Re: [Freesurfer] Orientation by direction cosines
Some documentaiotn is here https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems?action=AttachFile=get=fscoordinates.pdf The matrix below is the Mdc in the PDF. The first column is the direction of the columns (ie, as you go from column 1 to column 2). In your case, it is [.999 -.009 .030]' in RAS coordinates. This vector means that you will mostly move in the R direction, a little bit in the P (negative A) direction, and a little bit in the S direction. Because it is mostly R, R is the first letter in the orientation string. The next column is the row direction. Is is mostly in the A direction. The slice direction is mostly in the S direction. So this would be RAS orientation. On 1/25/19 9:06 PM, Ritesh Mahajan wrote: > External Email - Use Caution > > Hi Bruce, Thanks for your response. > > It would be really helpful if you explain how does it interpret from matrix. > > Thanks, > Ritesh Mahajan > > - Original Message - > From: "Greve, Douglas N.,Ph.D." > To: "freesurfer" > Sent: Friday, January 25, 2019 10:26:47 PM > Subject: Re: [Freesurfer] Orientation by direction cosines > > mri_info will do it. If you just want the orientation string, you can > add --orientation. Or do you still want the interpretation of the matrix? > > On 1/25/19 10:10 AM, Bruce Fischl wrote: >> Hi Ritesh >> >> I think that mri_info will try to figure this out and tell you (in the >> "Orientation" output). >> >> cheers >> Bruce >> >> >> On Fri, 25 Jan 2019, Ritesh Mahajan wrote: >> >>> External Email - Use Caution >>> >>> Hello Team, >>> >>> Can any one please explain how we come to know whether it is RAI or RAS or >>> any other orientation through direction cosines: >>> >>> Below is the direction cosine: I saw some non zero and negative values in >>> non diagonal values of matrix. What does this signify ? >>> >>> 0.9993770-0.0352819 >>> -0.00916448 0.965676-0.259588 >>> 0.0340709 0.25975 0.965075 >>> >>> Suppose it is Head First Supine. Any help will be really appreciated. >>> >>> Thanks, >>> Ritesh Mahajan >>> >>> ___ >>> 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 > > ___ > 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Orientation by direction cosines
here's the code if it is any help:
for (c = 0; c < 3; c++) ostr[c] = '\0';
for (c = 0; c < 3; c++) {
sag = Mdc[0][c]; // LR axis
cor = Mdc[1][c]; // PA axis
ax = Mdc[2][c]; // IS axis
// printf("c = %d, sag = %g, cor = %g, ax = %g\n",c,sag,cor,ax);
if (fabs(sag) > fabs(cor) && fabs(sag) > fabs(ax)) {
if (sag > 0)
ostr[c] = 'R';
else
ostr[c] = 'L';
continue;
}
if (fabs(cor) > fabs(ax)) {
if (cor > 0)
ostr[c] = 'A';
else
ostr[c] = 'P';
continue;
}
if (ax > 0)
ostr[c] = 'S';
else
ostr[c] = 'I';
}
return(ostr);
On Sat,
26 Jan 2019, Ritesh Mahajan
wrote:
External Email - Use Caution
Hi Bruce, Thanks for your response.
It would be really helpful if you explain how does it interpret from matrix.
Thanks,
Ritesh Mahajan
- Original Message -
From: "Greve, Douglas N.,Ph.D."
To: "freesurfer"
Sent: Friday, January 25, 2019 10:26:47 PM
Subject: Re: [Freesurfer] Orientation by direction cosines
mri_info will do it. If you just want the orientation string, you can
add --orientation. Or do you still want the interpretation of the matrix?
On 1/25/19 10:10 AM, Bruce Fischl wrote:
Hi Ritesh
I think that mri_info will try to figure this out and tell you (in the
"Orientation" output).
cheers
Bruce
On Fri, 25 Jan 2019, Ritesh Mahajan wrote:
External Email - Use Caution
Hello Team,
Can any one please explain how we come to know whether it is RAI or RAS or any
other orientation through direction cosines:
Below is the direction cosine: I saw some non zero and negative values in non
diagonal values of matrix. What does this signify ?
0.9993770-0.0352819
-0.00916448 0.965676-0.259588
0.0340709 0.25975 0.965075
Suppose it is Head First Supine. Any help will be really appreciated.
Thanks,
Ritesh Mahajan
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Re: [Freesurfer] Orientation by direction cosines
External Email - Use Caution Hi Bruce, Thanks for your response. It would be really helpful if you explain how does it interpret from matrix. Thanks, Ritesh Mahajan - Original Message - From: "Greve, Douglas N.,Ph.D." To: "freesurfer" Sent: Friday, January 25, 2019 10:26:47 PM Subject: Re: [Freesurfer] Orientation by direction cosines mri_info will do it. If you just want the orientation string, you can add --orientation. Or do you still want the interpretation of the matrix? On 1/25/19 10:10 AM, Bruce Fischl wrote: > Hi Ritesh > > I think that mri_info will try to figure this out and tell you (in the > "Orientation" output). > > cheers > Bruce > > > On Fri, 25 Jan 2019, Ritesh Mahajan wrote: > >> External Email - Use Caution >> >> Hello Team, >> >> Can any one please explain how we come to know whether it is RAI or RAS or >> any other orientation through direction cosines: >> >> Below is the direction cosine: I saw some non zero and negative values in >> non diagonal values of matrix. What does this signify ? >> >> 0.9993770-0.0352819 >> -0.00916448 0.965676-0.259588 >> 0.0340709 0.25975 0.965075 >> >> Suppose it is Head First Supine. Any help will be really appreciated. >> >> Thanks, >> Ritesh Mahajan >> >> ___ >> 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 ___ 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
Re: [Freesurfer] Orientation by direction cosines
mri_info will do it. If you just want the orientation string, you can add --orientation. Or do you still want the interpretation of the matrix? On 1/25/19 10:10 AM, Bruce Fischl wrote: > Hi Ritesh > > I think that mri_info will try to figure this out and tell you (in the > "Orientation" output). > > cheers > Bruce > > > On Fri, 25 Jan 2019, Ritesh Mahajan wrote: > >> External Email - Use Caution >> >> Hello Team, >> >> Can any one please explain how we come to know whether it is RAI or RAS or >> any other orientation through direction cosines: >> >> Below is the direction cosine: I saw some non zero and negative values in >> non diagonal values of matrix. What does this signify ? >> >> 0.9993770-0.0352819 >> -0.00916448 0.965676-0.259588 >> 0.0340709 0.25975 0.965075 >> >> Suppose it is Head First Supine. Any help will be really appreciated. >> >> Thanks, >> Ritesh Mahajan >> >> ___ >> 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Orientation by direction cosines
Hi Ritesh I think that mri_info will try to figure this out and tell you (in the "Orientation" output). cheers Bruce On Fri, 25 Jan 2019, Ritesh Mahajan wrote: >External Email - Use Caution > > Hello Team, > > Can any one please explain how we come to know whether it is RAI or RAS or > any other orientation through direction cosines: > > Below is the direction cosine: I saw some non zero and negative values in non > diagonal values of matrix. What does this signify ? > > 0.9993770-0.0352819 > -0.00916448 0.965676-0.259588 > 0.0340709 0.25975 0.965075 > > Suppose it is Head First Supine. Any help will be really appreciated. > > Thanks, > Ritesh Mahajan > > ___ > 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
[Freesurfer] Orientation by direction cosines
External Email - Use Caution Hello Team, Can any one please explain how we come to know whether it is RAI or RAS or any other orientation through direction cosines: Below is the direction cosine: I saw some non zero and negative values in non diagonal values of matrix. What does this signify ? 0.9993770-0.0352819 -0.00916448 0.965676-0.259588 0.0340709 0.25975 0.965075 Suppose it is Head First Supine. Any help will be really appreciated. Thanks, Ritesh Mahajan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
