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
Tg trisanna@kaplan:/data-01/trisanna/freesurfer/fsaverage/DISPLAY_overlays_fsavee_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_fsaverage_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. Candidate McGill 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_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 <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 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 > <greve@nmr.mgh.harvard.edu <mailto:greve@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 > > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@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 > > <fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@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 > greve@nmr.mgh.harvard.edu mailto:greve@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%3E > 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 greve@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.