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 > <fis...@nmr.mgh.harvard.edu <mailto:fis...@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-m...@mail.mcgill.ca > <mailto:trisanna.sprung-m...@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 >> <fis...@nmr.mgh.harvard.edu <mailto:fis...@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 >> <fis...@nmr.mgh.harvard.edu >> <mailto:fis...@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 >> <fis...@nmr.mgh.harvard.edu >> <mailto:fis...@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-m...@mail.mcgill.ca >> <mailto:trisanna.sprung-m...@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 >> <fis...@nmr.mgh.harvard.edu >> <mailto:fis...@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 >> <fis...@nmr.mgh.harvard.edu >> <mailto:fis...@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 >> >> <fis...@nmr.mgh.harvard.edu >> <mailto:fis...@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-m...@mail.mcgill.ca >> <mailto:trisanna.sprung-m...@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> >> 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 >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> 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 > > > 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
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