Dear all,
indeed all my T1-scans were recorded with a 3T scanner. So what can I do about it or do you have something in progress which would fix this problem anytime soon? Thanks, Maria
----- Original Message ----- From: "Avi Snyder" avi@npg.wustl.edu To: "Sita Kakunoori" sita@nmr.mgh.harvard.edu, felber@cbs.mpg.de, "Avi Snyder" avi@npg.wustl.edu Cc: "Bruce Fischl" fischl@nmr.mgh.harvard.edu Sent: Tuesday, September 13, 2011 11:03:28 PM Subject: Re: [Freesurfer] Talairach transformation
Hi Sita,
Wrong-stretch (e.g., too fat or too thin) MP-RAGE atlas transforms are expected if the contrast properties of the sample image are far from those of the target. This condition can easily occur if the target is based on 1.5T data and the sample is acquired at 3T. (3T but not 1.5T T1W images tend to be relatively bright in the center of the head.) Gd++ contrasted MP-RAGE scans routinely do not produce decent atlas transforms unless special measures are taken. A FreeSurfer fix for this problem is theoretically feasible.
Avi ----------------------------------------------- On 9/13/11 2:26 PM, "Sita Kakunoori" sita@nmr.mgh.harvard.edu wrote:
I might have seen this in a dataset. I am cc'ing Dr.Avi Anyder on this e-mail. Hi Dr.Snyder, Not sure if you remember but we saw something similar in a dataset here at the center where the talairach was much smaller than the orig.mgz volume and you created a new talairach template to be used with that dataset. I just wondered if this issue is similar to that.
Thanks much, Sita. ---------- Forwarded message ---------- Date: Tue, 13 Sep 2011 16:27:17 +0200 (CEST) From: Maria Felber felber@cbs.mpg.de To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Talairach transformation
Hi Bruce,
so we are back at the beginning. After I ran recon-all -all, I did exactly that and checked the xform using tkregister2. And here I always see that my talairach volume (the transform) is always smaller, which can be very well seen as the orig surfaces of the subjects are always a little outside the brain and reach well into the skull areas. Of course I can make the adjustments as descriped in the short instructions. But this also means I ran the recon-all precess anew for another 30 h per subject. And that is the reason, why I asked if this is normal that the tailarach transform is a) always smaller than the original brain, and b) if I can make any adjustments to prevent that from happening and thus saving another 30h per subject. In short: How acurate hat the talairach.xfm has to be and is it possible to change some parameters to make this transformation a little more accurate while running the recon-all process only once? Best, Maria
----- Original Message ----- From: "Bruce Fischl" fischl@nmr.mgh.harvard.edu To: "Maria Felber" felber@cbs.mpg.de Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, September 13, 2011 4:07:55 PM Subject: Re: [Freesurfer] Talairach transformation
Hi Maria
you can use tkregister2 to check the accuracy of the talairach.xfm transform ("xform" for short), and correct it if you want.
cheers Bruce On Tue, 13 Sep 2011, Maria Felber wrote:
Hi Bruce,
thanks for the first response. I tried to find some information on the webpage about xform, but failed. So what is xform standing for and where/how can I check it? As in the later processing stages I want to do localization and
DCM-Modeling with my data, I guess the correct talairach coords are kind of important for later comparisons.
Thanks again, Maria
----- Original Message ----- From: "Bruce Fischl" fischl@nmr.mgh.harvard.edu To: "Maria Felber" felber@cbs.mpg.de Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, September 9, 2011 2:13:05 PM Subject: Re: [Freesurfer] Talairach transformation
Hi Maria
as long as the tal xform is reasonable I wouldn't worry about it, unless for some reason you care a lot about the accuracy of the talairach coords.
cheers Bruce
p.s. not sure why it would be smaller
On Fri, 9 Sep 2011, Maria Felber wrote:
Dear all,
sorry, if that question came up before in the mailing list and I simple have been unable to find the thread.
Following the wiki reconstruction workflow, I ran yesterday the recon-all -all process. The process finished without errors. So the next step was to check the talairach transform. Now, according to the FsTutorial/Talairach I have to make some adjustments and then run the whole process again. That is all nice and good.
However, why is it, that the talairach volume is always, no matter which subject I look at, is always significantly smaller than the target volume? Is that normal? Has it to be fixed? Or is that just normal? Attached find one example. As I am using freesurfer for the first time, I am really unsure about that.
Thanks for the help, Maria
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.
-- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522
-- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Ms. Kakunoori,
sorry to bother you again, but as I did not get a reply to my last message to everyone so far troubled with my question, I am trying here for a second time. It is indeed the case, that all my data were scanned with a 3T. And if that is indeed the problem Dr. Snyder figured out, then what can I do about it? Or is anyone already working on this problem? I can hardly imagine I am the only one recording with a 3T instead of a 1.5T. Yours sincerely, Maria Felber
----- Forwarded Message ----- From: "Maria Felber" felber@cbs.mpg.de To: "Avi Snyder" avi@npg.wustl.edu Cc: "Sita Kakunoori", felber@cbs.mpg.de, "Avi Snyder" <avi@npg.wustl.edu, Bruce Fischl" sita@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu Sent: Thursday, September 15, 2011 10:46:55 AM Subject: Re: [Freesurfer] Talairach transformation
Dear all,
indeed all my T1-scans were recorded with a 3T scanner. So what can I do about it or do you have something in progress which would fix this problem anytime soon? Thanks, Maria
----- Original Message ----- From: "Avi Snyder" avi@npg.wustl.edu To: "Sita Kakunoori" sita@nmr.mgh.harvard.edu, felber@cbs.mpg.de, "Avi Snyder" avi@npg.wustl.edu Cc: "Bruce Fischl" fischl@nmr.mgh.harvard.edu Sent: Tuesday, September 13, 2011 11:03:28 PM Subject: Re: [Freesurfer] Talairach transformation
Hi Sita,
Wrong-stretch (e.g., too fat or too thin) MP-RAGE atlas transforms are expected if the contrast properties of the sample image are far from those of the target. This condition can easily occur if the target is based on 1.5T data and the sample is acquired at 3T. (3T but not 1.5T T1W images tend to be relatively bright in the center of the head.) Gd++ contrasted MP-RAGE scans routinely do not produce decent atlas transforms unless special measures are taken. A FreeSurfer fix for this problem is theoretically feasible.
Avi ----------------------------------------------- On 9/13/11 2:26 PM, "Sita Kakunoori" sita@nmr.mgh.harvard.edu wrote:
I might have seen this in a dataset. I am cc'ing Dr.Avi Anyder on this e-mail. Hi Dr.Snyder, Not sure if you remember but we saw something similar in a dataset here at the center where the talairach was much smaller than the orig.mgz volume and you created a new talairach template to be used with that dataset. I just wondered if this issue is similar to that.
Thanks much, Sita. ---------- Forwarded message ---------- Date: Tue, 13 Sep 2011 16:27:17 +0200 (CEST) From: Maria Felber felber@cbs.mpg.de To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Talairach transformation
Hi Bruce,
so we are back at the beginning. After I ran recon-all -all, I did exactly that and checked the xform using tkregister2. And here I always see that my talairach volume (the transform) is always smaller, which can be very well seen as the orig surfaces of the subjects are always a little outside the brain and reach well into the skull areas. Of course I can make the adjustments as descriped in the short instructions. But this also means I ran the recon-all precess anew for another 30 h per subject. And that is the reason, why I asked if this is normal that the tailarach transform is a) always smaller than the original brain, and b) if I can make any adjustments to prevent that from happening and thus saving another 30h per subject. In short: How acurate hat the talairach.xfm has to be and is it possible to change some parameters to make this transformation a little more accurate while running the recon-all process only once? Best, Maria
----- Original Message ----- From: "Bruce Fischl" fischl@nmr.mgh.harvard.edu To: "Maria Felber" felber@cbs.mpg.de Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, September 13, 2011 4:07:55 PM Subject: Re: [Freesurfer] Talairach transformation
Hi Maria
you can use tkregister2 to check the accuracy of the talairach.xfm transform ("xform" for short), and correct it if you want.
cheers Bruce On Tue, 13 Sep 2011, Maria Felber wrote:
Hi Bruce,
thanks for the first response. I tried to find some information on the webpage about xform, but failed. So what is xform standing for and where/how can I check it? As in the later processing stages I want to do localization and
DCM-Modeling with my data, I guess the correct talairach coords are kind of important for later comparisons.
Thanks again, Maria
----- Original Message ----- From: "Bruce Fischl" fischl@nmr.mgh.harvard.edu To: "Maria Felber" felber@cbs.mpg.de Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, September 9, 2011 2:13:05 PM Subject: Re: [Freesurfer] Talairach transformation
Hi Maria
as long as the tal xform is reasonable I wouldn't worry about it, unless for some reason you care a lot about the accuracy of the talairach coords.
cheers Bruce
p.s. not sure why it would be smaller
On Fri, 9 Sep 2011, Maria Felber wrote:
Dear all,
sorry, if that question came up before in the mailing list and I simple have been unable to find the thread.
Following the wiki reconstruction workflow, I ran yesterday the recon-all -all process. The process finished without errors. So the next step was to check the talairach transform. Now, according to the FsTutorial/Talairach I have to make some adjustments and then run the whole process again. That is all nice and good.
However, why is it, that the talairach volume is always, no matter which subject I look at, is always significantly smaller than the target volume? Is that normal? Has it to be fixed? Or is that just normal? Attached find one example. As I am using freesurfer for the first time, I am really unsure about that.
Thanks for the help, Maria
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.
-- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522
-- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Maria
have you tried running without the talairach stuff? Try -notalairach and see if it works for you
cheers Bruce On Wed, 28 Sep 2011, Maria Felber wrote:
Dear Ms. Kakunoori,
sorry to bother you again, but as I did not get a reply to my last message to everyone so far troubled with my question, I am trying here for a second time. It is indeed the case, that all my data were scanned with a 3T. And if that is indeed the problem Dr. Snyder figured out, then what can I do about it? Or is anyone already working on this problem? I can hardly imagine I am the only one recording with a 3T instead of a 1.5T. Yours sincerely, Maria Felber
----- Forwarded Message ----- From: "Maria Felber" felber@cbs.mpg.de To: "Avi Snyder" avi@npg.wustl.edu Cc: "Sita Kakunoori", felber@cbs.mpg.de, "Avi Snyder" <avi@npg.wustl.edu, Bruce Fischl" sita@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu Sent: Thursday, September 15, 2011 10:46:55 AM Subject: Re: [Freesurfer] Talairach transformation
Dear all,
indeed all my T1-scans were recorded with a 3T scanner. So what can I do about it or do you have something in progress which would fix this problem anytime soon? Thanks, Maria
----- Original Message ----- From: "Avi Snyder" avi@npg.wustl.edu To: "Sita Kakunoori" sita@nmr.mgh.harvard.edu, felber@cbs.mpg.de, "Avi Snyder" avi@npg.wustl.edu Cc: "Bruce Fischl" fischl@nmr.mgh.harvard.edu Sent: Tuesday, September 13, 2011 11:03:28 PM Subject: Re: [Freesurfer] Talairach transformation
Hi Sita,
Wrong-stretch (e.g., too fat or too thin) MP-RAGE atlas transforms are expected if the contrast properties of the sample image are far from those of the target. This condition can easily occur if the target is based on 1.5T data and the sample is acquired at 3T. (3T but not 1.5T T1W images tend to be relatively bright in the center of the head.) Gd++ contrasted MP-RAGE scans routinely do not produce decent atlas transforms unless special measures are taken. A FreeSurfer fix for this problem is theoretically feasible.
Avi
On 9/13/11 2:26 PM, "Sita Kakunoori" sita@nmr.mgh.harvard.edu wrote:
I might have seen this in a dataset. I am cc'ing Dr.Avi Anyder on this e-mail. Hi Dr.Snyder, Not sure if you remember but we saw something similar in a dataset here at the center where the talairach was much smaller than the orig.mgz volume and you created a new talairach template to be used with that dataset. I just wondered if this issue is similar to that.
Thanks much, Sita. ---------- Forwarded message ---------- Date: Tue, 13 Sep 2011 16:27:17 +0200 (CEST) From: Maria Felber felber@cbs.mpg.de To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Talairach transformation
Hi Bruce,
so we are back at the beginning. After I ran recon-all -all, I did exactly that and checked the xform using tkregister2. And here I always see that my talairach volume (the transform) is always smaller, which can be very well seen as the orig surfaces of the subjects are always a little outside the brain and reach well into the skull areas. Of course I can make the adjustments as descriped in the short instructions. But this also means I ran the recon-all precess anew for another 30 h per subject. And that is the reason, why I asked if this is normal that the tailarach transform is a) always smaller than the original brain, and b) if I can make any adjustments to prevent that from happening and thus saving another 30h per subject. In short: How acurate hat the talairach.xfm has to be and is it possible to change some parameters to make this transformation a little more accurate while running the recon-all process only once? Best, Maria
----- Original Message ----- From: "Bruce Fischl" fischl@nmr.mgh.harvard.edu To: "Maria Felber" felber@cbs.mpg.de Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, September 13, 2011 4:07:55 PM Subject: Re: [Freesurfer] Talairach transformation
Hi Maria
you can use tkregister2 to check the accuracy of the talairach.xfm transform ("xform" for short), and correct it if you want.
cheers Bruce On Tue, 13 Sep 2011, Maria Felber wrote:
Hi Bruce,
thanks for the first response. I tried to find some information on the webpage about xform, but failed. So what is xform standing for and where/how can I check it? As in the later processing stages I want to do localization and
DCM-Modeling with my data, I guess the correct talairach coords are kind of important for later comparisons.
Thanks again, Maria
----- Original Message ----- From: "Bruce Fischl" fischl@nmr.mgh.harvard.edu To: "Maria Felber" felber@cbs.mpg.de Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, September 9, 2011 2:13:05 PM Subject: Re: [Freesurfer] Talairach transformation
Hi Maria
as long as the tal xform is reasonable I wouldn't worry about it, unless for some reason you care a lot about the accuracy of the talairach coords.
cheers Bruce
p.s. not sure why it would be smaller
On Fri, 9 Sep 2011, Maria Felber wrote:
Dear all,
sorry, if that question came up before in the mailing list and I simple have been unable to find the thread.
Following the wiki reconstruction workflow, I ran yesterday the recon-all -all process. The process finished without errors. So the next step was to check the talairach transform. Now, according to the FsTutorial/Talairach I have to make some adjustments and then run the whole process again. That is all nice and good.
However, why is it, that the talairach volume is always, no matter which subject I look at, is always significantly smaller than the target volume? Is that normal? Has it to be fixed? Or is that just normal? Attached find one example. As I am using freesurfer for the first time, I am really unsure about that.
Thanks for the help, Maria
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.
-- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522
-- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
you could also try:
-talairach -use-mritotal
which will use an alternate talarairch alignment scheme (from the MNI). it sometimes works better (not necessary for 3T).
you should also probably add:
-nuintensitycor-3T
to the end of your recon-all command, which will run the nu_correct stage optimized for 3T. it wont help you with your talairach issue, but will produce better results for 3T data downstream.
n.
On Wed, 2011-09-28 at 16:38 -0400, Bruce Fischl wrote:
Hi Maria
have you tried running without the talairach stuff? Try -notalairach and see if it works for you
cheers Bruce On Wed, 28 Sep 2011, Maria Felber wrote:
Dear Ms. Kakunoori,
sorry to bother you again, but as I did not get a reply to my last message to everyone so far troubled with my question, I am trying here for a second time. It is indeed the case, that all my data were scanned with a 3T. And if that is indeed the problem Dr. Snyder figured out, then what can I do about it? Or is anyone already working on this problem? I can hardly imagine I am the only one recording with a 3T instead of a 1.5T. Yours sincerely, Maria Felber
----- Forwarded Message ----- From: "Maria Felber" felber@cbs.mpg.de To: "Avi Snyder" avi@npg.wustl.edu Cc: "Sita Kakunoori", felber@cbs.mpg.de, "Avi Snyder" <avi@npg.wustl.edu, Bruce Fischl" sita@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu Sent: Thursday, September 15, 2011 10:46:55 AM Subject: Re: [Freesurfer] Talairach transformation
Dear all,
indeed all my T1-scans were recorded with a 3T scanner. So what can I do about it or do you have something in progress which would fix this problem anytime soon? Thanks, Maria
----- Original Message ----- From: "Avi Snyder" avi@npg.wustl.edu To: "Sita Kakunoori" sita@nmr.mgh.harvard.edu, felber@cbs.mpg.de, "Avi Snyder" avi@npg.wustl.edu Cc: "Bruce Fischl" fischl@nmr.mgh.harvard.edu Sent: Tuesday, September 13, 2011 11:03:28 PM Subject: Re: [Freesurfer] Talairach transformation
Hi Sita,
Wrong-stretch (e.g., too fat or too thin) MP-RAGE atlas transforms are expected if the contrast properties of the sample image are far from those of the target. This condition can easily occur if the target is based on 1.5T data and the sample is acquired at 3T. (3T but not 1.5T T1W images tend to be relatively bright in the center of the head.) Gd++ contrasted MP-RAGE scans routinely do not produce decent atlas transforms unless special measures are taken. A FreeSurfer fix for this problem is theoretically feasible.
Avi
On 9/13/11 2:26 PM, "Sita Kakunoori" sita@nmr.mgh.harvard.edu wrote:
I might have seen this in a dataset. I am cc'ing Dr.Avi Anyder on this e-mail. Hi Dr.Snyder, Not sure if you remember but we saw something similar in a dataset here at the center where the talairach was much smaller than the orig.mgz volume and you created a new talairach template to be used with that dataset. I just wondered if this issue is similar to that.
Thanks much, Sita. ---------- Forwarded message ---------- Date: Tue, 13 Sep 2011 16:27:17 +0200 (CEST) From: Maria Felber felber@cbs.mpg.de To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Talairach transformation
Hi Bruce,
so we are back at the beginning. After I ran recon-all -all, I did exactly that and checked the xform using tkregister2. And here I always see that my talairach volume (the transform) is always smaller, which can be very well seen as the orig surfaces of the subjects are always a little outside the brain and reach well into the skull areas. Of course I can make the adjustments as descriped in the short instructions. But this also means I ran the recon-all precess anew for another 30 h per subject. And that is the reason, why I asked if this is normal that the tailarach transform is a) always smaller than the original brain, and b) if I can make any adjustments to prevent that from happening and thus saving another 30h per subject. In short: How acurate hat the talairach.xfm has to be and is it possible to change some parameters to make this transformation a little more accurate while running the recon-all process only once? Best, Maria
----- Original Message ----- From: "Bruce Fischl" fischl@nmr.mgh.harvard.edu To: "Maria Felber" felber@cbs.mpg.de Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, September 13, 2011 4:07:55 PM Subject: Re: [Freesurfer] Talairach transformation
Hi Maria
you can use tkregister2 to check the accuracy of the talairach.xfm transform ("xform" for short), and correct it if you want.
cheers Bruce On Tue, 13 Sep 2011, Maria Felber wrote:
Hi Bruce,
thanks for the first response. I tried to find some information on the webpage about xform, but failed. So what is xform standing for and where/how can I check it? As in the later processing stages I want to do localization and
DCM-Modeling with my data, I guess the correct talairach coords are kind of important for later comparisons.
Thanks again, Maria
----- Original Message ----- From: "Bruce Fischl" fischl@nmr.mgh.harvard.edu To: "Maria Felber" felber@cbs.mpg.de Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, September 9, 2011 2:13:05 PM Subject: Re: [Freesurfer] Talairach transformation
Hi Maria
as long as the tal xform is reasonable I wouldn't worry about it, unless for some reason you care a lot about the accuracy of the talairach coords.
cheers Bruce
p.s. not sure why it would be smaller
On Fri, 9 Sep 2011, Maria Felber wrote:
Dear all,
sorry, if that question came up before in the mailing list and I simple have been unable to find the thread.
Following the wiki reconstruction workflow, I ran yesterday the recon-all -all process. The process finished without errors. So the next step was to check the talairach transform. Now, according to the FsTutorial/Talairach I have to make some adjustments and then run the whole process again. That is all nice and good.
However, why is it, that the talairach volume is always, no matter which subject I look at, is always significantly smaller than the target volume? Is that normal? Has it to be fixed? Or is that just normal? Attached find one example. As I am using freesurfer for the first time, I am really unsure about that.
Thanks for the help, Maria
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.
-- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522
-- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522
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
Dear Nick,
how do I best implement your suggestions in my command line?
e.g. recon-all -all -use-mritotal -nuintensitycor-3T -s im30 or
recon-all -motioncor -s im30 recon-all -talairach -use-mritotal -s im30 recon-all -all -nuintensitycor-3T -s im30
As I have not a clue what changes will be saved by freesurfer or wethere they are just overwritten by a new command, please advise have best to follow you advise. Thank you. Sincerely, Maria
----- Original Message ----- From: "Nick Schmansky" nicks@nmr.mgh.harvard.edu To: "Bruce Fischl" fischl@nmr.mgh.harvard.edu Cc: "Maria Felber" felber@cbs.mpg.de, sita@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, September 28, 2011 10:53:08 PM Subject: Re: [Freesurfer] Fwd: Talairach transformation
you could also try:
-talairach -use-mritotal
which will use an alternate talarairch alignment scheme (from the MNI). it sometimes works better (not necessary for 3T).
you should also probably add:
-nuintensitycor-3T
to the end of your recon-all command, which will run the nu_correct stage optimized for 3T. it wont help you with your talairach issue, but will produce better results for 3T data downstream.
n.
On Wed, 2011-09-28 at 16:38 -0400, Bruce Fischl wrote:
Hi Maria
have you tried running without the talairach stuff? Try -notalairach and see if it works for you
cheers Bruce On Wed, 28 Sep 2011, Maria Felber wrote:
Dear Ms. Kakunoori,
sorry to bother you again, but as I did not get a reply to my last message to everyone so far troubled with my question, I am trying here for a second time. It is indeed the case, that all my data were scanned with a 3T. And if that is indeed the problem Dr. Snyder figured out, then what can I do about it? Or is anyone already working on this problem? I can hardly imagine I am the only one recording with a 3T instead of a 1.5T. Yours sincerely, Maria Felber
----- Forwarded Message ----- From: "Maria Felber" felber@cbs.mpg.de To: "Avi Snyder" avi@npg.wustl.edu Cc: "Sita Kakunoori", felber@cbs.mpg.de, "Avi Snyder" <avi@npg.wustl.edu, Bruce Fischl" sita@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu Sent: Thursday, September 15, 2011 10:46:55 AM Subject: Re: [Freesurfer] Talairach transformation
Dear all,
indeed all my T1-scans were recorded with a 3T scanner. So what can I do about it or do you have something in progress which would fix this problem anytime soon? Thanks, Maria
----- Original Message ----- From: "Avi Snyder" avi@npg.wustl.edu To: "Sita Kakunoori" sita@nmr.mgh.harvard.edu, felber@cbs.mpg.de, "Avi Snyder" avi@npg.wustl.edu Cc: "Bruce Fischl" fischl@nmr.mgh.harvard.edu Sent: Tuesday, September 13, 2011 11:03:28 PM Subject: Re: [Freesurfer] Talairach transformation
Hi Sita,
Wrong-stretch (e.g., too fat or too thin) MP-RAGE atlas transforms are expected if the contrast properties of the sample image are far from those of the target. This condition can easily occur if the target is based on 1.5T data and the sample is acquired at 3T. (3T but not 1.5T T1W images tend to be relatively bright in the center of the head.) Gd++ contrasted MP-RAGE scans routinely do not produce decent atlas transforms unless special measures are taken. A FreeSurfer fix for this problem is theoretically feasible.
Avi
On 9/13/11 2:26 PM, "Sita Kakunoori" sita@nmr.mgh.harvard.edu wrote:
I might have seen this in a dataset. I am cc'ing Dr.Avi Anyder on this e-mail. Hi Dr.Snyder, Not sure if you remember but we saw something similar in a dataset here at the center where the talairach was much smaller than the orig.mgz volume and you created a new talairach template to be used with that dataset. I just wondered if this issue is similar to that.
Thanks much, Sita. ---------- Forwarded message ---------- Date: Tue, 13 Sep 2011 16:27:17 +0200 (CEST) From: Maria Felber felber@cbs.mpg.de To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Talairach transformation
Hi Bruce,
so we are back at the beginning. After I ran recon-all -all, I did exactly that and checked the xform using tkregister2. And here I always see that my talairach volume (the transform) is always smaller, which can be very well seen as the orig surfaces of the subjects are always a little outside the brain and reach well into the skull areas. Of course I can make the adjustments as descriped in the short instructions. But this also means I ran the recon-all precess anew for another 30 h per subject. And that is the reason, why I asked if this is normal that the tailarach transform is a) always smaller than the original brain, and b) if I can make any adjustments to prevent that from happening and thus saving another 30h per subject. In short: How acurate hat the talairach.xfm has to be and is it possible to change some parameters to make this transformation a little more accurate while running the recon-all process only once? Best, Maria
----- Original Message ----- From: "Bruce Fischl" fischl@nmr.mgh.harvard.edu To: "Maria Felber" felber@cbs.mpg.de Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, September 13, 2011 4:07:55 PM Subject: Re: [Freesurfer] Talairach transformation
Hi Maria
you can use tkregister2 to check the accuracy of the talairach.xfm transform ("xform" for short), and correct it if you want.
cheers Bruce On Tue, 13 Sep 2011, Maria Felber wrote:
Hi Bruce,
thanks for the first response. I tried to find some information on the webpage about xform, but failed. So what is xform standing for and where/how can I check it? As in the later processing stages I want to do localization and
DCM-Modeling with my data, I guess the correct talairach coords are kind of important for later comparisons.
Thanks again, Maria
----- Original Message ----- From: "Bruce Fischl" fischl@nmr.mgh.harvard.edu To: "Maria Felber" felber@cbs.mpg.de Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, September 9, 2011 2:13:05 PM Subject: Re: [Freesurfer] Talairach transformation
Hi Maria
as long as the tal xform is reasonable I wouldn't worry about it, unless for some reason you care a lot about the accuracy of the talairach coords.
cheers Bruce
p.s. not sure why it would be smaller
On Fri, 9 Sep 2011, Maria Felber wrote:
Dear all,
sorry, if that question came up before in the mailing list and I simple have been unable to find the thread.
Following the wiki reconstruction workflow, I ran yesterday the recon-all -all process. The process finished without errors. So the next step was to check the talairach transform. Now, according to the FsTutorial/Talairach I have to make some adjustments and then run the whole process again. That is all nice and good.
However, why is it, that the talairach volume is always, no matter which subject I look at, is always significantly smaller than the target volume? Is that normal? Has it to be fixed? Or is that just normal? Attached find one example. As I am using freesurfer for the first time, I am really unsure about that.
Thanks for the help, Maria
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.
-- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522
-- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522
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 first command you show is what you should use (all flags on one line).
permanent changes are listed here: https://surfer.nmr.mgh.harvard.edu/fswiki/Edits
note that since you have run talairach once already, it will keep that prior run, so you will also want to include -clean-tal at the end of your recon-all command.
n.
On Thu, 2011-10-06 at 13:22 +0200, Maria Felber wrote:
Dear Nick,
how do I best implement your suggestions in my command line?
e.g. recon-all -all -use-mritotal -nuintensitycor-3T -s im30 or
recon-all -motioncor -s im30 recon-all -talairach -use-mritotal -s im30 recon-all -all -nuintensitycor-3T -s im30
As I have not a clue what changes will be saved by freesurfer or wethere they are just overwritten by a new command, please advise have best to follow you advise. Thank you. Sincerely, Maria
----- Original Message ----- From: "Nick Schmansky" nicks@nmr.mgh.harvard.edu To: "Bruce Fischl" fischl@nmr.mgh.harvard.edu Cc: "Maria Felber" felber@cbs.mpg.de, sita@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, September 28, 2011 10:53:08 PM Subject: Re: [Freesurfer] Fwd: Talairach transformation
you could also try:
-talairach -use-mritotal
which will use an alternate talarairch alignment scheme (from the MNI). it sometimes works better (not necessary for 3T).
you should also probably add:
-nuintensitycor-3T
to the end of your recon-all command, which will run the nu_correct stage optimized for 3T. it wont help you with your talairach issue, but will produce better results for 3T data downstream.
n.
On Wed, 2011-09-28 at 16:38 -0400, Bruce Fischl wrote:
Hi Maria
have you tried running without the talairach stuff? Try -notalairach and see if it works for you
cheers Bruce On Wed, 28 Sep 2011, Maria Felber wrote:
Dear Ms. Kakunoori,
sorry to bother you again, but as I did not get a reply to my last message to everyone so far troubled with my question, I am trying here for a second time. It is indeed the case, that all my data were scanned with a 3T. And if that is indeed the problem Dr. Snyder figured out, then what can I do about it? Or is anyone already working on this problem? I can hardly imagine I am the only one recording with a 3T instead of a 1.5T. Yours sincerely, Maria Felber
----- Forwarded Message ----- From: "Maria Felber" felber@cbs.mpg.de To: "Avi Snyder" avi@npg.wustl.edu Cc: "Sita Kakunoori", felber@cbs.mpg.de, "Avi Snyder" <avi@npg.wustl.edu, Bruce Fischl" sita@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu Sent: Thursday, September 15, 2011 10:46:55 AM Subject: Re: [Freesurfer] Talairach transformation
Dear all,
indeed all my T1-scans were recorded with a 3T scanner. So what can I do about it or do you have something in progress which would fix this problem anytime soon? Thanks, Maria
----- Original Message ----- From: "Avi Snyder" avi@npg.wustl.edu To: "Sita Kakunoori" sita@nmr.mgh.harvard.edu, felber@cbs.mpg.de, "Avi Snyder" avi@npg.wustl.edu Cc: "Bruce Fischl" fischl@nmr.mgh.harvard.edu Sent: Tuesday, September 13, 2011 11:03:28 PM Subject: Re: [Freesurfer] Talairach transformation
Hi Sita,
Wrong-stretch (e.g., too fat or too thin) MP-RAGE atlas transforms are expected if the contrast properties of the sample image are far from those of the target. This condition can easily occur if the target is based on 1.5T data and the sample is acquired at 3T. (3T but not 1.5T T1W images tend to be relatively bright in the center of the head.) Gd++ contrasted MP-RAGE scans routinely do not produce decent atlas transforms unless special measures are taken. A FreeSurfer fix for this problem is theoretically feasible.
Avi
On 9/13/11 2:26 PM, "Sita Kakunoori" sita@nmr.mgh.harvard.edu wrote:
I might have seen this in a dataset. I am cc'ing Dr.Avi Anyder on this e-mail. Hi Dr.Snyder, Not sure if you remember but we saw something similar in a dataset here at the center where the talairach was much smaller than the orig.mgz volume and you created a new talairach template to be used with that dataset. I just wondered if this issue is similar to that.
Thanks much, Sita. ---------- Forwarded message ---------- Date: Tue, 13 Sep 2011 16:27:17 +0200 (CEST) From: Maria Felber felber@cbs.mpg.de To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Talairach transformation
Hi Bruce,
so we are back at the beginning. After I ran recon-all -all, I did exactly that and checked the xform using tkregister2. And here I always see that my talairach volume (the transform) is always smaller, which can be very well seen as the orig surfaces of the subjects are always a little outside the brain and reach well into the skull areas. Of course I can make the adjustments as descriped in the short instructions. But this also means I ran the recon-all precess anew for another 30 h per subject. And that is the reason, why I asked if this is normal that the tailarach transform is a) always smaller than the original brain, and b) if I can make any adjustments to prevent that from happening and thus saving another 30h per subject. In short: How acurate hat the talairach.xfm has to be and is it possible to change some parameters to make this transformation a little more accurate while running the recon-all process only once? Best, Maria
----- Original Message ----- From: "Bruce Fischl" fischl@nmr.mgh.harvard.edu To: "Maria Felber" felber@cbs.mpg.de Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, September 13, 2011 4:07:55 PM Subject: Re: [Freesurfer] Talairach transformation
Hi Maria
you can use tkregister2 to check the accuracy of the talairach.xfm transform ("xform" for short), and correct it if you want.
cheers Bruce On Tue, 13 Sep 2011, Maria Felber wrote:
Hi Bruce,
thanks for the first response. I tried to find some information on the webpage about xform, but failed. So what is xform standing for and where/how can I check it? As in the later processing stages I want to do localization and
DCM-Modeling with my data, I guess the correct talairach coords are kind of important for later comparisons.
Thanks again, Maria
----- Original Message ----- From: "Bruce Fischl" fischl@nmr.mgh.harvard.edu To: "Maria Felber" felber@cbs.mpg.de Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, September 9, 2011 2:13:05 PM Subject: Re: [Freesurfer] Talairach transformation
Hi Maria
as long as the tal xform is reasonable I wouldn't worry about it, unless for some reason you care a lot about the accuracy of the talairach coords.
cheers Bruce
p.s. not sure why it would be smaller
On Fri, 9 Sep 2011, Maria Felber wrote:
Dear all,
sorry, if that question came up before in the mailing list and I simple have been unable to find the thread.
Following the wiki reconstruction workflow, I ran yesterday the recon-all -all process. The process finished without errors. So the next step was to check the talairach transform. Now, according to the FsTutorial/Talairach I have to make some adjustments and then run the whole process again. That is all nice and good.
However, why is it, that the talairach volume is always, no matter which subject I look at, is always significantly smaller than the target volume? Is that normal? Has it to be fixed? Or is that just normal? Attached find one example. As I am using freesurfer for the first time, I am really unsure about that.
Thanks for the help, Maria
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.
-- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522
-- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522
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 all,
I have the same problem. I'm also working with 3T, and I need to stretch the movable template with tkregister2 in almost every subject. It would be nice if this wasn't necessary, is there a workaround?
Thanks, Andreia
Citando Maria Felber felber@cbs.mpg.de:
Dear Ms. Kakunoori,
sorry to bother you again, but as I did not get a reply to my last message to everyone so far troubled with my question, I am trying here for a second time. It is indeed the case, that all my data were scanned with a 3T. And if that is indeed the problem Dr. Snyder figured out, then what can I do about it? Or is anyone already working on this problem? I can hardly imagine I am the only one recording with a 3T instead of a 1.5T. Yours sincerely, Maria Felber
----- Forwarded Message ----- From: "Maria Felber" felber@cbs.mpg.de To: "Avi Snyder" avi@npg.wustl.edu Cc: "Sita Kakunoori", felber@cbs.mpg.de, "Avi Snyder" <avi@npg.wustl.edu, Bruce Fischl" sita@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu Sent: Thursday, September 15, 2011 10:46:55 AM Subject: Re: [Freesurfer] Talairach transformation
Dear all,
indeed all my T1-scans were recorded with a 3T scanner. So what can I do about it or do you have something in progress which would fix this problem anytime soon? Thanks, Maria
----- Original Message ----- From: "Avi Snyder" avi@npg.wustl.edu To: "Sita Kakunoori" sita@nmr.mgh.harvard.edu, felber@cbs.mpg.de, "Avi Snyder" avi@npg.wustl.edu Cc: "Bruce Fischl" fischl@nmr.mgh.harvard.edu Sent: Tuesday, September 13, 2011 11:03:28 PM Subject: Re: [Freesurfer] Talairach transformation
Hi Sita,
Wrong-stretch (e.g., too fat or too thin) MP-RAGE atlas transforms are expected if the contrast properties of the sample image are far from those of the target. This condition can easily occur if the target is based on 1.5T data and the sample is acquired at 3T. (3T but not 1.5T T1W images tend to be relatively bright in the center of the head.) Gd++ contrasted MP-RAGE scans routinely do not produce decent atlas transforms unless special measures are taken. A FreeSurfer fix for this problem is theoretically feasible.
Avi
On 9/13/11 2:26 PM, "Sita Kakunoori" sita@nmr.mgh.harvard.edu wrote:
I might have seen this in a dataset. I am cc'ing Dr.Avi Anyder on this e-mail. Hi Dr.Snyder, Not sure if you remember but we saw something similar in a dataset here at the center where the talairach was much smaller than the orig.mgz volume and you created a new talairach template to be used with that dataset. I just wondered if this issue is similar to that.
Thanks much, Sita. ---------- Forwarded message ---------- Date: Tue, 13 Sep 2011 16:27:17 +0200 (CEST) From: Maria Felber felber@cbs.mpg.de To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Talairach transformation
Hi Bruce,
so we are back at the beginning. After I ran recon-all -all, I did exactly that and checked the xform using tkregister2. And here I always see that my talairach volume (the transform) is always smaller, which can be very well seen as the orig surfaces of the subjects are always a little outside the brain and reach well into the skull areas. Of course I can make the adjustments as descriped in the short instructions. But this also means I ran the recon-all precess anew for another 30 h per subject. And that is the reason, why I asked if this is normal that the tailarach transform is a) always smaller than the original brain, and b) if I can make any adjustments to prevent that from happening and thus saving another 30h per subject. In short: How acurate hat the talairach.xfm has to be and is it possible to change some parameters to make this transformation a little more accurate while running the recon-all process only once? Best, Maria
----- Original Message ----- From: "Bruce Fischl" fischl@nmr.mgh.harvard.edu To: "Maria Felber" felber@cbs.mpg.de Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, September 13, 2011 4:07:55 PM Subject: Re: [Freesurfer] Talairach transformation
Hi Maria
you can use tkregister2 to check the accuracy of the talairach.xfm transform ("xform" for short), and correct it if you want.
cheers Bruce On Tue, 13 Sep 2011, Maria Felber wrote:
Hi Bruce,
thanks for the first response. I tried to find some information on the webpage about xform, but failed. So what is xform standing for and where/how can I check it? As in the later processing stages I want to do localization and
DCM-Modeling with my data, I guess the correct talairach coords are kind of important for later comparisons.
Thanks again, Maria
----- Original Message ----- From: "Bruce Fischl" fischl@nmr.mgh.harvard.edu To: "Maria Felber" felber@cbs.mpg.de Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, September 9, 2011 2:13:05 PM Subject: Re: [Freesurfer] Talairach transformation
Hi Maria
as long as the tal xform is reasonable I wouldn't worry about it, unless for some reason you care a lot about the accuracy of the talairach coords.
cheers Bruce
p.s. not sure why it would be smaller
On Fri, 9 Sep 2011, Maria Felber wrote:
Dear all,
sorry, if that question came up before in the mailing list and I simple have been unable to find the thread.
Following the wiki reconstruction workflow, I ran yesterday the recon-all -all process. The process finished without errors. So the next step was to check the talairach transform. Now, according to the FsTutorial/Talairach I have to make some adjustments and then run the whole process again. That is all nice and good.
However, why is it, that the talairach volume is always, no matter which subject I look at, is always significantly smaller than the target volume? Is that normal? Has it to be fixed? Or is that just normal? Attached find one example. As I am using freesurfer for the first time, I am really unsure about that.
Thanks for the help, Maria
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.
-- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522
-- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522
-- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
you can try:
-talairach -use-mritotal
which will use an alternate talarairch alignment scheme (from the MNI). it sometimes works better.
you should also probably add:
-nuintensitycor-3T
to the end of your recon-all command, which will run the nu_correct stage optimized for 3T. it wont help you with your talairach issue, but people have found that it produces better results for 3T data (versus the default nu_correct parameters, which are optimized for 1.5T).
n.
On Mon, 2011-10-03 at 15:53 +0100, _andreia_@sapo.pt wrote:
Hi all,
I have the same problem. I'm also working with 3T, and I need to stretch the movable template with tkregister2 in almost every subject. It would be nice if this wasn't necessary, is there a workaround?
Thanks, Andreia
Citando Maria Felber felber@cbs.mpg.de:
Dear Ms. Kakunoori,
sorry to bother you again, but as I did not get a reply to my last message to everyone so far troubled with my question, I am trying here for a second time. It is indeed the case, that all my data were scanned with a 3T. And if that is indeed the problem Dr. Snyder figured out, then what can I do about it? Or is anyone already working on this problem? I can hardly imagine I am the only one recording with a 3T instead of a 1.5T. Yours sincerely, Maria Felber
----- Forwarded Message ----- From: "Maria Felber" felber@cbs.mpg.de To: "Avi Snyder" avi@npg.wustl.edu Cc: "Sita Kakunoori", felber@cbs.mpg.de, "Avi Snyder" <avi@npg.wustl.edu, Bruce Fischl" sita@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu Sent: Thursday, September 15, 2011 10:46:55 AM Subject: Re: [Freesurfer] Talairach transformation
Dear all,
indeed all my T1-scans were recorded with a 3T scanner. So what can I do about it or do you have something in progress which would fix this problem anytime soon? Thanks, Maria
----- Original Message ----- From: "Avi Snyder" avi@npg.wustl.edu To: "Sita Kakunoori" sita@nmr.mgh.harvard.edu, felber@cbs.mpg.de, "Avi Snyder" avi@npg.wustl.edu Cc: "Bruce Fischl" fischl@nmr.mgh.harvard.edu Sent: Tuesday, September 13, 2011 11:03:28 PM Subject: Re: [Freesurfer] Talairach transformation
Hi Sita,
Wrong-stretch (e.g., too fat or too thin) MP-RAGE atlas transforms are expected if the contrast properties of the sample image are far from those of the target. This condition can easily occur if the target is based on 1.5T data and the sample is acquired at 3T. (3T but not 1.5T T1W images tend to be relatively bright in the center of the head.) Gd++ contrasted MP-RAGE scans routinely do not produce decent atlas transforms unless special measures are taken. A FreeSurfer fix for this problem is theoretically feasible.
Avi
On 9/13/11 2:26 PM, "Sita Kakunoori" sita@nmr.mgh.harvard.edu wrote:
I might have seen this in a dataset. I am cc'ing Dr.Avi Anyder on this e-mail. Hi Dr.Snyder, Not sure if you remember but we saw something similar in a dataset here at the center where the talairach was much smaller than the orig.mgz volume and you created a new talairach template to be used with that dataset. I just wondered if this issue is similar to that.
Thanks much, Sita. ---------- Forwarded message ---------- Date: Tue, 13 Sep 2011 16:27:17 +0200 (CEST) From: Maria Felber felber@cbs.mpg.de To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Talairach transformation
Hi Bruce,
so we are back at the beginning. After I ran recon-all -all, I did exactly that and checked the xform using tkregister2. And here I always see that my talairach volume (the transform) is always smaller, which can be very well seen as the orig surfaces of the subjects are always a little outside the brain and reach well into the skull areas. Of course I can make the adjustments as descriped in the short instructions. But this also means I ran the recon-all precess anew for another 30 h per subject. And that is the reason, why I asked if this is normal that the tailarach transform is a) always smaller than the original brain, and b) if I can make any adjustments to prevent that from happening and thus saving another 30h per subject. In short: How acurate hat the talairach.xfm has to be and is it possible to change some parameters to make this transformation a little more accurate while running the recon-all process only once? Best, Maria
----- Original Message ----- From: "Bruce Fischl" fischl@nmr.mgh.harvard.edu To: "Maria Felber" felber@cbs.mpg.de Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, September 13, 2011 4:07:55 PM Subject: Re: [Freesurfer] Talairach transformation
Hi Maria
you can use tkregister2 to check the accuracy of the talairach.xfm transform ("xform" for short), and correct it if you want.
cheers Bruce On Tue, 13 Sep 2011, Maria Felber wrote:
Hi Bruce,
thanks for the first response. I tried to find some information on the webpage about xform, but failed. So what is xform standing for and where/how can I check it? As in the later processing stages I want to do localization and
DCM-Modeling with my data, I guess the correct talairach coords are kind of important for later comparisons.
Thanks again, Maria
----- Original Message ----- From: "Bruce Fischl" fischl@nmr.mgh.harvard.edu To: "Maria Felber" felber@cbs.mpg.de Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, September 9, 2011 2:13:05 PM Subject: Re: [Freesurfer] Talairach transformation
Hi Maria
as long as the tal xform is reasonable I wouldn't worry about it, unless for some reason you care a lot about the accuracy of the talairach coords.
cheers Bruce
p.s. not sure why it would be smaller
On Fri, 9 Sep 2011, Maria Felber wrote:
Dear all,
sorry, if that question came up before in the mailing list and I simple have been unable to find the thread.
Following the wiki reconstruction workflow, I ran yesterday the recon-all -all process. The process finished without errors. So the next step was to check the talairach transform. Now, according to the FsTutorial/Talairach I have to make some adjustments and then run the whole process again. That is all nice and good.
However, why is it, that the talairach volume is always, no matter which subject I look at, is always significantly smaller than the target volume? Is that normal? Has it to be fixed? Or is that just normal? Attached find one example. As I am using freesurfer for the first time, I am really unsure about that.
Thanks for the help, Maria
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.
-- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522
-- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522
-- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522
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
Thanks! I'll try that!
Andreia
Citando Nick Schmansky nicks@nmr.mgh.harvard.edu:
you can try:
-talairach -use-mritotal
which will use an alternate talarairch alignment scheme (from the MNI). it sometimes works better.
you should also probably add:
-nuintensitycor-3T
to the end of your recon-all command, which will run the nu_correct stage optimized for 3T. it wont help you with your talairach issue, but people have found that it produces better results for 3T data (versus the default nu_correct parameters, which are optimized for 1.5T).
n.
On Mon, 2011-10-03 at 15:53 +0100, _andreia_@sapo.pt wrote:
Hi all,
I have the same problem. I'm also working with 3T, and I need to stretch the movable template with tkregister2 in almost every subject. It would be nice if this wasn't necessary, is there a workaround?
Thanks, Andreia
Citando Maria Felber felber@cbs.mpg.de:
Dear Ms. Kakunoori,
sorry to bother you again, but as I did not get a reply to my last message to everyone so far troubled with my question, I am trying here for a second time. It is indeed the case, that all my data were scanned with a 3T. And if that is indeed the problem Dr. Snyder figured out, then what can I do about it? Or is anyone already working on this problem? I can hardly imagine I am the only one recording with a 3T instead of a 1.5T. Yours sincerely, Maria Felber
----- Forwarded Message ----- From: "Maria Felber" felber@cbs.mpg.de To: "Avi Snyder" avi@npg.wustl.edu Cc: "Sita Kakunoori", felber@cbs.mpg.de, "Avi Snyder" <avi@npg.wustl.edu, Bruce Fischl" sita@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu Sent: Thursday, September 15, 2011 10:46:55 AM Subject: Re: [Freesurfer] Talairach transformation
Dear all,
indeed all my T1-scans were recorded with a 3T scanner. So what can I do about it or do you have something in progress which would fix this problem anytime soon? Thanks, Maria
----- Original Message ----- From: "Avi Snyder" avi@npg.wustl.edu To: "Sita Kakunoori" sita@nmr.mgh.harvard.edu, felber@cbs.mpg.de, "Avi Snyder" avi@npg.wustl.edu Cc: "Bruce Fischl" fischl@nmr.mgh.harvard.edu Sent: Tuesday, September 13, 2011 11:03:28 PM Subject: Re: [Freesurfer] Talairach transformation
Hi Sita,
Wrong-stretch (e.g., too fat or too thin) MP-RAGE atlas transforms are expected if the contrast properties of the sample image are far from those of the target. This condition can easily occur if the target is based on 1.5T data and the sample is acquired at 3T. (3T but not 1.5T T1W images tend to be relatively bright in the center of the head.) Gd++ contrasted MP-RAGE scans routinely do not produce decent atlas transforms unless special measures are taken. A FreeSurfer fix for this problem is theoretically feasible.
Avi
On 9/13/11 2:26 PM, "Sita Kakunoori" sita@nmr.mgh.harvard.edu wrote:
I might have seen this in a dataset. I am cc'ing Dr.Avi Anyder on this e-mail. Hi Dr.Snyder, Not sure if you remember but we saw something similar in a dataset here at the center where the talairach was much smaller than the orig.mgz volume and you created a new talairach template to be used with that dataset. I just wondered if this issue is similar to that.
Thanks much, Sita. ---------- Forwarded message ---------- Date: Tue, 13 Sep 2011 16:27:17 +0200 (CEST) From: Maria Felber felber@cbs.mpg.de To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Talairach transformation
Hi Bruce,
so we are back at the beginning. After I ran recon-all -all, I did exactly that and checked the xform using tkregister2. And here I always see that my talairach volume (the transform) is always smaller, which can be very well seen as the orig surfaces of the subjects are always a little outside the brain and reach well into the skull areas. Of course I can make the adjustments as descriped in the short instructions. But this also means I ran the recon-all precess anew for another 30 h per subject. And that is the reason, why I asked if this is normal that the tailarach transform is a) always smaller than the original brain, and b) if I can make any adjustments to prevent that from happening and thus saving another 30h per subject. In short: How acurate hat the talairach.xfm has to be and is it possible to change some parameters to make this transformation a little more accurate while running the recon-all process only once? Best, Maria
----- Original Message ----- From: "Bruce Fischl" fischl@nmr.mgh.harvard.edu To: "Maria Felber" felber@cbs.mpg.de Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, September 13, 2011 4:07:55 PM Subject: Re: [Freesurfer] Talairach transformation
Hi Maria
you can use tkregister2 to check the accuracy of the talairach.xfm transform ("xform" for short), and correct it if you want.
cheers Bruce On Tue, 13 Sep 2011, Maria Felber wrote:
Hi Bruce,
thanks for the first response. I tried to find some information on the webpage about xform, but failed. So what is xform standing for and where/how can I check it? As in the later processing stages I want to do localization and
DCM-Modeling with my data, I guess the correct talairach coords are kind of important for later comparisons.
Thanks again, Maria
----- Original Message ----- From: "Bruce Fischl" fischl@nmr.mgh.harvard.edu To: "Maria Felber" felber@cbs.mpg.de Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, September 9, 2011 2:13:05 PM Subject: Re: [Freesurfer] Talairach transformation
Hi Maria
as long as the tal xform is reasonable I wouldn't worry about it, unless for some reason you care a lot about the accuracy of the talairach coords.
cheers Bruce
p.s. not sure why it would be smaller
On Fri, 9 Sep 2011, Maria Felber wrote:
Dear all,
sorry, if that question came up before in the mailing list and I simple have been unable to find the thread.
Following the wiki reconstruction workflow, I ran yesterday the recon-all -all process. The process finished without errors. So the next step was to check the talairach transform. Now, according to the FsTutorial/Talairach I have to make some adjustments and then run the whole process again. That is all nice and good.
However, why is it, that the talairach volume is always, no matter which subject I look at, is always significantly smaller than the target volume? Is that normal? Has it to be fixed? Or is that just normal? Attached find one example. As I am using freesurfer for the first time, I am really unsure about that.
Thanks for the help, Maria
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.
-- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522
-- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522
-- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522
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
Hello,
I'm having similar issues with a 1.5T data set from here that used a custom head coil. The talairach transforms are skewed and scaled incorrectly. Some are not correctable by tkmedit as the movable is too skewed (almost to a rhomboid shape). I'm fairly new to freesurfer so any suggestions would be greatly appreciated.
-James __ James Sheehan Research Laboratory Technologist GI Research, Massachusetts General Hospital Cell: (978) 505-5135
you can try:
-talairach -use-mritotal
which will use an alternate talarairch alignment scheme (from the MNI). it sometimes works better.
you should also probably add:
-nuintensitycor-3T
to the end of your recon-all command, which will run the nu_correct stage optimized for 3T. it wont help you with your talairach issue, but people have found that it produces better results for 3T data (versus the default nu_correct parameters, which are optimized for 1.5T).
n.
On Mon, 2011-10-03 at 15:53 +0100, _andreia_@sapo.pt wrote:
Hi all,
I have the same problem. I'm also working with 3T, and I need to stretch the movable template with tkregister2 in almost every subject. It would be nice if this wasn't necessary, is there a workaround?
Thanks, Andreia
Citando Maria Felber felber@cbs.mpg.de:
Dear Ms. Kakunoori,
sorry to bother you again, but as I did not get a reply to my last message to everyone so far troubled with my question, I am trying here for a second time. It is indeed the case, that all my data were scanned with a 3T. And if that is indeed the problem Dr. Snyder figured out, then what can I do about it? Or is anyone already working on this problem? I can hardly imagine I am the only one recording with a 3T instead of a 1.5T. Yours sincerely, Maria Felber
----- Forwarded Message ----- From: "Maria Felber" felber@cbs.mpg.de To: "Avi Snyder" avi@npg.wustl.edu Cc: "Sita Kakunoori", felber@cbs.mpg.de, "Avi Snyder" <avi@npg.wustl.edu, Bruce Fischl" sita@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu Sent: Thursday, September 15, 2011 10:46:55 AM Subject: Re: [Freesurfer] Talairach transformation
Dear all,
indeed all my T1-scans were recorded with a 3T scanner. So what can I do about it or do you have something in progress which would fix this problem anytime soon? Thanks, Maria
----- Original Message ----- From: "Avi Snyder" avi@npg.wustl.edu To: "Sita Kakunoori" sita@nmr.mgh.harvard.edu, felber@cbs.mpg.de, "Avi Snyder" avi@npg.wustl.edu Cc: "Bruce Fischl" fischl@nmr.mgh.harvard.edu Sent: Tuesday, September 13, 2011 11:03:28 PM Subject: Re: [Freesurfer] Talairach transformation
Hi Sita,
Wrong-stretch (e.g., too fat or too thin) MP-RAGE atlas transforms are expected if the contrast properties of the sample image are far from
those
of the target. This condition can easily occur if the target is based
on
1.5T data and the sample is acquired at 3T. (3T but not 1.5T T1W
images
tend to be relatively bright in the center of the head.) Gd++
contrasted
MP-RAGE scans routinely do not produce decent atlas transforms unless special measures are taken. A FreeSurfer fix for this problem is theoretically feasible.
Avi
On 9/13/11 2:26 PM, "Sita Kakunoori" sita@nmr.mgh.harvard.edu wrote:
I might have seen this in a dataset. I am cc'ing Dr.Avi Anyder on
this
e-mail. Hi Dr.Snyder, Not sure if you remember but we saw something similar
in a
dataset here at the center where the talairach was much smaller than
the
orig.mgz volume and you created a new talairach template to be used
with
that dataset. I just wondered if this issue is similar to that.
Thanks much, Sita. ---------- Forwarded message ---------- Date: Tue, 13 Sep 2011 16:27:17 +0200 (CEST) From: Maria Felber felber@cbs.mpg.de To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Talairach transformation
Hi Bruce,
so we are back at the beginning. After I ran recon-all -all, I did exactly that and checked the xform using tkregister2. And here I
always
see that my talairach volume (the transform) is always smaller, which
can
be very well seen as the orig surfaces of the subjects are always a little outside the brain and reach well into the skull areas. Of
course I
can make the adjustments as descriped in the short instructions. But
this
also means I ran the recon-all precess anew for another 30 h per
subject.
And that is the reason, why I asked if this is normal that the
tailarach
transform is a) always smaller than the original brain, and b) if I
can
make any adjustments to prevent that from happening and thus saving another 30h per subject. In short: How acurate hat the talairach.xfm has to be and is it
possible
to change some parameters to make this transformation a little more accurate while running the recon-all process only once? Best, Maria
----- Original Message ----- From: "Bruce Fischl" fischl@nmr.mgh.harvard.edu To: "Maria Felber" felber@cbs.mpg.de Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, September 13, 2011 4:07:55 PM Subject: Re: [Freesurfer] Talairach transformation
Hi Maria
you can use tkregister2 to check the accuracy of the talairach.xfm transform ("xform" for short), and correct it if you want.
cheers Bruce On Tue, 13 Sep 2011, Maria Felber wrote:
Hi Bruce,
thanks for the first response. I tried to find some information on
the
webpage about xform, but failed. So what is xform standing for and where/how can I check it? As in the later processing stages I want to do localization and
DCM-Modeling with my data, I guess the correct talairach coords are
kind
of important for later comparisons.
Thanks again, Maria
----- Original Message ----- From: "Bruce Fischl" fischl@nmr.mgh.harvard.edu To: "Maria Felber" felber@cbs.mpg.de Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, September 9, 2011 2:13:05 PM Subject: Re: [Freesurfer] Talairach transformation
Hi Maria
as long as the tal xform is reasonable I wouldn't worry about it,
unless
for some reason you care a lot about the accuracy of the talairach coords.
cheers Bruce
p.s. not sure why it would be smaller
On Fri, 9 Sep 2011, Maria Felber wrote:
Dear all,
sorry, if that question came up before in the mailing list and I simple have been unable to find the thread.
Following the wiki reconstruction workflow, I ran yesterday the recon-all -all process. The process finished without errors. So the next step was to check the talairach transform. Now, according to the FsTutorial/Talairach I have to make some adjustments and then run the whole process again. That is all nice
and
good.
However, why is it, that the talairach volume is always, no matter which subject I look at, is always significantly smaller than the target volume? Is that normal? Has it to be fixed? Or is that just normal? Attached find one example. As I am using freesurfer for the first time, I am really unsure
about
that.
Thanks for the help, Maria
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.
-- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences StephanstraÃe 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522
-- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences StephanstraÃe 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences StephanstraÃe 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522
-- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences StephanstraÃe 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522
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
What version are you running?
On Oct 11, 2011, at 4:21 PM, "James Sheehan" jds69@nmr.mgh.harvard.edu wrote:
Hello,
I'm having similar issues with a 1.5T data set from here that used a custom head coil. The talairach transforms are skewed and scaled incorrectly. Some are not correctable by tkmedit as the movable is too skewed (almost to a rhomboid shape). I'm fairly new to freesurfer so any suggestions would be greatly appreciated.
-James __ James Sheehan Research Laboratory Technologist GI Research, Massachusetts General Hospital Cell: (978) 505-5135
you can try:
-talairach -use-mritotal
which will use an alternate talarairch alignment scheme (from the MNI). it sometimes works better.
you should also probably add:
-nuintensitycor-3T
to the end of your recon-all command, which will run the nu_correct stage optimized for 3T. it wont help you with your talairach issue, but people have found that it produces better results for 3T data (versus the default nu_correct parameters, which are optimized for 1.5T).
n.
On Mon, 2011-10-03 at 15:53 +0100, _andreia_@sapo.pt wrote:
Hi all,
I have the same problem. I'm also working with 3T, and I need to stretch the movable template with tkregister2 in almost every subject. It would be nice if this wasn't necessary, is there a workaround?
Thanks, Andreia
Citando Maria Felber felber@cbs.mpg.de:
Dear Ms. Kakunoori,
sorry to bother you again, but as I did not get a reply to my last message to everyone so far troubled with my question, I am trying here for a second time. It is indeed the case, that all my data were scanned with a 3T. And if that is indeed the problem Dr. Snyder figured out, then what can I do about it? Or is anyone already working on this problem? I can hardly imagine I am the only one recording with a 3T instead of a 1.5T. Yours sincerely, Maria Felber
----- Forwarded Message ----- From: "Maria Felber" felber@cbs.mpg.de To: "Avi Snyder" avi@npg.wustl.edu Cc: "Sita Kakunoori", felber@cbs.mpg.de, "Avi Snyder" <avi@npg.wustl.edu, Bruce Fischl" sita@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu Sent: Thursday, September 15, 2011 10:46:55 AM Subject: Re: [Freesurfer] Talairach transformation
Dear all,
indeed all my T1-scans were recorded with a 3T scanner. So what can I do about it or do you have something in progress which would fix this problem anytime soon? Thanks, Maria
----- Original Message ----- From: "Avi Snyder" avi@npg.wustl.edu To: "Sita Kakunoori" sita@nmr.mgh.harvard.edu, felber@cbs.mpg.de, "Avi Snyder" avi@npg.wustl.edu Cc: "Bruce Fischl" fischl@nmr.mgh.harvard.edu Sent: Tuesday, September 13, 2011 11:03:28 PM Subject: Re: [Freesurfer] Talairach transformation
Hi Sita,
Wrong-stretch (e.g., too fat or too thin) MP-RAGE atlas transforms are expected if the contrast properties of the sample image are far from
those
of the target. This condition can easily occur if the target is based
on
1.5T data and the sample is acquired at 3T. (3T but not 1.5T T1W
images
tend to be relatively bright in the center of the head.) Gd++
contrasted
MP-RAGE scans routinely do not produce decent atlas transforms unless special measures are taken. A FreeSurfer fix for this problem is theoretically feasible.
Avi
On 9/13/11 2:26 PM, "Sita Kakunoori" sita@nmr.mgh.harvard.edu wrote:
I might have seen this in a dataset. I am cc'ing Dr.Avi Anyder on
this
e-mail. Hi Dr.Snyder, Not sure if you remember but we saw something similar
in a
dataset here at the center where the talairach was much smaller than
the
orig.mgz volume and you created a new talairach template to be used
with
that dataset. I just wondered if this issue is similar to that.
Thanks much, Sita. ---------- Forwarded message ---------- Date: Tue, 13 Sep 2011 16:27:17 +0200 (CEST) From: Maria Felber felber@cbs.mpg.de To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Talairach transformation
Hi Bruce,
so we are back at the beginning. After I ran recon-all -all, I did exactly that and checked the xform using tkregister2. And here I
always
see that my talairach volume (the transform) is always smaller, which
can
be very well seen as the orig surfaces of the subjects are always a little outside the brain and reach well into the skull areas. Of
course I
can make the adjustments as descriped in the short instructions. But
this
also means I ran the recon-all precess anew for another 30 h per
subject.
And that is the reason, why I asked if this is normal that the
tailarach
transform is a) always smaller than the original brain, and b) if I
can
make any adjustments to prevent that from happening and thus saving another 30h per subject. In short: How acurate hat the talairach.xfm has to be and is it
possible
to change some parameters to make this transformation a little more accurate while running the recon-all process only once? Best, Maria
----- Original Message ----- From: "Bruce Fischl" fischl@nmr.mgh.harvard.edu To: "Maria Felber" felber@cbs.mpg.de Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, September 13, 2011 4:07:55 PM Subject: Re: [Freesurfer] Talairach transformation
Hi Maria
you can use tkregister2 to check the accuracy of the talairach.xfm transform ("xform" for short), and correct it if you want.
cheers Bruce On Tue, 13 Sep 2011, Maria Felber wrote:
Hi Bruce,
thanks for the first response. I tried to find some information on
the
webpage about xform, but failed. So what is xform standing for and where/how can I check it? As in the later processing stages I want to do localization and
DCM-Modeling with my data, I guess the correct talairach coords are
kind
of important for later comparisons.
Thanks again, Maria
----- Original Message ----- From: "Bruce Fischl" fischl@nmr.mgh.harvard.edu To: "Maria Felber" felber@cbs.mpg.de Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, September 9, 2011 2:13:05 PM Subject: Re: [Freesurfer] Talairach transformation
Hi Maria
as long as the tal xform is reasonable I wouldn't worry about it,
unless
for some reason you care a lot about the accuracy of the talairach coords.
cheers Bruce
p.s. not sure why it would be smaller
On Fri, 9 Sep 2011, Maria Felber wrote:
Dear all,
sorry, if that question came up before in the mailing list and I simple have been unable to find the thread.
Following the wiki reconstruction workflow, I ran yesterday the recon-all -all process. The process finished without errors. So the next step was to check the talairach transform. Now, according to the FsTutorial/Talairach I have to make some adjustments and then run the whole process again. That is all nice
and
good.
However, why is it, that the talairach volume is always, no matter which subject I look at, is always significantly smaller than the target volume? Is that normal? Has it to be fixed? Or is that just normal? Attached find one example. As I am using freesurfer for the first time, I am really unsure
about
that.
Thanks for the help, Maria
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.
-- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences StephanstraÃe 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522
-- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences StephanstraÃe 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences StephanstraÃe 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522
-- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences StephanstraÃe 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522
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
-
_andreia_＠sapo.pt -
Bruce Fischl -
James Sheehan -
Maria Felber -
Nick Schmansky