29 Jun
2016
29 Jun
'16
1:19 p.m.
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 fischl@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 < fischl@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 <trisanna.sprung-much@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. CandidateMcGill University Integrated Program in Neuroscience Psychology On Wed, Jun 22, 2016 at 9:32 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> 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 <fischl@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 <fischl@nmr.mgh.harvard.edu> 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: 1.0000, 1.0000, 1.0000 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 = 1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.5000 : x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = -17.5000 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 18.5000 talairach xfm : Orientation : RAS Primary Slice Direction: axial voxel to ras transform: 1.0000 0.0000 0.0000 -81920.5000 0.0000 1.0000 0.0000 -18.0000 0.0000 0.0000 1.0000 18.0000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant 1 ras to voxel transform: 1.0000 -0.0000 -0.0000 81920.5000 -0.0000 1.0000 -0.0000 18.0000 -0.0000 -0.0000 1.0000 -18.0000 0.0000 0.0000 0.0000 1.0000 trisanna@kaplan:/data-01/trisanna/freesurfer/fsaverage/DISPLAY_overlays_f s a
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: 1.0000, 1.0000, 1.0000 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 = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.5000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = -17.5000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, 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 <trisanna.sprung-much@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: 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 of 51: reading fsaverage_overlay_aalf_icbm-143_left.mgz... embedding and interpolating volume MRIchangeType: Building histogram 37 of 51: reading fsaverage_overlay_aalf_icbm-144_left.mgz... embedding and interpolating volume MRIchangeType: Building histogram 38 of 51: reading fsaverage_overlay_aalf_icbm-145_left.mgz... embedding and interpolating volume MRIchangeType: Building histogram 39 of 51: reading fsaverage_overlay_aalf_icbm-146_left.mgz... embedding and interpolating volume MRIchangeType: Building histogram 40 of 51: reading fsaverage_overlay_aalf_icbm-150_left.mgz... embedding and interpolating volume MRIchangeType: Building histogram 41 of 51: reading fsaverage_overlay_aalf_icbm-158_left.mgz... embedding and interpolating volume MRIchangeType: Building histogram 42 of 51: reading fsaverage_overlay_aalf_icbm-200_left.mgz... embedding and interpolating volume MRIchangeType: Building histogram 43 of 51: reading fsaverage_overlay_aalf_icbm-201_left.mgz... embedding and interpolating volume MRIchangeType: Building histogram 44 of 51: reading fsaverage_overlay_aalf_icbm-203_left.mgz... embedding and interpolating volume MRIchangeType: Building histogram 45 of 51: reading fsaverage_overlay_aalf_icbm-204_left.mgz... embedding and interpolating volume MRIchangeType: Building histogram 46 of 51: reading fsaverage_overlay_aalf_icbm-205_left.mgz... embedding and interpolating volume MRIchangeType: Building histogram 47 of 51: reading fsaverage_overlay_aalf_icbm-209_left.mgz... embedding and interpolating volume MRIchangeType: Building histogram 48 of 51: reading fsaverage_overlay_aalf_icbm-340_left.mgz... embedding and interpolating volume MRIchangeType: Building histogram 49 of 51: reading fsaverage_overlay_aalf_icbm-347_left.mgz... embedding and interpolating volume MRIchangeType: Building histogram 50 of 51: reading fsaverage_overlay_aalf_icbm-350_left.mgz... embedding and interpolating volume MRIchangeType: Building histogram 51 of 51: reading test.mgz...mghRead(/data-01/trisanna/freesurfer/fsaverage/DISPLAY_overlays_fsaverage_l
eft/aalf_lh/test.mgz, -1): could not open file mri_average: MRIread(test.mgz) failed -- Ph.D. CandidateMcGill University Integrated Program in Neuroscience Psychology On Sun, Jun 19, 2016 at 12:46 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: 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 <fischl@nmr.mgh.harvard.edu> 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 <trisanna.sprung-much@mail.mcgill.ca> 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 <trisanna.sprung-much@mail.mcgill.ca> 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 <greve@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...
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