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 fischl@nmr.mgh.harvard.edu 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-much@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 < greve@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 seemsthat > 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 > <greve@nmr.mgh.harvard.edu mailto:greve@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 >> <greve@nmr.mgh.harvard.edu mailto:greve@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 >> > <greve@nmr.mgh.harvard.edu mailto: greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu >> mailto:greve@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 >> > > <greve@nmr.mgh.harvard.edu >> mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu >> mailto:greve@nmr.mgh.harvard.edu> >> > <mailto:greve@nmr.mgh.harvard.edu >> mailto:greve@nmr.mgh.harvard.edu >> > <mailto:greve@nmr.mgh.harvard.edu >> mailto:greve@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. 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> > <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/
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