Re: [Freesurfer] mri_average vs mri_concat

2016-11-07 Thread Douglas N Greve 
I did not see binary values. The values were 255 in the mnc volume. The 
caveat here is that I can only read it in using FS, so if there is 
something burried in the FS code that causes the values to change from 1 
to 255, I might not see it. Is there a minc viewer you can use to 
resolve this?


On 11/07/2016 04:23 PM, Trisanna Sprung-Much wrote:
> Hi Doug
>
> I am confused. The values of the input .mnc for mri_vol2surf are 0 and 
> 1.*I attach a snapshot using an inhouse software where you can see the 
> "1" highlighted in blue.* We also used the following command to ensure 
> they are 0 and 1:
>
> minclookup ' label_folder '/labels_final_minc1.mnc ' label_folder 
> '/label_aalf.mnc -discrete -lut_string "4 1" -clobber --> this 
> extracts my id 4 that I painted this sulcus with and gives it a value 
> of 1.
>
> Do you mean you do not see the binary values on your end?
>
> Trisanna
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Mon, Nov 7, 2016 at 3:53 PM, Douglas N Greve 
> > wrote:
>
> It looks like the input has values of 255 and 0, not 1 and 0. How
> do you
> verify that the values are 0 and 1?
>
>
> On 11/07/2016 03:43 PM, Trisanna Sprung-Much wrote:
> > Hi Doug
> >
> > I have uploaded the label_aalf.mnc and testsurfaceoverlay.mgz
> >
> > Here is an example of the mri_vol2surf that I use
> >
> > *
> > trisanna@kaplan:~$ mri_vol2surf --mov
> > /data-01/trisanna/freesurfer/icbm-113/label/label_aalf.mnc --o
> > /data-01/trisanna/freesurfer/icbm-113/testsurfaceoverlay.mgz
> --hemi lh
> > *--surf pial --regheader icbm-113
> > srcvol = /data-01/trisanna/freesurfer/icbm-113/label/label_aalf.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/icbm-113/mri/orig.mgz as target
> > reference.
> > Reading surface /data-01/trisanna/freesurfer/icbm-113/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 = 53960
> > Writing to
> /data-01/trisanna/freesurfer/icbm-113/testsurfaceoverlay.mgz
> > Dim: 159741 1 1
> > *
> > When I open this in Freeview, the values are either 0 or 255. However,
> > they were binary (0 or 1) in the label_aalf.mnc input file.*
> >
> >
> > The mri_concat command that I ran on label_aalf for 20
> hemispheres is:
> >
> > *trisanna@kaplan:~$ mri_concat
> >
> 
> /data-01/trisanna/freesurfer/fsaverage/committee_meeting/DISPLAY_overlays_fsaverage_left/aalf_lh/*.mgz
> > --o
> >
> 
> /data-01/trisanna/freesurfer/fsaverage/committee_meeting/DISPLAY_overlays_fsaverage_left/aalf_lh/mri_concat_test.mgz
> > --mean*
> > ninputs = 20
> > Checking inputs
> > nframestot = 20
> > Allocing output
> > Done allocing
> > nframes = 20
> > Computing mean across frames
> > Writing to
> >
> 
> /data-01/trisanna/freesurfer/fsaverage/committee_meeting/DISPLAY_overlays_fsaverage_left/aalf_lh/mri_concat_test.mgz
> >
> >
> > thanks
> >
> > Trisanna
> >
> > --
> > Ph.D. Candidate
> > McGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> > On Tue, Nov 1, 2016 at 2:45 PM, Douglas N Greve
> > 
>  >> wrote:
> >
> > Can you send me the mri_concat command and also upload the
> input files
> > to our filedrop?
> >
> > https://gate.nmr.mgh.harvard.edu/filedrop2
> 
> >  >
> >
> > On 11/01/2016 02:31 PM, Trisanna Sprung-Much wrote:
> > > Does anyone know who wrote the script for mri_concat? I
> would really
> > > like to get this figured out.
> > >
> > > thanks
> > >
> > > Trisanna
> > >
> > > --
> > > Ph.D. Candidate
> > > McGill University
> > > Integrated Program in Neuroscience
> > > Psychology
> > >
> > >
> > > On Fri, Oct 21, 2016 at 12:13 PM, Trisanna Sprung-Much
> > >  
> >

Re: [Freesurfer] mri_average vs mri_concat

2016-11-07 Thread Douglas N Greve 
It looks like the input has values of 255 and 0, not 1 and 0. How do you 
verify that the values are 0 and 1?


On 11/07/2016 03:43 PM, Trisanna Sprung-Much wrote:
> Hi Doug
>
> I have uploaded the label_aalf.mnc and testsurfaceoverlay.mgz
>
> Here is an example of the mri_vol2surf that I use
>
> *
> trisanna@kaplan:~$ mri_vol2surf --mov 
> /data-01/trisanna/freesurfer/icbm-113/label/label_aalf.mnc --o 
> /data-01/trisanna/freesurfer/icbm-113/testsurfaceoverlay.mgz --hemi lh 
> *--surf pial --regheader icbm-113
> srcvol = /data-01/trisanna/freesurfer/icbm-113/label/label_aalf.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/icbm-113/mri/orig.mgz as target 
> reference.
> Reading surface /data-01/trisanna/freesurfer/icbm-113/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 = 53960
> Writing to /data-01/trisanna/freesurfer/icbm-113/testsurfaceoverlay.mgz
> Dim: 159741 1 1
> *
> When I open this in Freeview, the values are either 0 or 255. However, 
> they were binary (0 or 1) in the label_aalf.mnc input file.*
>
>
> The mri_concat command that I ran on label_aalf for 20 hemispheres is:
>
> *trisanna@kaplan:~$ mri_concat 
> /data-01/trisanna/freesurfer/fsaverage/committee_meeting/DISPLAY_overlays_fsaverage_left/aalf_lh/*.mgz
>  
> --o 
> /data-01/trisanna/freesurfer/fsaverage/committee_meeting/DISPLAY_overlays_fsaverage_left/aalf_lh/mri_concat_test.mgz
>  
> --mean*
> ninputs = 20
> Checking inputs
> nframestot = 20
> Allocing output
> Done allocing
> nframes = 20
> Computing mean across frames
> Writing to 
> /data-01/trisanna/freesurfer/fsaverage/committee_meeting/DISPLAY_overlays_fsaverage_left/aalf_lh/mri_concat_test.mgz
>
>
> thanks
>
> Trisanna
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Tue, Nov 1, 2016 at 2:45 PM, Douglas N Greve 
> > wrote:
>
> Can you send me the mri_concat command and also upload the input files
> to our filedrop?
>
> https://gate.nmr.mgh.harvard.edu/filedrop2
> 
>
> On 11/01/2016 02:31 PM, Trisanna Sprung-Much wrote:
> > Does anyone know who wrote the script for mri_concat? I would really
> > like to get this figured out.
> >
> > thanks
> >
> > Trisanna
> >
> > --
> > Ph.D. Candidate
> > McGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> > On Fri, Oct 21, 2016 at 12:13 PM, Trisanna Sprung-Much
> >  
> >  >> wrote:
> >
> > thanks Bruce - I had indeed used this months ago but at the
> > workshop this semester Doug had suggested mri_concat as it is a
> > newer command and also doesn't blur the data. I am just having
> > problems creating percentage values with mri_concat.
> >
> > *Would you know why mri_vol2surf is taking a binary minc
> file and
> > creating values ranging from 0-255 that mri_concat then
> preserves?*
> >
> > best
> > Trisanna
> >
> > --
> > Ph.D. Candidate
> > McGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> > On Fri, Oct 21, 2016 at 9:29 AM, Bruce Fischl
> >  
>  >>
> > wrote:
> >
> > Hi Trisanna
> >
> > not sure about mri_concat, but mri_average -noconform -p ...
> > should do the trick
> >
> > cheers
> > Bruce
> > On Wed, 19 Oct 2016, Trisanna Sprung-Much wrote:
> >
> > Something weird is happening with mri_vol2surf - even
> > though the data looks great, the values are odd
> > which carries over when I try to average with
> mri_concat.
> > I would just like to get percentage values
> > with mri_concat.
> > thanks!
> >
> > Trisanna
> >
> > --
> > Ph.D. CandidateMcGill University
> >
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> > On Mon, Oct 17, 2016 at 5:21 PM,

Re: [Freesurfer] mri_average vs mri_concat

2016-11-01 Thread Douglas N Greve 
Can you send me the mri_concat command and also upload the input files 
to our filedrop?

https://gate.nmr.mgh.harvard.edu/filedrop2

On 11/01/2016 02:31 PM, Trisanna Sprung-Much wrote:
> Does anyone know who wrote the script for mri_concat? I would really 
> like to get this figured out.
>
> thanks
>
> Trisanna
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Fri, Oct 21, 2016 at 12:13 PM, Trisanna Sprung-Much 
>  > wrote:
>
> thanks Bruce - I had indeed used this months ago but at the
> workshop this semester Doug had suggested mri_concat as it is a
> newer command and also doesn't blur the data. I am just having
> problems creating percentage values with mri_concat.
>
> *Would you know why mri_vol2surf is taking a binary minc file and
> creating values ranging from 0-255 that mri_concat then preserves?*
>
> best
> Trisanna
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Fri, Oct 21, 2016 at 9:29 AM, Bruce Fischl
> >
> wrote:
>
> Hi Trisanna
>
> not sure about mri_concat, but mri_average -noconform -p ...
> should do the trick
>
> cheers
> Bruce
> On Wed, 19 Oct 2016, Trisanna Sprung-Much wrote:
>
> Something weird is happening with mri_vol2surf - even
> though the data looks great, the values are odd
> which carries over when I try to average with mri_concat.
> I would just like to get percentage values
> with mri_concat.
> thanks!
>
> Trisanna
>
> --
> Ph.D. CandidateMcGill University
>
> Integrated Program in Neuroscience
> Psychology
>
>
> On Mon, Oct 17, 2016 at 5:21 PM, Trisanna Sprung-Much
>  > wrote:
>   Hi Doug
>
> Here is what I ran:
>
> trisanna@kaplan:~$ mri_vol2surf --mov
> /data-01/trisanna/freesurfer/icbm-113/label/label_aalf.mnc
> --o
> /data-01/trisanna/freesurfer/icbm-113/testsurfaceoverlay.mgz
> --hemi lh --surf pial --regheader
> icbm-113
> srcvol =
> /data-01/trisanna/freesurfer/icbm-113/label/label_aalf.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/icbm-113/mri/orig.mgz
> as target reference.
> Reading surface
> /data-01/trisanna/freesurfer/icbm-113/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 = 53960
> Writing to
> /data-01/trisanna/freesurfer/icbm-113/testsurfaceoverlay.mgz
> Dim: 159741 1 1
>
> When I open this in Freeview, the values are either 0 or
> 255 (see attached image). However, they
> were binary (0 or 1) in the label_aalf.mnc input file...
>
> Trisanna
>
>
> --
> Ph.D. CandidateMcGill University
>
> Integrated Program in Neuroscience
> Psychology
>
>
> On Wed, Oct 12, 2016 at 2:09 PM, Douglas N Greve
>  > wrote:
>   Hmmm, I don't know what could be going on. Can you
> send the command line
>   and all terminal output?
>
>
>   On 10/06/2016 10:37 PM, Trisanna Sprung-Much wrote:
>   > Hi Doug
>   >
>   > So the pixel values are 0 and 1 *in the original
> .mnc*. It seems that
>   > after performing mri_vol2surf they become 0 and
> 255, and stay this way
>   > after mri_surf2surf as well. So, why would
> mri_vol2surf be changing
>   > the values?
>   >
>   > Trisanna
>   >
>   >
>   >
>   > --
>   > Ph.D. Candidate
>   > McGill

Re: [Freesurfer] mri_average vs mri_concat

2016-11-01 Thread Trisanna Sprung-Much 
Does anyone know who wrote the script for mri_concat? I would really like
to get this figured out.

thanks

Trisanna

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


On Fri, Oct 21, 2016 at 12:13 PM, Trisanna Sprung-Much <
trisanna.sprung-m...@mail.mcgill.ca> wrote:

> thanks Bruce - I had indeed used this months ago but at the workshop this
> semester Doug had suggested mri_concat as it is a newer command and also
> doesn't blur the data. I am just having problems creating percentage values
> with mri_concat.
>
> *Would you know why mri_vol2surf is taking a binary minc file and creating
> values ranging from 0-255 that mri_concat then preserves?*
>
> best
> Trisanna
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Fri, Oct 21, 2016 at 9:29 AM, Bruce Fischl 
> wrote:
>
>> Hi Trisanna
>>
>> not sure about mri_concat, but mri_average -noconform -p ... should do
>> the trick
>>
>> cheers
>> Bruce
>> On Wed, 19 Oct 2016, Trisanna Sprung-Much wrote:
>>
>> Something weird is happening with mri_vol2surf - even though the data
>>> looks great, the values are odd
>>> which carries over when I try to average with mri_concat. I would just
>>> like to get percentage values
>>> with mri_concat.
>>> thanks!
>>>
>>> Trisanna
>>>
>>> --
>>> Ph.D. CandidateMcGill University
>>>
>>> Integrated Program in Neuroscience
>>> Psychology
>>>
>>>
>>> On Mon, Oct 17, 2016 at 5:21 PM, Trisanna Sprung-Much <
>>> trisanna.sprung-m...@mail.mcgill.ca> wrote:
>>>   Hi Doug
>>>
>>> Here is what I ran:
>>>
>>> trisanna@kaplan:~$ mri_vol2surf --mov /data-01/trisanna/freesurfer/i
>>> cbm-113/label/label_aalf.mnc
>>> --o /data-01/trisanna/freesurfer/icbm-113/testsurfaceoverlay.mgz --hemi
>>> lh --surf pial --regheader
>>> icbm-113
>>> srcvol = /data-01/trisanna/freesurfer/icbm-113/label/label_aalf.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/icbm-113/mri/orig.mgz as target
>>> reference.
>>> Reading surface /data-01/trisanna/freesurfer/icbm-113/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 = 53960
>>> Writing to /data-01/trisanna/freesurfer/icbm-113/testsurfaceoverlay.mgz
>>> Dim: 159741 1 1
>>>
>>> When I open this in Freeview, the values are either 0 or 255 (see
>>> attached image). However, they
>>> were binary (0 or 1) in the label_aalf.mnc input file...
>>>
>>> Trisanna
>>>
>>>
>>> --
>>> Ph.D. CandidateMcGill University
>>>
>>> Integrated Program in Neuroscience
>>> Psychology
>>>
>>>
>>> On Wed, Oct 12, 2016 at 2:09 PM, Douglas N Greve <
>>> gr...@nmr.mgh.harvard.edu> wrote:
>>>   Hmmm, I don't know what could be going on. Can you send the
>>> command line
>>>   and all terminal output?
>>>
>>>
>>>   On 10/06/2016 10:37 PM, Trisanna Sprung-Much wrote:
>>>   > Hi Doug
>>>   >
>>>   > So the pixel values are 0 and 1 *in the original .mnc*. It seems
>>> that
>>>   > after performing mri_vol2surf they become 0 and 255, and stay
>>> this way
>>>   > after mri_surf2surf as well. So, why would mri_vol2surf be
>>> changing
>>>   > the values?
>>>   >
>>>   > Trisanna
>>>   >
>>>   >
>>>   >
>>>   > --
>>>   > Ph.D. Candidate
>>>   > McGill University
>>>   > Integrated Program in Neuroscience
>>>   > Psychology
>>>   >
>>>   >
>>>   > On Thu, Oct 6, 2016 at 11:30 AM, Douglas Greve
>>>   > >
>>> wrote:
>>>   >
>>>   > What are the pixel values in the mgz file? They should be
>>> binary,
>>>   > ie, 1=in a label, 0 = out of label
>>>   >
>>>   >
>>>   > On 10/6/16 10:22 AM, Trisanna Sprung-Much wrote:
>>>   >> Overlays in .mgz format using mri_vol2surf
>>>   >>
>>>   >> --
>>>   >> Ph.D. Candidate
>>>   >> McGill University
>>>   >> Integrated Program in Neuroscience
>>>   >> Psychology
>>>   >>
>>>   >>
>>>   >> On Wed, Oct 5, 2016 at 5:56 PM, Douglas N Greve
>>>   >> >> edu>> wrote:
>>>   >>
>>>   >> what is a labeled vertex? What file format? mgz? annot?
>>>   >>
>>>   >>
>>>   >> On 10/05/2016 05:03 PM, Trisanna Sprung-Much wrote:
>>>   >> > the source files are labelled vertices from 20
>>> subjects:
>>>   >> >
>>>   >> > -T1s were labelled using an MNI software
>>>   >> >

Re: [Freesurfer] mri_average vs mri_concat

2016-10-21 Thread Trisanna Sprung-Much 
thanks Bruce - I had indeed used this months ago but at the workshop this
semester Doug had suggested mri_concat as it is a newer command and also
doesn't blur the data. I am just having problems creating percentage values
with mri_concat.

*Would you know why mri_vol2surf is taking a binary minc file and creating
values ranging from 0-255 that mri_concat then preserves?*

best
Trisanna

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


On Fri, Oct 21, 2016 at 9:29 AM, Bruce Fischl 
wrote:

> Hi Trisanna
>
> not sure about mri_concat, but mri_average -noconform -p ... should do the
> trick
>
> cheers
> Bruce
> On Wed, 19 Oct 2016, Trisanna Sprung-Much wrote:
>
> Something weird is happening with mri_vol2surf - even though the data
>> looks great, the values are odd
>> which carries over when I try to average with mri_concat. I would just
>> like to get percentage values
>> with mri_concat.
>> thanks!
>>
>> Trisanna
>>
>> --
>> Ph.D. CandidateMcGill University
>>
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Mon, Oct 17, 2016 at 5:21 PM, Trisanna Sprung-Much <
>> trisanna.sprung-m...@mail.mcgill.ca> wrote:
>>   Hi Doug
>>
>> Here is what I ran:
>>
>> trisanna@kaplan:~$ mri_vol2surf --mov /data-01/trisanna/freesurfer/i
>> cbm-113/label/label_aalf.mnc
>> --o /data-01/trisanna/freesurfer/icbm-113/testsurfaceoverlay.mgz --hemi
>> lh --surf pial --regheader
>> icbm-113
>> srcvol = /data-01/trisanna/freesurfer/icbm-113/label/label_aalf.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/icbm-113/mri/orig.mgz as target
>> reference.
>> Reading surface /data-01/trisanna/freesurfer/icbm-113/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 = 53960
>> Writing to /data-01/trisanna/freesurfer/icbm-113/testsurfaceoverlay.mgz
>> Dim: 159741 1 1
>>
>> When I open this in Freeview, the values are either 0 or 255 (see
>> attached image). However, they
>> were binary (0 or 1) in the label_aalf.mnc input file...
>>
>> Trisanna
>>
>>
>> --
>> Ph.D. CandidateMcGill University
>>
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Wed, Oct 12, 2016 at 2:09 PM, Douglas N Greve <
>> gr...@nmr.mgh.harvard.edu> wrote:
>>   Hmmm, I don't know what could be going on. Can you send the command
>> line
>>   and all terminal output?
>>
>>
>>   On 10/06/2016 10:37 PM, Trisanna Sprung-Much wrote:
>>   > Hi Doug
>>   >
>>   > So the pixel values are 0 and 1 *in the original .mnc*. It seems
>> that
>>   > after performing mri_vol2surf they become 0 and 255, and stay
>> this way
>>   > after mri_surf2surf as well. So, why would mri_vol2surf be
>> changing
>>   > the values?
>>   >
>>   > Trisanna
>>   >
>>   >
>>   >
>>   > --
>>   > Ph.D. Candidate
>>   > McGill University
>>   > Integrated Program in Neuroscience
>>   > Psychology
>>   >
>>   >
>>   > On Thu, Oct 6, 2016 at 11:30 AM, Douglas Greve
>>   > >
>> wrote:
>>   >
>>   > What are the pixel values in the mgz file? They should be
>> binary,
>>   > ie, 1=in a label, 0 = out of label
>>   >
>>   >
>>   > On 10/6/16 10:22 AM, Trisanna Sprung-Much wrote:
>>   >> Overlays in .mgz format using mri_vol2surf
>>   >>
>>   >> --
>>   >> Ph.D. Candidate
>>   >> McGill University
>>   >> Integrated Program in Neuroscience
>>   >> Psychology
>>   >>
>>   >>
>>   >> On Wed, Oct 5, 2016 at 5:56 PM, Douglas N Greve
>>   >> >
>> wrote:
>>   >>
>>   >> what is a labeled vertex? What file format? mgz? annot?
>>   >>
>>   >>
>>   >> On 10/05/2016 05:03 PM, Trisanna Sprung-Much wrote:
>>   >> > the source files are labelled vertices from 20
>> subjects:
>>   >> >
>>   >> > -T1s were labelled using an MNI software
>>   >> > -Surfaces were created in FreeSurfer and surface
>> overlays
>>   >> of the
>>   >> > labels were created using mri_vol2surf
>>   >> > -Surface overlays were registered to fsaverage using
>>   >> mri_surf2surf and
>>   >> > then averaged to create a probability map, originally
>> using
>>   >> "mri_average"
>>   >> >
>>   >> > So, essentially the overlays are binary files of my
>> labels

Re: [Freesurfer] mri_average vs mri_concat

2016-10-21 Thread Bruce Fischl 

Hi Trisanna

not sure about mri_concat, but mri_average -noconform -p ... should do 
the trick


cheers
Bruce
On Wed, 19 Oct 2016, Trisanna Sprung-Much wrote:


Something weird is happening with mri_vol2surf - even though the data looks 
great, the values are odd
which carries over when I try to average with mri_concat. I would just like to 
get percentage values
with mri_concat.
thanks!

Trisanna

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


On Mon, Oct 17, 2016 at 5:21 PM, Trisanna Sprung-Much 
 wrote:
  Hi Doug

Here is what I ran:

trisanna@kaplan:~$ mri_vol2surf --mov 
/data-01/trisanna/freesurfer/icbm-113/label/label_aalf.mnc
--o /data-01/trisanna/freesurfer/icbm-113/testsurfaceoverlay.mgz --hemi lh 
--surf pial --regheader
icbm-113
srcvol = /data-01/trisanna/freesurfer/icbm-113/label/label_aalf.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/icbm-113/mri/orig.mgz as target reference.
Reading surface /data-01/trisanna/freesurfer/icbm-113/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 = 53960
Writing to /data-01/trisanna/freesurfer/icbm-113/testsurfaceoverlay.mgz
Dim: 159741 1 1

When I open this in Freeview, the values are either 0 or 255 (see attached 
image). However, they
were binary (0 or 1) in the label_aalf.mnc input file...

Trisanna


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


On Wed, Oct 12, 2016 at 2:09 PM, Douglas N Greve  
wrote:
  Hmmm, I don't know what could be going on. Can you send the command line
  and all terminal output?


  On 10/06/2016 10:37 PM, Trisanna Sprung-Much wrote:
  > Hi Doug
  >
  > So the pixel values are 0 and 1 *in the original .mnc*. It seems that
  > after performing mri_vol2surf they become 0 and 255, and stay this way
  > after mri_surf2surf as well. So, why would mri_vol2surf be changing
  > the values?
  >
  > Trisanna
  >
  >
  >
  > --
  > Ph.D. Candidate
  > McGill University
  > Integrated Program in Neuroscience
  > Psychology
  >
  >
  > On Thu, Oct 6, 2016 at 11:30 AM, Douglas Greve
  > > wrote:
  >
  >     What are the pixel values in the mgz file? They should be binary,
  >     ie, 1=in a label, 0 = out of label
  >
  >
  >     On 10/6/16 10:22 AM, Trisanna Sprung-Much wrote:
  >>     Overlays in .mgz format using mri_vol2surf
  >>
  >>     --
  >>     Ph.D. Candidate
  >>     McGill University
  >>     Integrated Program in Neuroscience
  >>     Psychology
  >>
  >>
  >>     On Wed, Oct 5, 2016 at 5:56 PM, Douglas N Greve
  >>     > 
wrote:
  >>
  >>         what is a labeled vertex? What file format? mgz? annot?
  >>
  >>
  >>         On 10/05/2016 05:03 PM, Trisanna Sprung-Much wrote:
  >>         > the source files are labelled vertices from 20 subjects:
  >>         >
  >>         > -T1s were labelled using an MNI software
  >>         > -Surfaces were created in FreeSurfer and surface overlays
  >>         of the
  >>         > labels were created using mri_vol2surf
  >>         > -Surface overlays were registered to fsaverage using
  >>         mri_surf2surf and
  >>         > then averaged to create a probability map, originally using
  >>         "mri_average"
  >>         >
  >>         > So, essentially the overlays are binary files of my labels
  >>         I believe
  >>         > - I can send one over if you wish.
  >>         >
  >>         > Trisanna
  >>         >
  >>         >
  >>         > --
  >>         > Ph.D. Candidate
  >>         > McGill University
  >>         > Integrated Program in Neuroscience
  >>         > Psychology
  >>         >
  >>         >
  >>         > On Wed, Oct 5, 2016 at 4:52 PM, Douglas N Greve
  >>         > 
  >>         >         >> wrote:
  >>         >
  >>         >     what are the source files ("all files"). What data
  >>         type, value range,
  >>         >     where did they come from?
  >>         >
  >>         >
  >>         >     On 10/05/2016 04:48 PM, Trisanna Sprung-Much wrote:
  >>         >     > Hi Doug

Re: [Freesurfer] mri_average vs mri_concat

2016-10-19 Thread Trisanna Sprung-Much 
Something weird is happening with mri_vol2surf - even though the data looks
great, the values are odd which carries over when I try to average with
mri_concat. I would just like to get percentage values with mri_concat.

thanks!

Trisanna

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


On Mon, Oct 17, 2016 at 5:21 PM, Trisanna Sprung-Much <
trisanna.sprung-m...@mail.mcgill.ca> wrote:

> Hi Doug
>
> *Here is what I ran:*
>
> *trisanna@kaplan:~$ mri_vol2surf --mov
> /data-01/trisanna/freesurfer/icbm-113/label/label_aalf.mnc --o
> /data-01/trisanna/freesurfer/icbm-113/testsurfaceoverlay.mgz --hemi lh
> --surf pial --regheader icbm-113*
> srcvol = /data-01/trisanna/freesurfer/icbm-113/label/label_aalf.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/icbm-113/mri/orig.mgz as target
> reference.
> Reading surface /data-01/trisanna/freesurfer/icbm-113/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 = 53960
> Writing to /data-01/trisanna/freesurfer/icbm-113/testsurfaceoverlay.mgz
> Dim: 159741 1 1
>
> When I open this in Freeview, the values are either 0 or 255 (see attached
> image). However, they were binary (0 or 1) in the label_aalf.mnc input
> file...
>
> Trisanna
>
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Wed, Oct 12, 2016 at 2:09 PM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>> Hmmm, I don't know what could be going on. Can you send the command line
>> and all terminal output?
>>
>>
>> On 10/06/2016 10:37 PM, Trisanna Sprung-Much wrote:
>> > Hi Doug
>> >
>> > So the pixel values are 0 and 1 *in the original .mnc*. It seems that
>> > after performing mri_vol2surf they become 0 and 255, and stay this way
>> > after mri_surf2surf as well. So, why would mri_vol2surf be changing
>> > the values?
>> >
>> > Trisanna
>> >
>> >
>> >
>> > --
>> > Ph.D. Candidate
>> > McGill University
>> > Integrated Program in Neuroscience
>> > Psychology
>> >
>> >
>> > On Thu, Oct 6, 2016 at 11:30 AM, Douglas Greve
>> > > wrote:
>> >
>> > What are the pixel values in the mgz file? They should be binary,
>> > ie, 1=in a label, 0 = out of label
>> >
>> >
>> > On 10/6/16 10:22 AM, Trisanna Sprung-Much wrote:
>> >> Overlays in .mgz format using mri_vol2surf
>> >>
>> >> --
>> >> Ph.D. Candidate
>> >> McGill University
>> >> Integrated Program in Neuroscience
>> >> Psychology
>> >>
>> >>
>> >> On Wed, Oct 5, 2016 at 5:56 PM, Douglas N Greve
>> >> >
>> wrote:
>> >>
>> >> what is a labeled vertex? What file format? mgz? annot?
>> >>
>> >>
>> >> On 10/05/2016 05:03 PM, Trisanna Sprung-Much wrote:
>> >> > the source files are labelled vertices from 20 subjects:
>> >> >
>> >> > -T1s were labelled using an MNI software
>> >> > -Surfaces were created in FreeSurfer and surface overlays
>> >> of the
>> >> > labels were created using mri_vol2surf
>> >> > -Surface overlays were registered to fsaverage using
>> >> mri_surf2surf and
>> >> > then averaged to create a probability map, originally using
>> >> "mri_average"
>> >> >
>> >> > So, essentially the overlays are binary files of my labels
>> >> I believe
>> >> > - I can send one over if you wish.
>> >> >
>> >> > Trisanna
>> >> >
>> >> >
>> >> > --
>> >> > Ph.D. Candidate
>> >> > McGill University
>> >> > Integrated Program in Neuroscience
>> >> > Psychology
>> >> >
>> >> >
>> >> > On Wed, Oct 5, 2016 at 4:52 PM, Douglas N Greve
>> >> > > >
>> >> > >> >> wrote:
>> >> >
>> >> > what are the source files ("all files"). What data
>> >> type, value range,
>> >> > where did they come from?
>> >> >
>> >> >
>> >> > On 10/05/2016 04:48 PM, Trisanna Sprung-Much wrote:
>> >> > > Hi Doug
>> >> > >
>> >> > > So, of course now it works without --keep-filetype...
>> >> :p it looks
>> >> > > pretty much the same was when I use --keep-filetype.
>> >> > >
>> >> > > However, the values of Min and Max are still odd (out
>> >>

Re: [Freesurfer] mri_average vs mri_concat

2016-10-12 Thread Douglas N Greve 
Hmmm, I don't know what could be going on. Can you send the command line 
and all terminal output?


On 10/06/2016 10:37 PM, Trisanna Sprung-Much wrote:
> Hi Doug
>
> So the pixel values are 0 and 1 *in the original .mnc*. It seems that 
> after performing mri_vol2surf they become 0 and 255, and stay this way 
> after mri_surf2surf as well. So, why would mri_vol2surf be changing 
> the values?
>
> Trisanna
>
>
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Thu, Oct 6, 2016 at 11:30 AM, Douglas Greve 
> > wrote:
>
> What are the pixel values in the mgz file? They should be binary,
> ie, 1=in a label, 0 = out of label
>
>
> On 10/6/16 10:22 AM, Trisanna Sprung-Much wrote:
>> Overlays in .mgz format using mri_vol2surf
>>
>> --
>> Ph.D. Candidate
>> McGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Wed, Oct 5, 2016 at 5:56 PM, Douglas N Greve
>> > wrote:
>>
>> what is a labeled vertex? What file format? mgz? annot?
>>
>>
>> On 10/05/2016 05:03 PM, Trisanna Sprung-Much wrote:
>> > the source files are labelled vertices from 20 subjects:
>> >
>> > -T1s were labelled using an MNI software
>> > -Surfaces were created in FreeSurfer and surface overlays
>> of the
>> > labels were created using mri_vol2surf
>> > -Surface overlays were registered to fsaverage using
>> mri_surf2surf and
>> > then averaged to create a probability map, originally using
>> "mri_average"
>> >
>> > So, essentially the overlays are binary files of my labels
>> I believe
>> > - I can send one over if you wish.
>> >
>> > Trisanna
>> >
>> >
>> > --
>> > Ph.D. Candidate
>> > McGill University
>> > Integrated Program in Neuroscience
>> > Psychology
>> >
>> >
>> > On Wed, Oct 5, 2016 at 4:52 PM, Douglas N Greve
>> > 
>> > >> wrote:
>> >
>> > what are the source files ("all files"). What data
>> type, value range,
>> > where did they come from?
>> >
>> >
>> > On 10/05/2016 04:48 PM, Trisanna Sprung-Much wrote:
>> > > Hi Doug
>> > >
>> > > So, of course now it works without --keep-filetype...
>> :p it looks
>> > > pretty much the same was when I use --keep-filetype.
>> > >
>> > > However, the values of Min and Max are still odd (out
>> of 256) - see
>> > > snapshot
>> > >
>> > > Trisanna
>> > >
>> > >
>> > >
>> > >
>> > >
>> > > --
>> > > Ph.D. Candidate
>> > > McGill University
>> > > Integrated Program in Neuroscience
>> > > Psychology
>> > >
>> > >
>> > > On Wed, Oct 5, 2016 at 4:23 PM, Douglas N Greve
>> > > > 
>> > >
>> > > 
>> >> > > >
>> > > Depending upon the type of the data, the
>> --keep-datatype may
>> > mess
>> > > things
>> > > up quite a bit. What happens if you don't include
>> that? It
>> > will not
>> > > create an annotation. maybe you mean some other
>> file type?
>> > >
>> > >
>> > > On 10/05/2016 02:36 PM, Trisanna Sprung-Much wrote:
>> > > >
>> > > > Hi Doug
>> > > >
>> > > > I spoke with you at the Freesurfer tutorial
>> last week
>> > about using
>> > > > mri_average to average my sulcal labels and get a
>> > probability map on
>> > > > fsaverage. You had suggested using "mri_concat"
>> instead,
>> > which is a
>> > > > newer command. So, I performed the following
>> command:
>> > > >
>> > > > *mri_concat all files --o output.mgz --mean
>> --keep-datatype*
>> > > >
>> > > > I had to put --keep-datatype or else

Re: [Freesurfer] mri_average vs mri_concat

2016-10-11 Thread Trisanna Sprung-Much 
Hi Doug

Any thoughts on this?

Trisanna

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


On Thu, Oct 6, 2016 at 10:37 PM, Trisanna Sprung-Much <
trisanna.sprung-m...@mail.mcgill.ca> wrote:

> Hi Doug
>
> So the pixel values are 0 and 1 *in the original .mnc*. It seems that
> after performing mri_vol2surf they become 0 and 255, and stay this way
> after mri_surf2surf as well. So, why would mri_vol2surf be changing the
> values?
>
> Trisanna
>
>
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Thu, Oct 6, 2016 at 11:30 AM, Douglas Greve 
> wrote:
>
>> What are the pixel values in the mgz file? They should be binary, ie,
>> 1=in a label, 0 = out of label
>>
>> On 10/6/16 10:22 AM, Trisanna Sprung-Much wrote:
>>
>> Overlays in .mgz format using mri_vol2surf
>>
>> --
>> Ph.D. Candidate
>> McGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Wed, Oct 5, 2016 at 5:56 PM, Douglas N Greve <
>> gr...@nmr.mgh.harvard.edu> wrote:
>>
>>> what is a labeled vertex? What file format? mgz? annot?
>>>
>>>
>>> On 10/05/2016 05:03 PM, Trisanna Sprung-Much wrote:
>>> > the source files are labelled vertices from 20 subjects:
>>> >
>>> > -T1s were labelled using an MNI software
>>> > -Surfaces were created in FreeSurfer and surface overlays of the
>>> > labels were created using mri_vol2surf
>>> > -Surface overlays were registered to fsaverage using mri_surf2surf and
>>> > then averaged to create a probability map, originally using
>>> "mri_average"
>>> >
>>> > So, essentially the overlays are binary files of my labels I believe
>>> > - I can send one over if you wish.
>>> >
>>> > Trisanna
>>> >
>>> >
>>> > --
>>> > Ph.D. Candidate
>>> > McGill University
>>> > Integrated Program in Neuroscience
>>> > Psychology
>>> >
>>> >
>>> > On Wed, Oct 5, 2016 at 4:52 PM, Douglas N Greve
>>> > > wrote:
>>> >
>>> > what are the source files ("all files"). What data type, value
>>> range,
>>> > where did they come from?
>>> >
>>> >
>>> > On 10/05/2016 04:48 PM, Trisanna Sprung-Much wrote:
>>> > > Hi Doug
>>> > >
>>> > > So, of course now it works without --keep-filetype... :p it looks
>>> > > pretty much the same was when I use --keep-filetype.
>>> > >
>>> > > However, the values of Min and Max are still odd (out of 256) -
>>> see
>>> > > snapshot
>>> > >
>>> > > Trisanna
>>> > >
>>> > >
>>> > >
>>> > >
>>> > >
>>> > > --
>>> > > Ph.D. Candidate
>>> > > McGill University
>>> > > Integrated Program in Neuroscience
>>> > > Psychology
>>> > >
>>> > >
>>> > > On Wed, Oct 5, 2016 at 4:23 PM, Douglas N Greve
>>> > > 
>>> > >> > >> wrote:
>>> > >
>>> > > Depending upon the type of the data, the --keep-datatype may
>>> > mess
>>> > > things
>>> > > up quite a bit. What happens if you don't include that? It
>>> > will not
>>> > > create an annotation. maybe you mean some other file type?
>>> > >
>>> > >
>>> > > On 10/05/2016 02:36 PM, Trisanna Sprung-Much wrote:
>>> > > >
>>> > > > Hi Doug
>>> > > >
>>> > > > I spoke with you at the Freesurfer tutorial last week
>>> > about using
>>> > > > mri_average to average my sulcal labels and get a
>>> > probability map on
>>> > > > fsaverage. You had suggested using "mri_concat" instead,
>>> > which is a
>>> > > > newer command. So, I performed the following command:
>>> > > >
>>> > > > *mri_concat all files --o output.mgz --mean
>>> --keep-datatype*
>>> > > >
>>> > > > I had to put --keep-datatype or else it tried to create an
>>> > annot
>>> > > file.
>>> > > >
>>> > > > This worked just fine.
>>> > > >
>>> > > > My question then is concerning *the min and max values
>>> > *when this
>>> > > > average is overlayed in Freeview. See the snapshot
>>> > attached. The
>>> > > > values seem to be based on 256 instead of percentage and
>>> > this is
>>> > > what
>>> > > > happens when I used "mri_average" without specifying the
>>> > "-p". Is
>>> > > > there a way to illustrate the values in percentage in a
>>> > similar way
>>> > > > with mri_concat?
>>> > > >
>>> > > > Many thanks!
>>> > > >
>>> > > > Trisanna
>>> > > >
>>> > > >
>>> > > > --
>>> > > > Ph.D. Candidate
>>> > > > McGill University
>>> > > > Integrated Program in Neuroscience
>>> > > > Psychology
>>> > > >
>>> > > >
>>> > > >

Re: [Freesurfer] mri_average vs mri_concat

2016-10-06 Thread Trisanna Sprung-Much 
Hi Doug

So the pixel values are 0 and 1 *in the original .mnc*. It seems that after
performing mri_vol2surf they become 0 and 255, and stay this way after
mri_surf2surf as well. So, why would mri_vol2surf be changing the values?

Trisanna



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


On Thu, Oct 6, 2016 at 11:30 AM, Douglas Greve 
wrote:

> What are the pixel values in the mgz file? They should be binary, ie, 1=in
> a label, 0 = out of label
>
> On 10/6/16 10:22 AM, Trisanna Sprung-Much wrote:
>
> Overlays in .mgz format using mri_vol2surf
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Wed, Oct 5, 2016 at 5:56 PM, Douglas N Greve  > wrote:
>
>> what is a labeled vertex? What file format? mgz? annot?
>>
>>
>> On 10/05/2016 05:03 PM, Trisanna Sprung-Much wrote:
>> > the source files are labelled vertices from 20 subjects:
>> >
>> > -T1s were labelled using an MNI software
>> > -Surfaces were created in FreeSurfer and surface overlays of the
>> > labels were created using mri_vol2surf
>> > -Surface overlays were registered to fsaverage using mri_surf2surf and
>> > then averaged to create a probability map, originally using
>> "mri_average"
>> >
>> > So, essentially the overlays are binary files of my labels I believe
>> > - I can send one over if you wish.
>> >
>> > Trisanna
>> >
>> >
>> > --
>> > Ph.D. Candidate
>> > McGill University
>> > Integrated Program in Neuroscience
>> > Psychology
>> >
>> >
>> > On Wed, Oct 5, 2016 at 4:52 PM, Douglas N Greve
>> > > wrote:
>> >
>> > what are the source files ("all files"). What data type, value
>> range,
>> > where did they come from?
>> >
>> >
>> > On 10/05/2016 04:48 PM, Trisanna Sprung-Much wrote:
>> > > Hi Doug
>> > >
>> > > So, of course now it works without --keep-filetype... :p it looks
>> > > pretty much the same was when I use --keep-filetype.
>> > >
>> > > However, the values of Min and Max are still odd (out of 256) -
>> see
>> > > snapshot
>> > >
>> > > Trisanna
>> > >
>> > >
>> > >
>> > >
>> > >
>> > > --
>> > > Ph.D. Candidate
>> > > McGill University
>> > > Integrated Program in Neuroscience
>> > > Psychology
>> > >
>> > >
>> > > On Wed, Oct 5, 2016 at 4:23 PM, Douglas N Greve
>> > > 
>> > > > >> wrote:
>> > >
>> > > Depending upon the type of the data, the --keep-datatype may
>> > mess
>> > > things
>> > > up quite a bit. What happens if you don't include that? It
>> > will not
>> > > create an annotation. maybe you mean some other file type?
>> > >
>> > >
>> > > On 10/05/2016 02:36 PM, Trisanna Sprung-Much wrote:
>> > > >
>> > > > Hi Doug
>> > > >
>> > > > I spoke with you at the Freesurfer tutorial last week
>> > about using
>> > > > mri_average to average my sulcal labels and get a
>> > probability map on
>> > > > fsaverage. You had suggested using "mri_concat" instead,
>> > which is a
>> > > > newer command. So, I performed the following command:
>> > > >
>> > > > *mri_concat all files --o output.mgz --mean --keep-datatype*
>> > > >
>> > > > I had to put --keep-datatype or else it tried to create an
>> > annot
>> > > file.
>> > > >
>> > > > This worked just fine.
>> > > >
>> > > > My question then is concerning *the min and max values
>> > *when this
>> > > > average is overlayed in Freeview. See the snapshot
>> > attached. The
>> > > > values seem to be based on 256 instead of percentage and
>> > this is
>> > > what
>> > > > happens when I used "mri_average" without specifying the
>> > "-p". Is
>> > > > there a way to illustrate the values in percentage in a
>> > similar way
>> > > > with mri_concat?
>> > > >
>> > > > Many thanks!
>> > > >
>> > > > Trisanna
>> > > >
>> > > >
>> > > > --
>> > > > Ph.D. Candidate
>> > > > McGill University
>> > > > Integrated Program in Neuroscience
>> > > > Psychology
>> > > >
>> > > >
>> > > >
>> > > > ___
>> > > > Freesurfer mailing list
>> > > > Freesurfer@nmr.mgh.harvard.edu
>> > 
>> > > > > >
>> > > >
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >

Re: [Freesurfer] mri_average vs mri_concat

2016-10-06 Thread Douglas Greve 
What are the pixel values in the mgz file? They should be binary, ie, 
1=in a label, 0 = out of label



On 10/6/16 10:22 AM, Trisanna Sprung-Much wrote:

Overlays in .mgz format using mri_vol2surf

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


On Wed, Oct 5, 2016 at 5:56 PM, Douglas N Greve 
> wrote:


what is a labeled vertex? What file format? mgz? annot?


On 10/05/2016 05:03 PM, Trisanna Sprung-Much wrote:
> the source files are labelled vertices from 20 subjects:
>
> -T1s were labelled using an MNI software
> -Surfaces were created in FreeSurfer and surface overlays of the
> labels were created using mri_vol2surf
> -Surface overlays were registered to fsaverage using
mri_surf2surf and
> then averaged to create a probability map, originally using
"mri_average"
>
> So, essentially the overlays are binary files of my labels I believe
> - I can send one over if you wish.
>
> Trisanna
>
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Wed, Oct 5, 2016 at 4:52 PM, Douglas N Greve
> 
>> wrote:
>
> what are the source files ("all files"). What data type,
value range,
> where did they come from?
>
>
> On 10/05/2016 04:48 PM, Trisanna Sprung-Much wrote:
> > Hi Doug
> >
> > So, of course now it works without --keep-filetype... :p
it looks
> > pretty much the same was when I use --keep-filetype.
> >
> > However, the values of Min and Max are still odd (out of
256) - see
> > snapshot
> >
> > Trisanna
> >
> >
> >
> >
> >
> > --
> > Ph.D. Candidate
> > McGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> > On Wed, Oct 5, 2016 at 4:23 PM, Douglas N Greve
> > 
>
> 
>  >
> > Depending upon the type of the data, the
--keep-datatype may
> mess
> > things
> > up quite a bit. What happens if you don't include that? It
> will not
> > create an annotation. maybe you mean some other file type?
> >
> >
> > On 10/05/2016 02:36 PM, Trisanna Sprung-Much wrote:
> > >
> > > Hi Doug
> > >
> > > I spoke with you at the Freesurfer tutorial last week
> about using
> > > mri_average to average my sulcal labels and get a
> probability map on
> > > fsaverage. You had suggested using "mri_concat" instead,
> which is a
> > > newer command. So, I performed the following command:
> > >
> > > *mri_concat all files --o output.mgz --mean
--keep-datatype*
> > >
> > > I had to put --keep-datatype or else it tried to
create an
> annot
> > file.
> > >
> > > This worked just fine.
> > >
> > > My question then is concerning *the min and max values
> *when this
> > > average is overlayed in Freeview. See the snapshot
> attached. The
> > > values seem to be based on 256 instead of percentage and
> this is
> > what
> > > happens when I used "mri_average" without specifying the
> "-p". Is
> > > there a way to illustrate the values in percentage in a
> similar way
> > > with mri_concat?
> > >
> > > Many thanks!
> > >
> > > Trisanna
> > >
> > >
> > > --
> > > Ph.D. Candidate
> > > McGill University
> > > Integrated Program in Neuroscience
> > > Psychology
> > >
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu

> >
> > 
>

Re: [Freesurfer] mri_average vs mri_concat

2016-10-06 Thread Trisanna Sprung-Much 
Overlays in .mgz format using mri_vol2surf

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


On Wed, Oct 5, 2016 at 5:56 PM, Douglas N Greve 
wrote:

> what is a labeled vertex? What file format? mgz? annot?
>
>
> On 10/05/2016 05:03 PM, Trisanna Sprung-Much wrote:
> > the source files are labelled vertices from 20 subjects:
> >
> > -T1s were labelled using an MNI software
> > -Surfaces were created in FreeSurfer and surface overlays of the
> > labels were created using mri_vol2surf
> > -Surface overlays were registered to fsaverage using mri_surf2surf and
> > then averaged to create a probability map, originally using "mri_average"
> >
> > So, essentially the overlays are binary files of my labels I believe
> > - I can send one over if you wish.
> >
> > Trisanna
> >
> >
> > --
> > Ph.D. Candidate
> > McGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> > On Wed, Oct 5, 2016 at 4:52 PM, Douglas N Greve
> > > wrote:
> >
> > what are the source files ("all files"). What data type, value range,
> > where did they come from?
> >
> >
> > On 10/05/2016 04:48 PM, Trisanna Sprung-Much wrote:
> > > Hi Doug
> > >
> > > So, of course now it works without --keep-filetype... :p it looks
> > > pretty much the same was when I use --keep-filetype.
> > >
> > > However, the values of Min and Max are still odd (out of 256) - see
> > > snapshot
> > >
> > > Trisanna
> > >
> > >
> > >
> > >
> > >
> > > --
> > > Ph.D. Candidate
> > > McGill University
> > > Integrated Program in Neuroscience
> > > Psychology
> > >
> > >
> > > On Wed, Oct 5, 2016 at 4:23 PM, Douglas N Greve
> > > 
> >  > >> wrote:
> > >
> > > Depending upon the type of the data, the --keep-datatype may
> > mess
> > > things
> > > up quite a bit. What happens if you don't include that? It
> > will not
> > > create an annotation. maybe you mean some other file type?
> > >
> > >
> > > On 10/05/2016 02:36 PM, Trisanna Sprung-Much wrote:
> > > >
> > > > Hi Doug
> > > >
> > > > I spoke with you at the Freesurfer tutorial last week
> > about using
> > > > mri_average to average my sulcal labels and get a
> > probability map on
> > > > fsaverage. You had suggested using "mri_concat" instead,
> > which is a
> > > > newer command. So, I performed the following command:
> > > >
> > > > *mri_concat all files --o output.mgz --mean --keep-datatype*
> > > >
> > > > I had to put --keep-datatype or else it tried to create an
> > annot
> > > file.
> > > >
> > > > This worked just fine.
> > > >
> > > > My question then is concerning *the min and max values
> > *when this
> > > > average is overlayed in Freeview. See the snapshot
> > attached. The
> > > > values seem to be based on 256 instead of percentage and
> > this is
> > > what
> > > > happens when I used "mri_average" without specifying the
> > "-p". Is
> > > > there a way to illustrate the values in percentage in a
> > similar way
> > > > with mri_concat?
> > > >
> > > > Many thanks!
> > > >
> > > > Trisanna
> > > >
> > > >
> > > > --
> > > > Ph.D. Candidate
> > > > McGill University
> > > > Integrated Program in Neuroscience
> > > > Psychology
> > > >
> > > >
> > > >
> > > > ___
> > > > Freesurfer mailing list
> > > > Freesurfer@nmr.mgh.harvard.edu
> > 
> > >  > >
> > > >
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > 
> > >  > >
> > >
> > > --
> > > Douglas N. Greve, Ph.D.
> > > MGH-NMR Center
> > > gr...@nmr.mgh.harvard.edu 
> >  >>
> > > Phone Number: 617-724-2358 
> > >
> > > Fax: 617-726-7422   > >
> > >
> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > 
> > >

Re: [Freesurfer] mri_average vs mri_concat

2016-10-05 Thread Douglas N Greve 
what is a labeled vertex? What file format? mgz? annot?


On 10/05/2016 05:03 PM, Trisanna Sprung-Much wrote:
> the source files are labelled vertices from 20 subjects:
>
> -T1s were labelled using an MNI software
> -Surfaces were created in FreeSurfer and surface overlays of the 
> labels were created using mri_vol2surf
> -Surface overlays were registered to fsaverage using mri_surf2surf and 
> then averaged to create a probability map, originally using "mri_average"
>
> So, essentially the overlays are binary files of my labels I believe  
> - I can send one over if you wish.
>
> Trisanna
>
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Wed, Oct 5, 2016 at 4:52 PM, Douglas N Greve 
> > wrote:
>
> what are the source files ("all files"). What data type, value range,
> where did they come from?
>
>
> On 10/05/2016 04:48 PM, Trisanna Sprung-Much wrote:
> > Hi Doug
> >
> > So, of course now it works without --keep-filetype... :p it looks
> > pretty much the same was when I use --keep-filetype.
> >
> > However, the values of Min and Max are still odd (out of 256) - see
> > snapshot
> >
> > Trisanna
> >
> >
> >
> >
> >
> > --
> > Ph.D. Candidate
> > McGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> > On Wed, Oct 5, 2016 at 4:23 PM, Douglas N Greve
> > 
>  >> wrote:
> >
> > Depending upon the type of the data, the --keep-datatype may
> mess
> > things
> > up quite a bit. What happens if you don't include that? It
> will not
> > create an annotation. maybe you mean some other file type?
> >
> >
> > On 10/05/2016 02:36 PM, Trisanna Sprung-Much wrote:
> > >
> > > Hi Doug
> > >
> > > I spoke with you at the Freesurfer tutorial last week
> about using
> > > mri_average to average my sulcal labels and get a
> probability map on
> > > fsaverage. You had suggested using "mri_concat" instead,
> which is a
> > > newer command. So, I performed the following command:
> > >
> > > *mri_concat all files --o output.mgz --mean --keep-datatype*
> > >
> > > I had to put --keep-datatype or else it tried to create an
> annot
> > file.
> > >
> > > This worked just fine.
> > >
> > > My question then is concerning *the min and max values
> *when this
> > > average is overlayed in Freeview. See the snapshot
> attached. The
> > > values seem to be based on 256 instead of percentage and
> this is
> > what
> > > happens when I used "mri_average" without specifying the
> "-p". Is
> > > there a way to illustrate the values in percentage in a
> similar way
> > > with mri_concat?
> > >
> > > Many thanks!
> > >
> > > Trisanna
> > >
> > >
> > > --
> > > Ph.D. Candidate
> > > McGill University
> > > Integrated Program in Neuroscience
> > > Psychology
> > >
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> 
> >  >
> > >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> >  >
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu 
> >
> > Phone Number: 617-724-2358 
> >
> > Fax: 617-726-7422   >
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> >  >
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> 
> >  >
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> >

Re: [Freesurfer] mri_average vs mri_concat

2016-10-05 Thread Trisanna Sprung-Much 
the source files are labelled vertices from 20 subjects:

-T1s were labelled using an MNI software
-Surfaces were created in FreeSurfer and surface overlays of the labels
were created using mri_vol2surf
-Surface overlays were registered to fsaverage using mri_surf2surf and then
averaged to create a probability map, originally using "mri_average"

So, essentially the overlays are binary files of my labels I believe  - I
can send one over if you wish.

Trisanna


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


On Wed, Oct 5, 2016 at 4:52 PM, Douglas N Greve 
wrote:

> what are the source files ("all files"). What data type, value range,
> where did they come from?
>
>
> On 10/05/2016 04:48 PM, Trisanna Sprung-Much wrote:
> > Hi Doug
> >
> > So, of course now it works without --keep-filetype... :p it looks
> > pretty much the same was when I use --keep-filetype.
> >
> > However, the values of Min and Max are still odd (out of 256) - see
> > snapshot
> >
> > Trisanna
> >
> >
> >
> >
> >
> > --
> > Ph.D. Candidate
> > McGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> > On Wed, Oct 5, 2016 at 4:23 PM, Douglas N Greve
> > > wrote:
> >
> > Depending upon the type of the data, the --keep-datatype may mess
> > things
> > up quite a bit. What happens if you don't include that? It will not
> > create an annotation. maybe you mean some other file type?
> >
> >
> > On 10/05/2016 02:36 PM, Trisanna Sprung-Much wrote:
> > >
> > > Hi Doug
> > >
> > > I spoke with you at the Freesurfer tutorial last week about using
> > > mri_average to average my sulcal labels and get a probability map
> on
> > > fsaverage. You had suggested using "mri_concat" instead, which is a
> > > newer command. So, I performed the following command:
> > >
> > > *mri_concat all files --o output.mgz --mean --keep-datatype*
> > >
> > > I had to put --keep-datatype or else it tried to create an annot
> > file.
> > >
> > > This worked just fine.
> > >
> > > My question then is concerning *the min and max values *when this
> > > average is overlayed in Freeview. See the snapshot attached. The
> > > values seem to be based on 256 instead of percentage and this is
> > what
> > > happens when I used "mri_average" without specifying the "-p". Is
> > > there a way to illustrate the values in percentage in a similar way
> > > with mri_concat?
> > >
> > > Many thanks!
> > >
> > > Trisanna
> > >
> > >
> > > --
> > > Ph.D. Candidate
> > > McGill University
> > > Integrated Program in Neuroscience
> > > Psychology
> > >
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > 
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > 
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu 
> > Phone Number: 617-724-2358 
> > Fax: 617-726-7422 
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > 
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > 
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > 
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > 
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu  harvard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > 
> >
> >
> > The information in this e-mail is intended only for the person to
> > whom it is
> > addressed. If you believe this e-mail was sent to you in error and
> > the e-mail
> > contains patient information, please contact the Partners
> > Compliance HelpLine at
> > http://www.partners.org/complianceline
> >  . If the e-mail was sent
> > to you in error
> > but does not contain patient information, please contact the
> > sender and properly
> > dispose of the e-mail.
> >
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N.

Re: [Freesurfer] mri_average vs mri_concat

2016-10-05 Thread Douglas N Greve 
what are the source files ("all files"). What data type, value range, 
where did they come from?


On 10/05/2016 04:48 PM, Trisanna Sprung-Much wrote:
> Hi Doug
>
> So, of course now it works without --keep-filetype... :p it looks 
> pretty much the same was when I use --keep-filetype.
>
> However, the values of Min and Max are still odd (out of 256) - see 
> snapshot
>
> Trisanna
>
>
>
>
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Wed, Oct 5, 2016 at 4:23 PM, Douglas N Greve 
> > wrote:
>
> Depending upon the type of the data, the --keep-datatype may mess
> things
> up quite a bit. What happens if you don't include that? It will not
> create an annotation. maybe you mean some other file type?
>
>
> On 10/05/2016 02:36 PM, Trisanna Sprung-Much wrote:
> >
> > Hi Doug
> >
> > I spoke with you at the Freesurfer tutorial last week about using
> > mri_average to average my sulcal labels and get a probability map on
> > fsaverage. You had suggested using "mri_concat" instead, which is a
> > newer command. So, I performed the following command:
> >
> > *mri_concat all files --o output.mgz --mean --keep-datatype*
> >
> > I had to put --keep-datatype or else it tried to create an annot
> file.
> >
> > This worked just fine.
> >
> > My question then is concerning *the min and max values *when this
> > average is overlayed in Freeview. See the snapshot attached. The
> > values seem to be based on 256 instead of percentage and this is
> what
> > happens when I used "mri_average" without specifying the "-p". Is
> > there a way to illustrate the values in percentage in a similar way
> > with mri_concat?
> >
> > Many thanks!
> >
> > Trisanna
> >
> >
> > --
> > Ph.D. Candidate
> > McGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358 
> Fax: 617-726-7422 
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> 
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> 
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
>
>
> The information in this e-mail is intended only for the person to
> whom it is
> addressed. If you believe this e-mail was sent to you in error and
> the e-mail
> contains patient information, please contact the Partners
> Compliance HelpLine at
> http://www.partners.org/complianceline
>  . If the e-mail was sent
> to you in error
> but does not contain patient information, please contact the
> sender and properly
> dispose of the e-mail.
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] mri_average vs mri_concat

2016-10-05 Thread Douglas N Greve 
Depending upon the type of the data, the --keep-datatype may mess things 
up quite a bit. What happens if you don't include that? It will not 
create an annotation. maybe you mean some other file type?


On 10/05/2016 02:36 PM, Trisanna Sprung-Much wrote:
>
> Hi Doug
>
> I spoke with you at the Freesurfer tutorial last week about using 
> mri_average to average my sulcal labels and get a probability map on 
> fsaverage. You had suggested using "mri_concat" instead, which is a 
> newer command. So, I performed the following command:
>
> *mri_concat all files --o output.mgz --mean --keep-datatype*
>
> I had to put --keep-datatype or else it tried to create an annot file.
>
> This worked just fine.
>
> My question then is concerning *the min and max values *when this 
> average is overlayed in Freeview. See the snapshot attached. The 
> values seem to be based on 256 instead of percentage and this is what 
> happens when I used "mri_average" without specifying the "-p". Is 
> there a way to illustrate the values in percentage in a similar way 
> with mri_concat?
>
> Many thanks!
>
> Trisanna
>
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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