Re: [Freesurfer] Input/Output to specific atlas space/dimensions?
Has anyone had a chance to take a further look at the output differences in using the -mprage option yet? (I'm still new at freesurfer and probably wouldn't know what to look for...) -Alex ~)--- -- Alexander Li Cohen al...@npg.wustl.edu (WORK Email) alexco...@gmail.com (Non-secure / rapid-response Email) Petersen/Schlaggar Lab Medical Scientist Training Program Washington University in St. Louis School of Medicine -- This message is intended only for the exclusive use of the intended recipient(s) named herein and may contain information that is PRIVILEGED and/or CONFIDENTIAL. If you are not the intended recipient, you are hereby notified that any use, dissemination, disclosure or copying of this communication is strictly prohibited. If you have received this communication in error, please destroy all copies of this message and its attachments and notify us immediately. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. On Aug 27, 2009, at 8:41 AM, Bruce Fischl wrote: yes, I think it will probably help a bit for mprage scans. Essentially it changes the default assumptions about noise and contrast characteristics (it assumes more of both) and will help the intensity normalization get a bit further out the thin white matter strands. Try it and see what you think On Thu, 27 Aug 2009, Michael Harms wrote: Is there any gain/benefit then by including this -mprage flag? In what circumstance is that flag to be used? I'm still confused what the purpose of that flag is. thanks, Mike H. On Thu, 2009-08-27 at 08:54 -0400, Bruce Fischl wrote: no, it's more agnostic. Optimized for both spgr and mprage (or neither, depending on your perspective). You're probably right that mp-rage is more common these days, but I think spgrs are still fairly widespread on GE. On Thu, 27 Aug 2009, Michael Harms wrote: So, are you saying that the default recon-all stream is really optimized for SPGR, and anyone running a MPRAGE should be including the - mprage flag when they run recon-all? If so, this is news to me, and I suspect many other FS users. The default recon-all setting is set IsMPRAGE = 0, but I suspect (just a hunch, no data) that MPRAGE is the most commonly used type of input to FS. thanks for clarifying, -Mike H. On Wed, 2009-08-26 at 12:53 -0400, Bruce Fischl wrote: yes, that's true. The difference is between the SPGR and the MP- RAGE. If we don't know which it is we have to try to figure out the contrast and noise characteristics (spgr has worse contrast and less noise) On Wed, 26 Aug 2009, Michael Harms wrote: Ok, now I'm confused again, because my understanding is that the Andre van de Kouwe mprage, Siemen's default mprage, and the ADNI mprage really are not very different in terms of their contrast. Is that not correct? Assuming they are indeed all similar, are you saying that a modern ADNI-like mprage benefits from the inclusion of this -mprage flag? thanks, Mike H. On Wed, 2009-08-26 at 12:18 -0400, Nick Schmansky wrote: There's also the flag -mpragewhich can be used, intended for the mprage developed by Andre van de Kouwe, which I believe is the same as that now used by Siemens. Nick On Wed, 2009-08-26 at 09:37 -0500, Michael Harms wrote: No, our current CAP MPRAGE at WU on the 3T TimTrio is very similar to the ADNI mprage, so that old flag shouldn't be used. -MH On Wed, 2009-08-26 at 09:24 -0500, Alexander Li Cohen wrote: Ah I see, this raises a question then, of whether the optimizations are still applicable to WU acquired MP-RAGE data, as we are currently collecting 3T Trio data, and I believe Randy's data is 1.5T Vision data, however the sequence (our CAP MP-RAGE) is quite similar... can anyone up there speak to this? -Alex ~)- -- Alexander Li Cohen al...@npg.wustl.edu (WORK Email) alexco...@gmail.com (Non-secure / rapid-response Email) Petersen/Schlaggar Lab Medical Scientist Training Program Washington University in St. Louis School of Medicine -- This message is intended only for the exclusive use of the intended recipient(s) named herein and may contain information that is PRIVILEGED and/or CONFIDENTIAL. If you are not the
Re: [Freesurfer] Input/Output to specific atlas space/dimensions?
So, are you saying that the default recon-all stream is really optimized for SPGR, and anyone running a MPRAGE should be including the -mprage flag when they run recon-all? If so, this is news to me, and I suspect many other FS users. The default recon-all setting is set IsMPRAGE = 0, but I suspect (just a hunch, no data) that MPRAGE is the most commonly used type of input to FS. thanks for clarifying, -Mike H. On Wed, 2009-08-26 at 12:53 -0400, Bruce Fischl wrote: yes, that's true. The difference is between the SPGR and the MP-RAGE. If we don't know which it is we have to try to figure out the contrast and noise characteristics (spgr has worse contrast and less noise) On Wed, 26 Aug 2009, Michael Harms wrote: Ok, now I'm confused again, because my understanding is that the Andre van de Kouwe mprage, Siemen's default mprage, and the ADNI mprage really are not very different in terms of their contrast. Is that not correct? Assuming they are indeed all similar, are you saying that a modern ADNI-like mprage benefits from the inclusion of this -mprage flag? thanks, Mike H. On Wed, 2009-08-26 at 12:18 -0400, Nick Schmansky wrote: There's also the flag -mpragewhich can be used, intended for the mprage developed by Andre van de Kouwe, which I believe is the same as that now used by Siemens. Nick On Wed, 2009-08-26 at 09:37 -0500, Michael Harms wrote: No, our current CAP MPRAGE at WU on the 3T TimTrio is very similar to the ADNI mprage, so that old flag shouldn't be used. -MH On Wed, 2009-08-26 at 09:24 -0500, Alexander Li Cohen wrote: Ah I see, this raises a question then, of whether the optimizations are still applicable to WU acquired MP-RAGE data, as we are currently collecting 3T Trio data, and I believe Randy's data is 1.5T Vision data, however the sequence (our CAP MP-RAGE) is quite similar... can anyone up there speak to this? -Alex ~)- -- Alexander Li Cohen al...@npg.wustl.edu (WORK Email) alexco...@gmail.com (Non-secure / rapid-response Email) Petersen/Schlaggar Lab Medical Scientist Training Program Washington University in St. Louis School of Medicine -- This message is intended only for the exclusive use of the intended recipient(s) named herein and may contain information that is PRIVILEGED and/or CONFIDENTIAL. If you are not the intended recipient, you are hereby notified that any use, dissemination, disclosure or copying of this communication is strictly prohibited. If you have received this communication in error, please destroy all copies of this message and its attachments and notify us immediately. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. On Aug 26, 2009, at 8:41 AM, Bruce Fischl wrote: yes, it was optimized for the mp-rages that Randy B used to collect there, not for example ADNI. On Tue, 25 Aug 2009, Michael Harms wrote: I assume that that flag (-washu_mprage) is somewhat antiquated, right? That is, it was included for an older set of scans (generated at WashU generated years ago before Siemens had its own MPRAGE sequence) that happened to have darker gray matter, and doesn't need to be applied for modern MPRAGE scans, correct? -MH On Tue, 2009-08-25 at 13:33 -0400, Nick Schmansky wrote: Alex, The -washu_mprage flag affects mri_normalize and mri_segment. It adjusts the parameters of those binaries to match the assumed intensity profile in mprage scans, eg. to account for darker grey matter. I've updated the help text in recon-all. Nick As a side note, there appears to be a switch for recon-all: -washu_mprage : assume scan parameters are Wash.U. MP-RAGE protocol yet there is no documentation as to what this determines, nor whether the raw, or locally atlas-aligned data should be provided. (Avi didn't know either...) Many Thanks! -Alex Li Cohen ~)- -- Alexander Li Cohen al...@npg.wustl.edu (WORK Email) alexco...@gmail.com (Non-secure / rapid-response Email) Petersen/Schlaggar Lab Medical Scientist Training Program Washington University in St. Louis School of Medicine -- This message is intended only for the exclusive use of the intended
Re: [Freesurfer] Input/Output to specific atlas space/dimensions?
no, it's more agnostic. Optimized for both spgr and mprage (or neither, depending on your perspective). You're probably right that mp-rage is more common these days, but I think spgrs are still fairly widespread on GE. On Thu, 27 Aug 2009, Michael Harms wrote: So, are you saying that the default recon-all stream is really optimized for SPGR, and anyone running a MPRAGE should be including the -mprage flag when they run recon-all? If so, this is news to me, and I suspect many other FS users. The default recon-all setting is set IsMPRAGE = 0, but I suspect (just a hunch, no data) that MPRAGE is the most commonly used type of input to FS. thanks for clarifying, -Mike H. On Wed, 2009-08-26 at 12:53 -0400, Bruce Fischl wrote: yes, that's true. The difference is between the SPGR and the MP-RAGE. If we don't know which it is we have to try to figure out the contrast and noise characteristics (spgr has worse contrast and less noise) On Wed, 26 Aug 2009, Michael Harms wrote: Ok, now I'm confused again, because my understanding is that the Andre van de Kouwe mprage, Siemen's default mprage, and the ADNI mprage really are not very different in terms of their contrast. Is that not correct? Assuming they are indeed all similar, are you saying that a modern ADNI-like mprage benefits from the inclusion of this -mprage flag? thanks, Mike H. On Wed, 2009-08-26 at 12:18 -0400, Nick Schmansky wrote: There's also the flag -mpragewhich can be used, intended for the mprage developed by Andre van de Kouwe, which I believe is the same as that now used by Siemens. Nick On Wed, 2009-08-26 at 09:37 -0500, Michael Harms wrote: No, our current CAP MPRAGE at WU on the 3T TimTrio is very similar to the ADNI mprage, so that old flag shouldn't be used. -MH On Wed, 2009-08-26 at 09:24 -0500, Alexander Li Cohen wrote: Ah I see, this raises a question then, of whether the optimizations are still applicable to WU acquired MP-RAGE data, as we are currently collecting 3T Trio data, and I believe Randy's data is 1.5T Vision data, however the sequence (our CAP MP-RAGE) is quite similar... can anyone up there speak to this? -Alex ~)- -- Alexander Li Cohen al...@npg.wustl.edu (WORK Email) alexco...@gmail.com (Non-secure / rapid-response Email) Petersen/Schlaggar Lab Medical Scientist Training Program Washington University in St. Louis School of Medicine -- This message is intended only for the exclusive use of the intended recipient(s) named herein and may contain information that is PRIVILEGED and/or CONFIDENTIAL. If you are not the intended recipient, you are hereby notified that any use, dissemination, disclosure or copying of this communication is strictly prohibited. If you have received this communication in error, please destroy all copies of this message and its attachments and notify us immediately. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. On Aug 26, 2009, at 8:41 AM, Bruce Fischl wrote: yes, it was optimized for the mp-rages that Randy B used to collect there, not for example ADNI. On Tue, 25 Aug 2009, Michael Harms wrote: I assume that that flag (-washu_mprage) is somewhat antiquated, right? That is, it was included for an older set of scans (generated at WashU generated years ago before Siemens had its own MPRAGE sequence) that happened to have darker gray matter, and doesn't need to be applied for modern MPRAGE scans, correct? -MH On Tue, 2009-08-25 at 13:33 -0400, Nick Schmansky wrote: Alex, The -washu_mprage flag affects mri_normalize and mri_segment. It adjusts the parameters of those binaries to match the assumed intensity profile in mprage scans, eg. to account for darker grey matter. I've updated the help text in recon-all. Nick As a side note, there appears to be a switch for recon-all: -washu_mprage : assume scan parameters are Wash.U. MP-RAGE protocol yet there is no documentation as to what this determines, nor whether the raw, or locally atlas-aligned data should be provided. (Avi didn't know either...) Many Thanks! -Alex Li Cohen ~)- -- Alexander Li Cohen al...@npg.wustl.edu (WORK Email) alexco...@gmail.com (Non-secure / rapid-response Email) Petersen/Schlaggar Lab Medical Scientist Training Program Washington University in St. Louis School of Medicine
Re: [Freesurfer] Input/Output to specific atlas space/dimensions?
Is there any gain/benefit then by including this -mprage flag? In what circumstance is that flag to be used? I'm still confused what the purpose of that flag is. thanks, Mike H. On Thu, 2009-08-27 at 08:54 -0400, Bruce Fischl wrote: no, it's more agnostic. Optimized for both spgr and mprage (or neither, depending on your perspective). You're probably right that mp-rage is more common these days, but I think spgrs are still fairly widespread on GE. On Thu, 27 Aug 2009, Michael Harms wrote: So, are you saying that the default recon-all stream is really optimized for SPGR, and anyone running a MPRAGE should be including the -mprage flag when they run recon-all? If so, this is news to me, and I suspect many other FS users. The default recon-all setting is set IsMPRAGE = 0, but I suspect (just a hunch, no data) that MPRAGE is the most commonly used type of input to FS. thanks for clarifying, -Mike H. On Wed, 2009-08-26 at 12:53 -0400, Bruce Fischl wrote: yes, that's true. The difference is between the SPGR and the MP-RAGE. If we don't know which it is we have to try to figure out the contrast and noise characteristics (spgr has worse contrast and less noise) On Wed, 26 Aug 2009, Michael Harms wrote: Ok, now I'm confused again, because my understanding is that the Andre van de Kouwe mprage, Siemen's default mprage, and the ADNI mprage really are not very different in terms of their contrast. Is that not correct? Assuming they are indeed all similar, are you saying that a modern ADNI-like mprage benefits from the inclusion of this -mprage flag? thanks, Mike H. On Wed, 2009-08-26 at 12:18 -0400, Nick Schmansky wrote: There's also the flag -mpragewhich can be used, intended for the mprage developed by Andre van de Kouwe, which I believe is the same as that now used by Siemens. Nick On Wed, 2009-08-26 at 09:37 -0500, Michael Harms wrote: No, our current CAP MPRAGE at WU on the 3T TimTrio is very similar to the ADNI mprage, so that old flag shouldn't be used. -MH On Wed, 2009-08-26 at 09:24 -0500, Alexander Li Cohen wrote: Ah I see, this raises a question then, of whether the optimizations are still applicable to WU acquired MP-RAGE data, as we are currently collecting 3T Trio data, and I believe Randy's data is 1.5T Vision data, however the sequence (our CAP MP-RAGE) is quite similar... can anyone up there speak to this? -Alex ~)- -- Alexander Li Cohen al...@npg.wustl.edu (WORK Email) alexco...@gmail.com (Non-secure / rapid-response Email) Petersen/Schlaggar Lab Medical Scientist Training Program Washington University in St. Louis School of Medicine -- This message is intended only for the exclusive use of the intended recipient(s) named herein and may contain information that is PRIVILEGED and/or CONFIDENTIAL. If you are not the intended recipient, you are hereby notified that any use, dissemination, disclosure or copying of this communication is strictly prohibited. If you have received this communication in error, please destroy all copies of this message and its attachments and notify us immediately. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. On Aug 26, 2009, at 8:41 AM, Bruce Fischl wrote: yes, it was optimized for the mp-rages that Randy B used to collect there, not for example ADNI. On Tue, 25 Aug 2009, Michael Harms wrote: I assume that that flag (-washu_mprage) is somewhat antiquated, right? That is, it was included for an older set of scans (generated at WashU generated years ago before Siemens had its own MPRAGE sequence) that happened to have darker gray matter, and doesn't need to be applied for modern MPRAGE scans, correct? -MH On Tue, 2009-08-25 at 13:33 -0400, Nick Schmansky wrote: Alex, The -washu_mprage flag affects mri_normalize and mri_segment. It adjusts the parameters of those binaries to match the assumed intensity profile in mprage scans, eg. to account for darker grey matter. I've updated the help text in recon-all. Nick As a side note, there appears to be a switch for recon-all: -washu_mprage : assume scan parameters are Wash.U. MP-RAGE protocol yet there is no documentation as to what this determines, nor whether the raw, or locally atlas-aligned data should be provided. (Avi didn't
Re: [Freesurfer] Input/Output to specific atlas space/dimensions?
yes, I think it will probably help a bit for mprage scans. Essentially it changes the default assumptions about noise and contrast characteristics (it assumes more of both) and will help the intensity normalization get a bit further out the thin white matter strands. Try it and see what you think On Thu, 27 Aug 2009, Michael Harms wrote: Is there any gain/benefit then by including this -mprage flag? In what circumstance is that flag to be used? I'm still confused what the purpose of that flag is. thanks, Mike H. On Thu, 2009-08-27 at 08:54 -0400, Bruce Fischl wrote: no, it's more agnostic. Optimized for both spgr and mprage (or neither, depending on your perspective). You're probably right that mp-rage is more common these days, but I think spgrs are still fairly widespread on GE. On Thu, 27 Aug 2009, Michael Harms wrote: So, are you saying that the default recon-all stream is really optimized for SPGR, and anyone running a MPRAGE should be including the -mprage flag when they run recon-all? If so, this is news to me, and I suspect many other FS users. The default recon-all setting is set IsMPRAGE = 0, but I suspect (just a hunch, no data) that MPRAGE is the most commonly used type of input to FS. thanks for clarifying, -Mike H. On Wed, 2009-08-26 at 12:53 -0400, Bruce Fischl wrote: yes, that's true. The difference is between the SPGR and the MP-RAGE. If we don't know which it is we have to try to figure out the contrast and noise characteristics (spgr has worse contrast and less noise) On Wed, 26 Aug 2009, Michael Harms wrote: Ok, now I'm confused again, because my understanding is that the Andre van de Kouwe mprage, Siemen's default mprage, and the ADNI mprage really are not very different in terms of their contrast. Is that not correct? Assuming they are indeed all similar, are you saying that a modern ADNI-like mprage benefits from the inclusion of this -mprage flag? thanks, Mike H. On Wed, 2009-08-26 at 12:18 -0400, Nick Schmansky wrote: There's also the flag -mpragewhich can be used, intended for the mprage developed by Andre van de Kouwe, which I believe is the same as that now used by Siemens. Nick On Wed, 2009-08-26 at 09:37 -0500, Michael Harms wrote: No, our current CAP MPRAGE at WU on the 3T TimTrio is very similar to the ADNI mprage, so that old flag shouldn't be used. -MH On Wed, 2009-08-26 at 09:24 -0500, Alexander Li Cohen wrote: Ah I see, this raises a question then, of whether the optimizations are still applicable to WU acquired MP-RAGE data, as we are currently collecting 3T Trio data, and I believe Randy's data is 1.5T Vision data, however the sequence (our CAP MP-RAGE) is quite similar... can anyone up there speak to this? -Alex ~)- -- Alexander Li Cohen al...@npg.wustl.edu (WORK Email) alexco...@gmail.com (Non-secure / rapid-response Email) Petersen/Schlaggar Lab Medical Scientist Training Program Washington University in St. Louis School of Medicine -- This message is intended only for the exclusive use of the intended recipient(s) named herein and may contain information that is PRIVILEGED and/or CONFIDENTIAL. If you are not the intended recipient, you are hereby notified that any use, dissemination, disclosure or copying of this communication is strictly prohibited. If you have received this communication in error, please destroy all copies of this message and its attachments and notify us immediately. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. On Aug 26, 2009, at 8:41 AM, Bruce Fischl wrote: yes, it was optimized for the mp-rages that Randy B used to collect there, not for example ADNI. On Tue, 25 Aug 2009, Michael Harms wrote: I assume that that flag (-washu_mprage) is somewhat antiquated, right? That is, it was included for an older set of scans (generated at WashU generated years ago before Siemens had its own MPRAGE sequence) that happened to have darker gray matter, and doesn't need to be applied for modern MPRAGE scans, correct? -MH On Tue, 2009-08-25 at 13:33 -0400, Nick Schmansky wrote: Alex, The -washu_mprage flag affects mri_normalize and mri_segment. It adjusts the parameters of those binaries to match the assumed intensity profile in mprage scans, eg. to account for darker grey matter. I've updated the help text in recon-all. Nick As a side note, there appears to be a switch for
Re: [Freesurfer] Input/Output to specific atlas space/dimensions?
Ah I see, this raises a question then, of whether the optimizations are still applicable to WU acquired MP-RAGE data, as we are currently collecting 3T Trio data, and I believe Randy's data is 1.5T Vision data, however the sequence (our CAP MP-RAGE) is quite similar... can anyone up there speak to this? -Alex ~)- -- Alexander Li Cohen al...@npg.wustl.edu (WORK Email) alexco...@gmail.com (Non-secure / rapid-response Email) Petersen/Schlaggar Lab Medical Scientist Training Program Washington University in St. Louis School of Medicine -- This message is intended only for the exclusive use of the intended recipient(s) named herein and may contain information that is PRIVILEGED and/or CONFIDENTIAL. If you are not the intended recipient, you are hereby notified that any use, dissemination, disclosure or copying of this communication is strictly prohibited. If you have received this communication in error, please destroy all copies of this message and its attachments and notify us immediately. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. On Aug 26, 2009, at 8:41 AM, Bruce Fischl wrote: yes, it was optimized for the mp-rages that Randy B used to collect there, not for example ADNI. On Tue, 25 Aug 2009, Michael Harms wrote: I assume that that flag (-washu_mprage) is somewhat antiquated, right? That is, it was included for an older set of scans (generated at WashU generated years ago before Siemens had its own MPRAGE sequence) that happened to have darker gray matter, and doesn't need to be applied for modern MPRAGE scans, correct? -MH On Tue, 2009-08-25 at 13:33 -0400, Nick Schmansky wrote: Alex, The -washu_mprage flag affects mri_normalize and mri_segment. It adjusts the parameters of those binaries to match the assumed intensity profile in mprage scans, eg. to account for darker grey matter. I've updated the help text in recon-all. Nick As a side note, there appears to be a switch for recon-all: -washu_mprage : assume scan parameters are Wash.U. MP-RAGE protocol yet there is no documentation as to what this determines, nor whether the raw, or locally atlas-aligned data should be provided. (Avi didn't know either...) Many Thanks! -Alex Li Cohen ~)- -- Alexander Li Cohen al...@npg.wustl.edu (WORK Email) alexco...@gmail.com (Non-secure / rapid-response Email) Petersen/Schlaggar Lab Medical Scientist Training Program Washington University in St. Louis School of Medicine -- This message is intended only for the exclusive use of the intended recipient(s) named herein and may contain information that is PRIVILEGED and/or CONFIDENTIAL. If you are not the intended recipient, you are hereby notified that any use, dissemination, disclosure or copying of this communication is strictly prohibited. If you have received this communication in error, please destroy all copies of this message and its attachments and notify us immediately. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return 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
Re: [Freesurfer] Input/Output to specific atlas space/dimensions?
if you send us a volume we'll take a look. Basically Randy's mp-rage had significantly darker gray matter than we were used to in SPGR and MPRAGE images. If wm was around 110, I think typical GM is around 75, but Randy's were around 60. cheers, Bruce On Wed, 26 Aug 2009, Alexander Li Cohen wrote: Ah I see, this raises a question then, of whether the optimizations are still applicable to WU acquired MP-RAGE data, as we are currently collecting 3T Trio data, and I believe Randy's data is 1.5T Vision data, however the sequence (our CAP MP-RAGE) is quite similar... can anyone up there speak to this? -Alex ~)- -- Alexander Li Cohen al...@npg.wustl.edu (WORK Email) alexco...@gmail.com (Non-secure / rapid-response Email) Petersen/Schlaggar Lab Medical Scientist Training Program Washington University in St. Louis School of Medicine -- This message is intended only for the exclusive use of the intended recipient(s) named herein and may contain information that is PRIVILEGED and/or CONFIDENTIAL. If you are not the intended recipient, you are hereby notified that any use, dissemination, disclosure or copying of this communication is strictly prohibited. If you have received this communication in error, please destroy all copies of this message and its attachments and notify us immediately. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. On Aug 26, 2009, at 8:41 AM, Bruce Fischl wrote: yes, it was optimized for the mp-rages that Randy B used to collect there, not for example ADNI. On Tue, 25 Aug 2009, Michael Harms wrote: I assume that that flag (-washu_mprage) is somewhat antiquated, right? That is, it was included for an older set of scans (generated at WashU generated years ago before Siemens had its own MPRAGE sequence) that happened to have darker gray matter, and doesn't need to be applied for modern MPRAGE scans, correct? -MH On Tue, 2009-08-25 at 13:33 -0400, Nick Schmansky wrote: Alex, The -washu_mprage flag affects mri_normalize and mri_segment. It adjusts the parameters of those binaries to match the assumed intensity profile in mprage scans, eg. to account for darker grey matter. I've updated the help text in recon-all. Nick As a side note, there appears to be a switch for recon-all: -washu_mprage : assume scan parameters are Wash.U. MP-RAGE protocol yet there is no documentation as to what this determines, nor whether the raw, or locally atlas-aligned data should be provided. (Avi didn't know either...) Many Thanks! -Alex Li Cohen ~)- -- Alexander Li Cohen al...@npg.wustl.edu (WORK Email) alexco...@gmail.com (Non-secure / rapid-response Email) Petersen/Schlaggar Lab Medical Scientist Training Program Washington University in St. Louis School of Medicine -- This message is intended only for the exclusive use of the intended recipient(s) named herein and may contain information that is PRIVILEGED and/or CONFIDENTIAL. If you are not the intended recipient, you are hereby notified that any use, dissemination, disclosure or copying of this communication is strictly prohibited. If you have received this communication in error, please destroy all copies of this message and its attachments and notify us immediately. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return 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
Re: [Freesurfer] Input/Output to specific atlas space/dimensions?
yes, it was optimized for the mp-rages that Randy B used to collect there, not for example ADNI. On Tue, 25 Aug 2009, Michael Harms wrote: I assume that that flag (-washu_mprage) is somewhat antiquated, right? That is, it was included for an older set of scans (generated at WashU generated years ago before Siemens had its own MPRAGE sequence) that happened to have darker gray matter, and doesn't need to be applied for modern MPRAGE scans, correct? -MH On Tue, 2009-08-25 at 13:33 -0400, Nick Schmansky wrote: Alex, The -washu_mprage flag affects mri_normalize and mri_segment. It adjusts the parameters of those binaries to match the assumed intensity profile in mprage scans, eg. to account for darker grey matter. I've updated the help text in recon-all. Nick As a side note, there appears to be a switch for recon-all: -washu_mprage : assume scan parameters are Wash.U. MP-RAGE protocol yet there is no documentation as to what this determines, nor whether the raw, or locally atlas-aligned data should be provided. (Avi didn't know either...) Many Thanks! -Alex Li Cohen ~)- -- Alexander Li Cohen al...@npg.wustl.edu (WORK Email) alexco...@gmail.com (Non-secure / rapid-response Email) Petersen/Schlaggar Lab Medical Scientist Training Program Washington University in St. Louis School of Medicine -- This message is intended only for the exclusive use of the intended recipient(s) named herein and may contain information that is PRIVILEGED and/or CONFIDENTIAL. If you are not the intended recipient, you are hereby notified that any use, dissemination, disclosure or copying of this communication is strictly prohibited. If you have received this communication in error, please destroy all copies of this message and its attachments and notify us immediately. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return 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
Re: [Freesurfer] Input/Output to specific atlas space/dimensions?
No, our current CAP MPRAGE at WU on the 3T TimTrio is very similar to the ADNI mprage, so that old flag shouldn't be used. -MH On Wed, 2009-08-26 at 09:24 -0500, Alexander Li Cohen wrote: Ah I see, this raises a question then, of whether the optimizations are still applicable to WU acquired MP-RAGE data, as we are currently collecting 3T Trio data, and I believe Randy's data is 1.5T Vision data, however the sequence (our CAP MP-RAGE) is quite similar... can anyone up there speak to this? -Alex ~)- -- Alexander Li Cohen al...@npg.wustl.edu (WORK Email) alexco...@gmail.com (Non-secure / rapid-response Email) Petersen/Schlaggar Lab Medical Scientist Training Program Washington University in St. Louis School of Medicine -- This message is intended only for the exclusive use of the intended recipient(s) named herein and may contain information that is PRIVILEGED and/or CONFIDENTIAL. If you are not the intended recipient, you are hereby notified that any use, dissemination, disclosure or copying of this communication is strictly prohibited. If you have received this communication in error, please destroy all copies of this message and its attachments and notify us immediately. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. On Aug 26, 2009, at 8:41 AM, Bruce Fischl wrote: yes, it was optimized for the mp-rages that Randy B used to collect there, not for example ADNI. On Tue, 25 Aug 2009, Michael Harms wrote: I assume that that flag (-washu_mprage) is somewhat antiquated, right? That is, it was included for an older set of scans (generated at WashU generated years ago before Siemens had its own MPRAGE sequence) that happened to have darker gray matter, and doesn't need to be applied for modern MPRAGE scans, correct? -MH On Tue, 2009-08-25 at 13:33 -0400, Nick Schmansky wrote: Alex, The -washu_mprage flag affects mri_normalize and mri_segment. It adjusts the parameters of those binaries to match the assumed intensity profile in mprage scans, eg. to account for darker grey matter. I've updated the help text in recon-all. Nick As a side note, there appears to be a switch for recon-all: -washu_mprage : assume scan parameters are Wash.U. MP-RAGE protocol yet there is no documentation as to what this determines, nor whether the raw, or locally atlas-aligned data should be provided. (Avi didn't know either...) Many Thanks! -Alex Li Cohen ~)- -- Alexander Li Cohen al...@npg.wustl.edu (WORK Email) alexco...@gmail.com (Non-secure / rapid-response Email) Petersen/Schlaggar Lab Medical Scientist Training Program Washington University in St. Louis School of Medicine -- This message is intended only for the exclusive use of the intended recipient(s) named herein and may contain information that is PRIVILEGED and/or CONFIDENTIAL. If you are not the intended recipient, you are hereby notified that any use, dissemination, disclosure or copying of this communication is strictly prohibited. If you have received this communication in error, please destroy all copies of this message and its attachments and notify us immediately. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return 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
Re: [Freesurfer] Input/Output to specific atlas space/dimensions?
There's also the flag -mpragewhich can be used, intended for the mprage developed by Andre van de Kouwe, which I believe is the same as that now used by Siemens. Nick On Wed, 2009-08-26 at 09:37 -0500, Michael Harms wrote: No, our current CAP MPRAGE at WU on the 3T TimTrio is very similar to the ADNI mprage, so that old flag shouldn't be used. -MH On Wed, 2009-08-26 at 09:24 -0500, Alexander Li Cohen wrote: Ah I see, this raises a question then, of whether the optimizations are still applicable to WU acquired MP-RAGE data, as we are currently collecting 3T Trio data, and I believe Randy's data is 1.5T Vision data, however the sequence (our CAP MP-RAGE) is quite similar... can anyone up there speak to this? -Alex ~)- -- Alexander Li Cohen al...@npg.wustl.edu (WORK Email) alexco...@gmail.com (Non-secure / rapid-response Email) Petersen/Schlaggar Lab Medical Scientist Training Program Washington University in St. Louis School of Medicine -- This message is intended only for the exclusive use of the intended recipient(s) named herein and may contain information that is PRIVILEGED and/or CONFIDENTIAL. If you are not the intended recipient, you are hereby notified that any use, dissemination, disclosure or copying of this communication is strictly prohibited. If you have received this communication in error, please destroy all copies of this message and its attachments and notify us immediately. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. On Aug 26, 2009, at 8:41 AM, Bruce Fischl wrote: yes, it was optimized for the mp-rages that Randy B used to collect there, not for example ADNI. On Tue, 25 Aug 2009, Michael Harms wrote: I assume that that flag (-washu_mprage) is somewhat antiquated, right? That is, it was included for an older set of scans (generated at WashU generated years ago before Siemens had its own MPRAGE sequence) that happened to have darker gray matter, and doesn't need to be applied for modern MPRAGE scans, correct? -MH On Tue, 2009-08-25 at 13:33 -0400, Nick Schmansky wrote: Alex, The -washu_mprage flag affects mri_normalize and mri_segment. It adjusts the parameters of those binaries to match the assumed intensity profile in mprage scans, eg. to account for darker grey matter. I've updated the help text in recon-all. Nick As a side note, there appears to be a switch for recon-all: -washu_mprage : assume scan parameters are Wash.U. MP-RAGE protocol yet there is no documentation as to what this determines, nor whether the raw, or locally atlas-aligned data should be provided. (Avi didn't know either...) Many Thanks! -Alex Li Cohen ~)- -- Alexander Li Cohen al...@npg.wustl.edu (WORK Email) alexco...@gmail.com (Non-secure / rapid-response Email) Petersen/Schlaggar Lab Medical Scientist Training Program Washington University in St. Louis School of Medicine -- This message is intended only for the exclusive use of the intended recipient(s) named herein and may contain information that is PRIVILEGED and/or CONFIDENTIAL. If you are not the intended recipient, you are hereby notified that any use, dissemination, disclosure or copying of this communication is strictly prohibited. If you have received this communication in error, please destroy all copies of this message and its attachments and notify us immediately. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Input/Output to specific atlas space/dimensions?
Ok, now I'm confused again, because my understanding is that the Andre van de Kouwe mprage, Siemen's default mprage, and the ADNI mprage really are not very different in terms of their contrast. Is that not correct? Assuming they are indeed all similar, are you saying that a modern ADNI-like mprage benefits from the inclusion of this -mprage flag? thanks, Mike H. On Wed, 2009-08-26 at 12:18 -0400, Nick Schmansky wrote: There's also the flag -mpragewhich can be used, intended for the mprage developed by Andre van de Kouwe, which I believe is the same as that now used by Siemens. Nick On Wed, 2009-08-26 at 09:37 -0500, Michael Harms wrote: No, our current CAP MPRAGE at WU on the 3T TimTrio is very similar to the ADNI mprage, so that old flag shouldn't be used. -MH On Wed, 2009-08-26 at 09:24 -0500, Alexander Li Cohen wrote: Ah I see, this raises a question then, of whether the optimizations are still applicable to WU acquired MP-RAGE data, as we are currently collecting 3T Trio data, and I believe Randy's data is 1.5T Vision data, however the sequence (our CAP MP-RAGE) is quite similar... can anyone up there speak to this? -Alex ~)- -- Alexander Li Cohen al...@npg.wustl.edu (WORK Email) alexco...@gmail.com (Non-secure / rapid-response Email) Petersen/Schlaggar Lab Medical Scientist Training Program Washington University in St. Louis School of Medicine -- This message is intended only for the exclusive use of the intended recipient(s) named herein and may contain information that is PRIVILEGED and/or CONFIDENTIAL. If you are not the intended recipient, you are hereby notified that any use, dissemination, disclosure or copying of this communication is strictly prohibited. If you have received this communication in error, please destroy all copies of this message and its attachments and notify us immediately. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. On Aug 26, 2009, at 8:41 AM, Bruce Fischl wrote: yes, it was optimized for the mp-rages that Randy B used to collect there, not for example ADNI. On Tue, 25 Aug 2009, Michael Harms wrote: I assume that that flag (-washu_mprage) is somewhat antiquated, right? That is, it was included for an older set of scans (generated at WashU generated years ago before Siemens had its own MPRAGE sequence) that happened to have darker gray matter, and doesn't need to be applied for modern MPRAGE scans, correct? -MH On Tue, 2009-08-25 at 13:33 -0400, Nick Schmansky wrote: Alex, The -washu_mprage flag affects mri_normalize and mri_segment. It adjusts the parameters of those binaries to match the assumed intensity profile in mprage scans, eg. to account for darker grey matter. I've updated the help text in recon-all. Nick As a side note, there appears to be a switch for recon-all: -washu_mprage : assume scan parameters are Wash.U. MP-RAGE protocol yet there is no documentation as to what this determines, nor whether the raw, or locally atlas-aligned data should be provided. (Avi didn't know either...) Many Thanks! -Alex Li Cohen ~)- -- Alexander Li Cohen al...@npg.wustl.edu (WORK Email) alexco...@gmail.com (Non-secure / rapid-response Email) Petersen/Schlaggar Lab Medical Scientist Training Program Washington University in St. Louis School of Medicine -- This message is intended only for the exclusive use of the intended recipient(s) named herein and may contain information that is PRIVILEGED and/or CONFIDENTIAL. If you are not the intended recipient, you are hereby notified that any use, dissemination, disclosure or copying of this communication is strictly prohibited. If you have received this communication in error, please destroy all copies of this message and its attachments and notify us immediately. The materials in this message are private and may contain Protected Healthcare Information or other information of a
Re: [Freesurfer] Input/Output to specific atlas space/dimensions?
Alex, We ran into the same problem a while ago for some of our studies. We did the following: 1. Convert an Avi preprocessed T1 MPRAGE into a FreeSurfer-native format and provided it the appropriate orientation and image center. 2. Next, we simply ran recon-all on this file (single MPRAGE). Then we take the the final segmentation output (at least the aseg file) and convert it back to a 4dfp file, which is perfectly aligned with the original T1 image. It is my understanding that FreeSurfer completes the segmentation on the orignal image in it's native space, hence the alignment. However, the FreeSurfer surfaces we get are misaligned with the T1 and I am assuming this is what you need for your work. Donna Dierker and I have a script that may make your life a lot easier by converting surfaces from FreeSurfer into Caret including creating a mid-thickness surface. However, I would need to know a bit more about what you are trying to accomplish and I can help you use the tools we have. Best, Alan On Aug 25, 2009, at 11:23 AM, Alexander Li Cohen wrote: Hi all, Just starting using Freesurfer, and while I did search the mailing list archive, I didn't see a ready answer for this question: I would like to use Freesurfer to generate surfaces for my subjects (currently using Caret's SureFit routine), however I need to maintain a specific atlas space for my subjects (in this case, the WU 711-2B, T88-derived space). I can imagine two possibilities, but not how to do them, nor which is more accurate/appropriate: 1. Input the raw T1 for my subject in scanner space (1x1x1 isovolumetric) and then convert the Freesurfer surface and volume outputs to my atlas space using a previously defined linear affine transform (using local scripts written by Avi). This requires Freesurfer to back-convert all results to the original supplied space, then for me to additionally learn how to transform the surfaces. 2. Input the T1 for my subject already in my atlas space, and have Freesurfer output all results in the original supplied space. This, however, will be providing Freesurfer with data that has undergone an additional transform, but is obviously simpler in either case, the methodological question becomes simply: how can I tell recon-all to output all files in the original space provided. Given that it must perform the necessary transforms to get into the internal MNI305 space (I'm assuming), I'm simply wanting to undo all of the applied transforms. For obvious reasons, I want to use the same affine transform and transform routine consistently across this and my other datatypes. As a side note, there appears to be a switch for recon-all: -washu_mprage : assume scan parameters are Wash.U. MP-RAGE protocol yet there is no documentation as to what this determines, nor whether the raw, or locally atlas-aligned data should be provided. (Avi didn't know either...) Many Thanks! -Alex Li Cohen ~)- -- Alexander Li Cohen al...@npg.wustl.edu (WORK Email) alexco...@gmail.com (Non-secure / rapid-response Email) Petersen/Schlaggar Lab Medical Scientist Training Program Washington University in St. Louis School of Medicine -- This message is intended only for the exclusive use of the intended recipient(s) named herein and may contain information that is PRIVILEGED and/or CONFIDENTIAL. If you are not the intended recipient, you are hereby notified that any use, dissemination, disclosure or copying of this communication is strictly prohibited. If you have received this communication in error, please destroy all copies of this message and its attachments and notify us immediately. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Alan Anticevic Department of Psychology - CCP Lab Washington University in St. Louis One Brookings Dr., Campus Box 1125 St. Louis, MO 63110 Phone: 314-935-8547 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Input/Output to specific atlas space/dimensions?
Yes, I am currently giving freesurfer an atlas (711-2B / TRIO_Y_NDC to be specific) transformed 111 MP-RAGE file. The concern is that if I use mri_convert, I want to specifically return to the same 111 volume size and space and I provided as accurately as possible (hopefully using the inverse of the total transform applied to the image during processing). I know Matt Glasser has worked out a way to convert (and apparently re-register?) surfaces to caret, and I will talk with him later this week to walk through this procedure, but I was hoping that freesurfer could directly output the surfaces in the original space. -Alex ~)- -- Alexander Li Cohen al...@npg.wustl.edu (WORK Email) alexco...@gmail.com (Non-secure / rapid-response Email) Petersen/Schlaggar Lab Medical Scientist Training Program Washington University in St. Louis School of Medicine -- This message is intended only for the exclusive use of the intended recipient(s) named herein and may contain information that is PRIVILEGED and/or CONFIDENTIAL. If you are not the intended recipient, you are hereby notified that any use, dissemination, disclosure or copying of this communication is strictly prohibited. If you have received this communication in error, please destroy all copies of this message and its attachments and notify us immediately. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. On Aug 25, 2009, at 11:57 AM, Donna Dierker wrote: Alan: Alex is detecting areal boundaries with functional connectivity on lots of subjects: Cohen, A.L., Fair, D.A., Dosenbach, N.U.F., Miezin, F.M., Dierker, D., Van Essen, D.C., Schlaggar, B.L., and Petersen, S.E. (2008) Defining functional areas in individual human brains using resting functional connectivity MRI. http://dx.doi.org/10.1016/j.neuroimage.2008.01.066 Alex: Freesurfer can write surfaces (and possibly volumes) out in multiple ways. See output of mri_convert and mris_convert for helpful details. I have also found this web site very helpful: http://www.wideman-one.com/gw/brain/fs/coords/fscoords.htm Just double-checking: So you are giving Freesurfer a T1 that has already been put through Avi's imgreg (i.e., in 711-2* space)? Donna On 08/25/2009 11:40 AM, Alan Anticevic wrote: Alex, We ran into the same problem a while ago for some of our studies. We did the following: 1. Convert an Avi preprocessed T1 MPRAGE into a FreeSurfer-native format and provided it the appropriate orientation and image center. 2. Next, we simply ran recon-all on this file (single MPRAGE). Then we take the the final segmentation output (at least the aseg file) and convert it back to a 4dfp file, which is perfectly aligned with the original T1 image. It is my understanding that FreeSurfer completes the segmentation on the orignal image in it's native space, hence the alignment. However, the FreeSurfer surfaces we get are misaligned with the T1 and I am assuming this is what you need for your work. Donna Dierker and I have a script that may make your life a lot easier by converting surfaces from FreeSurfer into Caret including creating a mid-thickness surface. However, I would need to know a bit more about what you are trying to accomplish and I can help you use the tools we have. Best, Alan On Aug 25, 2009, at 11:23 AM, Alexander Li Cohen wrote: Hi all, Just starting using Freesurfer, and while I did search the mailing list archive, I didn't see a ready answer for this question: I would like to use Freesurfer to generate surfaces for my subjects (currently using Caret's SureFit routine), however I need to maintain a specific atlas space for my subjects (in this case, the WU 711-2B, T88-derived space). I can imagine two possibilities, but not how to do them, nor which is more accurate/appropriate: 1. Input the raw T1 for my subject in scanner space (1x1x1 isovolumetric) and then convert the Freesurfer surface and volume outputs to my atlas space using a previously defined linear affine transform (using local scripts written by Avi). This requires Freesurfer to back-convert all results to the original supplied space, then for me to additionally learn how to transform the surfaces. 2. Input the T1 for my subject already in my atlas space, and have Freesurfer output all results in the original supplied space. This, however,
Re: [Freesurfer] Input/Output to specific atlas space/dimensions?
Alex, The -washu_mprage flag affects mri_normalize and mri_segment. It adjusts the parameters of those binaries to match the assumed intensity profile in mprage scans, eg. to account for darker grey matter. I've updated the help text in recon-all. Nick As a side note, there appears to be a switch for recon-all: -washu_mprage : assume scan parameters are Wash.U. MP-RAGE protocol yet there is no documentation as to what this determines, nor whether the raw, or locally atlas-aligned data should be provided. (Avi didn't know either...) Many Thanks! -Alex Li Cohen ~)- -- Alexander Li Cohen al...@npg.wustl.edu (WORK Email) alexco...@gmail.com (Non-secure / rapid-response Email) Petersen/Schlaggar Lab Medical Scientist Training Program Washington University in St. Louis School of Medicine -- This message is intended only for the exclusive use of the intended recipient(s) named herein and may contain information that is PRIVILEGED and/or CONFIDENTIAL. If you are not the intended recipient, you are hereby notified that any use, dissemination, disclosure or copying of this communication is strictly prohibited. If you have received this communication in error, please destroy all copies of this message and its attachments and notify us immediately. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return 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
Re: [Freesurfer] Input/Output to specific atlas space/dimensions?
Alex, My code converts the FreeSurfer surfaces into caret format and applies the appropriate transformations when Freesurfer is given data that is already in Wash U standard space. It is based on things that Donna originally figured out. Shortly, I will extend this to the volume parcellations output by FreeSurfer (Bruce told me how to do it; I just need to implement it in my script). Peace, Matt. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Alexander Li Cohen Sent: Tuesday, August 25, 2009 12:15 PM To: Donna Dierker Cc: Alan Anticevic; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Input/Output to specific atlas space/dimensions? Yes, I am currently giving freesurfer an atlas (711-2B / TRIO_Y_NDC to be specific) transformed 111 MP-RAGE file. The concern is that if I use mri_convert, I want to specifically return to the same 111 volume size and space and I provided as accurately as possible (hopefully using the inverse of the total transform applied to the image during processing). I know Matt Glasser has worked out a way to convert (and apparently re-register?) surfaces to caret, and I will talk with him later this week to walk through this procedure, but I was hoping that freesurfer could directly output the surfaces in the original space. -Alex ~)- -- Alexander Li Cohen al...@npg.wustl.edu (WORK Email) alexco...@gmail.com (Non-secure / rapid-response Email) Petersen/Schlaggar Lab Medical Scientist Training Program Washington University in St. Louis School of Medicine -- This message is intended only for the exclusive use of the intended recipient(s) named herein and may contain information that is PRIVILEGED and/or CONFIDENTIAL. If you are not the intended recipient, you are hereby notified that any use, dissemination, disclosure or copying of this communication is strictly prohibited. If you have received this communication in error, please destroy all copies of this message and its attachments and notify us immediately. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. On Aug 25, 2009, at 11:57 AM, Donna Dierker wrote: Alan: Alex is detecting areal boundaries with functional connectivity on lots of subjects: Cohen, A.L., Fair, D.A., Dosenbach, N.U.F., Miezin, F.M., Dierker, D., Van Essen, D.C., Schlaggar, B.L., and Petersen, S.E. (2008) Defining functional areas in individual human brains using resting functional connectivity MRI. http://dx.doi.org/10.1016/j.neuroimage.2008.01.066 Alex: Freesurfer can write surfaces (and possibly volumes) out in multiple ways. See output of mri_convert and mris_convert for helpful details. I have also found this web site very helpful: http://www.wideman-one.com/gw/brain/fs/coords/fscoords.htm Just double-checking: So you are giving Freesurfer a T1 that has already been put through Avi's imgreg (i.e., in 711-2* space)? Donna On 08/25/2009 11:40 AM, Alan Anticevic wrote: Alex, We ran into the same problem a while ago for some of our studies. We did the following: 1. Convert an Avi preprocessed T1 MPRAGE into a FreeSurfer-native format and provided it the appropriate orientation and image center. 2. Next, we simply ran recon-all on this file (single MPRAGE). Then we take the the final segmentation output (at least the aseg file) and convert it back to a 4dfp file, which is perfectly aligned with the original T1 image. It is my understanding that FreeSurfer completes the segmentation on the orignal image in it's native space, hence the alignment. However, the FreeSurfer surfaces we get are misaligned with the T1 and I am assuming this is what you need for your work. Donna Dierker and I have a script that may make your life a lot easier by converting surfaces from FreeSurfer into Caret including creating a mid-thickness surface. However, I would need to know a bit more about what you are trying to accomplish and I can help you use the tools we have. Best, Alan On Aug 25, 2009, at 11:23 AM, Alexander Li Cohen wrote: Hi all, Just starting using Freesurfer, and while I did search the mailing list archive, I didn't see a ready answer for this question: I would like to use Freesurfer to generate surfaces for my subjects (currently using Caret's SureFit routine), however I need to maintain
Re: [Freesurfer] Input/Output to specific atlas space/dimensions?
I assume that that flag (-washu_mprage) is somewhat antiquated, right? That is, it was included for an older set of scans (generated at WashU generated years ago before Siemens had its own MPRAGE sequence) that happened to have darker gray matter, and doesn't need to be applied for modern MPRAGE scans, correct? -MH On Tue, 2009-08-25 at 13:33 -0400, Nick Schmansky wrote: Alex, The -washu_mprage flag affects mri_normalize and mri_segment. It adjusts the parameters of those binaries to match the assumed intensity profile in mprage scans, eg. to account for darker grey matter. I've updated the help text in recon-all. Nick As a side note, there appears to be a switch for recon-all: -washu_mprage : assume scan parameters are Wash.U. MP-RAGE protocol yet there is no documentation as to what this determines, nor whether the raw, or locally atlas-aligned data should be provided. (Avi didn't know either...) Many Thanks! -Alex Li Cohen ~)- -- Alexander Li Cohen al...@npg.wustl.edu (WORK Email) alexco...@gmail.com (Non-secure / rapid-response Email) Petersen/Schlaggar Lab Medical Scientist Training Program Washington University in St. Louis School of Medicine -- This message is intended only for the exclusive use of the intended recipient(s) named herein and may contain information that is PRIVILEGED and/or CONFIDENTIAL. If you are not the intended recipient, you are hereby notified that any use, dissemination, disclosure or copying of this communication is strictly prohibited. If you have received this communication in error, please destroy all copies of this message and its attachments and notify us immediately. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return 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
