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/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 <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
> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> 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 <mailto: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
>> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
>> <mailto:gr...@nmr.mgh.harvard.edu
>> <mailto:gr...@nmr.mgh.harvard.edu>>> 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
>> > > <gr...@nmr.mgh.harvard.edu
>> <mailto:gr...@nmr.mgh.harvard.edu>
>> <mailto:gr...@nmr.mgh.harvard.edu
>> <mailto:gr...@nmr.mgh.harvard.edu>>
>> > <mailto:gr...@nmr.mgh.harvard.edu
>> <mailto:gr...@nmr.mgh.harvard.edu>
>> > <mailto:gr...@nmr.mgh.harvard.edu
>> <mailto:gr...@nmr.mgh.harvard.edu>>>> 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
>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>> > <mailto:Freesurfer@nmr.mgh.harvard.edu
>> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>> > <mailto:Freesurfer@nmr.mgh.harvard.edu
>> <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
>> > > >
>> >
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>> >
>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
>> > >
>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>> >
>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>
>> > >
>> > > --
>> > > Douglas N. Greve, Ph.D.
>> > > MGH-NMR Center
>> > > gr...@nmr.mgh.harvard.edu
>> <mailto:gr...@nmr.mgh.harvard.edu>
>> <mailto:gr...@nmr.mgh.harvard.edu
>> <mailto:gr...@nmr.mgh.harvard.edu>>
>> > <mailto:gr...@nmr.mgh.harvard.edu
>> <mailto:gr...@nmr.mgh.harvard.edu>
>> <mailto:gr...@nmr.mgh.harvard.edu
>> <mailto:gr...@nmr.mgh.harvard.edu>>>
>> > > Phone Number:617-724-2358 <tel:617-724-2358>
<tel:617-724-2358
>> <tel:617-724-2358>>
>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358
>> <tel:617-724-2358>>>
>> > > Fax: 617-726-7422 <tel:617-726-7422>
>> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422
>> <tel:617-726-7422>
>> > <tel:617-726-7422 <tel:617-726-7422>>>
>> > >
>> > > Bugs:
>> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>
>> > >
>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>>
>> > > FileDrop:
>> https://gate.nmr.mgh.harvard.edu/filedrop2
>> <https://gate.nmr.mgh.harvard.edu/filedrop2>
>> > <https://gate.nmr.mgh.harvard.edu/filedrop2
>> <https://gate.nmr.mgh.harvard.edu/filedrop2>>
>> > > <https://gate.nmr.mgh.harvard.edu/filedrop2
>> <https://gate.nmr.mgh.harvard.edu/filedrop2>
>> > <https://gate.nmr.mgh.harvard.edu/filedrop2
>> <https://gate.nmr.mgh.harvard.edu/filedrop2>>>
>> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>> >
>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>
>> > >
>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>>
>> > > Outgoing:
>> > >
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
>> >
>> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>
>> > >
>> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
>> >
>> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>>
>> > >
>> > > _______________________________________________
>> > > Freesurfer mailing list
>> > > Freesurfer@nmr.mgh.harvard.edu
>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>> > <mailto:Freesurfer@nmr.mgh.harvard.edu
>> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>> > <mailto:Freesurfer@nmr.mgh.harvard.edu
>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>> > <mailto:Freesurfer@nmr.mgh.harvard.edu
>> <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
>> > >
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>> >
>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
>> > >
>> >
>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>> >
>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> <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
>> <http://www.partners.org/complianceline>
>> > <http://www.partners.org/complianceline
>> <http://www.partners.org/complianceline>>
>> > > <http://www.partners.org/complianceline
>> <http://www.partners.org/complianceline>
>> > <http://www.partners.org/complianceline
>> <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
>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>> > <mailto:Freesurfer@nmr.mgh.harvard.edu
>> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>> > >
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>> >
>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
>> >
>> > --
>> > Douglas N. Greve, Ph.D.
>> > MGH-NMR Center
>> > gr...@nmr.mgh.harvard.edu
>> <mailto:gr...@nmr.mgh.harvard.edu>
>> <mailto:gr...@nmr.mgh.harvard.edu
>> <mailto:gr...@nmr.mgh.harvard.edu>>
>> > Phone Number: 617-724-2358 <tel:617-724-2358>
>> <tel:617-724-2358 <tel:617-724-2358>>
>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422
>> <tel:617-726-7422>>
>> >
>> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>
>> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> <https://gate.nmr.mgh.harvard.edu/filedrop2>
>> > <https://gate.nmr.mgh.harvard.edu/filedrop2
>> <https://gate.nmr.mgh.harvard.edu/filedrop2>>
>> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>> >
>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>
>> > Outgoing:
>> >
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
>> >
>> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>
>> >
>> > _______________________________________________
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>> <mailto:Freesurfer@nmr.mgh.harvard.edu
>> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>> >
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>> >
>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
>> >
>> >
>> >
>> >
>> > _______________________________________________
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>> >
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
>> Phone Number: 617-724-2358 <tel:617-724-2358>
>> Fax: 617-726-7422 <tel:617-726-7422>
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> <https://gate.nmr.mgh.harvard.edu/filedrop2>
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>> Outgoing:
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>>
>>
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> _______________________________________________ Freesurfer mailing
> list Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <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
> <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
_______________________________________________
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.
