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_left/aalf_lh/test.mgz, -1): could not open file mri_average: MRIread(test.mgz) failed -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Sun, Jun 19, 2016 at 12:46 PM, Bruce Fischl <fis...@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 < >> fis...@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-m...@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-m...@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 >> <gr...@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 >> sulcus as a .label >> > and then try the mri_label2label? Someone >> suggested perhaps the >> > colours are overlapping with the overlay.... >> > >> > -- >> > Ph.D. Candidate >> > McGill University >> > Integrated Program in Neuroscience >> > Psychology >> > >> > >> > On Wed, Jun 15, 2016 at 4:10 PM, Douglas N >> Greve >> > <gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> > >> > The problem is probably that the >> vol2surf >> command did not properly >> > sample the labels onto the surface. Do >> the >> labels on subject 00350 >> > surfaces look ok? >> > >> > On 06/15/2016 04:00 PM, Trisanna >> Sprung-Much >> wrote: >> > > thanks Dr. Fischl >> > > >> > > So the command seems to have worked! I >> have >> copied what ran in my >> > > terminal. When I open the test.mgz >> overlay >> on the fsaverage pial >> > > surface, things look ok but a bit >> funny. I >> am wondering if there is >> > > anything I can do to the mri_surf2surf >> command to improve the >> > > registration to fsaverage? *See my >> snapshots >> attached.* >> > > >> > > trisanna@kaplan:~$ mri_surf2surf >> --srcsubject 00350 --sval >> > > >> >> /data-01/trisanna/freesurfer/00350/surfaceoverlay_left.mgz >> > > --trgsubject fsaverage --tval test.mgz >> --hemi lh >> > > srcsubject = 00350 >> > > srcval = >> > >> >> /data-01/trisanna/freesurfer/00350/surfaceoverlay_left.mgz >> > > srctype = >> > > trgsubject = fsaverage >> > > trgval = test.mgz >> > > trgtype = >> > > srcsurfreg = sphere.reg >> > > trgsurfreg = sphere.reg >> > > srchemi = lh >> > > trghemi = lh >> > > frame = 0 >> > > fwhm-in = 0 >> > > fwhm-out = 0 >> > > label-src = (null) >> > > label-trg = (null) >> > > OKToRevFaceOrder = 1 >> > > Reading source surface reg >> > > >> >> /data-01/trisanna/freesurfer/00350/surf/lh.sphere.reg >> > > Loading source data >> > > Reading target surface reg >> > > >> >> /data-01/trisanna/freesurfer/fsaverage/surf/lh.sphere.reg >> > > Done >> > > Mapping Source Volume onto Source >> Subject >> Surface >> > > surf2surf_nnfr: building source hash >> (res=16). >> > > Surf2Surf: Forward Loop (163842) >> > > >> > > surf2surf_nnfr: building target hash >> (res=16). >> > > Surf2Surf: Reverse Loop (166912) >> > > Reverse Loop had 41306 hits >> > > Surf2Surf: Dividing by number of hits >> (163842) >> > > INFO: nSrcLost = 0 >> > > nTrg121 = 132490, nTrgMulti = 31352, >> MnTrgMultiHits = 2.31749 >> > > nSrc121 = 137180, nSrcLost = 0, >> nSrcMulti = >> 29732, MnSrcMultiHits = >> > > 2.28602 >> > > Saving target data >> > > Saving to test.mgz >> > > >> > > best >> > > >> > > Trisanna >> > > >> > > -- >> > > Ph.D. Candidate >> > > McGill University >> > > Integrated Program in Neuroscience >> > > Psychology >> > > >> > > >> > > On Wed, Jun 15, 2016 at 12:13 PM, >> Bruce >> Fischl >> > > <fis...@nmr.mgh.harvard.edu >> <mailto:fis...@nmr.mgh.harvard.edu> >> > <mailto:fis...@nmr.mgh.harvard.edu >> > <mailto:fis...@nmr.mgh.harvard.edu>>> wrote: >> > > >> > > Hi Trisanna >> > > >> > > you would only use those options of if >> you >> were transforming >> > a surface >> > > Bruce >> > > >> > > >> > > On Wed, 15 Jun 2016, Trisanna >> Sprung-Much >> wrote: >> > > >> > > thanks Dr. Fischl >> > > >> > > I assume that for surface overlays >> one >> cannot specify >> > > --sval-xyz and --tval-xyz or the >> command >> will treat the >> > input >> > > as a surface >> > > itself? >> > > >> > > best >> > > >> > > Trisanna >> > > >> > > >> > > >> > > >> > > -- >> > > Ph.D. CandidateMcGill University >> > > Integrated Program in Neuroscience >> > > Psychology >> > > >> > > >> > > On Wed, Jun 15, 2016 at 11:11 AM, >> Bruce >> Fischl >> > > <fis...@nmr.mgh.harvard.edu >> > <mailto:fis...@nmr.mgh.harvard.edu> >> > > <mailto:fis...@nmr.mgh.harvard.edu >> > <mailto:fis...@nmr.mgh.harvard.edu>>> wrote: >> > > Hi Trisanna >> > > >> > > you don't need to inflate the >> overlays. They can just >> > > use the existing surface-based >> (sphere.reg) registration. >> > > >> > > cheers >> > > Bruce >> > > On Wed, 15 Jun 2016, Trisanna >> Sprung-Much wrote: >> > > >> > > Hi there >> > > So I have sulcal labels >> from >> another software >> > > (.mnc format) from which I am trying >> to >> generate some >> > > probability maps. I was >> able >> > > to convert the .mnc to >> .mgz >> surface overlay >> > using >> > > mri_vol2surf for my MRIs after >> running all >> MRIs in >> > > recon-all. So, now I >> have >> > > all my painted voxels as >> surface overlays, as I >> > > was instructed to do a few months >> ago. >> > > >> > > I was told that the next >> step >> would be to use >> > > mri_surf2surf to resample the >> overlays to >> fsaverage. >> > > >> > > I am a bit confused as I >> would >> think that >> > the next >> > > step would be to take the surface >> overlays >> and >> > > inflate them before I >> register >> > > them to fsaverage. I see >> that >> when recon-all >> > runs, >> > > it computes the registration of the >> MRI >> surface to >> > > fsaverage and saves it >> as >> > > sphere.reg. Is there a >> way I >> can inflate my >> > > surface overlays in a similar manner >> and >> then apply this >> > > same registration to my >> > > surface overlays? Or am >> I >> missing something? >> > > >> > > thanks very much! >> > > >> > > Trisanna >> > > >> > > >> > > -- >> > > Ph.D. CandidateMcGill >> 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>> >> > >> > >> 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> >> > <mailto: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 >> > >> > -- >> > 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 >> > >> 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/ >> > >> > >> _______________________________________________ >> > 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 >> > >> 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. >> >> >> >> > _______________________________________________ > 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. > >
_______________________________________________ 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.
