Hi:
I have an mprage image with nframes = 2... how can I convert it to use it in freesurfer ?...
Sincerely,
Gonzalo Rojas Costa
-------------------------------- Gonzalo Rojas Costa Advanced Medical Image Processing Laboratory Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl
Hi Gonzalo
what is in the two frames? Bruce On Tue, 2 Sep 2014, Gonzalo Rojas Costa wrote:
Hi:
I have an mprage image with nframes = 2... how can I convert it to use it in freesurfer ?...
Sincerely,
Gonzalo Rojas Costa
Gonzalo Rojas Costa Advanced Medical Image Processing Laboratory Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl
Hi:
I don't know.... it is an mprage got in our center using a Siemens Avanto equipment.... freesurfer specify that the images has two nframes and for that reason freesurfer could not process it...
Sincerely
Gonzalo Rojas Costa
Hi Gonzalo
what is in the two frames? Bruce On Tue, 2 Sep 2014, Gonzalo Rojas Costa wrote:
Hi:
I have an mprage image with nframes = 2... how >>can I convert it to use
it in
freesurfer ?...
Sincerely,
Gonzalo Rojas Costa
-------------------------------- Gonzalo Rojas Costa Advanced Medical Image Processing Laboratory Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl
Hi Gonzalo
is it multi-echo? Phase and mag? You need to find out before you can process it properly. You can extract the frames via:
mri_convert -nth <frame #> <input dicom> <output.mgz>
cheers Bruce
On Wed, 3 Sep 2014, Gonzalo Rojas Costa wrote:
Hi:
I don't know.... it is an mprage got in our center using a Siemens Avanto equipment.... freesurfer specify that the images has two nframes and for that reason freesurfer could not process it...
Sincerely
Gonzalo Rojas Costa
Hi Gonzalo
what is in the two frames? Bruce On Tue, 2 Sep 2014, Gonzalo Rojas Costa wrote:
Hi:
I have an mprage image with nframes = 2... how >>can I convert it to use
it in
freesurfer ?...
Sincerely,
Gonzalo Rojas Costa
Gonzalo Rojas Costa Advanced Medical Image Processing Laboratory Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl
Hello,
I did all of my DTI preprocessing through tracula. I now am using FSL probtractx (which utilizes the bedpost stage output) to explore pathways from the amygdala to the ventromedial prefontal cortex.
When I used FSL's probtractx, when I viewed the tract. The tract was in the wrong area of the brain.
So, I think this may have something to do with the transfromation matrices I gave it via tracula.
*FSL asks for the seed to diffusion transformation matrix so that it can convert your seed masks from MNI space to diffusion space. I gave the transformation matrix in the dmri folder under xfms, titled mni2diff.bbr.mat. I have a feeling this may be the issue.
* I then tried to use the FLIRT registration tool through FSL to get the appropriate transformation matrices. It asks for the bedpost directory. I got an error saying it could not read my no_dif_brain_mask.nii.
I am not sure what transformation matrix to give and was wondering if you could give me some guidance.
Thanks,
Emily
Hi Emily - Is your amygdala seed ROI in MNI space? Only in that case the seed-to-diffusion transformation would be the MNI-to-diffusion transformation.
a.y
On Wed, 3 Sep 2014, Emily Louise Belleau wrote:
Hello,
I did all of my DTI preprocessing through tracula. I now am using FSL probtractx (which utilizes the bedpost stage output) to explore pathways from the amygdala to the ventromedial prefontal cortex.
When I used FSL's probtractx, when I viewed the tract. The tract was in the wrong area of the brain.
So, I think this may have something to do with the transfromation matrices I gave it via tracula.
*FSL asks for the seed to diffusion transformation matrix so that it can convert your seed masks from MNI space to diffusion space. I gave the transformation matrix in the dmri folder under xfms, titled mni2diff.bbr.mat. I have a feeling this may be the issue.
- I then tried to use the FLIRT registration tool through FSL to get the appropriate transformation matrices. It asks for the bedpost directory. I got an error saying it could not read my no_dif_brain_mask.nii.
I am not sure what transformation matrix to give and was wondering if you could give me some guidance.
Thanks,
Emily
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Anastasia,
Yes my amygdala seed is in MNI space. When I used the MNI to diffusion.mat file in the dmri folder and placed it into FSL's probtractx, I developed a track that was in the wrong area of the brain, so I am thinking there is something wrong happening with the transformation to diffusion space.
Can I transform the amygdala mask into diffusion space prior to putting it into FSL's probtrackx viz bb register. If so, how might I go about doing that?
Thanks so much for your help,
Emily ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu Sent: Thursday, September 04, 2014 4:26 PM To: Freesurfer support list Subject: Re: [Freesurfer] Tracula
Hi Emily - Is your amygdala seed ROI in MNI space? Only in that case the seed-to-diffusion transformation would be the MNI-to-diffusion transformation.
a.y
On Wed, 3 Sep 2014, Emily Louise Belleau wrote:
Hello,
I did all of my DTI preprocessing through tracula. I now am using FSL probtractx (which utilizes the bedpost stage output) to explore pathways from the amygdala to the ventromedial prefontal cortex.
When I used FSL's probtractx, when I viewed the tract. The tract was in the wrong area of the brain.
So, I think this may have something to do with the transfromation matrices I gave it via tracula.
*FSL asks for the seed to diffusion transformation matrix so that it can convert your seed masks from MNI space to diffusion space. I gave the transformation matrix in the dmri folder under xfms, titled mni2diff.bbr.mat. I have a feeling this may be the issue.
- I then tried to use the FLIRT registration tool through FSL to get the appropriate transformation matrices. It asks for the bedpost directory. I got an error saying it could not read my no_dif_brain_mask.nii.
I am not sure what transformation matrix to give and was wondering if you could give me some guidance.
Thanks,
Emily
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.
Certainly you can, and it's a good idea for troubleshooting this. In FSL you can do it with:
flirt -in your_label_in_MNI_space.nii.gz -out your_label_in_diff_space.nii.gz -ref dmri/lowb.nii.gz -applyxfm -init dmri/xfms/mni2diff.bbr.mat -interp nearestneighbour
Then you can overlay the transformed label on some of the other inputs that you're giving probtrackx (e.g. a volume from the bedpostx directory) to make sure they look right in fslview.
On Thu, 4 Sep 2014, Emily Louise Belleau wrote:
Hi Anastasia,
Yes my amygdala seed is in MNI space. When I used the MNI to diffusion.mat file in the dmri folder and placed it into FSL's probtractx, I developed a track that was in the wrong area of the brain, so I am thinking there is something wrong happening with the transformation to diffusion space.
Can I transform the amygdala mask into diffusion space prior to putting it into FSL's probtrackx viz bb register. If so, how might I go about doing that?
Thanks so much for your help,
Emily ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu Sent: Thursday, September 04, 2014 4:26 PM To: Freesurfer support list Subject: Re: [Freesurfer] Tracula
Hi Emily - Is your amygdala seed ROI in MNI space? Only in that case the seed-to-diffusion transformation would be the MNI-to-diffusion transformation.
a.y
On Wed, 3 Sep 2014, Emily Louise Belleau wrote:
Hello,
I did all of my DTI preprocessing through tracula. I now am using FSL probtractx (which utilizes the bedpost stage output) to explore pathways from the amygdala to the ventromedial prefontal cortex.
When I used FSL's probtractx, when I viewed the tract. The tract was in the wrong area of the brain.
So, I think this may have something to do with the transfromation matrices I gave it via tracula.
*FSL asks for the seed to diffusion transformation matrix so that it can convert your seed masks from MNI space to diffusion space. I gave the transformation matrix in the dmri folder under xfms, titled mni2diff.bbr.mat. I have a feeling this may be the issue.
- I then tried to use the FLIRT registration tool through FSL to get the appropriate transformation matrices. It asks for the bedpost directory. I got an error saying it could not read my no_dif_brain_mask.nii.
I am not sure what transformation matrix to give and was wondering if you could give me some guidance.
Thanks,
Emily
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Anastasia,
I am still having a bit of trouble understanding how to properly view my tract through fsl view.
What is the appropriate underlay to use/settings?
Thanks again for your continued help!
Emily ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu Sent: Thursday, September 04, 2014 4:54 PM To: Freesurfer support list Subject: Re: [Freesurfer] Tracula
Certainly you can, and it's a good idea for troubleshooting this. In FSL you can do it with:
flirt -in your_label_in_MNI_space.nii.gz -out your_label_in_diff_space.nii.gz -ref dmri/lowb.nii.gz -applyxfm -init dmri/xfms/mni2diff.bbr.mat -interp nearestneighbour
Then you can overlay the transformed label on some of the other inputs that you're giving probtrackx (e.g. a volume from the bedpostx directory) to make sure they look right in fslview.
On Thu, 4 Sep 2014, Emily Louise Belleau wrote:
Hi Anastasia,
Yes my amygdala seed is in MNI space. When I used the MNI to diffusion.mat file in the dmri folder and placed it into FSL's probtractx, I developed a track that was in the wrong area of the brain, so I am thinking there is something wrong happening with the transformation to diffusion space.
Can I transform the amygdala mask into diffusion space prior to putting it into FSL's probtrackx viz bb register. If so, how might I go about doing that?
Thanks so much for your help,
Emily ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu Sent: Thursday, September 04, 2014 4:26 PM To: Freesurfer support list Subject: Re: [Freesurfer] Tracula
Hi Emily - Is your amygdala seed ROI in MNI space? Only in that case the seed-to-diffusion transformation would be the MNI-to-diffusion transformation.
a.y
On Wed, 3 Sep 2014, Emily Louise Belleau wrote:
Hello,
I did all of my DTI preprocessing through tracula. I now am using FSL probtractx (which utilizes the bedpost stage output) to explore pathways from the amygdala to the ventromedial prefontal cortex.
When I used FSL's probtractx, when I viewed the tract. The tract was in the wrong area of the brain.
So, I think this may have something to do with the transfromation matrices I gave it via tracula.
*FSL asks for the seed to diffusion transformation matrix so that it can convert your seed masks from MNI space to diffusion space. I gave the transformation matrix in the dmri folder under xfms, titled mni2diff.bbr.mat. I have a feeling this may be the issue.
- I then tried to use the FLIRT registration tool through FSL to get the appropriate transformation matrices. It asks for the bedpost directory. I got an error saying it could not read my no_dif_brain_mask.nii.
I am not sure what transformation matrix to give and was wondering if you could give me some guidance.
Thanks,
Emily
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
To view your label over the MNI average brain:
fslview $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz your_label_in_MNI_space.nii.gz -l Red
There are no settings, other than choosing a different color for the label.
On Fri, 5 Sep 2014, Emily Louise Belleau wrote:
Hi Anastasia,
I am still having a bit of trouble understanding how to properly view my tract through fsl view.
What is the appropriate underlay to use/settings?
Thanks again for your continued help!
Emily ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu Sent: Thursday, September 04, 2014 4:54 PM To: Freesurfer support list Subject: Re: [Freesurfer] Tracula
Certainly you can, and it's a good idea for troubleshooting this. In FSL you can do it with:
flirt -in your_label_in_MNI_space.nii.gz -out your_label_in_diff_space.nii.gz -ref dmri/lowb.nii.gz -applyxfm -init dmri/xfms/mni2diff.bbr.mat -interp nearestneighbour
Then you can overlay the transformed label on some of the other inputs that you're giving probtrackx (e.g. a volume from the bedpostx directory) to make sure they look right in fslview.
On Thu, 4 Sep 2014, Emily Louise Belleau wrote:
Hi Anastasia,
Yes my amygdala seed is in MNI space. When I used the MNI to diffusion.mat file in the dmri folder and placed it into FSL's probtractx, I developed a track that was in the wrong area of the brain, so I am thinking there is something wrong happening with the transformation to diffusion space.
Can I transform the amygdala mask into diffusion space prior to putting it into FSL's probtrackx viz bb register. If so, how might I go about doing that?
Thanks so much for your help,
Emily ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu Sent: Thursday, September 04, 2014 4:26 PM To: Freesurfer support list Subject: Re: [Freesurfer] Tracula
Hi Emily - Is your amygdala seed ROI in MNI space? Only in that case the seed-to-diffusion transformation would be the MNI-to-diffusion transformation.
a.y
On Wed, 3 Sep 2014, Emily Louise Belleau wrote:
Hello,
I did all of my DTI preprocessing through tracula. I now am using FSL probtractx (which utilizes the bedpost stage output) to explore pathways from the amygdala to the ventromedial prefontal cortex.
When I used FSL's probtractx, when I viewed the tract. The tract was in the wrong area of the brain.
So, I think this may have something to do with the transfromation matrices I gave it via tracula.
*FSL asks for the seed to diffusion transformation matrix so that it can convert your seed masks from MNI space to diffusion space. I gave the transformation matrix in the dmri folder under xfms, titled mni2diff.bbr.mat. I have a feeling this may be the issue.
- I then tried to use the FLIRT registration tool through FSL to get the appropriate transformation matrices. It asks for the bedpost directory. I got an error saying it could not read my no_dif_brain_mask.nii.
I am not sure what transformation matrix to give and was wondering if you could give me some guidance.
Thanks,
Emily
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
Hi Anastasia,
This would be in diffusion space though. Since I converted all of my seeds to diffusion space.
Emily ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu Sent: Friday, September 05, 2014 11:32 AM To: Freesurfer support list Subject: Re: [Freesurfer] Tracula
To view your label over the MNI average brain:
fslview $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz your_label_in_MNI_space.nii.gz -l Red
There are no settings, other than choosing a different color for the label.
On Fri, 5 Sep 2014, Emily Louise Belleau wrote:
Hi Anastasia,
I am still having a bit of trouble understanding how to properly view my tract through fsl view.
What is the appropriate underlay to use/settings?
Thanks again for your continued help!
Emily ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu Sent: Thursday, September 04, 2014 4:54 PM To: Freesurfer support list Subject: Re: [Freesurfer] Tracula
Certainly you can, and it's a good idea for troubleshooting this. In FSL you can do it with:
flirt -in your_label_in_MNI_space.nii.gz -out your_label_in_diff_space.nii.gz -ref dmri/lowb.nii.gz -applyxfm -init dmri/xfms/mni2diff.bbr.mat -interp nearestneighbour
Then you can overlay the transformed label on some of the other inputs that you're giving probtrackx (e.g. a volume from the bedpostx directory) to make sure they look right in fslview.
On Thu, 4 Sep 2014, Emily Louise Belleau wrote:
Hi Anastasia,
Yes my amygdala seed is in MNI space. When I used the MNI to diffusion.mat file in the dmri folder and placed it into FSL's probtractx, I developed a track that was in the wrong area of the brain, so I am thinking there is something wrong happening with the transformation to diffusion space.
Can I transform the amygdala mask into diffusion space prior to putting it into FSL's probtrackx viz bb register. If so, how might I go about doing that?
Thanks so much for your help,
Emily ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu Sent: Thursday, September 04, 2014 4:26 PM To: Freesurfer support list Subject: Re: [Freesurfer] Tracula
Hi Emily - Is your amygdala seed ROI in MNI space? Only in that case the seed-to-diffusion transformation would be the MNI-to-diffusion transformation.
a.y
On Wed, 3 Sep 2014, Emily Louise Belleau wrote:
Hello,
I did all of my DTI preprocessing through tracula. I now am using FSL probtractx (which utilizes the bedpost stage output) to explore pathways from the amygdala to the ventromedial prefontal cortex.
When I used FSL's probtractx, when I viewed the tract. The tract was in the wrong area of the brain.
So, I think this may have something to do with the transfromation matrices I gave it via tracula.
*FSL asks for the seed to diffusion transformation matrix so that it can convert your seed masks from MNI space to diffusion space. I gave the transformation matrix in the dmri folder under xfms, titled mni2diff.bbr.mat. I have a feeling this may be the issue.
- I then tried to use the FLIRT registration tool through FSL to get the appropriate transformation matrices. It asks for the bedpost directory. I got an error saying it could not read my no_dif_brain_mask.nii.
I am not sure what transformation matrix to give and was wondering if you could give me some guidance.
Thanks,
Emily
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
If your label is in diffusion space, then replace the MNI brain with any volume that's in diffusion space.
On Fri, 5 Sep 2014, Emily Louise Belleau wrote:
Hi Anastasia,
This would be in diffusion space though. Since I converted all of my seeds to diffusion space.
Emily ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu Sent: Friday, September 05, 2014 11:32 AM To: Freesurfer support list Subject: Re: [Freesurfer] Tracula
To view your label over the MNI average brain:
fslview $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz your_label_in_MNI_space.nii.gz -l Red
There are no settings, other than choosing a different color for the label.
On Fri, 5 Sep 2014, Emily Louise Belleau wrote:
Hi Anastasia,
I am still having a bit of trouble understanding how to properly view my tract through fsl view.
What is the appropriate underlay to use/settings?
Thanks again for your continued help!
Emily ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu Sent: Thursday, September 04, 2014 4:54 PM To: Freesurfer support list Subject: Re: [Freesurfer] Tracula
Certainly you can, and it's a good idea for troubleshooting this. In FSL you can do it with:
flirt -in your_label_in_MNI_space.nii.gz -out your_label_in_diff_space.nii.gz -ref dmri/lowb.nii.gz -applyxfm -init dmri/xfms/mni2diff.bbr.mat -interp nearestneighbour
Then you can overlay the transformed label on some of the other inputs that you're giving probtrackx (e.g. a volume from the bedpostx directory) to make sure they look right in fslview.
On Thu, 4 Sep 2014, Emily Louise Belleau wrote:
Hi Anastasia,
Yes my amygdala seed is in MNI space. When I used the MNI to diffusion.mat file in the dmri folder and placed it into FSL's probtractx, I developed a track that was in the wrong area of the brain, so I am thinking there is something wrong happening with the transformation to diffusion space.
Can I transform the amygdala mask into diffusion space prior to putting it into FSL's probtrackx viz bb register. If so, how might I go about doing that?
Thanks so much for your help,
Emily ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu Sent: Thursday, September 04, 2014 4:26 PM To: Freesurfer support list Subject: Re: [Freesurfer] Tracula
Hi Emily - Is your amygdala seed ROI in MNI space? Only in that case the seed-to-diffusion transformation would be the MNI-to-diffusion transformation.
a.y
On Wed, 3 Sep 2014, Emily Louise Belleau wrote:
Hello,
I did all of my DTI preprocessing through tracula. I now am using FSL probtractx (which utilizes the bedpost stage output) to explore pathways from the amygdala to the ventromedial prefontal cortex.
When I used FSL's probtractx, when I viewed the tract. The tract was in the wrong area of the brain.
So, I think this may have something to do with the transfromation matrices I gave it via tracula.
*FSL asks for the seed to diffusion transformation matrix so that it can convert your seed masks from MNI space to diffusion space. I gave the transformation matrix in the dmri folder under xfms, titled mni2diff.bbr.mat. I have a feeling this may be the issue.
- I then tried to use the FLIRT registration tool through FSL to get the appropriate transformation matrices. It asks for the bedpost directory. I got an error saying it could not read my no_dif_brain_mask.nii.
I am not sure what transformation matrix to give and was wondering if you could give me some guidance.
Thanks,
Emily
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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@nmr.mgh.harvard.edu
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Anastasia Yendiki -
Bruce Fischl -
Emily Louise Belleau -
Gonzalo Rojas Costa