Well, I tried to avoid FSL, and used only Freesurfer tool to do the same thing. I found there was the same issue when an image with 32-bit float point data type converts to 32-bit integer. No problem for the convertion from 32-bit float point to 8-bit unsigned integer.
Wayne
On 05/10/10 10:44 AM, "Wayne Su" wsu@interchange.ubc.ca wrote:
Hello Freesurfer Users,
I am feeling very bad when I am using mri_convert. There are two problems:
- When I converted a file in mgz format to nii.gz format, and did some
volume calculation (mask and addition) by using fslmaths from FSL, then converted back to mgz. If the image type is uchar, it works fine. If the image type is int, the intensities changed. The 0¹ value is changed to 2.1e+09¹, others also in very large number (look like read the data from wrong place). Here is the code I used:
${FREESURFER_HOME}/bin/mri_convert aparc+aseg.mgz aparc+aseg.nii.gz-odt int ${FSLDIR}/bin/fslmaths aparc+aseg -mas right_vect_mask_inv -add right_vect_mask aparc+aseg ${FREESURFER_HOME}/bin/mri_convert aparc+aseg.nii.gz aparc+aseg.mgz -odt int
If no fslmaths calculation, convert back to mgz right way, no problemfound.
- when the conform is used, some head were rotated a little bit, but not for
others. I am wondering how to avoid the rotation?
Regards, Wayne
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 Wayne,
can you check to see whether it's an FSL problem or a FreeSurfer one? If you don't use FSL do you still have the problem?
cheers Bruce On Tue, 5 Oct 2010, Wayne Su wrote:
Well, I tried to avoid FSL, and used only Freesurfer tool to do the same thing. I found there was the same issue when an image with 32-bit float point data type converts to 32-bit integer. No problem for the convertion from 32-bit float point to 8-bit unsigned integer.
Wayne
On 05/10/10 10:44 AM, "Wayne Su" wsu@interchange.ubc.ca wrote:
Hello Freesurfer Users,
I am feeling very bad when I am using mri_convert. There are two problems:
- When I converted a file in mgz format to nii.gz format, and did some
volume calculation (mask and addition) by using fslmaths from FSL, then converted back to mgz. If the image type is uchar, it works fine. If the image type is int, the intensities changed. The 0¹ value is changed to 2.1e+09¹, others also in very large number (look like read the data from wrong place). Here is the code I used:
${FREESURFER_HOME}/bin/mri_convert aparc+aseg.mgz aparc+aseg.nii.gz-odt int ${FSLDIR}/bin/fslmaths aparc+aseg -mas right_vect_mask_inv -add right_vect_mask aparc+aseg ${FREESURFER_HOME}/bin/mri_convert aparc+aseg.nii.gz aparc+aseg.mgz -odt int
If no fslmaths calculation, convert back to mgz right way, no problemfound.
- when the conform is used, some head were rotated a little bit, but not for
others. I am wondering how to avoid the rotation?
Regards, Wayne
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, I used just mri_binarize, mri_mask and mri_concat and all in mgz format. I got a 32-bit floating point image with intensity range from 0~2031. Then I used the mri_convert to convert it to 32-bit integer also both in mgz format. Here is the message on the screen.
mri_convert aparc+aseg.mgz aparc+aseg2.mgz -odt int $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from aparc+aseg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.77636e-15, -1.88564e-15) j_ras = (0, -4.3715e-16, -1) k_ras = (0, 1, -3.72529e-09) changing data type from float to int (noscale = 0)... MRIchangeType: Building histogram writing to aparc+aseg2.mgz...
The intensity range of new image is -214783648.00 ~ 214551xxx.00 showed by DTI_TK Quick Look.
Wayne
On 05/10/10 1:30 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Wayne,
can you check to see whether it's an FSL problem or a FreeSurfer one? If you don't use FSL do you still have the problem?
cheers Bruce On Tue, 5 Oct 2010, Wayne Su wrote:
Well, I tried to avoid FSL, and used only Freesurfer tool to do the same thing. I found there was the same issue when an image with 32-bit float point data type converts to 32-bit integer. No problem for the convertion from 32-bit float point to 8-bit unsigned integer.
Wayne
On 05/10/10 10:44 AM, "Wayne Su" wsu@interchange.ubc.ca wrote:
Hello Freesurfer Users,
I am feeling very bad when I am using mri_convert. There are two problems:
- When I converted a file in mgz format to nii.gz format, and did some
volume calculation (mask and addition) by using fslmaths from FSL, then converted back to mgz. If the image type is uchar, it works fine. If the image type is int, the intensities changed. The 0¹ value is changed to 2.1e+09¹, others also in very large number (look like read the data from wrong place). Here is the code I used:
${FREESURFER_HOME}/bin/mri_convert aparc+aseg.mgz aparc+aseg.nii.gz-odt int ${FSLDIR}/bin/fslmaths aparc+aseg -mas right_vect_mask_inv -add right_vect_mask aparc+aseg ${FREESURFER_HOME}/bin/mri_convert aparc+aseg.nii.gz aparc+aseg.mgz -odt int
If no fslmaths calculation, convert back to mgz right way, noproblem found.
- when the conform is used, some head were rotated a little bit, but not
for others. I am wondering how to avoid the rotation?
Regards, Wayne
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
I've never heard of DTI_TK Quick Look. Does it actually read mgz files? What value does it give for aparc+aseg.mgz? Try loading the file into matlab with the FreeSurfer MRIread.m function and see what it gives for the max. Or just run
mris_calc aparc+aseg2.mgz max
doug
Wayne Su wrote:
Hi Bruce, I used just mri_binarize, mri_mask and mri_concat and all in mgz format. I got a 32-bit floating point image with intensity range from 0~2031. Then I used the mri_convert to convert it to 32-bit integer also both in mgz format. Here is the message on the screen.
mri_convert aparc+aseg.mgz aparc+aseg2.mgz -odt int $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from aparc+aseg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.77636e-15, -1.88564e-15) j_ras = (0, -4.3715e-16, -1) k_ras = (0, 1, -3.72529e-09) changing data type from float to int (noscale = 0)... MRIchangeType: Building histogram writing to aparc+aseg2.mgz...
The intensity range of new image is -214783648.00 ~ 214551xxx.00 showed by DTI_TK Quick Look.
Wayne
On 05/10/10 1:30 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Wayne,
can you check to see whether it's an FSL problem or a FreeSurfer one? If you don't use FSL do you still have the problem?
cheers Bruce On Tue, 5 Oct 2010, Wayne Su wrote:
Well, I tried to avoid FSL, and used only Freesurfer tool to do the same thing. I found there was the same issue when an image with 32-bit float point data type converts to 32-bit integer. No problem for the convertion from 32-bit float point to 8-bit unsigned integer.
Wayne
On 05/10/10 10:44 AM, "Wayne Su" wsu@interchange.ubc.ca wrote:
Hello Freesurfer Users,
I am feeling very bad when I am using mri_convert. There are two problems:
- When I converted a file in mgz format to nii.gz format, and did some
volume calculation (mask and addition) by using fslmaths from FSL, then converted back to mgz. If the image type is uchar, it works fine. If the image type is int, the intensities changed. The Œ0¹ value is changed to Œ2.1e+09¹, others also in very large number (look like read the data from wrong place). Here is the code I used:
${FREESURFER_HOME}/bin/mri_convert aparc+aseg.mgz aparc+aseg.nii.gz-odt int ${FSLDIR}/bin/fslmaths aparc+aseg -mas right_vect_mask_inv -add right_vect_mask aparc+aseg ${FREESURFER_HOME}/bin/mri_convert aparc+aseg.nii.gz aparc+aseg.mgz -odt int
If no fslmaths calculation, convert back to mgz right way, noproblem found.
- when the conform is used, some head were rotated a little bit, but not
for others. I am wondering how to avoid the rotation?
Regards, Wayne
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Here is the output from mris_calc: mris_calc aparc+aseg2.mgz max Max@(index) [ 2145516800.000000 (6400402) ] Wayne
On 05/10/10 2:05 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
I've never heard of DTI_TK Quick Look. Does it actually read mgz files? What value does it give for aparc+aseg.mgz? Try loading the file into matlab with the FreeSurfer MRIread.m function and see what it gives for the max. Or just run
mris_calc aparc+aseg2.mgz max
doug
Wayne Su wrote:
Hi Bruce, I used just mri_binarize, mri_mask and mri_concat and all in mgz format. I got a 32-bit floating point image with intensity range from 0~2031. Then I used the mri_convert to convert it to 32-bit integer also both in mgz format. Here is the message on the screen.
mri_convert aparc+aseg.mgz aparc+aseg2.mgz -odt int $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from aparc+aseg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.77636e-15, -1.88564e-15) j_ras = (0, -4.3715e-16, -1) k_ras = (0, 1, -3.72529e-09) changing data type from float to int (noscale = 0)... MRIchangeType: Building histogram writing to aparc+aseg2.mgz...
The intensity range of new image is -214783648.00 ~ 214551xxx.00 showed by DTI_TK Quick Look.
Wayne
On 05/10/10 1:30 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Wayne,
can you check to see whether it's an FSL problem or a FreeSurfer one? If you don't use FSL do you still have the problem?
cheers Bruce On Tue, 5 Oct 2010, Wayne Su wrote:
Well, I tried to avoid FSL, and used only Freesurfer tool to do the same thing. I found there was the same issue when an image with 32-bit float point data type converts to 32-bit integer. No problem for the convertion from 32-bit float point to 8-bit unsigned integer.
Wayne
On 05/10/10 10:44 AM, "Wayne Su" wsu@interchange.ubc.ca wrote:
Hello Freesurfer Users,
I am feeling very bad when I am using mri_convert. There are two problems:
- When I converted a file in mgz format to nii.gz format, and did some
volume calculation (mask and addition) by using fslmaths from FSL, then converted back to mgz. If the image type is uchar, it works fine. If the image type is int, the intensities changed. The Œ0¹ value is changed to Œ2.1e+09¹, others also in very large number (look like read the data from wrong place). Here is the code I used:
${FREESURFER_HOME}/bin/mri_convert aparc+aseg.mgzaparc+aseg.nii.gz -odt int ${FSLDIR}/bin/fslmaths aparc+aseg -mas right_vect_mask_inv -add right_vect_mask aparc+aseg ${FREESURFER_HOME}/bin/mri_convert aparc+aseg.nii.gz aparc+aseg.mgz -odt int
If no fslmaths calculation, convert back to mgz right way, noproblem found.
- when the conform is used, some head were rotated a little bit, but not
for others. I am wondering how to avoid the rotation?
Regards, Wayne
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
And what do you get when you run mris_calc on aparc+aseg.mgz?
Wayne Su wrote:
Here is the output from mris_calc: mris_calc aparc+aseg2.mgz max Max@(index) [ 2145516800.000000 (6400402) ] Wayne
On 05/10/10 2:05 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
I've never heard of DTI_TK Quick Look. Does it actually read mgz files? What value does it give for aparc+aseg.mgz? Try loading the file into matlab with the FreeSurfer MRIread.m function and see what it gives for the max. Or just run
mris_calc aparc+aseg2.mgz max
doug
Wayne Su wrote:
Hi Bruce, I used just mri_binarize, mri_mask and mri_concat and all in mgz format. I got a 32-bit floating point image with intensity range from 0~2031. Then I used the mri_convert to convert it to 32-bit integer also both in mgz format. Here is the message on the screen.
mri_convert aparc+aseg.mgz aparc+aseg2.mgz -odt int $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from aparc+aseg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.77636e-15, -1.88564e-15) j_ras = (0, -4.3715e-16, -1) k_ras = (0, 1, -3.72529e-09) changing data type from float to int (noscale = 0)... MRIchangeType: Building histogram writing to aparc+aseg2.mgz...
The intensity range of new image is -214783648.00 ~ 214551xxx.00 showed by DTI_TK Quick Look.
Wayne
On 05/10/10 1:30 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Wayne,
can you check to see whether it's an FSL problem or a FreeSurfer one? If you don't use FSL do you still have the problem?
cheers Bruce On Tue, 5 Oct 2010, Wayne Su wrote:
Well, I tried to avoid FSL, and used only Freesurfer tool to do the same thing. I found there was the same issue when an image with 32-bit float point data type converts to 32-bit integer. No problem for the convertion from 32-bit float point to 8-bit unsigned integer.
Wayne
On 05/10/10 10:44 AM, "Wayne Su" wsu@interchange.ubc.ca wrote:
Hello Freesurfer Users,
I am feeling very bad when I am using mri_convert. There are two problems:
- When I converted a file in mgz format to nii.gz format, and did some
volume calculation (mask and addition) by using fslmaths from FSL, then converted back to mgz. If the image type is uchar, it works fine. If the image type is int, the intensities changed. The Œ0¹ value is changed to Œ2.1e+09¹, others also in very large number (look like read the data from wrong place). Here is the code I used:
${FREESURFER_HOME}/bin/mri_convert aparc+aseg.mgzaparc+aseg.nii.gz -odt int ${FSLDIR}/bin/fslmaths aparc+aseg -mas right_vect_mask_inv -add right_vect_mask aparc+aseg ${FREESURFER_HOME}/bin/mri_convert aparc+aseg.nii.gz aparc+aseg.mgz -odt int
If no fslmaths calculation, convert back to mgz right way, noproblem found.
- when the conform is used, some head were rotated a little bit, but not
for others. I am wondering how to avoid the rotation?
Regards, Wayne
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
btw, I mean the original aparc+aseg.mgz, not the one created after you made changes using those FSL commands.
doug
Douglas N Greve wrote:
And what do you get when you run mris_calc on aparc+aseg.mgz?
Wayne Su wrote:
Here is the output from mris_calc: mris_calc aparc+aseg2.mgz max Max@(index) [ 2145516800.000000 (6400402) ] Wayne
On 05/10/10 2:05 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
I've never heard of DTI_TK Quick Look. Does it actually read mgz files? What value does it give for aparc+aseg.mgz? Try loading the file into matlab with the FreeSurfer MRIread.m function and see what it gives for the max. Or just run
mris_calc aparc+aseg2.mgz max
doug
Wayne Su wrote:
Hi Bruce, I used just mri_binarize, mri_mask and mri_concat and all in mgz format. I got a 32-bit floating point image with intensity range from 0~2031. Then I used the mri_convert to convert it to 32-bit integer also both in mgz format. Here is the message on the screen.
mri_convert aparc+aseg.mgz aparc+aseg2.mgz -odt int $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from aparc+aseg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.77636e-15, -1.88564e-15) j_ras = (0, -4.3715e-16, -1) k_ras = (0, 1, -3.72529e-09) changing data type from float to int (noscale = 0)... MRIchangeType: Building histogram writing to aparc+aseg2.mgz...
The intensity range of new image is -214783648.00 ~ 214551xxx.00 showed by DTI_TK Quick Look.
Wayne
On 05/10/10 1:30 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Wayne,
can you check to see whether it's an FSL problem or a FreeSurfer one? If you don't use FSL do you still have the problem?
cheers Bruce On Tue, 5 Oct 2010, Wayne Su wrote:
Well, I tried to avoid FSL, and used only Freesurfer tool to do the same thing. I found there was the same issue when an image with 32-bit float point data type converts to 32-bit integer. No problem for the convertion from 32-bit float point to 8-bit unsigned integer.
Wayne
On 05/10/10 10:44 AM, "Wayne Su" wsu@interchange.ubc.ca wrote:
> Hello Freesurfer Users, > > I am feeling very bad when I am using mri_convert. There are two problems: > 1. When I converted a file in mgz format to nii.gz format, and did some > volume calculation (mask and addition) by using fslmaths from FSL, then > converted back to mgz. If the image type is uchar, it works fine. If the > image type is int, the intensities changed. The Œ0¹ value is changed to > Œ2.1e+09¹, others also in very large number (look like read the data from > wrong place). Here is the code I used: > > ${FREESURFER_HOME}/bin/mri_convert aparc+aseg.mgz > aparc+aseg.nii.gz > -odt int > ${FSLDIR}/bin/fslmaths aparc+aseg -mas right_vect_mask_inv -add > right_vect_mask aparc+aseg > ${FREESURFER_HOME}/bin/mri_convert aparc+aseg.nii.gz > aparc+aseg.mgz > -odt int > > If no fslmaths calculation, convert back to mgz right way, no > problem > found. > > 2. when the conform is used, some head were rotated a little bit, but not > for > others. I am wondering how to avoid the rotation? > > Regards, > Wayne > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Here is: mris_calc aparc+aseg.mgz max Max@(index) [ 2035.000000 (7772808) ]
On 05/10/10 2:20 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
btw, I mean the original aparc+aseg.mgz, not the one created after you
made
changes using those FSL commands.
doug
Douglas N Greve wrote:
And what do you get when you run mris_calc on aparc+aseg.mgz?
Wayne Su wrote:
Here is the output from mris_calc:
mris_calc aparc+aseg2.mgz max
Max@(index) [ 2145516800.000000 (6400402) ]
Wayne
On 05/10/10 2:05
PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
I've never heard of DTI_TK Quick Look. Does it actually read mgz files?
What value does it give for aparc+aseg.mgz? Try loading the file into
matlab with the FreeSurfer MRIread.m function and see what it gives for
the max. Or just run
mris_calc aparc+aseg2.mgz max
doug
Wayne Su wrote:
Hi Bruce, I used
just mri_binarize, mri_mask and mri_concat and all in mgz format. I
got a
32-bit floating point image with intensity range from 0~2031. Then I
used
the mri_convert to convert it to 32-bit integer also both in mgz
format.
Here is the message on the screen.
mri_convert aparc+aseg.mgz
aparc+aseg2.mgz -odt int
$Id: mri_convert.c,v 1.166.2.2 2010/08/10
19:11:50 greve Exp $
reading from aparc+aseg.mgz... TR=0.00,
TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -1.77636e-15,
-1.88564e-15)
j_ras = (0, -4.3715e-16, -1) k_ras = (0, 1,
-3.72529e-09)
changing data type from float to int (noscale = 0)...
MRIchangeType: Building histogram
writing to aparc+aseg2.mgz...
The intensity range of new image is -214783648.00 ~ 214551xxx.00 showed by
DTI_TK Quick Look.
Wayne
On 05/10/10
1:30 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Wayne,
can you check to see whether it's
an FSL problem or a FreeSurfer one? If
you don't use FSL do you still
have the problem?
cheers Bruce On Tue, 5 Oct 2010,
Wayne
Su wrote:
Well, I tried to avoid FSL, and used only Freesurfer tool to do the same
thing. I found there was the same issue when an image with 32-bit
float
point data type converts to 32-bit integer. No problem for the
convertion
from 32-bit float point to 8-bit unsigned
integer.
Wayne
On 05/10/10 10:44 AM, "Wayne
Su" wsu@interchange.ubc.ca wrote:
> Hello Freesurfer Users, > > I am
feeling very bad when I am using mri_convert. There are two problems:
>
- When I converted a file in mgz format to nii.gz format, and did
some
> volume calculation (mask and addition) by using fslmaths from
FSL, then
> converted back to mgz. If the image type is uchar, it works
fine. If the
> image type is int, the intensities changed. The Œ0¹ value
is changed to
> Œ2.1e+09¹, others also in very large number (look like
read the data from
> wrong place). Here is the code I
used:
> > ${FREESURFER_HOME}/bin/mri_convert
aparc+aseg.mgz
> aparc+aseg.nii.gz > -odt int >
${FSLDIR}/bin/fslmaths aparc+aseg -mas right_vect_mask_inv -add
>
right_vect_mask aparc+aseg
> ${FREESURFER_HOME}/bin/mri_convert
aparc+aseg.nii.gz
> aparc+aseg.mgz > -odt int > >
If no fslmaths calculation, convert back to mgz right way, no
>
problem
> found. > > 2. when the conform is used, some head
were rotated a little bit, but not
> for > others. I am wondering
how to avoid the rotation?
> > Regards, >
Wayne
> > _______________________________________________ >
Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> The information in this e-mail is intended only for the person to whom
it
> is > addressed. If you believe this e-mail was sent to you in
error and the
> e-mail > contains patient information, please
contact the Partners Compliance
> HelpLine > at >
http://www.partners.org/complianceline . If the e-mail was sent to you in
> error > but does not contain patient information, please
contact the sender and
> properly > dispose of the e-mail. >
> >
Freesurfer mailing
list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and
the
e-mail contains patient information, please contact the
Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in
error but does not contain patient information, please contact
the sender and
properly dispose of the e-mail.
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
And when you run
mri_convert aparc+aseg.mgz aparc+aseg2.mgz -odt int
And then
mris_calc aparc+aseg2.mgz max
you get that crazy number?
I've tried this here with version 5 and cannot replicate. What version are you using?
doug
Wayne Su wrote:
Here is: mris_calc aparc+aseg.mgz max Max@(index) [ 2035.000000 (7772808) ]
On 05/10/10 2:20 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
btw, I mean the original aparc+aseg.mgz, not the one created after you
made
changes using those FSL commands.
doug
Douglas N Greve wrote:
And what do you get when you run mris_calc on aparc+aseg.mgz?
Wayne Su wrote:
Here is the output from mris_calc:
mris_calc aparc+aseg2.mgz max
Max@(index) [ 2145516800.000000 (6400402) ]
Wayne
On 05/10/10 2:05
PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
I've never heard of DTI_TK Quick Look. Does it actually read mgz files?
What value does it give for aparc+aseg.mgz? Try loading the file into
matlab with the FreeSurfer MRIread.m function and see what it gives for
the max. Or just run
mris_calc aparc+aseg2.mgz max
doug
Wayne Su wrote:
Hi Bruce, I used
just mri_binarize, mri_mask and mri_concat and all in mgz format. I
got a
32-bit floating point image with intensity range from 0~2031. Then I
used
the mri_convert to convert it to 32-bit integer also both in mgz
format.
Here is the message on the screen.
mri_convert aparc+aseg.mgz
aparc+aseg2.mgz -odt int
$Id: mri_convert.c,v 1.166.2.2 2010/08/10
19:11:50 greve Exp $
reading from aparc+aseg.mgz... TR=0.00,
TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -1.77636e-15,
-1.88564e-15)
j_ras = (0, -4.3715e-16, -1) k_ras = (0, 1,
-3.72529e-09)
changing data type from float to int (noscale = 0)...
MRIchangeType: Building histogram
writing to aparc+aseg2.mgz...
The intensity range of new image is -214783648.00 ~ 214551xxx.00 showed by
DTI_TK Quick Look.
Wayne
On 05/10/10
1:30 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Wayne,
can you check to see whether it's
an FSL problem or a FreeSurfer one? If
you don't use FSL do you still
have the problem?
cheers Bruce On Tue, 5 Oct 2010,
Wayne
Su wrote:
Well, I tried to avoid FSL, and used only Freesurfer tool to do the same
> thing. I found there was the same issue when an image with 32-bit >
float
> point data type converts to 32-bit integer. No problem for the >
convertion
> from 32-bit float point to 8-bit unsigned >
integer.
> Wayne > > > On 05/10/10 10:44 AM, "Wayne >
Su" wsu@interchange.ubc.ca wrote:
> > > > > >> Hello Freesurfer Users, >> >> I am >>
feeling very bad when I am using mri_convert. There are two problems:
- When I converted a file in mgz format to nii.gz format, and did
some
>> volume calculation (mask and addition) by using fslmaths from >>
FSL, then
>> converted back to mgz. If the image type is uchar, it works >>
fine. If the
>> image type is int, the intensities changed. The Œ0¹ value >>
is changed to
>> Œ2.1e+09¹, others also in very large number (look like >>
read the data from
>> wrong place). Here is the code I >>
used:
>> ${FREESURFER_HOME}/bin/mri_convert >>
aparc+aseg.mgz
>> aparc+aseg.nii.gz >> -odt int >> >>
${FSLDIR}/bin/fslmaths aparc+aseg -mas right_vect_mask_inv -add
right_vect_mask aparc+aseg
>> ${FREESURFER_HOME}/bin/mri_convert >>
aparc+aseg.nii.gz
>> aparc+aseg.mgz >> -odt int >> >> >>
If no fslmaths calculation, convert back to mgz right way, no
problem
>> found. >> >> 2. when the conform is used, some head >>
were rotated a little bit, but not
>> for >> others. I am wondering >>
how to avoid the rotation?
>> Regards, >> >>
Wayne
>> _______________________________________________ >> >>
Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu >> >>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >> The information in this e-mail is intended only for the person to whom >>
it
>> is >> addressed. If you believe this e-mail was sent to you in >>
error and the
>> e-mail >> contains patient information, please >>
contact the Partners Compliance
>> HelpLine >> at >> >>
http://www.partners.org/complianceline . If the e-mail was sent to you in
>> error >> but does not contain patient information, please >>
contact the sender and
>> properly >> dispose of the e-mail. >> >> >> >> >> > > > > >
Freesurfer mailing
list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and
the
e-mail contains patient information, please contact the
Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in
error but does not contain patient information, please contact
the sender and
properly dispose of the e-mail.
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Maybe my email is not clear. Try this to see what you get:
mri_convert aparc+aseg.mgz aparc+aseg1.mgz -odt float mri_convert aparc+aseg1.mgz aparc+aseg2.mgz -odt int mris_calc aparc+aseg2.mgz max
I tried 'mris_calc'. The output is in floating format. I have no way to avoid converting back to int format.
I am using Freesurfer version 5.
Wayne
On 05/10/10 2:33 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
And when you run
mri_convert aparc+aseg.mgz aparc+aseg2.mgz -odt int
And
then
mris_calc aparc+aseg2.mgz max
you get that crazy number?
I've tried
this here with version 5 and cannot replicate. What version
are you
using?
doug
Wayne Su wrote:
Here is: mris_calc aparc+aseg.mgz max
Max@(index) [ 2035.000000 (7772808) ]
On 05/10/10 2:20 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
btw, I mean the original
aparc+aseg.mgz, not the one created after you
made
changes
using those FSL commands.
doug
Douglas N Greve wrote:
And what do
you get when you run mris_calc on aparc+aseg.mgz?
Wayne
Su wrote:
Here is the output from mris_calc:
mris_calc aparc+aseg2.mgz max
Max@(index) [
2145516800.000000 (6400402) ]
Wayne
On 05/10/10
2:05
PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
I've never heard of DTI_TK Quick Look. Does it
actually read mgz files?
What value does it give for
aparc+aseg.mgz? Try loading the file into
matlab with the
FreeSurfer MRIread.m function and see what it gives for
the max. Or
just run
mris_calc aparc+aseg2.mgz max
doug
Wayne Su wrote:
Hi
Bruce,
I used
just mri_binarize, mri_mask and
mri_concat and all in mgz format. I
got a
32-bit floating point image with intensity range from 0~2031. Then I
used
the mri_convert to convert it to 32-bit
integer also both in mgz
format.
Here is the
message on the screen.
mri_convert aparc+aseg.mgz
aparc+aseg2.mgz -odt int
$Id: mri_convert.c,v 1.166.2.2
2010/08/10
19:11:50 greve Exp $
reading from
aparc+aseg.mgz...
TR=0.00,
TE=0.00, TI=0.00, flip
angle=0.00
i_ras = (-1, -1.77636e-15,
-1.88564e-15)
j_ras = (0, -4.3715e-16, -1) k_ras = (0,
1,
-3.72529e-09)
changing data type from
float to int (noscale = 0)...
MRIchangeType:
Building histogram
writing to
aparc+aseg2.mgz...
The intensity range of new
image is -214783648.00 ~ 214551xxx.00 showed
by
DTI_TK Quick
Look.
Wayne
On 05/10/10
1:30 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi
Wayne,
can you check to see whether it's
an FSL problem or a FreeSurfer one? If
you don't use FSL do you
still
have the problem?
cheers
Bruce
On Tue, 5 Oct 2010,
Wayne
Su wrote:
Well, I tried to avoid FSL, and used only Freesurfer tool to do the
same
> thing. I found there was the same issue when an image
with 32-bit
>
float
> point data type
converts to 32-bit integer. No problem for the
>
convertion
> from 32-bit float point to 8-bit unsigned >
integer.
> Wayne > > > On 05/10/10 10:44
AM, "Wayne
>
Su" wsu@interchange.ubc.ca wrote:
> > > > >
>> Hello Freesurfer Users, >> >> I am >>
feeling very bad when I am using mri_convert. There are two problems:
- When I converted a file in mgz format to nii.gz format, and did
some
>> volume calculation (mask and addition) by using fslmaths
from
>>
FSL, then
>> converted back to
mgz. If the image type is uchar, it works
>>
fine.
If the
>> image type is int, the intensities changed. The Œ0¹
value
>>
is changed to
>> Œ2.1e+09¹,
others also in very large number (look like
>>
read
the data from
>> wrong place). Here is the code I >>
used:
>> ${FREESURFER_HOME}/bin/mri_convert >>
aparc+aseg.mgz
>> aparc+aseg.nii.gz >> -odt
int
>> >>
${FSLDIR}/bin/fslmaths aparc+aseg
-mas right_vect_mask_inv -add
right_vect_mask aparc+aseg
>> ${FREESURFER_HOME}/bin/mri_convert >>
aparc+aseg.nii.gz
>> aparc+aseg.mgz >> -odt
int
>> >> >>
If no fslmaths calculation,
convert back to mgz right way, no
problem
>>
found.
>> >> 2. when the conform is used, some head >>
were rotated a little bit, but not
>> for >> others. I
am wondering
>>
how to avoid the rotation?
>> Regards, >> >>
Wayne
>> _______________________________________________ >> >>
Freesurfer mailing list
>>
Freesurfer@nmr.mgh.harvard.edu
>> >>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> The information in this e-mail is intended only for the person to
whom
>>
it
>> is >> addressed.
If you believe this e-mail was sent to you in
>>
error and the
>> e-mail >> contains patient information,
please
>>
contact the Partners Compliance
>> HelpLine >> at >> >>
http://www.partners.org/complianceline . If the e-mail was sent to you
in
>> error >> but does not contain patient information,
please
>>
contact the sender and
>>
properly
>> dispose of the e-mail. >> >>
>> >> >>
> > > > >
Freesurfer
mailing
list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only
for the person to whom it
is
addressed. If you believe this
e-mail was sent to you in error and
the
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
Ah, I see, that I can replicate. As Bruce says, use -ns 1 to keep it from doing a funny rescaling when converting from float to int.
doug
Wayne Su wrote:
Maybe my email is not clear. Try this to see what you get:
mri_convert aparc+aseg.mgz aparc+aseg1.mgz -odt float mri_convert aparc+aseg1.mgz aparc+aseg2.mgz -odt int mris_calc aparc+aseg2.mgz max
I tried 'mris_calc'. The output is in floating format. I have no way to avoid converting back to int format.
I am using Freesurfer version 5.
Wayne
On 05/10/10 2:33 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
And when you run
mri_convert aparc+aseg.mgz aparc+aseg2.mgz -odt int
And
then
mris_calc aparc+aseg2.mgz max
you get that crazy number?
I've tried
this here with version 5 and cannot replicate. What version
are you
using?
doug
Wayne Su wrote:
Here is: mris_calc aparc+aseg.mgz max
Max@(index) [ 2035.000000 (7772808) ]
On 05/10/10 2:20 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
btw, I mean the original
aparc+aseg.mgz, not the one created after you
made
changes
using those FSL commands.
doug
Douglas N Greve wrote:
And what do
you get when you run mris_calc on aparc+aseg.mgz?
Wayne
Su wrote:
Here is the output from mris_calc:
mris_calc aparc+aseg2.mgz max
Max@(index) [
2145516800.000000 (6400402) ]
Wayne
On 05/10/10
2:05
PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
I've never heard of DTI_TK Quick Look. Does it
actually read mgz files?
What value does it give for
aparc+aseg.mgz? Try loading the file into
matlab with the
FreeSurfer MRIread.m function and see what it gives for
the max. Or
just run
mris_calc aparc+aseg2.mgz max
doug
Wayne Su wrote:
Hi
Bruce,
I used
just mri_binarize, mri_mask and
mri_concat and all in mgz format. I
got a
32-bit floating point image with intensity range from 0~2031. Then I
used
the mri_convert to convert it to 32-bit
integer also both in mgz
format.
Here is the
message on the screen.
mri_convert aparc+aseg.mgz
aparc+aseg2.mgz -odt int
$Id: mri_convert.c,v 1.166.2.2
2010/08/10
19:11:50 greve Exp $
reading from
aparc+aseg.mgz...
TR=0.00,
TE=0.00, TI=0.00, flip
angle=0.00
i_ras = (-1, -1.77636e-15,
-1.88564e-15)
j_ras = (0, -4.3715e-16, -1) k_ras = (0,
1,
-3.72529e-09)
changing data type from
float to int (noscale = 0)...
MRIchangeType:
Building histogram
writing to
aparc+aseg2.mgz...
The intensity range of new
image is -214783648.00 ~ 214551xxx.00 showed
by
DTI_TK Quick
Look.
Wayne
On 05/10/10
1:30 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
> Hi >
Wayne,
> can you check to see whether it's > >
an FSL problem or a FreeSurfer one? If
> you don't use FSL do you >
still
> >
have the problem?
> cheers > >
Bruce
> On Tue, 5 Oct 2010, > >
Wayne
Su wrote:
> > > > >
Well, I tried to avoid FSL, and used only Freesurfer tool to do the
same
>> thing. I found there was the same issue when an image >>
with 32-bit
>> >>
float
>> point data type >>
converts to 32-bit integer. No problem for the
>> >>
convertion
>> from 32-bit float point to 8-bit unsigned >> >>
integer.
>> Wayne >> >> >> On 05/10/10 10:44 >>
AM, "Wayne
>> >>
Su" wsu@interchange.ubc.ca wrote:
>> >> >> >> >> >> >>> Hello Freesurfer Users, >>> >>> I am >>> >>>
feeling very bad when I am using mri_convert. There are two problems:
- When I converted a file in mgz format to nii.gz format, and did
some
>>> volume calculation (mask and addition) by using fslmaths >>>
from
>>> >>>
FSL, then
>>> converted back to >>>
mgz. If the image type is uchar, it works
>>> >>>
fine.
If the
>>> image type is int, the intensities changed. The Œ0¹ >>>
value
>>> >>>
is changed to
>>> Œ2.1e+09¹, >>>
others also in very large number (look like
>>> >>>
read
the data from
>>> wrong place). Here is the code I >>> >>>
used:
>>> ${FREESURFER_HOME}/bin/mri_convert >>> >>>
aparc+aseg.mgz
>>> aparc+aseg.nii.gz >>> -odt >>>
int
>>> >>>
${FSLDIR}/bin/fslmaths aparc+aseg
-mas right_vect_mask_inv -add
right_vect_mask aparc+aseg
>>> ${FREESURFER_HOME}/bin/mri_convert >>> >>>
aparc+aseg.nii.gz
>>> aparc+aseg.mgz >>> -odt >>>
int
>>> >>>
If no fslmaths calculation,
convert back to mgz right way, no
problem
found.
>>> 2. when the conform is used, some head >>> >>>
were rotated a little bit, but not
>>> for >>> others. I >>>
am wondering
>>> >>>
how to avoid the rotation?
>>> Regards, >>> >>> >>>
Wayne
>>> _______________________________________________ >>> >>> >>>
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
>>> >>>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> The information in this e-mail is intended only for the person to >>>
whom
>>> >>>
it
>>> is >>> addressed. >>>
If you believe this e-mail was sent to you in
>>> >>>
error and the
>>> e-mail >>> contains patient information, >>>
please
>>> >>>
contact the Partners Compliance
>>> HelpLine >>> at >>> >>> >>>
http://www.partners.org/complianceline . If the e-mail was sent to you
in
>>> error >>> but does not contain patient information, >>>
please
>>> >>>
contact the sender and
properly
>>> dispose of the e-mail. >>> >>> >>> >>> >>> >>> >>> >> >> >> >> >> >>
> Freesurfer >
mailing
> >
list
Freesurfer@nmr.mgh.harvard.edu
> >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
The information in this e-mail is intended only
for the person to whom it
is
> addressed. If you believe this >
e-mail was sent to you in error and
> >
the
> 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
you want noscale to be 1 (-ns 1) otherwise it will rescale the image "intensities" in teh aparc+aseg and you'll got nonsense On Tue, 5 Oct 2010, Douglas N Greve wrote:
I've never heard of DTI_TK Quick Look. Does it actually read mgz files? What value does it give for aparc+aseg.mgz? Try loading the file into matlab with the FreeSurfer MRIread.m function and see what it gives for the max. Or just run
mris_calc aparc+aseg2.mgz max
doug
Wayne Su wrote:
Hi Bruce, I used just mri_binarize, mri_mask and mri_concat and all in mgz format. I got a 32-bit floating point image with intensity range from 0~2031. Then I used the mri_convert to convert it to 32-bit integer also both in mgz format. Here is the message on the screen.
mri_convert aparc+aseg.mgz aparc+aseg2.mgz -odt int $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from aparc+aseg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.77636e-15, -1.88564e-15) j_ras = (0, -4.3715e-16, -1) k_ras = (0, 1, -3.72529e-09) changing data type from float to int (noscale = 0)... MRIchangeType: Building histogram writing to aparc+aseg2.mgz...
The intensity range of new image is -214783648.00 ~ 214551xxx.00 showed by DTI_TK Quick Look.
Wayne
On 05/10/10 1:30 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Wayne,
can you check to see whether it's an FSL problem or a FreeSurfer one? If you don't use FSL do you still have the problem?
cheers Bruce On Tue, 5 Oct 2010, Wayne Su wrote:
Well, I tried to avoid FSL, and used only Freesurfer tool to do the same thing. I found there was the same issue when an image with 32-bit float point data type converts to 32-bit integer. No problem for the convertion from 32-bit float point to 8-bit unsigned integer.
Wayne
On 05/10/10 10:44 AM, "Wayne Su" wsu@interchange.ubc.ca wrote:
Hello Freesurfer Users,
I am feeling very bad when I am using mri_convert. There are two problems:
- When I converted a file in mgz format to nii.gz format, and did some
volume calculation (mask and addition) by using fslmaths from FSL, then converted back to mgz. If the image type is uchar, it works fine. If the image type is int, the intensities changed. The ?0¹ value is changed to ?2.1e+09¹, others also in very large number (look like read the data from wrong place). Here is the code I used:
${FREESURFER_HOME}/bin/mri_convert aparc+aseg.mgzaparc+aseg.nii.gz -odt int ${FSLDIR}/bin/fslmaths aparc+aseg -mas right_vect_mask_inv -add right_vect_mask aparc+aseg ${FREESURFER_HOME}/bin/mri_convert aparc+aseg.nii.gz aparc+aseg.mgz -odt int
If no fslmaths calculation, convert back to mgz right way, noproblem found.
- when the conform is used, some head were rotated a little bit, but
not for others. I am wondering how to avoid the rotation?
Regards, Wayne
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Thank you, Bruce. That solved my problem. Wayne
On 05/10/10 3:21 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
you want noscale to be 1 (-ns 1) otherwise it will rescale the image "intensities" in teh aparc+aseg and you'll got nonsense On Tue, 5 Oct 2010, Douglas N Greve wrote:
I've never heard of DTI_TK Quick Look. Does it actually read mgz files? What value does it give for aparc+aseg.mgz? Try loading the file into matlab with the FreeSurfer MRIread.m function and see what it gives for the max. Or just run
mris_calc aparc+aseg2.mgz max
doug
Wayne Su wrote:
Hi Bruce, I used just mri_binarize, mri_mask and mri_concat and all in mgz format. I got a 32-bit floating point image with intensity range from 0~2031. Then I used the mri_convert to convert it to 32-bit integer also both in mgz format. Here is the message on the screen.
mri_convert aparc+aseg.mgz aparc+aseg2.mgz -odt int $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from aparc+aseg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.77636e-15, -1.88564e-15) j_ras = (0, -4.3715e-16, -1) k_ras = (0, 1, -3.72529e-09) changing data type from float to int (noscale = 0)... MRIchangeType: Building histogram writing to aparc+aseg2.mgz...
The intensity range of new image is -214783648.00 ~ 214551xxx.00 showed by DTI_TK Quick Look.
Wayne
On 05/10/10 1:30 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Wayne,
can you check to see whether it's an FSL problem or a FreeSurfer one? If you don't use FSL do you still have the problem?
cheers Bruce On Tue, 5 Oct 2010, Wayne Su wrote:
Well, I tried to avoid FSL, and used only Freesurfer tool to do the same thing. I found there was the same issue when an image with 32-bit float point data type converts to 32-bit integer. No problem for the convertion from 32-bit float point to 8-bit unsigned integer.
Wayne
On 05/10/10 10:44 AM, "Wayne Su" wsu@interchange.ubc.ca wrote:
Hello Freesurfer Users,
I am feeling very bad when I am using mri_convert. There are two problems:
- When I converted a file in mgz format to nii.gz format, and did some
volume calculation (mask and addition) by using fslmaths from FSL, then converted back to mgz. If the image type is uchar, it works fine. If the image type is int, the intensities changed. The ?0¹ value is changed to ?2.1e+09¹, others also in very large number (look like read the data from wrong place). Here is the code I used:
${FREESURFER_HOME}/bin/mri_convert aparc+aseg.mgzaparc+aseg.nii.gz -odt int ${FSLDIR}/bin/fslmaths aparc+aseg -mas right_vect_mask_inv -add right_vect_mask aparc+aseg ${FREESURFER_HOME}/bin/mri_convert aparc+aseg.nii.gz aparc+aseg.mgz -odt int
If no fslmaths calculation, convert back to mgz right way, noproblem found.
- when the conform is used, some head were rotated a little bit, but
not for others. I am wondering how to avoid the rotation?
Regards, Wayne
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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FreeSurfer offers 'mris_calc' which is similar to 'fslmaths'. I'm a bit confused with your fslmaths line, but you should be able to do a similar operation using 'mris_calc':
(assuming you have 'right_vect_mask_inv.nii.gz' and right_vect_mask.nii.gz')
$>mris_calc -o aparc+aseg_masked.mgz aparc+aseg.mgz maskedby right_vect_inv.nii.gz
$>mris_calc -o aparc+aseg2.mgz aparc+aseg_masked.mgz add right_vect_mask.nii.gz
will result in 'aparc+aseg2.mgz' which is the original aparc+aseg.mgz masked by the right_vect_inv.nii.gz added to right_vect_mask.nii.gz
Perhaps worth trying with 'mris_calc'?
On 10/5/10 16:24 , Wayne Su wrote:
Well, I tried to avoid FSL, and used only Freesurfer tool to do the same thing. I found there was the same issue when an image with 32-bit float point data type converts to 32-bit integer. No problem for the convertion from 32-bit float point to 8-bit unsigned integer.
Wayne
On 05/10/10 10:44 AM, "Wayne Su" wsu@interchange.ubc.ca wrote:
Hello Freesurfer Users, I am feeling very bad when I am using mri_convert. There are two problems: 1. When I converted a file in mgz format to nii.gz format, and did some volume calculation (mask and addition) by using fslmaths from FSL, then converted back to mgz. If the image type is uchar, it works fine. If the image type is int, the intensities changed. The ‘0’ value is changed to ‘–2.1e+09’, others also in very large number (look like read the data from wrong place). Here is the code I used: ${FREESURFER_HOME}/bin/mri_convert aparc+aseg.mgz aparc+aseg.nii.gz -odt int ${FSLDIR}/bin/fslmaths aparc+aseg -mas right_vect_mask_inv -add right_vect_mask aparc+aseg ${FREESURFER_HOME}/bin/mri_convert aparc+aseg.nii.gz aparc+aseg.mgz -odt int If no fslmaths calculation, convert back to mgz right way, no problem found. 2. when the –conform is used, some head were rotated a little bit, but not for others. I am wondering how to avoid the rotation? Regards, Wayne ------------------------------------------------------------------------ _______________________________________________ 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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