for_label_id_4_blur_minc1.mnc
> > --o
> >
> /data-01/trisanna/freesurfer/MNI_average_2009a_asymm/spam_for_label_id_4_blur_overlay.mgz
> > --hemi lh --surf pial --regheader MNI_average_2009a_asymm
> > srcvol =
> >
> /data-01/trisanna/freesurfer/MNI_average_2009a_asymm/spam_for_label_id_4_blur_minc1.mnc
> > srcreg unspecified
> > srcregold = 0
> > srcwarp unspecified
> > surf = pial
> > hemi = lh
> > reshape = 0
> > interp = nearest
> > float2int = round
> > GetProjMax = 0
> > INFO: float2int code = 0
> > INFO: changing type to float
> > Done loading volume
> > Computing registration from header.
> >   Using
> > /data-01/trisanna/freesurfer/MNI_average_2009a_asymm/mri/orig.mgz as
> > target reference.
> > Reading surface
> > /data-01/trisanna/freesurfer/MNI_average_2009a_asymm/surf/lh.pial
> > Done reading source surface
> > Mapping Source Volume onto Source Subject Surface
> >  1 0 0 0
> > using old
> > Done mapping volume to surface
> > Number of source voxels hit = 95521
> > Writing to
> >
> /data-01/trisanna/freesurfer/MNI_average_2009a_asymm/spam_for_label_id_4_blur_overlay.mgz
> > Dim: 152257 1 1
> >
> >
> > --
> > Ph.D. Candidate
> > McGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> > On Wed, Jun 29, 2016 at 8:10 PM, Bruce Fischl
> > > wrote:
> >
> > Can you send the full output of that command?
> >
> > On Jun 29, 2016, at 2:54 PM, Trisanna Sprung-Much
> >  > > wrote:
> >
> >> Hi Bruce
> >>
> >> I simply use
> >>
> >> mri_vol2surf --mov spam.mnc --output overlayspam.mgz --regheader
> >> subject --hemi lh --surf pial
> >>
> >> Trisanna
> >>
> >> --
> >> Ph.D. Candidate
> >> McGill University
> >> Integrated Program in Neuroscience
> >> Psychology
> >>
> >>
> >> On Wed, Jun 29, 2016 at 1:23 PM, Bruce Fischl
> >> >
> >> wrote:
> >>
> >> how do you create the overlay?
> >> On Wed, 29 Jun 2016, Trisanna Sprung-Much wrote:
> >>
> >> Hi Bruce
> >>
> >> To create the spam I used minctools:
> >>
> >>  mincaverage  input.mnc output.mnc
> >>
> >> I blurred the spam using
> >>
> >> mincblur input.mnc output.mnc -fwhm 3
> >>
> >> When I open the spams using minc software, the % shown is
> >> from about 10-40%
> >> (i.e. the max overlap). For some reason when I create an
> >> overlay from this
> >> it displays the % from 1-255.
> >>
> >> Trisanna
> >>
> >> --
> >> Ph.D. CandidateMcGill University
> >> Integrated Program in Neuroscience
> >> Psychology
> >>
> >>
> >> On Wed, Jun 29, 2016 at 12:20 PM, Bruce Fischl
> >>  >> >
> >> wrote:
> >>   Hi Trisanna
> >>
> >>   what commands did you use to generate the
> >> volumetric probability
> >>   map?
> >>
> >>   Bruce
> >>
> >>
> >>
> >>   On Wed, 29 Jun 2016, Trisanna Sprung-Much wrote:
> >>
> >> Hi Bruce
> >> So, when I take a probability map formed using
> >> linear volumetric
> >> registration with minc tools and saved as
> >> .mnc and
> >> convert it to an
> >> overlay.mgz and open it in Freeview, the
> >> probability
> >> seems to be out of 255
> >> (See the image attached). This is different
> >> from my
> >> Freesurfer generated
> >> probability 

Re: [Freesurfer] registering to fsaverage

[Douglas N Greve]

Trisanna, has this issue been resolved?
doug

On 06/30/2016 01:26 PM, Trisanna Sprung-Much wrote:
> Hi Bruce
>
> here is the output of my mri_vol2surf for a volumetric spam created in 
> minc tools. When I then overlay this result in Freeview, it displays a 
> Min of 127 and a Max of 255.
>
> trisanna@kaplan:~$ mri_vol2surf --mov 
> /data-01/trisanna/freesurfer/MNI_average_2009a_asymm/spam_for_label_id_4_blur_minc1.mnc
>  
> --o 
> /data-01/trisanna/freesurfer/MNI_average_2009a_asymm/spam_for_label_id_4_blur_overlay.mgz
>  
> --hemi lh --surf pial --regheader MNI_average_2009a_asymm
> srcvol = 
> /data-01/trisanna/freesurfer/MNI_average_2009a_asymm/spam_for_label_id_4_blur_minc1.mnc
> srcreg unspecified
> srcregold = 0
> srcwarp unspecified
> surf = pial
> hemi = lh
> reshape = 0
> interp = nearest
> float2int = round
> GetProjMax = 0
> INFO: float2int code = 0
> INFO: changing type to float
> Done loading volume
> Computing registration from header.
>   Using 
> /data-01/trisanna/freesurfer/MNI_average_2009a_asymm/mri/orig.mgz as 
> target reference.
> Reading surface 
> /data-01/trisanna/freesurfer/MNI_average_2009a_asymm/surf/lh.pial
> Done reading source surface
> Mapping Source Volume onto Source Subject Surface
>  1 0 0 0
> using old
> Done mapping volume to surface
> Number of source voxels hit = 95521
> Writing to 
> /data-01/trisanna/freesurfer/MNI_average_2009a_asymm/spam_for_label_id_4_blur_overlay.mgz
> Dim: 152257 1 1
>
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Wed, Jun 29, 2016 at 8:10 PM, Bruce Fischl 
> > wrote:
>
> Can you send the full output of that command?
>
> On Jun 29, 2016, at 2:54 PM, Trisanna Sprung-Much
>  > wrote:
>
>> Hi Bruce
>>
>> I simply use
>>
>> mri_vol2surf --mov spam.mnc --output overlayspam.mgz --regheader
>> subject --hemi lh --surf pial
>>
>> Trisanna
>>
>> --
>> Ph.D. Candidate
>> McGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Wed, Jun 29, 2016 at 1:23 PM, Bruce Fischl
>> >
>> wrote:
>>
>> how do you create the overlay?
>> On Wed, 29 Jun 2016, Trisanna Sprung-Much wrote:
>>
>> Hi Bruce
>>
>> To create the spam I used minctools:
>>
>>  mincaverage  input.mnc output.mnc
>>
>> I blurred the spam using
>>
>> mincblur input.mnc output.mnc -fwhm 3
>>
>> When I open the spams using minc software, the % shown is
>> from about 10-40%
>> (i.e. the max overlap). For some reason when I create an
>> overlay from this
>> it displays the % from 1-255.
>>
>> Trisanna
>>
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Wed, Jun 29, 2016 at 12:20 PM, Bruce Fischl
>> > >
>> wrote:
>>   Hi Trisanna
>>
>>   what commands did you use to generate the
>> volumetric probability
>>   map?
>>
>>   Bruce
>>
>>
>>
>>   On Wed, 29 Jun 2016, Trisanna Sprung-Much wrote:
>>
>> Hi Bruce
>> So, when I take a probability map formed using
>> linear volumetric
>> registration with minc tools and saved as
>> .mnc and
>> convert it to an
>> overlay.mgz and open it in Freeview, the
>> probability
>> seems to be out of 255
>> (See the image attached). This is different
>> from my
>> Freesurfer generated
>> probability maps where I use -p in the
>> mri_average
>> command.
>>
>> Is there a way to change these probability values
>> that are displaying from
>> 1-255?
>>
>> many thanks
>>
>> Trisanna
>>
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Mon, Jun 27, 2016 at 10:28 AM, Bruce Fischl
>> > >
>> wrote:
>>   Hi Trisanna
>>
>>   

Re: [Freesurfer] registering to fsaverage

[Bruce Fischl]

Hi Trisanna

what does mri_info show about spam_for_label_id_4_blur_minc1.mnc? You said 
it has the range of values in [0,100]? Or [0,1]? I'm not sure why 
mri_vol2surf would modify the values - this might have to wait for Doug to 
get back

Bruce


On Thu, 30 Jun 2016, Trisanna 
Sprung-Much wrote:



Hi Bruce

here is the output of my mri_vol2surf for a volumetric spam created in minc
tools. When I then overlay this result in Freeview, it displays a Min of 127
and a Max of 255.

trisanna@kaplan:~$ mri_vol2surf 
--mov/data-01/trisanna/freesurfer/MNI_average_2009a_asymm/spam_for_label_id_4_bl
ur_minc1.mnc 
--o/data-01/trisanna/freesurfer/MNI_average_2009a_asymm/spam_for_label_id_4_bl
ur_overlay.mgz --hemi lh --surf pial --regheader MNI_average_2009a_asymm 
srcvol 
=/data-01/trisanna/freesurfer/MNI_average_2009a_asymm/spam_for_label_id_4_bl
ur_minc1.mnc
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = pial
hemi = lh
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
Computing registration from header.
  Using /data-01/trisanna/freesurfer/MNI_average_2009a_asymm/mri/orig.mgz as
target reference.
Reading surface
/data-01/trisanna/freesurfer/MNI_average_2009a_asymm/surf/lh.pial
Done reading source surface
Mapping Source Volume onto Source Subject Surface
 1 0 0 0
using old
Done mapping volume to surface
Number of source voxels hit = 95521
Writing 
to/data-01/trisanna/freesurfer/MNI_average_2009a_asymm/spam_for_label_id_4_bl
ur_overlay.mgz
Dim: 152257 1 1


--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Wed, Jun 29, 2016 at 8:10 PM, Bruce Fischl 
wrote:
Can you send the full output of that command?

On Jun 29, 2016, at 2:54 PM, Trisanna Sprung-Much
 wrote:

  Hi Bruce

I simply use

mri_vol2surf --mov spam.mnc --output overlayspam.mgz --regheader
subject --hemi lh --surf pial

Trisanna

--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Wed, Jun 29, 2016 at 1:23 PM, Bruce Fischl
 wrote:
  how do you create the overlay?
  On Wed, 29 Jun 2016, Trisanna Sprung-Much wrote:

Hi Bruce

To create the spam I used minctools:

 mincaverage  input.mnc output.mnc 

I blurred the spam using

mincblur input.mnc output.mnc -fwhm 3 

When I open the spams using minc
software, the % shown is from about
10-40%
(i.e. the max overlap). For some reason
when I create an overlay from this
it displays the % from 1-255.

Trisanna

--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Wed, Jun 29, 2016 at 12:20 PM, Bruce
Fischl 
wrote:
      Hi Trisanna

      what commands did you use to
generate the volumetric probability
      map?

      Bruce



      On Wed, 29 Jun 2016, Trisanna
Sprung-Much wrote:

            Hi Bruce
            So, when I take a
probability map formed using
            linear volumetric
            registration with minc tools
and saved as .mnc and
            convert it to an
            overlay.mgz and open it in
Freeview, the probability
            seems to be out of 255
            (See the image attached).
This is different from my
            Freesurfer generated
            probability maps where I use
-p in the mri_average
            command.

            Is there a way to change
these probability values
            that are displaying from
            1-255?

            many thanks

            Trisanna

            --
            Ph.D. CandidateMcGill
University
            Integrated Program in
Neuroscience
            Psychology


            On Mon, Jun 27, 2016 at
10:28 AM, Bruce Fischl
            
            wrote:
                  Hi Trisanna

                  we need more
information if you want us to
            help you. What does
                  "very odd mean"? If
you do it in .mgz do you
            get a different
                  answer than in .mnc?
If so, why not just
            compute them in .mgz
   

Re: [Freesurfer] registering to fsaverage

[Trisanna Sprung-Much]

Hi Bruce

here is the output of my mri_vol2surf for a volumetric spam created in minc
tools. When I then overlay this result in Freeview, it displays a Min of
127 and a Max of 255.

trisanna@kaplan:~$ mri_vol2surf --mov
/data-01/trisanna/freesurfer/MNI_average_2009a_asymm/spam_for_label_id_4_blur_minc1.mnc
--o
/data-01/trisanna/freesurfer/MNI_average_2009a_asymm/spam_for_label_id_4_blur_overlay.mgz
--hemi lh --surf pial --regheader MNI_average_2009a_asymm
srcvol =
/data-01/trisanna/freesurfer/MNI_average_2009a_asymm/spam_for_label_id_4_blur_minc1.mnc
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = pial
hemi = lh
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
Computing registration from header.
  Using /data-01/trisanna/freesurfer/MNI_average_2009a_asymm/mri/orig.mgz
as target reference.
Reading surface
/data-01/trisanna/freesurfer/MNI_average_2009a_asymm/surf/lh.pial
Done reading source surface
Mapping Source Volume onto Source Subject Surface
 1 0 0 0
using old
Done mapping volume to surface
Number of source voxels hit = 95521
Writing to
/data-01/trisanna/freesurfer/MNI_average_2009a_asymm/spam_for_label_id_4_blur_overlay.mgz
Dim: 152257 1 1


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


On Wed, Jun 29, 2016 at 8:10 PM, Bruce Fischl 
wrote:

> Can you send the full output of that command?
>
> On Jun 29, 2016, at 2:54 PM, Trisanna Sprung-Much <
> trisanna.sprung-m...@mail.mcgill.ca> wrote:
>
> Hi Bruce
>
> I simply use
>
> mri_vol2surf --mov spam.mnc --output overlayspam.mgz --regheader subject
> --hemi lh --surf pial
>
> Trisanna
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Wed, Jun 29, 2016 at 1:23 PM, Bruce Fischl 
> wrote:
>
>> how do you create the overlay?
>> On Wed, 29 Jun 2016, Trisanna Sprung-Much wrote:
>>
>> Hi Bruce
>>>
>>> To create the spam I used minctools:
>>>
>>>  mincaverage  input.mnc output.mnc
>>>
>>> I blurred the spam using
>>>
>>> mincblur input.mnc output.mnc -fwhm 3
>>>
>>> When I open the spams using minc software, the % shown is from about
>>> 10-40%
>>> (i.e. the max overlap). For some reason when I create an overlay from
>>> this
>>> it displays the % from 1-255.
>>>
>>> Trisanna
>>>
>>> --
>>> Ph.D. CandidateMcGill University
>>> Integrated Program in Neuroscience
>>> Psychology
>>>
>>>
>>> On Wed, Jun 29, 2016 at 12:20 PM, Bruce Fischl <
>>> fis...@nmr.mgh.harvard.edu>
>>> wrote:
>>>   Hi Trisanna
>>>
>>>   what commands did you use to generate the volumetric probability
>>>   map?
>>>
>>>   Bruce
>>>
>>>
>>>
>>>   On Wed, 29 Jun 2016, Trisanna Sprung-Much wrote:
>>>
>>> Hi Bruce
>>> So, when I take a probability map formed using
>>> linear volumetric
>>> registration with minc tools and saved as .mnc and
>>> convert it to an
>>> overlay.mgz and open it in Freeview, the probability
>>> seems to be out of 255
>>> (See the image attached). This is different from my
>>> Freesurfer generated
>>> probability maps where I use -p in the mri_average
>>> command.
>>>
>>> Is there a way to change these probability values
>>> that are displaying from
>>> 1-255?
>>>
>>> many thanks
>>>
>>> Trisanna
>>>
>>> --
>>> Ph.D. CandidateMcGill University
>>> Integrated Program in Neuroscience
>>> Psychology
>>>
>>>
>>> On Mon, Jun 27, 2016 at 10:28 AM, Bruce Fischl
>>> 
>>> wrote:
>>>   Hi Trisanna
>>>
>>>   we need more information if you want us to
>>> help you. What does
>>>   "very odd mean"? If you do it in .mgz do you
>>> get a different
>>>   answer than in .mnc? If so, why not just
>>> compute them in .mgz
>>>   and convert to .mnc at the end?
>>>
>>>   cheers
>>>   Bruce
>>>
>>>
>>>   On Mon, 27 Jun 2016, Trisanna Sprung-Much
>>> wrote:
>>>
>>> any ideas?
>>> Thanks!
>>>
>>> Trisanna
>>>
>>> --
>>> Ph.D. CandidateMcGill University
>>> Integrated Program in Neuroscience
>>> Psychology
>>>
>>>
>>> On Wed, Jun 22, 2016 at 10:22 PM,
>>> Trisanna
>>> Sprung-Much
>>> 
>>> wrote:
>>>   thanks Bruce - I had found that
>>> 

Re: [Freesurfer] registering to fsaverage

[Trisanna Sprung-Much]

Hi Bruce

I simply use

mri_vol2surf --mov spam.mnc --output overlayspam.mgz --regheader subject
--hemi lh --surf pial

Trisanna

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


On Wed, Jun 29, 2016 at 1:23 PM, Bruce Fischl 
wrote:

> how do you create the overlay?
> On Wed, 29 Jun 2016, Trisanna Sprung-Much wrote:
>
> Hi Bruce
>>
>> To create the spam I used minctools:
>>
>>  mincaverage  input.mnc output.mnc
>>
>> I blurred the spam using
>>
>> mincblur input.mnc output.mnc -fwhm 3
>>
>> When I open the spams using minc software, the % shown is from about
>> 10-40%
>> (i.e. the max overlap). For some reason when I create an overlay from this
>> it displays the % from 1-255.
>>
>> Trisanna
>>
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Wed, Jun 29, 2016 at 12:20 PM, Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu>
>> wrote:
>>   Hi Trisanna
>>
>>   what commands did you use to generate the volumetric probability
>>   map?
>>
>>   Bruce
>>
>>
>>
>>   On Wed, 29 Jun 2016, Trisanna Sprung-Much wrote:
>>
>> Hi Bruce
>> So, when I take a probability map formed using
>> linear volumetric
>> registration with minc tools and saved as .mnc and
>> convert it to an
>> overlay.mgz and open it in Freeview, the probability
>> seems to be out of 255
>> (See the image attached). This is different from my
>> Freesurfer generated
>> probability maps where I use -p in the mri_average
>> command.
>>
>> Is there a way to change these probability values
>> that are displaying from
>> 1-255?
>>
>> many thanks
>>
>> Trisanna
>>
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Mon, Jun 27, 2016 at 10:28 AM, Bruce Fischl
>> 
>> wrote:
>>   Hi Trisanna
>>
>>   we need more information if you want us to
>> help you. What does
>>   "very odd mean"? If you do it in .mgz do you
>> get a different
>>   answer than in .mnc? If so, why not just
>> compute them in .mgz
>>   and convert to .mnc at the end?
>>
>>   cheers
>>   Bruce
>>
>>
>>   On Mon, 27 Jun 2016, Trisanna Sprung-Much
>> wrote:
>>
>> any ideas?
>> Thanks!
>>
>> Trisanna
>>
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Wed, Jun 22, 2016 at 10:22 PM,
>> Trisanna
>> Sprung-Much
>> 
>> wrote:
>>   thanks Bruce - I had found that
>> option for my
>> fsaverage maps and
>>   it worked.
>> What about if I am importing probability
>> maps formed
>> as .mnc and
>> creating overlays from them? The
>> percentages seem to
>> be very odd for
>> min and max threshold.
>>
>> Trisanna
>>
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Wed, Jun 22, 2016 at 9:32 PM, Bruce
>> Fischl
>>  wrote:
>>   Hi Trisanna
>>
>>   if you are using mri_average you
>> can give it
>> -p as the
>>   first argument and it will compute
>> a percent
>> at the end
>>   Bruce
>>   On Wed, 22 Jun 2016, Trisanna
>> Sprung-Much
>> wrote:
>>
>>   Hi Bruce
>>
>>   Is there is a way to set the
>> probability of an
>>   overlay between 0 and 1?
>>   Would this have to be done when
>> creating the
>> overlay
>>   using mri_vol2surf?
>>
>>   thanks
>>
>>  

Re: [Freesurfer] registering to fsaverage

[Bruce Fischl]

how do you create the overlay?
On Wed, 29 Jun 2016, Trisanna Sprung-Much 
wrote:



Hi Bruce

To create the spam I used minctools:

 mincaverage  input.mnc output.mnc 

I blurred the spam using

mincblur input.mnc output.mnc -fwhm 3 

When I open the spams using minc software, the % shown is from about 10-40%
(i.e. the max overlap). For some reason when I create an overlay from this
it displays the % from 1-255.

Trisanna

--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Wed, Jun 29, 2016 at 12:20 PM, Bruce Fischl 
wrote:
  Hi Trisanna

  what commands did you use to generate the volumetric probability
  map?

  Bruce



  On Wed, 29 Jun 2016, Trisanna Sprung-Much wrote:

Hi Bruce
So, when I take a probability map formed using
linear volumetric
registration with minc tools and saved as .mnc and
convert it to an
overlay.mgz and open it in Freeview, the probability
seems to be out of 255
(See the image attached). This is different from my
Freesurfer generated
probability maps where I use -p in the mri_average
command.

Is there a way to change these probability values
that are displaying from
1-255?

many thanks

Trisanna

--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Mon, Jun 27, 2016 at 10:28 AM, Bruce Fischl

wrote:
      Hi Trisanna

      we need more information if you want us to
help you. What does
      "very odd mean"? If you do it in .mgz do you
get a different
      answer than in .mnc? If so, why not just
compute them in .mgz
      and convert to .mnc at the end?

      cheers
      Bruce


      On Mon, 27 Jun 2016, Trisanna Sprung-Much
wrote:

            any ideas?
            Thanks!

            Trisanna

            --
            Ph.D. CandidateMcGill University
            Integrated Program in Neuroscience
            Psychology


            On Wed, Jun 22, 2016 at 10:22 PM,
Trisanna
            Sprung-Much
            
wrote:
                  thanks Bruce - I had found that
option for my
            fsaverage maps and
                  it worked.
            What about if I am importing probability
maps formed
            as .mnc and
            creating overlays from them? The
percentages seem to
            be very odd for
            min and max threshold.

            Trisanna

            --
            Ph.D. CandidateMcGill University
            Integrated Program in Neuroscience
            Psychology


            On Wed, Jun 22, 2016 at 9:32 PM, Bruce
Fischl
             wrote:
                  Hi Trisanna

                  if you are using mri_average you
can give it
            -p as the
                  first argument and it will compute
a percent
            at the end
                  Bruce
                  On Wed, 22 Jun 2016, Trisanna
Sprung-Much
            wrote:

                  Hi Bruce

                  Is there is a way to set the
probability of an
                  overlay between 0 and 1?
                  Would this have to be done when
creating the
            overlay
                  using mri_vol2surf?

                  thanks

                  Trisanna

                  --
                  Ph.D. CandidateMcGill University
                  Integrated Program in Neuroscience
                  Psychology


                  On Mon, Jun 20, 2016 at 12:11 PM,
Bruce Fischl
                  
                  wrote:
                        Hi Trisanna

                        the binaries that take
mandatory
            command-line
                  arguments (i.e.
                        without a -- or - in 

Re: [Freesurfer] registering to fsaverage

[Trisanna Sprung-Much]

Hi Bruce

To create the spam I used minctools:

 mincaverage  input.mnc output.mnc

I blurred the spam using

mincblur input.mnc output.mnc -fwhm 3

When I open the spams using minc software, the % shown is from about 10-40%
(i.e. the max overlap). For some reason when I create an overlay from this
it displays the % from 1-255.

Trisanna

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


On Wed, Jun 29, 2016 at 12:20 PM, Bruce Fischl 
wrote:

> Hi Trisanna
>
> what commands did you use to generate the volumetric probability map?
>
> Bruce
>
>
>
> On Wed, 29 Jun 2016, Trisanna Sprung-Much wrote:
>
> Hi Bruce
>> So, when I take a probability map formed using linear volumetric
>> registration with minc tools and saved as .mnc and convert it to an
>> overlay.mgz and open it in Freeview, the probability seems to be out of
>> 255
>> (See the image attached). This is different from my Freesurfer generated
>> probability maps where I use -p in the mri_average command.
>>
>> Is there a way to change these probability values that are displaying from
>> 1-255?
>>
>> many thanks
>>
>> Trisanna
>>
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Mon, Jun 27, 2016 at 10:28 AM, Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu>
>> wrote:
>>   Hi Trisanna
>>
>>   we need more information if you want us to help you. What does
>>   "very odd mean"? If you do it in .mgz do you get a different
>>   answer than in .mnc? If so, why not just compute them in .mgz
>>   and convert to .mnc at the end?
>>
>>   cheers
>>   Bruce
>>
>>
>>   On Mon, 27 Jun 2016, Trisanna Sprung-Much wrote:
>>
>> any ideas?
>> Thanks!
>>
>> Trisanna
>>
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Wed, Jun 22, 2016 at 10:22 PM, Trisanna
>> Sprung-Much
>>  wrote:
>>   thanks Bruce - I had found that option for my
>> fsaverage maps and
>>   it worked.
>> What about if I am importing probability maps formed
>> as .mnc and
>> creating overlays from them? The percentages seem to
>> be very odd for
>> min and max threshold.
>>
>> Trisanna
>>
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Wed, Jun 22, 2016 at 9:32 PM, Bruce Fischl
>>  wrote:
>>   Hi Trisanna
>>
>>   if you are using mri_average you can give it
>> -p as the
>>   first argument and it will compute a percent
>> at the end
>>   Bruce
>>   On Wed, 22 Jun 2016, Trisanna Sprung-Much
>> wrote:
>>
>>   Hi Bruce
>>
>>   Is there is a way to set the probability of an
>>   overlay between 0 and 1?
>>   Would this have to be done when creating the
>> overlay
>>   using mri_vol2surf?
>>
>>   thanks
>>
>>   Trisanna
>>
>>   --
>>   Ph.D. CandidateMcGill University
>>   Integrated Program in Neuroscience
>>   Psychology
>>
>>
>>   On Mon, Jun 20, 2016 at 12:11 PM, Bruce Fischl
>>   
>>   wrote:
>> Hi Trisanna
>>
>> the binaries that take mandatory
>> command-line
>>   arguments (i.e.
>> without a -- or - in front of them)
>> require
>>   all options to be
>> given before the mandatory arguments
>>
>> cheers
>> Bruce
>>
>> On Mon, 20 Jun 2016, Trisanna
>> Sprung-Much
>>   wrote:
>>
>>   thanks, Bruce. Yes in the end
>> through
>>   trial and
>>   error I tried "mri_average
>> -noconform
>>   input output"
>>   and it worked. I was
>>   surprised that I had to put the
>>   -noconform first as
>>   normally one can put the argument
>>   anywhere in the
>>   command.
>>
>>   Best
>>
>>   Trisanna
>>
>>   --
>>

Re: [Freesurfer] registering to fsaverage

[Bruce Fischl]

Hi Trisanna

what commands did you use to generate the volumetric probability map?

Bruce



On 
Wed, 29 Jun 2016, Trisanna Sprung-Much wrote:



Hi Bruce
So, when I take a probability map formed using linear volumetric
registration with minc tools and saved as .mnc and convert it to an
overlay.mgz and open it in Freeview, the probability seems to be out of 255
(See the image attached). This is different from my Freesurfer generated
probability maps where I use -p in the mri_average command.

Is there a way to change these probability values that are displaying from
1-255?

many thanks

Trisanna

--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Mon, Jun 27, 2016 at 10:28 AM, Bruce Fischl 
wrote:
  Hi Trisanna

  we need more information if you want us to help you. What does
  "very odd mean"? If you do it in .mgz do you get a different
  answer than in .mnc? If so, why not just compute them in .mgz
  and convert to .mnc at the end?

  cheers
  Bruce


  On Mon, 27 Jun 2016, Trisanna Sprung-Much wrote:

any ideas?
Thanks!

Trisanna

--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Wed, Jun 22, 2016 at 10:22 PM, Trisanna
Sprung-Much
 wrote:
      thanks Bruce - I had found that option for my
fsaverage maps and
      it worked.
What about if I am importing probability maps formed
as .mnc and
creating overlays from them? The percentages seem to
be very odd for
min and max threshold.

Trisanna

--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Wed, Jun 22, 2016 at 9:32 PM, Bruce Fischl
 wrote:
      Hi Trisanna

      if you are using mri_average you can give it
-p as the
      first argument and it will compute a percent
at the end
      Bruce
      On Wed, 22 Jun 2016, Trisanna Sprung-Much
wrote:

      Hi Bruce

      Is there is a way to set the probability of an
      overlay between 0 and 1?
      Would this have to be done when creating the
overlay
      using mri_vol2surf?

      thanks

      Trisanna

      --
      Ph.D. CandidateMcGill University
      Integrated Program in Neuroscience
      Psychology


      On Mon, Jun 20, 2016 at 12:11 PM, Bruce Fischl
      
      wrote:
            Hi Trisanna

            the binaries that take mandatory
command-line
      arguments (i.e.
            without a -- or - in front of them)
require
      all options to be
            given before the mandatory arguments

            cheers
            Bruce

            On Mon, 20 Jun 2016, Trisanna
Sprung-Much
      wrote:

                  thanks, Bruce. Yes in the end
through
      trial and
                  error I tried "mri_average
-noconform
      input output"
                  and it worked. I was
                  surprised that I had to put the
      -noconform first as
                  normally one can put the argument
      anywhere in the
                  command.

                  Best

                  Trisanna

                  --
                  Ph.D. CandidateMcGill University
                  Integrated Program in Neuroscience
                  Psychology


                  On Mon, Jun 20, 2016 at 9:27 AM,
Bruce
      Fischl
                  
wrote:
                        yes, your last file on the
command
      line should
                  be the output file (the average)

                        cheers
                        Bruce

                        On Mon, 20 Jun 2016,
Trisanna
      Sprung-Much
                  wrote:

                        As a follow-up, here is the
      mri_info for one
                  of my overlays in the 

Re: [Freesurfer] registering to fsaverage

[Bruce Fischl]

Hi Trisanna

we need more information if you want us to help you. What does "very odd 
mean"? If you do it in .mgz do you get a different answer than in .mnc? 
If so, why not just compute them in .mgz and convert to .mnc at the end?


cheers
Bruce


On Mon, 27 Jun 2016, Trisanna Sprung-Much wrote:


any ideas?
Thanks!

Trisanna

--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Wed, Jun 22, 2016 at 10:22 PM, Trisanna Sprung-Much
 wrote:
  thanks Bruce - I had found that option for my fsaverage maps and
  it worked.
What about if I am importing probability maps formed as .mnc and
creating overlays from them? The percentages seem to be very odd for
min and max threshold.

Trisanna

--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Wed, Jun 22, 2016 at 9:32 PM, Bruce Fischl
 wrote:
  Hi Trisanna

  if you are using mri_average you can give it -p as the
  first argument and it will compute a percent at the end
  Bruce
  On Wed, 22 Jun 2016, Trisanna Sprung-Much wrote:

  Hi Bruce

  Is there is a way to set the probability of an
  overlay between 0 and 1?
  Would this have to be done when creating the overlay
  using mri_vol2surf?

  thanks

  Trisanna

  --
  Ph.D. CandidateMcGill University
  Integrated Program in Neuroscience
  Psychology


  On Mon, Jun 20, 2016 at 12:11 PM, Bruce Fischl
  
  wrote:
        Hi Trisanna

        the binaries that take mandatory command-line
  arguments (i.e.
        without a -- or - in front of them) require
  all options to be
        given before the mandatory arguments

        cheers
        Bruce

        On Mon, 20 Jun 2016, Trisanna Sprung-Much
  wrote:

              thanks, Bruce. Yes in the end through
  trial and
              error I tried "mri_average -noconform
  input output"
              and it worked. I was
              surprised that I had to put the
  -noconform first as
              normally one can put the argument
  anywhere in the
              command.

              Best

              Trisanna

              --
              Ph.D. CandidateMcGill University
              Integrated Program in Neuroscience
              Psychology


              On Mon, Jun 20, 2016 at 9:27 AM, Bruce
  Fischl
               wrote:
                    yes, your last file on the command
  line should
              be the output file (the average)

                    cheers
                    Bruce

                    On Mon, 20 Jun 2016, Trisanna
  Sprung-Much
              wrote:

                    As a follow-up, here is the
  mri_info for one
              of my overlays in the folder
                    and the output file that
  mri_average seems to
              create (if I don't specify an
                    output and it re-writes my last
  file). The
              dimensions are off:
                    Any ideas?

                    Trisanna


                  
Tgtrisanna@kaplan:/data-01/trisanna/freesurfer/fsaverage/DISPLAY_overlays_
  f
              sa
                    vee_left/aalf_lh$ mri_info
             
  fsaverage_overlay_aalf_icbm-102_left.mgz 
                    Volume information for
              fsaverage_overlay_aalf_icbm-102_left.mgz
                              type: MGH
                        dimensions: 163842 x 1 x 1
                       voxel sizes: 1., 1.,
  1.
                              type: FLOAT (3)
                               fov: 163842.000
                               dof: 0
                            xstart: -81921.0, xend:
  81921.0
                            ystart: -0.5, yend: 0.5
                            zstart: -0.5, zend: 0.5
                                TR: 0.00 msec, TE:
  0.00 msec, TI:
              0.00 msec, flip angle: 0.00
                    degrees
                           nframes: 1
                           PhEncDir: UNKNOWN
                    ras xform present
                        xform info: x_r =   1.,
  y_r =  
              0., z_r =   0., c_r =    
                    0.5000
                                  : x_a =   0.,
  y_a =  
              1., z_a =   0., c_a =  
                    -17.5000
                                  : x_s =   0.,
  y_s =  
              0., z_s =   1., c_s =  
                     18.5000

                    talairach xfm : 
                    Orientation   : 

Re: [Freesurfer] registering to fsaverage

[Trisanna Sprung-Much]

any ideas?

Thanks!

Trisanna

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


On Wed, Jun 22, 2016 at 10:22 PM, Trisanna Sprung-Much <
trisanna.sprung-m...@mail.mcgill.ca> wrote:

> thanks Bruce - I had found that option for my fsaverage maps and it worked.
>
> What about if I am importing probability maps formed as .mnc and creating
> overlays from them? The percentages seem to be very odd for min and max
> threshold.
>
> Trisanna
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Wed, Jun 22, 2016 at 9:32 PM, Bruce Fischl 
> wrote:
>
>> Hi Trisanna
>>
>> if you are using mri_average you can give it -p as the first argument and
>> it will compute a percent at the end
>> Bruce
>> On Wed, 22 Jun 2016, Trisanna Sprung-Much wrote:
>>
>> Hi Bruce
>>>
>>> Is there is a way to set the probability of an overlay between 0 and 1?
>>> Would this have to be done when creating the overlay using mri_vol2surf?
>>>
>>> thanks
>>>
>>> Trisanna
>>>
>>> --
>>> Ph.D. CandidateMcGill University
>>> Integrated Program in Neuroscience
>>> Psychology
>>>
>>>
>>> On Mon, Jun 20, 2016 at 12:11 PM, Bruce Fischl <
>>> fis...@nmr.mgh.harvard.edu>
>>> wrote:
>>>   Hi Trisanna
>>>
>>>   the binaries that take mandatory command-line arguments (i.e.
>>>   without a -- or - in front of them) require all options to be
>>>   given before the mandatory arguments
>>>
>>>   cheers
>>>   Bruce
>>>
>>>   On Mon, 20 Jun 2016, Trisanna Sprung-Much wrote:
>>>
>>> thanks, Bruce. Yes in the end through trial and
>>> error I tried "mri_average -noconform input output"
>>> and it worked. I was
>>> surprised that I had to put the -noconform first as
>>> normally one can put the argument anywhere in the
>>> command.
>>>
>>> Best
>>>
>>> Trisanna
>>>
>>> --
>>> Ph.D. CandidateMcGill University
>>> Integrated Program in Neuroscience
>>> Psychology
>>>
>>>
>>> On Mon, Jun 20, 2016 at 9:27 AM, Bruce Fischl
>>>  wrote:
>>>   yes, your last file on the command line should
>>> be the output file (the average)
>>>
>>>   cheers
>>>   Bruce
>>>
>>>   On Mon, 20 Jun 2016, Trisanna Sprung-Much
>>> wrote:
>>>
>>>   As a follow-up, here is the mri_info for one
>>> of my overlays in the folder
>>>   and the output file that mri_average seems to
>>> create (if I don't specify an
>>>   output and it re-writes my last file). The
>>> dimensions are off:
>>>   Any ideas?
>>>
>>>   Trisanna
>>>
>>>
>>>  Tgtrisanna@kaplan
>>> :/data-01/trisanna/freesurfer/fsaverage/DISPLAY_overlays_f
>>> sa
>>>   vee_left/aalf_lh$ mri_info
>>> fsaverage_overlay_aalf_icbm-102_left.mgz
>>>   Volume information for
>>> fsaverage_overlay_aalf_icbm-102_left.mgz
>>> type: MGH
>>>   dimensions: 163842 x 1 x 1
>>>  voxel sizes: 1., 1., 1.
>>> type: FLOAT (3)
>>>  fov: 163842.000
>>>  dof: 0
>>>   xstart: -81921.0, xend: 81921.0
>>>   ystart: -0.5, yend: 0.5
>>>   zstart: -0.5, zend: 0.5
>>>   TR: 0.00 msec, TE: 0.00 msec, TI:
>>> 0.00 msec, flip angle: 0.00
>>>   degrees
>>>  nframes: 1
>>>  PhEncDir: UNKNOWN
>>>   ras xform present
>>>   xform info: x_r =   1., y_r =
>>> 0., z_r =   0., c_r =
>>>   0.5000
>>> : x_a =   0., y_a =
>>> 1., z_a =   0., c_a =
>>>   -17.5000
>>> : x_s =   0., y_s =
>>> 0., z_s =   1., c_s =
>>>18.5000
>>>
>>>   talairach xfm :
>>>   Orientation   : RAS
>>>   Primary Slice Direction: axial
>>>
>>>   voxel to ras transform:
>>>   1.   0.   0.
>>> -81920.5000
>>>   0.   1.   0.
>>> -18.
>>>   0.   0.   1.
>>>  18.
>>>   0.   0.   0.
>>> 1.
>>>
>>>   voxel-to-ras determinant 1
>>>
>>>  

Re: [Freesurfer] registering to fsaverage

[Trisanna Sprung-Much]

thanks Bruce - I had found that option for my fsaverage maps and it worked.

What about if I am importing probability maps formed as .mnc and creating
overlays from them? The percentages seem to be very odd for min and max
threshold.

Trisanna

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


On Wed, Jun 22, 2016 at 9:32 PM, Bruce Fischl 
wrote:

> Hi Trisanna
>
> if you are using mri_average you can give it -p as the first argument and
> it will compute a percent at the end
> Bruce
> On Wed, 22 Jun 2016, Trisanna Sprung-Much wrote:
>
> Hi Bruce
>>
>> Is there is a way to set the probability of an overlay between 0 and 1?
>> Would this have to be done when creating the overlay using mri_vol2surf?
>>
>> thanks
>>
>> Trisanna
>>
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Mon, Jun 20, 2016 at 12:11 PM, Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu>
>> wrote:
>>   Hi Trisanna
>>
>>   the binaries that take mandatory command-line arguments (i.e.
>>   without a -- or - in front of them) require all options to be
>>   given before the mandatory arguments
>>
>>   cheers
>>   Bruce
>>
>>   On Mon, 20 Jun 2016, Trisanna Sprung-Much wrote:
>>
>> thanks, Bruce. Yes in the end through trial and
>> error I tried "mri_average -noconform input output"
>> and it worked. I was
>> surprised that I had to put the -noconform first as
>> normally one can put the argument anywhere in the
>> command.
>>
>> Best
>>
>> Trisanna
>>
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Mon, Jun 20, 2016 at 9:27 AM, Bruce Fischl
>>  wrote:
>>   yes, your last file on the command line should
>> be the output file (the average)
>>
>>   cheers
>>   Bruce
>>
>>   On Mon, 20 Jun 2016, Trisanna Sprung-Much
>> wrote:
>>
>>   As a follow-up, here is the mri_info for one
>> of my overlays in the folder
>>   and the output file that mri_average seems to
>> create (if I don't specify an
>>   output and it re-writes my last file). The
>> dimensions are off:
>>   Any ideas?
>>
>>   Trisanna
>>
>>
>>  Tgtrisanna@kaplan
>> :/data-01/trisanna/freesurfer/fsaverage/DISPLAY_overlays_f
>> sa
>>   vee_left/aalf_lh$ mri_info
>> fsaverage_overlay_aalf_icbm-102_left.mgz
>>   Volume information for
>> fsaverage_overlay_aalf_icbm-102_left.mgz
>> type: MGH
>>   dimensions: 163842 x 1 x 1
>>  voxel sizes: 1., 1., 1.
>> type: FLOAT (3)
>>  fov: 163842.000
>>  dof: 0
>>   xstart: -81921.0, xend: 81921.0
>>   ystart: -0.5, yend: 0.5
>>   zstart: -0.5, zend: 0.5
>>   TR: 0.00 msec, TE: 0.00 msec, TI:
>> 0.00 msec, flip angle: 0.00
>>   degrees
>>  nframes: 1
>>  PhEncDir: UNKNOWN
>>   ras xform present
>>   xform info: x_r =   1., y_r =
>> 0., z_r =   0., c_r =
>>   0.5000
>> : x_a =   0., y_a =
>> 1., z_a =   0., c_a =
>>   -17.5000
>> : x_s =   0., y_s =
>> 0., z_s =   1., c_s =
>>18.5000
>>
>>   talairach xfm :
>>   Orientation   : RAS
>>   Primary Slice Direction: axial
>>
>>   voxel to ras transform:
>>   1.   0.   0.
>> -81920.5000
>>   0.   1.   0.
>> -18.
>>   0.   0.   1.
>>  18.
>>   0.   0.   0.
>> 1.
>>
>>   voxel-to-ras determinant 1
>>
>>   ras to voxel transform:
>>   1.  -0.  -0.
>> 81920.5000
>>  -0.   1.  -0.
>>  18.
>>  -0.  -0.   1.
>> -18.
>>   0.   0.   0.
>> 

Re: [Freesurfer] registering to fsaverage

[Bruce Fischl]

Hi Trisanna

if you are using mri_average you can give it -p as the first argument and 
it will compute a percent at the end

Bruce
On Wed, 22 Jun 2016, Trisanna 
Sprung-Much wrote:



Hi Bruce

Is there is a way to set the probability of an overlay between 0 and 1?
Would this have to be done when creating the overlay using mri_vol2surf?

thanks

Trisanna

--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Mon, Jun 20, 2016 at 12:11 PM, Bruce Fischl 
wrote:
  Hi Trisanna

  the binaries that take mandatory command-line arguments (i.e.
  without a -- or - in front of them) require all options to be
  given before the mandatory arguments

  cheers
  Bruce

  On Mon, 20 Jun 2016, Trisanna Sprung-Much wrote:

thanks, Bruce. Yes in the end through trial and
error I tried "mri_average -noconform input output"
and it worked. I was
surprised that I had to put the -noconform first as
normally one can put the argument anywhere in the
command.

Best

Trisanna

--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Mon, Jun 20, 2016 at 9:27 AM, Bruce Fischl
 wrote:
      yes, your last file on the command line should
be the output file (the average)

      cheers
      Bruce

      On Mon, 20 Jun 2016, Trisanna Sprung-Much
wrote:

      As a follow-up, here is the mri_info for one
of my overlays in the folder
      and the output file that mri_average seems to
create (if I don't specify an
      output and it re-writes my last file). The
dimensions are off:
      Any ideas?

      Trisanna


     
Tgtrisanna@kaplan:/data-01/trisanna/freesurfer/fsaverage/DISPLAY_overlays_f
sa
      vee_left/aalf_lh$ mri_info
fsaverage_overlay_aalf_icbm-102_left.mgz 
      Volume information for
fsaverage_overlay_aalf_icbm-102_left.mgz
                type: MGH
          dimensions: 163842 x 1 x 1
         voxel sizes: 1., 1., 1.
                type: FLOAT (3)
                 fov: 163842.000
                 dof: 0
              xstart: -81921.0, xend: 81921.0
              ystart: -0.5, yend: 0.5
              zstart: -0.5, zend: 0.5
                  TR: 0.00 msec, TE: 0.00 msec, TI:
0.00 msec, flip angle: 0.00
      degrees
             nframes: 1
             PhEncDir: UNKNOWN
      ras xform present
          xform info: x_r =   1., y_r =  
0., z_r =   0., c_r =    
      0.5000
                    : x_a =   0., y_a =  
1., z_a =   0., c_a =  
      -17.5000
                    : x_s =   0., y_s =  
0., z_s =   1., c_s =  
       18.5000

      talairach xfm : 
      Orientation   : RAS
      Primary Slice Direction: axial

      voxel to ras transform:
                      1.   0.   0.
-81920.5000
                      0.   1.   0.  
-18.
                      0.   0.   1.  
 18.
                      0.   0.   0.    
1.

      voxel-to-ras determinant 1

      ras to voxel transform:
                      1.  -0.  -0.
81920.5000
                     -0.   1.  -0.  
 18.
                     -0.  -0.   1.  
-18.
                      0.   0.   0.    
1.


     
trisanna@kaplan:/data-01/trisanna/freesurfer/fsaverage/DISPLAY_overlays_fsa

      verage_left/aalf_lh$ mri_info
fsaverage_overlay_aalf_icbm-350_left.mgz 
      Volume information for
fsaverage_overlay_aalf_icbm-350_left.mgz
                type: MGH
          dimensions: 256 x 256 x 256
         voxel sizes: 1., 1., 1.
                type: FLOAT (3)
                 fov: 256.000
                 dof: 0
              xstart: -128.0, xend: 128.0
              ystart: -128.0, yend: 128.0
              zstart: -128.0, zend: 128.0
  

Re: [Freesurfer] registering to fsaverage

[Trisanna Sprung-Much]

Hi Bruce

Is there is a way to set the probability of an overlay between 0 and 1?
Would this have to be done when creating the overlay using mri_vol2surf?

thanks

Trisanna

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


On Mon, Jun 20, 2016 at 12:11 PM, Bruce Fischl 
wrote:

> Hi Trisanna
>
> the binaries that take mandatory command-line arguments (i.e. without a --
> or - in front of them) require all options to be given before the mandatory
> arguments
>
> cheers
> Bruce
>
> On Mon, 20 Jun 2016, Trisanna Sprung-Much wrote:
>
> thanks, Bruce. Yes in the end through trial and error I tried "mri_average
>> -noconform input output" and it worked. I was
>> surprised that I had to put the -noconform first as normally one can put
>> the argument anywhere in the command.
>>
>> Best
>>
>> Trisanna
>>
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Mon, Jun 20, 2016 at 9:27 AM, Bruce Fischl 
>> wrote:
>>   yes, your last file on the command line should be the output file
>> (the average)
>>
>>   cheers
>>   Bruce
>>
>>   On Mon, 20 Jun 2016, Trisanna Sprung-Much wrote:
>>
>>   As a follow-up, here is the mri_info for one of my overlays in the
>> folder
>>   and the output file that mri_average seems to create (if I don't
>> specify an
>>   output and it re-writes my last file). The dimensions are off:
>>   Any ideas?
>>
>>   Trisanna
>>
>>
>>   Tgtrisanna@kaplan
>> :/data-01/trisanna/freesurfer/fsaverage/DISPLAY_overlays_fsa
>>   vee_left/aalf_lh$ mri_info fsaverage_overlay_aalf_icbm-102_left.mgz
>>   Volume information for fsaverage_overlay_aalf_icbm-102_left.mgz
>> type: MGH
>>   dimensions: 163842 x 1 x 1
>>  voxel sizes: 1., 1., 1.
>> type: FLOAT (3)
>>  fov: 163842.000
>>  dof: 0
>>   xstart: -81921.0, xend: 81921.0
>>   ystart: -0.5, yend: 0.5
>>   zstart: -0.5, zend: 0.5
>>   TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip
>> angle: 0.00
>>   degrees
>>  nframes: 1
>>  PhEncDir: UNKNOWN
>>   ras xform present
>>   xform info: x_r =   1., y_r =   0., z_r =   0., c_r
>> =
>>   0.5000
>> : x_a =   0., y_a =   1., z_a =   0., c_a
>> =
>>   -17.5000
>> : x_s =   0., y_s =   0., z_s =   1., c_s
>> =
>>18.5000
>>
>>   talairach xfm :
>>   Orientation   : RAS
>>   Primary Slice Direction: axial
>>
>>   voxel to ras transform:
>>   1.   0.   0. -81920.5000
>>   0.   1.   0.   -18.
>>   0.   0.   1.18.
>>   0.   0.   0. 1.
>>
>>   voxel-to-ras determinant 1
>>
>>   ras to voxel transform:
>>   1.  -0.  -0. 81920.5000
>>  -0.   1.  -0.18.
>>  -0.  -0.   1.   -18.
>>   0.   0.   0. 1.
>>
>>
>>   trisanna@kaplan
>> :/data-01/trisanna/freesurfer/fsaverage/DISPLAY_overlays_fsa
>>   verage_left/aalf_lh$ mri_info
>> fsaverage_overlay_aalf_icbm-350_left.mgz
>>   Volume information for fsaverage_overlay_aalf_icbm-350_left.mgz
>> type: MGH
>>   dimensions: 256 x 256 x 256
>>  voxel sizes: 1., 1., 1.
>> type: FLOAT (3)
>>  fov: 256.000
>>  dof: 0
>>   xstart: -128.0, xend: 128.0
>>   ystart: -128.0, yend: 128.0
>>   zstart: -128.0, zend: 128.0
>>   TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip
>> angle: 0.00
>>   degrees
>>  nframes: 1
>>  PhEncDir: UNKNOWN
>>   ras xform present
>>   xform info: x_r =  -1., y_r =   0., z_r =   0., c_r
>> =
>>   0.5000
>> : x_a =   0., y_a =   0., z_a =   1., c_a
>> =
>>   -17.5000
>> : x_s =   0., y_s =  -1., z_s =   0., c_s
>> =
>>18.5000
>>
>>   talairach xfm :
>>   Orientation   : LIA
>>   Primary Slice Direction: coronal
>>
>>   --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Mon, Jun 20, 2016 at 12:32 AM, Trisanna Sprung-Much
>>  wrote:
>>   Hi Dr. Fischl
>> I ran the following mri_average and consistently get this message. It
>> seems to be trying to read my output as one of the input volumes. If I
>> don't specify an output it re-writes my last file in the input folder
>> and when I try to open this it 

Re: [Freesurfer] registering to fsaverage

[Bruce Fischl]

Hi Trisanna

the binaries that take mandatory command-line arguments (i.e. without a -- 
or - in front of them) require all options to be given before the mandatory 
arguments


cheers
Bruce

On Mon, 20 Jun 2016, Trisanna Sprung-Much 
wrote:



thanks, Bruce. Yes in the end through trial and error I tried "mri_average 
-noconform input output" and it worked. I was
surprised that I had to put the -noconform first as normally one can put the 
argument anywhere in the command.

Best

Trisanna

--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Mon, Jun 20, 2016 at 9:27 AM, Bruce Fischl  
wrote:
  yes, your last file on the command line should be the output file (the 
average)

  cheers
  Bruce

  On Mon, 20 Jun 2016, Trisanna Sprung-Much wrote:

  As a follow-up, here is the mri_info for one of my overlays in the folder
  and the output file that mri_average seems to create (if I don't specify 
an
  output and it re-writes my last file). The dimensions are off:
  Any ideas?

  Trisanna


  
Tgtrisanna@kaplan:/data-01/trisanna/freesurfer/fsaverage/DISPLAY_overlays_fsa
  vee_left/aalf_lh$ mri_info fsaverage_overlay_aalf_icbm-102_left.mgz 
  Volume information for fsaverage_overlay_aalf_icbm-102_left.mgz
            type: MGH
      dimensions: 163842 x 1 x 1
     voxel sizes: 1., 1., 1.
            type: FLOAT (3)
             fov: 163842.000
             dof: 0
          xstart: -81921.0, xend: 81921.0
          ystart: -0.5, yend: 0.5
          zstart: -0.5, zend: 0.5
              TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
  degrees
         nframes: 1
         PhEncDir: UNKNOWN
  ras xform present
      xform info: x_r =   1., y_r =   0., z_r =   0., c_r =    
  0.5000
                : x_a =   0., y_a =   1., z_a =   0., c_a =  
  -17.5000
                : x_s =   0., y_s =   0., z_s =   1., c_s =  
   18.5000

  talairach xfm : 
  Orientation   : RAS
  Primary Slice Direction: axial

  voxel to ras transform:
                  1.   0.   0. -81920.5000
                  0.   1.   0.   -18.
                  0.   0.   1.    18.
                  0.   0.   0.     1.

  voxel-to-ras determinant 1

  ras to voxel transform:
                  1.  -0.  -0. 81920.5000
                 -0.   1.  -0.    18.
                 -0.  -0.   1.   -18.
                  0.   0.   0.     1.


  
trisanna@kaplan:/data-01/trisanna/freesurfer/fsaverage/DISPLAY_overlays_fsa
  verage_left/aalf_lh$ mri_info fsaverage_overlay_aalf_icbm-350_left.mgz 
  Volume information for fsaverage_overlay_aalf_icbm-350_left.mgz
            type: MGH
      dimensions: 256 x 256 x 256
     voxel sizes: 1., 1., 1.
            type: FLOAT (3)
             fov: 256.000
             dof: 0
          xstart: -128.0, xend: 128.0
          ystart: -128.0, yend: 128.0
          zstart: -128.0, zend: 128.0
              TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
  degrees
         nframes: 1
         PhEncDir: UNKNOWN
  ras xform present
      xform info: x_r =  -1., y_r =   0., z_r =   0., c_r =    
  0.5000
                : x_a =   0., y_a =   0., z_a =   1., c_a =  
  -17.5000
                : x_s =   0., y_s =  -1., z_s =   0., c_s =  
   18.5000

  talairach xfm : 
  Orientation   : LIA
  Primary Slice Direction: coronal

  --
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Mon, Jun 20, 2016 at 12:32 AM, Trisanna Sprung-Much
 wrote:
      Hi Dr. Fischl
I ran the following mri_average and consistently get this message. It
seems to be trying to read my output as one of the input volumes. If I
don't specify an output it re-writes my last file in the input folder
and when I try to open this it doesn't work at all.

What exactly does MRIchangeType mean?



(navigated to folder with all .mgz volumes want to average)
mri_average *.mgz test.mgz --noconform

1 of 51: reading fsaverage_overlay_aalf_icbm-102_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
2 of 51: reading fsaverage_overlay_aalf_icbm-103_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
3 of 51: reading fsaverage_overlay_aalf_icbm-104_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
4 of 51: reading fsaverage_overlay_aalf_icbm-105_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
5 of 51: 

Re: [Freesurfer] registering to fsaverage

[Trisanna Sprung-Much]

thanks, Bruce. Yes in the end through trial and error I tried "mri_average
-noconform input output" and it worked. I was surprised that I had to put
the -noconform first as normally one can put the argument anywhere in the
command.

Best

Trisanna

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


On Mon, Jun 20, 2016 at 9:27 AM, Bruce Fischl 
wrote:

> yes, your last file on the command line should be the output file (the
> average)
>
> cheers
> Bruce
>
>
> On Mon, 20 Jun 2016, Trisanna Sprung-Much wrote:
>
> As a follow-up, here is the mri_info for one of my overlays in the folder
>> and the output file that mri_average seems to create (if I don't specify
>> an
>> output and it re-writes my last file). The dimensions are off:
>> Any ideas?
>>
>> Trisanna
>>
>>
>> Tgtrisanna@kaplan
>> :/data-01/trisanna/freesurfer/fsaverage/DISPLAY_overlays_fsa
>> vee_left/aalf_lh$ mri_info fsaverage_overlay_aalf_icbm-102_left.mgz
>> Volume information for fsaverage_overlay_aalf_icbm-102_left.mgz
>>   type: MGH
>> dimensions: 163842 x 1 x 1
>>voxel sizes: 1., 1., 1.
>>   type: FLOAT (3)
>>fov: 163842.000
>>dof: 0
>> xstart: -81921.0, xend: 81921.0
>> ystart: -0.5, yend: 0.5
>> zstart: -0.5, zend: 0.5
>> TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
>> degrees
>>nframes: 1
>>PhEncDir: UNKNOWN
>> ras xform present
>> xform info: x_r =   1., y_r =   0., z_r =   0., c_r =
>> 0.5000
>>   : x_a =   0., y_a =   1., z_a =   0., c_a =
>> -17.5000
>>   : x_s =   0., y_s =   0., z_s =   1., c_s =
>>  18.5000
>>
>> talairach xfm :
>> Orientation   : RAS
>> Primary Slice Direction: axial
>>
>> voxel to ras transform:
>> 1.   0.   0. -81920.5000
>> 0.   1.   0.   -18.
>> 0.   0.   1.18.
>> 0.   0.   0. 1.
>>
>> voxel-to-ras determinant 1
>>
>> ras to voxel transform:
>> 1.  -0.  -0. 81920.5000
>>-0.   1.  -0.18.
>>-0.  -0.   1.   -18.
>> 0.   0.   0. 1.
>>
>>
>> trisanna@kaplan
>> :/data-01/trisanna/freesurfer/fsaverage/DISPLAY_overlays_fsa
>> verage_left/aalf_lh$ mri_info fsaverage_overlay_aalf_icbm-350_left.mgz
>> Volume information for fsaverage_overlay_aalf_icbm-350_left.mgz
>>   type: MGH
>> dimensions: 256 x 256 x 256
>>voxel sizes: 1., 1., 1.
>>   type: FLOAT (3)
>>fov: 256.000
>>dof: 0
>> xstart: -128.0, xend: 128.0
>> ystart: -128.0, yend: 128.0
>> zstart: -128.0, zend: 128.0
>> TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
>> degrees
>>nframes: 1
>>PhEncDir: UNKNOWN
>> ras xform present
>> xform info: x_r =  -1., y_r =   0., z_r =   0., c_r =
>> 0.5000
>>   : x_a =   0., y_a =   0., z_a =   1., c_a =
>> -17.5000
>>   : x_s =   0., y_s =  -1., z_s =   0., c_s =
>>  18.5000
>>
>> talairach xfm :
>> Orientation   : LIA
>> Primary Slice Direction: coronal
>>
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Mon, Jun 20, 2016 at 12:32 AM, Trisanna Sprung-Much
>>  wrote:
>>   Hi Dr. Fischl
>> I ran the following mri_average and consistently get this message. It
>> seems to be trying to read my output as one of the input volumes. If I
>> don't specify an output it re-writes my last file in the input folder
>> and when I try to open this it doesn't work at all.
>>
>> What exactly does MRIchangeType mean?
>>
>>
>>
>> (navigated to folder with all .mgz volumes want to average)
>> mri_average *.mgz test.mgz --noconform
>>
>> 1 of 51: reading fsaverage_overlay_aalf_icbm-102_left.mgz...
>> embedding and interpolating volume
>> MRIchangeType: Building histogram
>> 2 of 51: reading fsaverage_overlay_aalf_icbm-103_left.mgz...
>> embedding and interpolating volume
>> MRIchangeType: Building histogram
>> 3 of 51: reading fsaverage_overlay_aalf_icbm-104_left.mgz...
>> embedding and interpolating volume
>> MRIchangeType: Building histogram
>> 4 of 51: reading fsaverage_overlay_aalf_icbm-105_left.mgz...
>> embedding and interpolating volume
>> MRIchangeType: Building histogram
>> 5 of 51: reading fsaverage_overlay_aalf_icbm-106_left.mgz...
>> embedding and interpolating volume
>> MRIchangeType: Building histogram
>> 6 of 51: reading fsaverage_overlay_aalf_icbm-107_left.mgz...
>> embedding and interpolating volume
>> MRIchangeType: Building histogram
>> 7 of 51: reading fsaverage_overlay_aalf_icbm-108_left.mgz...
>> embedding and interpolating volume
>> 

Re: [Freesurfer] registering to fsaverage

[Bruce Fischl]

yes, your last file on the command line should be the output file (the 
average)


cheers
Bruce

On Mon, 20 Jun 2016, Trisanna Sprung-Much wrote:


As a follow-up, here is the mri_info for one of my overlays in the folder
and the output file that mri_average seems to create (if I don't specify an
output and it re-writes my last file). The dimensions are off:
Any ideas?

Trisanna


Tgtrisanna@kaplan:/data-01/trisanna/freesurfer/fsaverage/DISPLAY_overlays_fsa
vee_left/aalf_lh$ mri_info fsaverage_overlay_aalf_icbm-102_left.mgz 
Volume information for fsaverage_overlay_aalf_icbm-102_left.mgz
          type: MGH
    dimensions: 163842 x 1 x 1
   voxel sizes: 1., 1., 1.
          type: FLOAT (3)
           fov: 163842.000
           dof: 0
        xstart: -81921.0, xend: 81921.0
        ystart: -0.5, yend: 0.5
        zstart: -0.5, zend: 0.5
            TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
       nframes: 1
       PhEncDir: UNKNOWN
ras xform present
    xform info: x_r =   1., y_r =   0., z_r =   0., c_r =    
0.5000
              : x_a =   0., y_a =   1., z_a =   0., c_a =  
-17.5000
              : x_s =   0., y_s =   0., z_s =   1., c_s =  
 18.5000

talairach xfm : 
Orientation   : RAS
Primary Slice Direction: axial

voxel to ras transform:
                1.   0.   0. -81920.5000
                0.   1.   0.   -18.
                0.   0.   1.    18.
                0.   0.   0.     1.

voxel-to-ras determinant 1

ras to voxel transform:
                1.  -0.  -0. 81920.5000
               -0.   1.  -0.    18.
               -0.  -0.   1.   -18.
                0.   0.   0.     1.


trisanna@kaplan:/data-01/trisanna/freesurfer/fsaverage/DISPLAY_overlays_fsa
verage_left/aalf_lh$ mri_info fsaverage_overlay_aalf_icbm-350_left.mgz 
Volume information for fsaverage_overlay_aalf_icbm-350_left.mgz
          type: MGH
    dimensions: 256 x 256 x 256
   voxel sizes: 1., 1., 1.
          type: FLOAT (3)
           fov: 256.000
           dof: 0
        xstart: -128.0, xend: 128.0
        ystart: -128.0, yend: 128.0
        zstart: -128.0, zend: 128.0
            TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
       nframes: 1
       PhEncDir: UNKNOWN
ras xform present
    xform info: x_r =  -1., y_r =   0., z_r =   0., c_r =    
0.5000
              : x_a =   0., y_a =   0., z_a =   1., c_a =  
-17.5000
              : x_s =   0., y_s =  -1., z_s =   0., c_s =  
 18.5000

talairach xfm : 
Orientation   : LIA
Primary Slice Direction: coronal

--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Mon, Jun 20, 2016 at 12:32 AM, Trisanna Sprung-Much
 wrote:
  Hi Dr. Fischl
I ran the following mri_average and consistently get this message. It
seems to be trying to read my output as one of the input volumes. If I
don't specify an output it re-writes my last file in the input folder
and when I try to open this it doesn't work at all.

What exactly does MRIchangeType mean?



(navigated to folder with all .mgz volumes want to average)
mri_average *.mgz test.mgz --noconform

1 of 51: reading fsaverage_overlay_aalf_icbm-102_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
2 of 51: reading fsaverage_overlay_aalf_icbm-103_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
3 of 51: reading fsaverage_overlay_aalf_icbm-104_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
4 of 51: reading fsaverage_overlay_aalf_icbm-105_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
5 of 51: reading fsaverage_overlay_aalf_icbm-106_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
6 of 51: reading fsaverage_overlay_aalf_icbm-107_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
7 of 51: reading fsaverage_overlay_aalf_icbm-108_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
8 of 51: reading fsaverage_overlay_aalf_icbm-109_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
9 of 51: reading fsaverage_overlay_aalf_icbm-110_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
10 of 51: reading fsaverage_overlay_aalf_icbm-111_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
11 of 51: reading fsaverage_overlay_aalf_icbm-112_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
12 of 51: reading fsaverage_overlay_aalf_icbm-113_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
13 of 51: reading fsaverage_overlay_aalf_icbm-114_left.mgz...

Re: [Freesurfer] registering to fsaverage

[Bruce Fischl]

try it with the noconform as the first argument. I think it will ignore it 
at the end






Hi Dr. Fischl
I ran the following mri_average and consistently get this message. It seems
to be trying to read my output as one of the input volumes. If I don't
specify an output it re-writes my last file in the input folder and when I
try to open this it doesn't work at all.

What exactly does MRIchangeType mean?



(navigated to folder with all .mgz volumes want to average)
mri_average *.mgz test.mgz --noconform

1 of 51: reading fsaverage_overlay_aalf_icbm-102_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
2 of 51: reading fsaverage_overlay_aalf_icbm-103_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
3 of 51: reading fsaverage_overlay_aalf_icbm-104_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
4 of 51: reading fsaverage_overlay_aalf_icbm-105_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
5 of 51: reading fsaverage_overlay_aalf_icbm-106_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
6 of 51: reading fsaverage_overlay_aalf_icbm-107_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
7 of 51: reading fsaverage_overlay_aalf_icbm-108_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
8 of 51: reading fsaverage_overlay_aalf_icbm-109_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
9 of 51: reading fsaverage_overlay_aalf_icbm-110_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
10 of 51: reading fsaverage_overlay_aalf_icbm-111_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
11 of 51: reading fsaverage_overlay_aalf_icbm-112_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
12 of 51: reading fsaverage_overlay_aalf_icbm-113_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
13 of 51: reading fsaverage_overlay_aalf_icbm-114_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
14 of 51: reading fsaverage_overlay_aalf_icbm-115_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
15 of 51: reading fsaverage_overlay_aalf_icbm-116_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
16 of 51: reading fsaverage_overlay_aalf_icbm-117_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
17 of 51: reading fsaverage_overlay_aalf_icbm-118_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
18 of 51: reading fsaverage_overlay_aalf_icbm-119_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
19 of 51: reading fsaverage_overlay_aalf_icbm-120_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
20 of 51: reading fsaverage_overlay_aalf_icbm-121_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
21 of 51: reading fsaverage_overlay_aalf_icbm-122_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
22 of 51: reading fsaverage_overlay_aalf_icbm-123_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
23 of 51: reading fsaverage_overlay_aalf_icbm-124_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
24 of 51: reading fsaverage_overlay_aalf_icbm-125_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
25 of 51: reading fsaverage_overlay_aalf_icbm-126_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
26 of 51: reading fsaverage_overlay_aalf_icbm-127_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
27 of 51: reading fsaverage_overlay_aalf_icbm-131_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
28 of 51: reading fsaverage_overlay_aalf_icbm-133_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
29 of 51: reading fsaverage_overlay_aalf_icbm-134_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
30 of 51: reading fsaverage_overlay_aalf_icbm-135_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
31 of 51: reading fsaverage_overlay_aalf_icbm-137_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
32 of 51: reading fsaverage_overlay_aalf_icbm-139_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
33 of 51: reading fsaverage_overlay_aalf_icbm-140_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
34 of 51: reading fsaverage_overlay_aalf_icbm-141_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram 
35 of 

Re: [Freesurfer] registering to fsaverage

[Trisanna Sprung-Much]

As a follow-up, here is the mri_info for one of my overlays in the folder
and the output file that mri_average seems to create (if I don't specify an
output and it re-writes my last file). The dimensions are off:

Any ideas?

Trisanna


Tg 
trisanna@kaplan:/data-01/trisanna/freesurfer/fsaverage/DISPLAY_overlays_fsavee_left/aalf_lh$
mri_info fsaverage_overlay_aalf_icbm-102_left.mgz
Volume information for fsaverage_overlay_aalf_icbm-102_left.mgz
  type: MGH
dimensions: 163842 x 1 x 1
   voxel sizes: 1., 1., 1.
  type: FLOAT (3)
   fov: 163842.000
   dof: 0
xstart: -81921.0, xend: 81921.0
ystart: -0.5, yend: 0.5
zstart: -0.5, zend: 0.5
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
   nframes: 1
   PhEncDir: UNKNOWN
ras xform present
xform info: x_r =   1., y_r =   0., z_r =   0., c_r =
0.5000
  : x_a =   0., y_a =   1., z_a =   0., c_a =
-17.5000
  : x_s =   0., y_s =   0., z_s =   1., c_s =
 18.5000

talairach xfm :
Orientation   : RAS
Primary Slice Direction: axial

voxel to ras transform:
1.   0.   0. -81920.5000
0.   1.   0.   -18.
0.   0.   1.18.
0.   0.   0. 1.

voxel-to-ras determinant 1

ras to voxel transform:
1.  -0.  -0. 81920.5000
   -0.   1.  -0.18.
   -0.  -0.   1.   -18.
0.   0.   0. 1.


trisanna@kaplan:/data-01/trisanna/freesurfer/fsaverage/DISPLAY_overlays_fsaverage_left/aalf_lh$
mri_info fsaverage_overlay_aalf_icbm-350_left.mgz
Volume information for fsaverage_overlay_aalf_icbm-350_left.mgz
  type: MGH
dimensions: 256 x 256 x 256
   voxel sizes: 1., 1., 1.
  type: FLOAT (3)
   fov: 256.000
   dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
   nframes: 1
   PhEncDir: UNKNOWN
ras xform present
xform info: x_r =  -1., y_r =   0., z_r =   0., c_r =
0.5000
  : x_a =   0., y_a =   0., z_a =   1., c_a =
-17.5000
  : x_s =   0., y_s =  -1., z_s =   0., c_s =
 18.5000

talairach xfm :
Orientation   : LIA
Primary Slice Direction: coronal

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


On Mon, Jun 20, 2016 at 12:32 AM, Trisanna Sprung-Much <
trisanna.sprung-m...@mail.mcgill.ca> wrote:

> Hi Dr. Fischl
>
> I ran the following mri_average and consistently get this message. It
> seems to be trying to read my output as one of the input volumes. If I
> don't specify an output it re-writes my last file in the input folder and
> when I try to open this it doesn't work at all.
>
> What exactly does MRIchangeType mean?
>
>
>
> (navigated to folder with all .mgz volumes want to average)
> mri_average *.mgz test.mgz --noconform
>
> 1 of 51: reading fsaverage_overlay_aalf_icbm-102_left.mgz...
> embedding and interpolating volume
> MRIchangeType: Building histogram
> 2 of 51: reading fsaverage_overlay_aalf_icbm-103_left.mgz...
> embedding and interpolating volume
> MRIchangeType: Building histogram
> 3 of 51: reading fsaverage_overlay_aalf_icbm-104_left.mgz...
> embedding and interpolating volume
> MRIchangeType: Building histogram
> 4 of 51: reading fsaverage_overlay_aalf_icbm-105_left.mgz...
> embedding and interpolating volume
> MRIchangeType: Building histogram
> 5 of 51: reading fsaverage_overlay_aalf_icbm-106_left.mgz...
> embedding and interpolating volume
> MRIchangeType: Building histogram
> 6 of 51: reading fsaverage_overlay_aalf_icbm-107_left.mgz...
> embedding and interpolating volume
> MRIchangeType: Building histogram
> 7 of 51: reading fsaverage_overlay_aalf_icbm-108_left.mgz...
> embedding and interpolating volume
> MRIchangeType: Building histogram
> 8 of 51: reading fsaverage_overlay_aalf_icbm-109_left.mgz...
> embedding and interpolating volume
> MRIchangeType: Building histogram
> 9 of 51: reading fsaverage_overlay_aalf_icbm-110_left.mgz...
> embedding and interpolating volume
> MRIchangeType: Building histogram
> 10 of 51: reading fsaverage_overlay_aalf_icbm-111_left.mgz...
> embedding and interpolating volume
> MRIchangeType: Building histogram
> 11 of 51: reading fsaverage_overlay_aalf_icbm-112_left.mgz...
> embedding and interpolating volume
> MRIchangeType: Building histogram
> 12 of 51: reading fsaverage_overlay_aalf_icbm-113_left.mgz...
> embedding and interpolating volume
> MRIchangeType: Building histogram
> 13 of 51: reading fsaverage_overlay_aalf_icbm-114_left.mgz...
> embedding and interpolating volume
> MRIchangeType: Building histogram
> 14 of 51: 

Re: [Freesurfer] registering to fsaverage

[Trisanna Sprung-Much]

Hi Dr. Fischl

I ran the following mri_average and consistently get this message. It seems
to be trying to read my output as one of the input volumes. If I don't
specify an output it re-writes my last file in the input folder and when I
try to open this it doesn't work at all.

What exactly does MRIchangeType mean?



(navigated to folder with all .mgz volumes want to average)
mri_average *.mgz test.mgz --noconform

1 of 51: reading fsaverage_overlay_aalf_icbm-102_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
2 of 51: reading fsaverage_overlay_aalf_icbm-103_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
3 of 51: reading fsaverage_overlay_aalf_icbm-104_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
4 of 51: reading fsaverage_overlay_aalf_icbm-105_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
5 of 51: reading fsaverage_overlay_aalf_icbm-106_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
6 of 51: reading fsaverage_overlay_aalf_icbm-107_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
7 of 51: reading fsaverage_overlay_aalf_icbm-108_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
8 of 51: reading fsaverage_overlay_aalf_icbm-109_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
9 of 51: reading fsaverage_overlay_aalf_icbm-110_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
10 of 51: reading fsaverage_overlay_aalf_icbm-111_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
11 of 51: reading fsaverage_overlay_aalf_icbm-112_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
12 of 51: reading fsaverage_overlay_aalf_icbm-113_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
13 of 51: reading fsaverage_overlay_aalf_icbm-114_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
14 of 51: reading fsaverage_overlay_aalf_icbm-115_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
15 of 51: reading fsaverage_overlay_aalf_icbm-116_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
16 of 51: reading fsaverage_overlay_aalf_icbm-117_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
17 of 51: reading fsaverage_overlay_aalf_icbm-118_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
18 of 51: reading fsaverage_overlay_aalf_icbm-119_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
19 of 51: reading fsaverage_overlay_aalf_icbm-120_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
20 of 51: reading fsaverage_overlay_aalf_icbm-121_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
21 of 51: reading fsaverage_overlay_aalf_icbm-122_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
22 of 51: reading fsaverage_overlay_aalf_icbm-123_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
23 of 51: reading fsaverage_overlay_aalf_icbm-124_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
24 of 51: reading fsaverage_overlay_aalf_icbm-125_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
25 of 51: reading fsaverage_overlay_aalf_icbm-126_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
26 of 51: reading fsaverage_overlay_aalf_icbm-127_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
27 of 51: reading fsaverage_overlay_aalf_icbm-131_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
28 of 51: reading fsaverage_overlay_aalf_icbm-133_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
29 of 51: reading fsaverage_overlay_aalf_icbm-134_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
30 of 51: reading fsaverage_overlay_aalf_icbm-135_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
31 of 51: reading fsaverage_overlay_aalf_icbm-137_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
32 of 51: reading fsaverage_overlay_aalf_icbm-139_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
33 of 51: reading fsaverage_overlay_aalf_icbm-140_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
34 of 51: reading fsaverage_overlay_aalf_icbm-141_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
35 of 51: reading fsaverage_overlay_aalf_icbm-142_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
36 

Re: [Freesurfer] registering to fsaverage

[Bruce Fischl]

no problem.

Bruce
On Sun, 19 Jun 2016, Trisanna Sprung-Much wrote:


thanks Dr. Fischl - I think sometimes my emails don't get sent out on the
first try and so I resend - don't mean to spam everyone.
Don't know how I missed the mri_average option - I think I need vacation
too.

thanks and have a lovely Sunday!

Trisanna

--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Sun, Jun 19, 2016 at 11:22 AM, Bruce Fischl 
wrote:
  Hi Trisanna

  Doug is on vacation and his response time is likely to be pretty
  slow. If any emails go unanswered you should repost them in a
  week or two.

  As for this, if you overlays are mapped to fsaverage you can
  just use mri_average to average them.

  cheers
  Bruce



  On Sun, 19 Jun 2016, Trisanna Sprung-Much wrote:

Hi Doug

So all of my overlays for each subject have been
registered to fsaverage
using mri_surf2surf. I am now wondering how I could
create an average in
"fsaverage space" using these overlays - I
understand that
mris_make_average_surface is an option but I cannot
seem to find whether
this works for overlays and not just surfaces
(white, pial). I want to take
each subject overlay on fsaverage and average them
to get a probability map.

thanks

--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Fri, Jun 17, 2016 at 5:48 PM, Trisanna
Sprung-Much
 wrote:
      Hi Doug

So all of my sulci for each subject have been
registered to fsaverage
using mri_surf2surf. I am now wondering how I could
create an average
of a sulcus using these overlays - I understand that
mris_make_average_surface is an option but I cannot
seem to find
whether this works for overlays and not just
surfaces (white, pial). I
want to take each subject overlay on fsaverage and
average them to get
a probability map for a single sulcus.

thanks

Trisanna

--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Wed, Jun 15, 2016 at 6:25 PM, Trisanna
Sprung-Much
 wrote:
      worked beautifully. Thank you!

--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Wed, Jun 15, 2016 at 4:41 PM, Douglas N Greve
 wrote:
      Try surf2surf with --mapmethod nnf

      On 06/15/2016 04:25 PM, Trisanna Sprung-Much
wrote:
      > Hi Doug - yes they do actually, I was quite
      pleased. I did some trials
      > with other subjects and the mri_vol2surf all
looks
      good. Very similar
      > to what I had in our in-house software.
      >
      > Would things be better if I were to isolate
each
      sulcus as a .label
      > and then try the mri_label2label? Someone
      suggested perhaps the
      > colours are overlapping with the overlay
      >
      > --
      > Ph.D. Candidate
      > McGill University
      > Integrated Program in Neuroscience
      > Psychology
      >
      >
      > On Wed, Jun 15, 2016 at 4:10 PM, Douglas N
Greve
      > > wrote:
      >
      >     The problem is probably that the
vol2surf
      command did not properly
      >     sample the labels onto the surface. Do
the
      labels on subject 00350
      >     surfaces look ok?
      >
      >     On 06/15/2016 04:00 PM, Trisanna
Sprung-Much
      wrote:
      >     > thanks Dr. Fischl
      >     >
      >     > So the command seems to have worked! I
have
      copied what ran in my
      >     > terminal. When I open the test.mgz
overlay
      on the fsaverage pial
      >     > surface, things look ok but a bit
funny. I
      am wondering if there is
  

Re: [Freesurfer] registering to fsaverage

[Trisanna Sprung-Much]

thanks Dr. Fischl - I think sometimes my emails don't get sent out on the
first try and so I resend - don't mean to spam everyone.

Don't know how I missed the mri_average option - I think I need vacation
too.

thanks and have a lovely Sunday!

Trisanna

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


On Sun, Jun 19, 2016 at 11:22 AM, Bruce Fischl 
wrote:

> Hi Trisanna
>
> Doug is on vacation and his response time is likely to be pretty slow. If
> any emails go unanswered you should repost them in a week or two.
>
> As for this, if you overlays are mapped to fsaverage you can just use
> mri_average to average them.
>
> cheers
> Bruce
>
>
>
> On Sun, 19 Jun 2016, Trisanna Sprung-Much wrote:
>
> Hi Doug
>>
>> So all of my overlays for each subject have been registered to fsaverage
>> using mri_surf2surf. I am now wondering how I could create an average in
>> "fsaverage space" using these overlays - I understand that
>> mris_make_average_surface is an option but I cannot seem to find whether
>> this works for overlays and not just surfaces (white, pial). I want to
>> take
>> each subject overlay on fsaverage and average them to get a probability
>> map.
>>
>> thanks
>>
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Fri, Jun 17, 2016 at 5:48 PM, Trisanna Sprung-Much
>>  wrote:
>>   Hi Doug
>>
>> So all of my sulci for each subject have been registered to fsaverage
>> using mri_surf2surf. I am now wondering how I could create an average
>> of a sulcus using these overlays - I understand that
>> mris_make_average_surface is an option but I cannot seem to find
>> whether this works for overlays and not just surfaces (white, pial). I
>> want to take each subject overlay on fsaverage and average them to get
>> a probability map for a single sulcus.
>>
>> thanks
>>
>> Trisanna
>>
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Wed, Jun 15, 2016 at 6:25 PM, Trisanna Sprung-Much
>>  wrote:
>>   worked beautifully. Thank you!
>>
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Wed, Jun 15, 2016 at 4:41 PM, Douglas N Greve
>>  wrote:
>>   Try surf2surf with --mapmethod nnf
>>
>>   On 06/15/2016 04:25 PM, Trisanna Sprung-Much wrote:
>>   > Hi Doug - yes they do actually, I was quite
>>   pleased. I did some trials
>>   > with other subjects and the mri_vol2surf all looks
>>   good. Very similar
>>   > to what I had in our in-house software.
>>   >
>>   > Would things be better if I were to isolate each
>>   sulcus as a .label
>>   > and then try the mri_label2label? Someone
>>   suggested perhaps the
>>   > colours are overlapping with the overlay
>>   >
>>   > --
>>   > Ph.D. Candidate
>>   > McGill University
>>   > Integrated Program in Neuroscience
>>   > Psychology
>>   >
>>   >
>>   > On Wed, Jun 15, 2016 at 4:10 PM, Douglas N Greve
>>   > >   > wrote:
>>   >
>>   > The problem is probably that the vol2surf
>>   command did not properly
>>   > sample the labels onto the surface. Do the
>>   labels on subject 00350
>>   > surfaces look ok?
>>   >
>>   > On 06/15/2016 04:00 PM, Trisanna Sprung-Much
>>   wrote:
>>   > > thanks Dr. Fischl
>>   > >
>>   > > So the command seems to have worked! I have
>>   copied what ran in my
>>   > > terminal. When I open the test.mgz overlay
>>   on the fsaverage pial
>>   > > surface, things look ok but a bit funny. I
>>   am wondering if there is
>>   > > anything I can do to the mri_surf2surf
>>   command to improve the
>>   > > registration to fsaverage? *See my snapshots
>>   attached.*
>>   > >
>>   > > trisanna@kaplan:~$ mri_surf2surf
>>   --srcsubject 00350 --sval
>>   > >
>>   /data-01/trisanna/freesurfer/00350/surfaceoverlay_left.mgz
>>   > > --trgsubject fsaverage --tval test.mgz
>>   --hemi lh
>>   > > srcsubject = 00350
>>   > > srcval =
>>   >
>>/data-01/trisanna/freesurfer/00350/surfaceoverlay_left.mgz
>>   > > srctype=
>>   > > trgsubject = fsaverage
>>   > > trgval = test.mgz
>>   > > trgtype=
>>   > > srcsurfreg = sphere.reg
>>   > > trgsurfreg = sphere.reg
>>   > > srchemi= lh
>>   > > trghemi= lh
>>   > > frame  = 0
>>   > > fwhm-in= 0
>>   > > fwhm-out   = 0
>>   > > label-src  = (null)
>>   > > label-trg  = (null)
>>   > > 

Re: [Freesurfer] registering to fsaverage

[Bruce Fischl]

Hi Trisanna

Doug is on vacation and his response time is likely to be pretty slow. If 
any emails go unanswered you should repost them in a week or two.


As for this, if you overlays are mapped to fsaverage you can just use 
mri_average to average them.


cheers
Bruce



On Sun, 19 
Jun 2016, Trisanna Sprung-Much wrote:



Hi Doug

So all of my overlays for each subject have been registered to fsaverage
using mri_surf2surf. I am now wondering how I could create an average in
"fsaverage space" using these overlays - I understand that
mris_make_average_surface is an option but I cannot seem to find whether
this works for overlays and not just surfaces (white, pial). I want to take
each subject overlay on fsaverage and average them to get a probability map.

thanks

--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Fri, Jun 17, 2016 at 5:48 PM, Trisanna Sprung-Much
 wrote:
  Hi Doug

So all of my sulci for each subject have been registered to fsaverage
using mri_surf2surf. I am now wondering how I could create an average
of a sulcus using these overlays - I understand that
mris_make_average_surface is an option but I cannot seem to find
whether this works for overlays and not just surfaces (white, pial). I
want to take each subject overlay on fsaverage and average them to get
a probability map for a single sulcus.

thanks

Trisanna

--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Wed, Jun 15, 2016 at 6:25 PM, Trisanna Sprung-Much
 wrote:
  worked beautifully. Thank you!

--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Wed, Jun 15, 2016 at 4:41 PM, Douglas N Greve
 wrote:
  Try surf2surf with --mapmethod nnf

  On 06/15/2016 04:25 PM, Trisanna Sprung-Much wrote:
  > Hi Doug - yes they do actually, I was quite
  pleased. I did some trials
  > with other subjects and the mri_vol2surf all looks
  good. Very similar
  > to what I had in our in-house software.
  >
  > Would things be better if I were to isolate each
  sulcus as a .label
  > and then try the mri_label2label? Someone
  suggested perhaps the
  > colours are overlapping with the overlay
  >
  > --
  > Ph.D. Candidate
  > McGill University
  > Integrated Program in Neuroscience
  > Psychology
  >
  >
  > On Wed, Jun 15, 2016 at 4:10 PM, Douglas N Greve
  > > wrote:
  >
  >     The problem is probably that the vol2surf
  command did not properly
  >     sample the labels onto the surface. Do the
  labels on subject 00350
  >     surfaces look ok?
  >
  >     On 06/15/2016 04:00 PM, Trisanna Sprung-Much
  wrote:
  >     > thanks Dr. Fischl
  >     >
  >     > So the command seems to have worked! I have
  copied what ran in my
  >     > terminal. When I open the test.mgz overlay
  on the fsaverage pial
  >     > surface, things look ok but a bit funny. I
  am wondering if there is
  >     > anything I can do to the mri_surf2surf
  command to improve the
  >     > registration to fsaverage? *See my snapshots
  attached.*
  >     >
  >     > trisanna@kaplan:~$ mri_surf2surf
  --srcsubject 00350 --sval
  >     >
  /data-01/trisanna/freesurfer/00350/surfaceoverlay_left.mgz
  >     > --trgsubject fsaverage --tval test.mgz
  --hemi lh
  >     > srcsubject = 00350
  >     > srcval     =
  >   
   /data-01/trisanna/freesurfer/00350/surfaceoverlay_left.mgz
  >     > srctype    =
  >     > trgsubject = fsaverage
  >     > trgval     = test.mgz
  >     > trgtype    =
  >     > srcsurfreg = sphere.reg
  >     > trgsurfreg = sphere.reg
  >     > srchemi    = lh
  >     > trghemi    = lh
  >     > frame      = 0
  >     > fwhm-in    = 0
  >     > fwhm-out   = 0
  >     > label-src  = (null)
  >     > label-trg  = (null)
  >     > OKToRevFaceOrder  = 1
  >     > Reading source surface reg
  >     >
  /data-01/trisanna/freesurfer/00350/surf/lh.sphere.reg
  >     > Loading source data
  >     > Reading target surface reg
  >     >
  /data-01/trisanna/freesurfer/fsaverage/surf/lh.sphere.reg
  >     > Done
  >     > Mapping Source Volume onto Source Subject
  Surface
  >     > surf2surf_nnfr: building source hash
  (res=16).
  >     > Surf2Surf: Forward Loop (163842)
  >     >
  >     > surf2surf_nnfr: building target hash
  (res=16).
  >     > Surf2Surf: Reverse Loop (166912)
  >     > Reverse Loop had 41306 hits
  >     > Surf2Surf: Dividing by number of hits
  (163842)
  >     > INFO: nSrcLost = 0
  >     > nTrg121 = 

Re: [Freesurfer] registering to fsaverage

[Trisanna Sprung-Much]

Hi Doug

So all of my sulci for each subject have been registered to fsaverage using
mri_surf2surf. I am now wondering how I could create an average of a sulcus
using these overlays - I understand that mris_make_average_surface is an
option but I cannot seem to find whether this works for overlays and not
just surfaces (white, pial). I want to take each subject overlay on
fsaverage and average them to get a probability map for a single sulcus.

thanks

Trisanna

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


On Wed, Jun 15, 2016 at 6:25 PM, Trisanna Sprung-Much <
trisanna.sprung-m...@mail.mcgill.ca> wrote:

> worked beautifully. Thank you!
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Wed, Jun 15, 2016 at 4:41 PM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>> Try surf2surf with --mapmethod nnf
>>
>> On 06/15/2016 04:25 PM, Trisanna Sprung-Much wrote:
>> > Hi Doug - yes they do actually, I was quite pleased. I did some trials
>> > with other subjects and the mri_vol2surf all looks good. Very similar
>> > to what I had in our in-house software.
>> >
>> > Would things be better if I were to isolate each sulcus as a .label
>> > and then try the mri_label2label? Someone suggested perhaps the
>> > colours are overlapping with the overlay
>> >
>> > --
>> > Ph.D. Candidate
>> > McGill University
>> > Integrated Program in Neuroscience
>> > Psychology
>> >
>> >
>> > On Wed, Jun 15, 2016 at 4:10 PM, Douglas N Greve
>> > > wrote:
>> >
>> > The problem is probably that the vol2surf command did not properly
>> > sample the labels onto the surface. Do the labels on subject 00350
>> > surfaces look ok?
>> >
>> > On 06/15/2016 04:00 PM, Trisanna Sprung-Much wrote:
>> > > thanks Dr. Fischl
>> > >
>> > > So the command seems to have worked! I have copied what ran in my
>> > > terminal. When I open the test.mgz overlay on the fsaverage pial
>> > > surface, things look ok but a bit funny. I am wondering if there
>> is
>> > > anything I can do to the mri_surf2surf command to improve the
>> > > registration to fsaverage? *See my snapshots attached.*
>> > >
>> > > trisanna@kaplan:~$ mri_surf2surf --srcsubject 00350 --sval
>> > > /data-01/trisanna/freesurfer/00350/surfaceoverlay_left.mgz
>> > > --trgsubject fsaverage --tval test.mgz --hemi lh
>> > > srcsubject = 00350
>> > > srcval =
>> > /data-01/trisanna/freesurfer/00350/surfaceoverlay_left.mgz
>> > > srctype=
>> > > trgsubject = fsaverage
>> > > trgval = test.mgz
>> > > trgtype=
>> > > srcsurfreg = sphere.reg
>> > > trgsurfreg = sphere.reg
>> > > srchemi= lh
>> > > trghemi= lh
>> > > frame  = 0
>> > > fwhm-in= 0
>> > > fwhm-out   = 0
>> > > label-src  = (null)
>> > > label-trg  = (null)
>> > > OKToRevFaceOrder  = 1
>> > > Reading source surface reg
>> > > /data-01/trisanna/freesurfer/00350/surf/lh.sphere.reg
>> > > Loading source data
>> > > Reading target surface reg
>> > > /data-01/trisanna/freesurfer/fsaverage/surf/lh.sphere.reg
>> > > Done
>> > > Mapping Source Volume onto Source Subject Surface
>> > > surf2surf_nnfr: building source hash (res=16).
>> > > Surf2Surf: Forward Loop (163842)
>> > >
>> > > surf2surf_nnfr: building target hash (res=16).
>> > > Surf2Surf: Reverse Loop (166912)
>> > > Reverse Loop had 41306 hits
>> > > Surf2Surf: Dividing by number of hits (163842)
>> > > INFO: nSrcLost = 0
>> > > nTrg121 = 132490, nTrgMulti = 31352, MnTrgMultiHits = 2.31749
>> > > nSrc121 = 137180, nSrcLost = 0, nSrcMulti = 29732, MnSrcMultiHits
>> =
>> > > 2.28602
>> > > Saving target data
>> > > Saving to test.mgz
>> > >
>> > > best
>> > >
>> > > Trisanna
>> > >
>> > > --
>> > > Ph.D. Candidate
>> > > McGill University
>> > > Integrated Program in Neuroscience
>> > > Psychology
>> > >
>> > >
>> > > On Wed, Jun 15, 2016 at 12:13 PM, Bruce Fischl
>> > > 
>> > > > >> wrote:
>> > >
>> > > Hi Trisanna
>> > >
>> > > you would only use those options of if you were transforming
>> > a surface
>> > > Bruce
>> > >
>> > >
>> > > On Wed, 15 Jun 2016, Trisanna Sprung-Much wrote:
>> > >
>> > > thanks Dr. Fischl
>> > >
>> > > I assume that for surface overlays one cannot specify
>> > > --sval-xyz and --tval-xyz or the command will treat the
>> > input
>> > > as a surface
>> > > itself?
>> > >
>> > > best
>> > >
>> > > Trisanna
>> > >

Re: [Freesurfer] registering to fsaverage

[Trisanna Sprung-Much]

worked beautifully. Thank you!

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


On Wed, Jun 15, 2016 at 4:41 PM, Douglas N Greve 
wrote:

> Try surf2surf with --mapmethod nnf
>
> On 06/15/2016 04:25 PM, Trisanna Sprung-Much wrote:
> > Hi Doug - yes they do actually, I was quite pleased. I did some trials
> > with other subjects and the mri_vol2surf all looks good. Very similar
> > to what I had in our in-house software.
> >
> > Would things be better if I were to isolate each sulcus as a .label
> > and then try the mri_label2label? Someone suggested perhaps the
> > colours are overlapping with the overlay
> >
> > --
> > Ph.D. Candidate
> > McGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> > On Wed, Jun 15, 2016 at 4:10 PM, Douglas N Greve
> > > wrote:
> >
> > The problem is probably that the vol2surf command did not properly
> > sample the labels onto the surface. Do the labels on subject 00350
> > surfaces look ok?
> >
> > On 06/15/2016 04:00 PM, Trisanna Sprung-Much wrote:
> > > thanks Dr. Fischl
> > >
> > > So the command seems to have worked! I have copied what ran in my
> > > terminal. When I open the test.mgz overlay on the fsaverage pial
> > > surface, things look ok but a bit funny. I am wondering if there is
> > > anything I can do to the mri_surf2surf command to improve the
> > > registration to fsaverage? *See my snapshots attached.*
> > >
> > > trisanna@kaplan:~$ mri_surf2surf --srcsubject 00350 --sval
> > > /data-01/trisanna/freesurfer/00350/surfaceoverlay_left.mgz
> > > --trgsubject fsaverage --tval test.mgz --hemi lh
> > > srcsubject = 00350
> > > srcval =
> > /data-01/trisanna/freesurfer/00350/surfaceoverlay_left.mgz
> > > srctype=
> > > trgsubject = fsaverage
> > > trgval = test.mgz
> > > trgtype=
> > > srcsurfreg = sphere.reg
> > > trgsurfreg = sphere.reg
> > > srchemi= lh
> > > trghemi= lh
> > > frame  = 0
> > > fwhm-in= 0
> > > fwhm-out   = 0
> > > label-src  = (null)
> > > label-trg  = (null)
> > > OKToRevFaceOrder  = 1
> > > Reading source surface reg
> > > /data-01/trisanna/freesurfer/00350/surf/lh.sphere.reg
> > > Loading source data
> > > Reading target surface reg
> > > /data-01/trisanna/freesurfer/fsaverage/surf/lh.sphere.reg
> > > Done
> > > Mapping Source Volume onto Source Subject Surface
> > > surf2surf_nnfr: building source hash (res=16).
> > > Surf2Surf: Forward Loop (163842)
> > >
> > > surf2surf_nnfr: building target hash (res=16).
> > > Surf2Surf: Reverse Loop (166912)
> > > Reverse Loop had 41306 hits
> > > Surf2Surf: Dividing by number of hits (163842)
> > > INFO: nSrcLost = 0
> > > nTrg121 = 132490, nTrgMulti = 31352, MnTrgMultiHits = 2.31749
> > > nSrc121 = 137180, nSrcLost = 0, nSrcMulti = 29732, MnSrcMultiHits =
> > > 2.28602
> > > Saving target data
> > > Saving to test.mgz
> > >
> > > best
> > >
> > > Trisanna
> > >
> > > --
> > > Ph.D. Candidate
> > > McGill University
> > > Integrated Program in Neuroscience
> > > Psychology
> > >
> > >
> > > On Wed, Jun 15, 2016 at 12:13 PM, Bruce Fischl
> > > 
> >  > >> wrote:
> > >
> > > Hi Trisanna
> > >
> > > you would only use those options of if you were transforming
> > a surface
> > > Bruce
> > >
> > >
> > > On Wed, 15 Jun 2016, Trisanna Sprung-Much wrote:
> > >
> > > thanks Dr. Fischl
> > >
> > > I assume that for surface overlays one cannot specify
> > > --sval-xyz and --tval-xyz or the command will treat the
> > input
> > > as a surface
> > > itself?
> > >
> > > best
> > >
> > > Trisanna
> > >
> > >
> > >
> > >
> > > --
> > > Ph.D. CandidateMcGill University
> > > Integrated Program in Neuroscience
> > > Psychology
> > >
> > >
> > > On Wed, Jun 15, 2016 at 11:11 AM, Bruce Fischl
> > >  > 
> > >  > >> wrote:
> > >   Hi Trisanna
> > >
> > >   you don't need to inflate the overlays. They can just
> > > use the existing surface-based (sphere.reg) registration.
> > >
> > >   cheers
> > >   Bruce
> > >   On Wed, 15 Jun 2016, Trisanna 

Re: [Freesurfer] registering to fsaverage

[Douglas N Greve]

Try surf2surf with --mapmethod nnf

On 06/15/2016 04:25 PM, Trisanna Sprung-Much wrote:
> Hi Doug - yes they do actually, I was quite pleased. I did some trials 
> with other subjects and the mri_vol2surf all looks good. Very similar 
> to what I had in our in-house software.
>
> Would things be better if I were to isolate each sulcus as a .label 
> and then try the mri_label2label? Someone suggested perhaps the 
> colours are overlapping with the overlay
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Wed, Jun 15, 2016 at 4:10 PM, Douglas N Greve 
> > wrote:
>
> The problem is probably that the vol2surf command did not properly
> sample the labels onto the surface. Do the labels on subject 00350
> surfaces look ok?
>
> On 06/15/2016 04:00 PM, Trisanna Sprung-Much wrote:
> > thanks Dr. Fischl
> >
> > So the command seems to have worked! I have copied what ran in my
> > terminal. When I open the test.mgz overlay on the fsaverage pial
> > surface, things look ok but a bit funny. I am wondering if there is
> > anything I can do to the mri_surf2surf command to improve the
> > registration to fsaverage? *See my snapshots attached.*
> >
> > trisanna@kaplan:~$ mri_surf2surf --srcsubject 00350 --sval
> > /data-01/trisanna/freesurfer/00350/surfaceoverlay_left.mgz
> > --trgsubject fsaverage --tval test.mgz --hemi lh
> > srcsubject = 00350
> > srcval =
> /data-01/trisanna/freesurfer/00350/surfaceoverlay_left.mgz
> > srctype=
> > trgsubject = fsaverage
> > trgval = test.mgz
> > trgtype=
> > srcsurfreg = sphere.reg
> > trgsurfreg = sphere.reg
> > srchemi= lh
> > trghemi= lh
> > frame  = 0
> > fwhm-in= 0
> > fwhm-out   = 0
> > label-src  = (null)
> > label-trg  = (null)
> > OKToRevFaceOrder  = 1
> > Reading source surface reg
> > /data-01/trisanna/freesurfer/00350/surf/lh.sphere.reg
> > Loading source data
> > Reading target surface reg
> > /data-01/trisanna/freesurfer/fsaverage/surf/lh.sphere.reg
> > Done
> > Mapping Source Volume onto Source Subject Surface
> > surf2surf_nnfr: building source hash (res=16).
> > Surf2Surf: Forward Loop (163842)
> >
> > surf2surf_nnfr: building target hash (res=16).
> > Surf2Surf: Reverse Loop (166912)
> > Reverse Loop had 41306 hits
> > Surf2Surf: Dividing by number of hits (163842)
> > INFO: nSrcLost = 0
> > nTrg121 = 132490, nTrgMulti = 31352, MnTrgMultiHits = 2.31749
> > nSrc121 = 137180, nSrcLost = 0, nSrcMulti = 29732, MnSrcMultiHits =
> > 2.28602
> > Saving target data
> > Saving to test.mgz
> >
> > best
> >
> > Trisanna
> >
> > --
> > Ph.D. Candidate
> > McGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> > On Wed, Jun 15, 2016 at 12:13 PM, Bruce Fischl
> > 
>  >> wrote:
> >
> > Hi Trisanna
> >
> > you would only use those options of if you were transforming
> a surface
> > Bruce
> >
> >
> > On Wed, 15 Jun 2016, Trisanna Sprung-Much wrote:
> >
> > thanks Dr. Fischl
> >
> > I assume that for surface overlays one cannot specify
> > --sval-xyz and --tval-xyz or the command will treat the
> input
> > as a surface
> > itself?
> >
> > best
> >
> > Trisanna
> >
> >
> >
> >
> > --
> > Ph.D. CandidateMcGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> > On Wed, Jun 15, 2016 at 11:11 AM, Bruce Fischl
> >  
> >  >> wrote:
> >   Hi Trisanna
> >
> >   you don't need to inflate the overlays. They can just
> > use the existing surface-based (sphere.reg) registration.
> >
> >   cheers
> >   Bruce
> >   On Wed, 15 Jun 2016, Trisanna Sprung-Much wrote:
> >
> > Hi there
> > So I have sulcal labels from another software
> > (.mnc format) from which I am trying to generate some
> > probability maps. I was able
> > to convert the .mnc to .mgz surface overlay
> using
> > mri_vol2surf for my MRIs after running all MRIs in
> > recon-all. So, now I 

Re: [Freesurfer] registering to fsaverage

[Trisanna Sprung-Much]

Hi Doug - yes they do actually, I was quite pleased. I did some trials with
other subjects and the mri_vol2surf all looks good. Very similar to what I
had in our in-house software.

Would things be better if I were to isolate each sulcus as a .label and
then try the mri_label2label? Someone suggested perhaps the colours are
overlapping with the overlay

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


On Wed, Jun 15, 2016 at 4:10 PM, Douglas N Greve 
wrote:

> The problem is probably that the vol2surf command did not properly
> sample the labels onto the surface. Do the labels on subject 00350
> surfaces look ok?
>
> On 06/15/2016 04:00 PM, Trisanna Sprung-Much wrote:
> > thanks Dr. Fischl
> >
> > So the command seems to have worked! I have copied what ran in my
> > terminal. When I open the test.mgz overlay on the fsaverage pial
> > surface, things look ok but a bit funny. I am wondering if there is
> > anything I can do to the mri_surf2surf command to improve the
> > registration to fsaverage? *See my snapshots attached.*
> >
> > trisanna@kaplan:~$ mri_surf2surf --srcsubject 00350 --sval
> > /data-01/trisanna/freesurfer/00350/surfaceoverlay_left.mgz
> > --trgsubject fsaverage --tval test.mgz --hemi lh
> > srcsubject = 00350
> > srcval = /data-01/trisanna/freesurfer/00350/surfaceoverlay_left.mgz
> > srctype=
> > trgsubject = fsaverage
> > trgval = test.mgz
> > trgtype=
> > srcsurfreg = sphere.reg
> > trgsurfreg = sphere.reg
> > srchemi= lh
> > trghemi= lh
> > frame  = 0
> > fwhm-in= 0
> > fwhm-out   = 0
> > label-src  = (null)
> > label-trg  = (null)
> > OKToRevFaceOrder  = 1
> > Reading source surface reg
> > /data-01/trisanna/freesurfer/00350/surf/lh.sphere.reg
> > Loading source data
> > Reading target surface reg
> > /data-01/trisanna/freesurfer/fsaverage/surf/lh.sphere.reg
> > Done
> > Mapping Source Volume onto Source Subject Surface
> > surf2surf_nnfr: building source hash (res=16).
> > Surf2Surf: Forward Loop (163842)
> >
> > surf2surf_nnfr: building target hash (res=16).
> > Surf2Surf: Reverse Loop (166912)
> > Reverse Loop had 41306 hits
> > Surf2Surf: Dividing by number of hits (163842)
> > INFO: nSrcLost = 0
> > nTrg121 = 132490, nTrgMulti = 31352, MnTrgMultiHits = 2.31749
> > nSrc121 = 137180, nSrcLost = 0, nSrcMulti = 29732, MnSrcMultiHits =
> > 2.28602
> > Saving target data
> > Saving to test.mgz
> >
> > best
> >
> > Trisanna
> >
> > --
> > Ph.D. Candidate
> > McGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> > On Wed, Jun 15, 2016 at 12:13 PM, Bruce Fischl
> > > wrote:
> >
> > Hi Trisanna
> >
> > you would only use those options of if you were transforming a
> surface
> > Bruce
> >
> >
> > On Wed, 15 Jun 2016, Trisanna Sprung-Much wrote:
> >
> > thanks Dr. Fischl
> >
> > I assume that for surface overlays one cannot specify
> > --sval-xyz and --tval-xyz or the command will treat the input
> > as a surface
> > itself?
> >
> > best
> >
> > Trisanna
> >
> >
> >
> >
> > --
> > Ph.D. CandidateMcGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> > On Wed, Jun 15, 2016 at 11:11 AM, Bruce Fischl
> >  > > wrote:
> >   Hi Trisanna
> >
> >   you don't need to inflate the overlays. They can just
> > use the existing surface-based (sphere.reg) registration.
> >
> >   cheers
> >   Bruce
> >   On Wed, 15 Jun 2016, Trisanna Sprung-Much wrote:
> >
> > Hi there
> > So I have sulcal labels from another software
> > (.mnc format) from which I am trying to generate some
> > probability maps. I was able
> > to convert the .mnc to .mgz surface overlay using
> > mri_vol2surf for my MRIs after running all MRIs in
> > recon-all. So, now I have
> > all my painted voxels as surface overlays, as I
> > was instructed to do a few months ago.
> >
> > I was told that the next step would be to use
> > mri_surf2surf to resample the overlays to fsaverage.
> >
> > I am a bit confused as I would think that the next
> > step would be to take the surface overlays and
> > inflate them before I register
> > them to fsaverage. I see that when recon-all runs,
> > it computes the registration of the MRI surface to
> > fsaverage and saves it as
> > sphere.reg. Is there a way I can inflate my
> > surface overlays in a similar manner and then apply this
> >   

Re: [Freesurfer] registering to fsaverage

[Douglas N Greve]

The problem is probably that the vol2surf command did not properly 
sample the labels onto the surface. Do the labels on subject 00350 
surfaces look ok?

On 06/15/2016 04:00 PM, Trisanna Sprung-Much wrote:
> thanks Dr. Fischl
>
> So the command seems to have worked! I have copied what ran in my 
> terminal. When I open the test.mgz overlay on the fsaverage pial 
> surface, things look ok but a bit funny. I am wondering if there is 
> anything I can do to the mri_surf2surf command to improve the 
> registration to fsaverage? *See my snapshots attached.*
>
> trisanna@kaplan:~$ mri_surf2surf --srcsubject 00350 --sval 
> /data-01/trisanna/freesurfer/00350/surfaceoverlay_left.mgz 
> --trgsubject fsaverage --tval test.mgz --hemi lh
> srcsubject = 00350
> srcval = /data-01/trisanna/freesurfer/00350/surfaceoverlay_left.mgz
> srctype=
> trgsubject = fsaverage
> trgval = test.mgz
> trgtype=
> srcsurfreg = sphere.reg
> trgsurfreg = sphere.reg
> srchemi= lh
> trghemi= lh
> frame  = 0
> fwhm-in= 0
> fwhm-out   = 0
> label-src  = (null)
> label-trg  = (null)
> OKToRevFaceOrder  = 1
> Reading source surface reg 
> /data-01/trisanna/freesurfer/00350/surf/lh.sphere.reg
> Loading source data
> Reading target surface reg 
> /data-01/trisanna/freesurfer/fsaverage/surf/lh.sphere.reg
> Done
> Mapping Source Volume onto Source Subject Surface
> surf2surf_nnfr: building source hash (res=16).
> Surf2Surf: Forward Loop (163842)
>
> surf2surf_nnfr: building target hash (res=16).
> Surf2Surf: Reverse Loop (166912)
> Reverse Loop had 41306 hits
> Surf2Surf: Dividing by number of hits (163842)
> INFO: nSrcLost = 0
> nTrg121 = 132490, nTrgMulti = 31352, MnTrgMultiHits = 2.31749
> nSrc121 = 137180, nSrcLost = 0, nSrcMulti = 29732, MnSrcMultiHits = 
> 2.28602
> Saving target data
> Saving to test.mgz
>
> best
>
> Trisanna
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Wed, Jun 15, 2016 at 12:13 PM, Bruce Fischl 
> > wrote:
>
> Hi Trisanna
>
> you would only use those options of if you were transforming a surface
> Bruce
>
>
> On Wed, 15 Jun 2016, Trisanna Sprung-Much wrote:
>
> thanks Dr. Fischl
>
> I assume that for surface overlays one cannot specify
> --sval-xyz and --tval-xyz or the command will treat the input
> as a surface
> itself?
>
> best
>
> Trisanna
>
>
>
>
> --
> Ph.D. CandidateMcGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Wed, Jun 15, 2016 at 11:11 AM, Bruce Fischl
>  > wrote:
>   Hi Trisanna
>
>   you don't need to inflate the overlays. They can just
> use the existing surface-based (sphere.reg) registration.
>
>   cheers
>   Bruce
>   On Wed, 15 Jun 2016, Trisanna Sprung-Much wrote:
>
> Hi there
> So I have sulcal labels from another software
> (.mnc format) from which I am trying to generate some
> probability maps. I was able
> to convert the .mnc to .mgz surface overlay using
> mri_vol2surf for my MRIs after running all MRIs in
> recon-all. So, now I have
> all my painted voxels as surface overlays, as I
> was instructed to do a few months ago.
>
> I was told that the next step would be to use
> mri_surf2surf to resample the overlays to fsaverage.
>
> I am a bit confused as I would think that the next
> step would be to take the surface overlays and
> inflate them before I register
> them to fsaverage. I see that when recon-all runs,
> it computes the registration of the MRI surface to
> fsaverage and saves it as
> sphere.reg. Is there a way I can inflate my
> surface overlays in a similar manner and then apply this
> same registration to my
> surface overlays? Or am I missing something?
>
> thanks very much!
>
> Trisanna
>
>
> --
> Ph.D. CandidateMcGill University
> Integrated Program in Neuroscience
> Psychology
>
>
>
>
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> 
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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 

Re: [Freesurfer] registering to fsaverage

[Bruce Fischl]

Hi Trisanna

you would only use those options of if you were transforming a surface
Bruce


On Wed, 15 Jun 2016, Trisanna Sprung-Much wrote:


thanks Dr. Fischl

I assume that for surface overlays one cannot specify --sval-xyz and --tval-xyz 
or the command will treat the input as a surface
itself?

best

Trisanna




--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Wed, Jun 15, 2016 at 11:11 AM, Bruce Fischl  
wrote:
  Hi Trisanna

  you don't need to inflate the overlays. They can just use the existing 
surface-based (sphere.reg) registration.

  cheers
  Bruce
  On Wed, 15 Jun 2016, Trisanna Sprung-Much wrote:

Hi there
So I have sulcal labels from another software (.mnc format) from 
which I am trying to generate some
probability maps. I was able
to convert the .mnc to .mgz surface overlay using mri_vol2surf for 
my MRIs after running all MRIs in
recon-all. So, now I have
all my painted voxels as surface overlays, as I was instructed to 
do a few months ago.

I was told that the next step would be to use mri_surf2surf to 
resample the overlays to fsaverage. 

I am a bit confused as I would think that the next step would be to 
take the surface overlays and
inflate them before I register
them to fsaverage. I see that when recon-all runs, it computes the 
registration of the MRI surface to
fsaverage and saves it as
sphere.reg. Is there a way I can inflate my surface overlays in a 
similar manner and then apply this
same registration to my
surface overlays? Or am I missing something?

thanks very much!

Trisanna


--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology




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Re: [Freesurfer] registering to fsaverage

[Trisanna Sprung-Much]

thanks Dr. Fischl

I assume that for surface overlays one cannot specify --sval-xyz and
--tval-xyz or the command will treat the input as a surface itself?

best

Trisanna




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


On Wed, Jun 15, 2016 at 11:11 AM, Bruce Fischl 
wrote:

> Hi Trisanna
>
> you don't need to inflate the overlays. They can just use the existing
> surface-based (sphere.reg) registration.
>
> cheers
> Bruce
> On Wed, 15 Jun 2016, Trisanna Sprung-Much wrote:
>
> Hi there
>> So I have sulcal labels from another software (.mnc format) from which I
>> am trying to generate some probability maps. I was able
>> to convert the .mnc to .mgz surface overlay using mri_vol2surf for my
>> MRIs after running all MRIs in recon-all. So, now I have
>> all my painted voxels as surface overlays, as I was instructed to do a
>> few months ago.
>>
>> I was told that the next step would be to use mri_surf2surf to resample
>> the overlays to fsaverage.
>>
>> I am a bit confused as I would think that the next step would be to take
>> the surface overlays and inflate them before I register
>> them to fsaverage. I see that when recon-all runs, it computes the
>> registration of the MRI surface to fsaverage and saves it as
>> sphere.reg. Is there a way I can inflate my surface overlays in a similar
>> manner and then apply this same registration to my
>> surface overlays? Or am I missing something?
>>
>> thanks very much!
>>
>> Trisanna
>>
>>
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>>
>>
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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
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> but does not contain patient information, please contact the sender and
> properly
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Re: [Freesurfer] registering to fsaverage

[Bruce Fischl]

Hi Trisanna

you don't need to inflate the overlays. They can just use the existing 
surface-based (sphere.reg) registration.


cheers
Bruce
On Wed, 15 Jun 2016, 
Trisanna Sprung-Much wrote:



Hi there
So I have sulcal labels from another software (.mnc format) from which I am 
trying to generate some probability maps. I was able
to convert the .mnc to .mgz surface overlay using mri_vol2surf for my MRIs 
after running all MRIs in recon-all. So, now I have
all my painted voxels as surface overlays, as I was instructed to do a few 
months ago.

I was told that the next step would be to use mri_surf2surf to resample the 
overlays to fsaverage. 

I am a bit confused as I would think that the next step would be to take the 
surface overlays and inflate them before I register
them to fsaverage. I see that when recon-all runs, it computes the registration 
of the MRI surface to fsaverage and saves it as
sphere.reg. Is there a way I can inflate my surface overlays in a similar 
manner and then apply this same registration to my
surface overlays? Or am I missing something?

thanks very much!

Trisanna


--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology



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contains patient information, please contact the Partners Compliance HelpLine at
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