mri_convert and image orientation

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Re: [Freesurfer] fast_selxavg3...

Yang, Daniel

25 Jan 2016 25 Jan '16

12:11 p.m.

Dear FreeSurfer experts,

I find that mri_convert will convert DICOM of structural scan to neurological orientation by default.

For example, mri_convert --in_type dicom --out_type mii <first file in the DICOM directory> <output.nii.gz>

Thus, the NII may need to be swapped in x for use in FSL.

In this the case?

Many thanks, Daniel

-- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.yang@yale.edu

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Douglas N Greve

25 Jan 25 Jan

1:47 p.m.

not necessarily. For FSL, the determinant must be less than 0 (see mri_info output). Having said that, even if the det<0, it may still show up funny in fslview

On 01/25/2016 12:11 PM, Yang, Daniel wrote:

...

Dear FreeSurfer experts,

I find that mri_convert will convert DICOM of structural scan to neurological orientation by default.

For example, mri_convert --in_type dicom --out_type mii <first file in the DICOM directory> <output.nii.gz>

Thus, the NII may need to be swapped in x for use in FSL.

In this the case?

Many thanks, Daniel

-- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.yang@yale.edu

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/

Yang, Daniel

26 Jan 26 Jan

4:20 p.m.

Dear Doug,

Thanks for your reply. Is it possible to upload the raw DICOM to a server so that you can see if mri_convert is making the orientation in the output NII file neurological? I just want to make sure what my image orientation is and how mri_convert interacts with it.

Many thanks! Daniel

-- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.yang@yale.edu On 1/25/16, 1:47 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@nmr.mgh.harvard.edu> wrote: >not necessarily. For FSL, the determinant must be less than 0 (see >mri_info output). Having said that, even if the det<0, it may still show >up funny in fslview > >On 01/25/2016 12:11 PM, Yang, Daniel wrote: >> Dear FreeSurfer experts, >> >> I find that mri_convert will convert DICOM of structural scan to >> neurological orientation by default. >> >> For example, mri_convert --in_type dicom --out_type mii <first file in >> the DICOM directory> <output.nii.gz> >> >> Thus, the NII may need to be swapped in x for use in FSL. >> >> In this the case? >> >> Many thanks, >> Daniel >> >> -- >> Daniel Yang, Ph.D. >> Yale Child Study Center >> E-mail: daniel.yj.yang@yale.edu >> >> >> _______________________________________________ >> 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 > > >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 >https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compl >ianceline&d=AwIBAg&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=vhD8z919MORXy6GkKdTAw3V58rxz >UZGOKpGXPDgqUHY&m=vPCUh0LHBB0FFqxEXa3WMuAGE7_uhojBsOWMI4IcGCE&s=hHbJW-rVbK >tbdsFRHLaY0s9EKUtssTAJmRyP2VVqzUE&e= . 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. >

Douglas N Greve

4:26 p.m.

If the determinant is less than 0, then it is radiological (probably it will be radiological).

On 01/26/2016 04:20 PM, Yang, Daniel wrote:

...

Dear Doug,

Thanks for your reply. Is it possible to upload the raw DICOM to a server so that you can see if mri_convert is making the orientation in the output NII file neurological? I just want to make sure what my image orientation is and how mri_convert interacts with it.

Many thanks! Daniel

Yang, Daniel

10:09 p.m.

Thanks so much, I see that voxel-to-ras determinant is -1 in my file, so it’s most likely to be radiological.

Just curious, so determinant > 0 means neurological then?

Daniel

-- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.yang@yale.edu On 1/26/16, 4:26 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@nmr.mgh.harvard.edu> wrote: >If the determinant is less than 0, then it is radiological (probably it >will be radiological). > >On 01/26/2016 04:20 PM, Yang, Daniel wrote: >> Dear Doug, >> >> Thanks for your reply. Is it possible to upload the raw DICOM to a >>server >> so that you can see if mri_convert is making the orientation in the >>output >> NII file neurological? I just want to make sure what my image >>orientation >> is and how mri_convert interacts with it. >> >> Many thanks! >> Daniel >> >> > >-- >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 > > >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 >https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compl >ianceline&d=AwIBAg&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=vhD8z919MORXy6GkKdTAw3V58rxz >UZGOKpGXPDgqUHY&m=WLltv6OcAkXClyk0AkG4dpyu2SPQluAJ6oEiH94MutM&s=TD-7P7MmdH >yxRXXCDN_76DHGG7ZDDwckhxJfe-wp-cU&e= . 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. >

Yang, Daniel

29 Jan 29 Jan

8:52 a.m.

Just to note for people who are interested:

It does seem that when voxel-to-ras determinant > 0, then the file is neurological.

-- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.yang@yale.edu On 1/26/16, 10:09 PM, "Yang, Daniel" daniel.yj.yang@yale.edu wrote: >Thanks so much, I see that voxel-to-ras determinant is -1 in my file, so >it’s most likely to be radiological. > >Just curious, so determinant > 0 means neurological then? > >Daniel > > >-- >Daniel Yang, Ph.D. >Yale Child Study Center > >E-mail: daniel.yj.yang@yale.edu > > > > >On 1/26/16, 4:26 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of >Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of >greve@nmr.mgh.harvard.edu> wrote: > >>If the determinant is less than 0, then it is radiological (probably it >>will be radiological). >> >>On 01/26/2016 04:20 PM, Yang, Daniel wrote: >>> Dear Doug, >>> >>> Thanks for your reply. Is it possible to upload the raw DICOM to a >>>server >>> so that you can see if mri_convert is making the orientation in the >>>output >>> NII file neurological? I just want to make sure what my image >>>orientation >>> is and how mri_convert interacts with it. >>> >>> Many thanks! >>> Daniel >>> >>> >> >>-- >>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 >> >> >>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 >>https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_comp >>l >>ianceline&d=AwIBAg&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=vhD8z919MORXy6GkKdTAw3V58rx >>z >>UZGOKpGXPDgqUHY&m=WLltv6OcAkXClyk0AkG4dpyu2SPQluAJ6oEiH94MutM&s=TD-7P7Mmd >>H >>yxRXXCDN_76DHGG7ZDDwckhxJfe-wp-cU&e= . 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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Douglas N Greve
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