6 Jul
2016
6 Jul
'16
1:28 p.m.
Trisanna, has this issue been resolved? doug
On 06/30/2016 01:26 PM, Trisanna Sprung-Much wrote:
Hi Bruce
here is the output of my mri_vol2surf for a volumetric spam created in minc tools. When I then overlay this result in Freeview, it displays a Min of 127 and a Max of 255.
trisanna@kaplan:~$ mri_vol2surf --mov /data-01/trisanna/freesurfer/MNI_average_2009a_asymm/spam_for_label_id_4_blur_minc1.mnc --o /data-01/trisanna/freesurfer/MNI_average_2009a_asymm/spam_for_label_id_4_blur_overlay.mgz --hemi lh --surf pial --regheader MNI_average_2009a_asymm srcvol = /data-01/trisanna/freesurfer/MNI_average_2009a_asymm/spam_for_label_id_4_blur_minc1.mnc srcreg unspecified srcregold = 0 srcwarp unspecified surf = pial hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /data-01/trisanna/freesurfer/MNI_average_2009a_asymm/mri/orig.mgz as target reference. Reading surface /data-01/trisanna/freesurfer/MNI_average_2009a_asymm/surf/lh.pial Done reading source surface Mapping Source Volume onto Source Subject Surface 1 0 0 0 using old Done mapping volume to surface Number of source voxels hit = 95521 Writing to /data-01/trisanna/freesurfer/MNI_average_2009a_asymm/spam_for_label_id_4_blur_overlay.mgz Dim: 152257 1 1
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Wed, Jun 29, 2016 at 8:10 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
Can you send the full output of that command? On Jun 29, 2016, at 2:54 PM, Trisanna Sprung-Much <trisanna.sprung-much@mail.mcgill.ca <mailto:trisanna.sprung-much@mail.mcgill.ca>> wrote:Hi Bruce I simply use mri_vol2surf --mov spam.mnc --output overlayspam.mgz --regheader subject --hemi lh --surf pial Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Wed, Jun 29, 2016 at 1:23 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: how do you create the overlay? On Wed, 29 Jun 2016, Trisanna Sprung-Much wrote: Hi Bruce To create the spam I used minctools: mincaverage input.mnc output.mnc I blurred the spam using mincblur input.mnc output.mnc -fwhm 3 When I open the spams using minc software, the % shown is from about 10-40% (i.e. the max overlap). For some reason when I create an overlay from this it displays the % from 1-255. Trisanna -- Ph.D. CandidateMcGill University Integrated Program in Neuroscience Psychology On Wed, Jun 29, 2016 at 12:20 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto: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_overlay s _ 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 <mailto: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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> 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