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. Candidate McGill University Integrated Program in Neuroscience Psychology
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
---------- Forwarded message ---------- From: Trisanna Sprung-Much trisanna.sprung-much@mail.mcgill.ca Date: Wed, Jun 15, 2016 at 10:49 AM Subject: registering to fsaverage To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
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. Candidate McGill University Integrated Program in Neuroscience Psychology
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
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. Candidate McGill University Integrated Program in Neuroscience Psychology
On Wed, Jun 15, 2016 at 11:11 AM, Bruce Fischl 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
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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 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 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.
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 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> wrote: Hi Trisanna
you don't need to inflate the overlays. They can just use theexisting 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_surf2surfto resample the overlays to fsaverage.
I am a bit confused as I would think that the next step wouldbe 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person towhom 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.
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> 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>> 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> 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 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
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 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> wrote:
Hi Trisanna you would only use those options of if you were transforming asurface
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>> 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> 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 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
-- 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/
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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> 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
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worked beautifully. Thank you!
-- Ph.D. Candidate McGill 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> 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
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. Candidate McGill 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. Candidate McGill 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 thereis
> 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 canjust
> 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, asI
> 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 sentto
> 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> 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
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-- 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
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. Candidate McGill 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. Candidate McGill 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. Candidate McGill 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 thereis
> 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 canjust
> 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 sentto
> 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> 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>
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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
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http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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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/
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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. Candidate McGill 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 youwere transforming
a surface > Bruce > > > On Wed, 15 Jun 2016, Trisanna Sprung-Muchwrote:
> > thanks Dr. Fischl > > I assume that for surface overlays onecannot specify
> --sval-xyz and --tval-xyz or the commandwill 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, BruceFischl
> <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 theoverlays. They can just
> use the existing surface-based(sphere.reg) registration.
> > cheers > Bruce > On Wed, 15 Jun 2016, TrisannaSprung-Much wrote:
> > Hi there > So I have sulcal labels fromanother software
> (.mnc format) from which I am trying togenerate some
> probability maps. I was able > to convert the .mnc to .mgzsurface overlay
using > mri_vol2surf for my MRIs after running allMRIs in
> recon-all. So, now I have > all my painted voxels assurface overlays, as I
> was instructed to do a few months ago. > > I was told that the next stepwould be to use
> mri_surf2surf to resample the overlays tofsaverage.
> > I am a bit confused as I wouldthink that
the next > step would be to take the surface overlaysand
> inflate them before I register > them to fsaverage. I see thatwhen recon-all
runs, > it computes the registration of the MRIsurface to
> fsaverage and saves it as > sphere.reg. Is there a way Ican inflate my
> surface overlays in a similar manner andthen apply this
> same registration to my > surface overlays? Or am Imissing something?
> > thanks very much! > > Trisanna > > > -- > Ph.D. CandidateMcGillUniversity
> Integrated Program inNeuroscience
> 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 thise-mail was sent to
you in > error and the e-mail > contains patient information, pleasecontact the
> Partners Compliance HelpLine at > http://www.partners.org/complianceline . If thee-mail was
> sent to you in error > but does not contain patientinformation, please
contact > the sender and properly > dispose of the e-mail. > > > > >
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu
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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> > 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
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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
> 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.
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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.
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 >
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-- 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
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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.
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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_fsa 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_fsa 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 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> > 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.
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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.
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. Candidate McGill 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_fsa 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_fsa 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 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. > > > > > > > > > >
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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_fsa 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_fsa 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 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 > 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
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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.
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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.
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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.
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. Candidate McGill 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 thefolder 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_fsa 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_fsa 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 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> 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/
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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_fsa 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 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> > 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. 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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. Candidate McGill 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_fsa
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 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
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any ideas?
Thanks!
Trisanna
-- Ph.D. Candidate McGill 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. Candidate McGill 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_fsa
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 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
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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_fs 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 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 itas > > sphere.reg. Is there a way I can inflate my > > surface overlays in a similar manner
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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. Candidate McGill 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_fs 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 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
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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 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 _______________________________________________ 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.
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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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 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_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> 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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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 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> 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_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> 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
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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.
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 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 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 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_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> 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 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
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 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> 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 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> 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_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> 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
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Hi Trisanna
what does mri_info show about spam_for_label_id_4_blur_minc1.mnc? You said it has the range of values in [0,100]? Or [0,1]? I'm not sure why mri_vol2surf would modify the values - this might have to wait for Doug to get back Bruce
On Thu, 30 Jun 2016, 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_bl ur_minc1.mnc --o/data-01/trisanna/freesurfer/MNI_average_2009a_asymm/spam_for_label_id_4_bl ur_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_bl ur_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_bl ur_overlay.mgz Dim: 152257 1 1
-- Ph.D. CandidateMcGill University Integrated Program in Neuroscience Psychology
On Wed, Jun 29, 2016 at 8:10 PM, Bruce Fischl 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 wrote:
Hi BruceI simply use
mri_vol2surf --mov spam.mnc --output overlayspam.mgz --regheader subject --hemi lh --surf pial
Trisanna
-- Ph.D. CandidateMcGill University Integrated Program in Neuroscience Psychology
On Wed, Jun 29, 2016 at 1:23 PM, Bruce Fischl 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> 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_overla y 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> 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 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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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Hi Doug
My apologies for the delay - I just returned from vacation.
Ok, so when I take a volumetric spam created using minc tools and create an overlay from it using mri_vol2surf, the min and max seems to be between 1 and 255. I am wondering if there is any where to change this into a %? When I open the spam using a minc software, for instance, it shows me the %.
best
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Wed, Jul 6, 2016 at 1:28 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
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 probabilityvalues
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 foundthat
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 donewhen
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 thefollowing
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>
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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try it with the noconform as the first argument. I think it will ignore it at the end
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 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> > 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.
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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@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas N Greve -
Trisanna Sprung-Much