Hello,
I am interested in doing some T1-mapping analyses on some ex vivo brains. We have collected flash sequences under multiple flip angles (5, 10, 15, 20, 25 and 30). How would you suggest that I proceed? Should I use the mri_ms_fitparms to come up with the T1 maps for each subject and then maybe calculate the signal intensity 1mm into the cortex, or is there another way that you would recommend?
Thanks in advance for any advice!
Best,
Panos
Panagiotis Fotiadis Senior Imaging Research Technologist J. P. Kistler Stroke Research Center, Department of Neurology Massachusetts General Hospital, Boston, MA T: (617) 643-3869
mri_fit_parms should do it. BTW, if you are using a siemens scanner, you should just collect an MP2RAGE. That automatically outputs a quantitative T1 map using the two inversion technique. The results are much more accurate than using multiple flip angles
On 8/8/18 5:00 PM, Fotiadis, Panagiotis wrote:
Hello,
I am interested in doing some T1-mapping analyses on some ex vivo brains. We have collected flash sequences under multiple flip angles (5, 10, 15, 20, 25 and 30). How would you suggest that I proceed? Should I use the mri_ms_fitparms to come up with the T1 maps for each subject and then maybe calculate the signal intensity 1mm into the cortex, or is there another way that you would recommend?
Thanks in advance for any advice!
Best,
Panos
Panagiotis Fotiadis Senior Imaging Research Technologist J. P. Kistler Stroke Research Center, Department of Neurology Massachusetts General Hospital, Boston, MA T: (617) 643-3869
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
Thanks for your response! I had a couple follow-up questions:
1) If I used mri_fit_parms to calculate the T1 maps, then created a surface mid-cortex (with mris_expand) with that T1 map as a reference, and uploaded that file into MATLAB through MRIread, would the resulting values represent absolute "pure" T1 values?
2) Even though we are scanning on a Siemens scanner we have been acquiring a tfl_mgh_multiecho_4E_P2_1MM_ISO sequence. Do you think I could do T1 mapping based on that sequence (with the same method as the one described in the previous question)?
Thanks again, and I apologize for the potential triviality of the questions!
Best,
Panos
Panagiotis Fotiadis Senior Imaging Research Technologist J. P. Kistler Stroke Research Center, Department of Neurology Massachusetts General Hospital, Boston, MA T: (617) 643-3869 ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve dgreve@mgh.harvard.edu Sent: Friday, August 10, 2018 1:59:47 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] T1 mapping
mri_fit_parms should do it. BTW, if you are using a siemens scanner, you should just collect an MP2RAGE. That automatically outputs a quantitative T1 map using the two inversion technique. The results are much more accurate than using multiple flip angles
On 8/8/18 5:00 PM, Fotiadis, Panagiotis wrote:
Hello,
I am interested in doing some T1-mapping analyses on some ex vivo brains. We have collected flash sequences under multiple flip angles (5, 10, 15, 20, 25 and 30). How would you suggest that I proceed? Should I use the mri_ms_fitparms to come up with the T1 maps for each subject and then maybe calculate the signal intensity 1mm into the cortex, or is there another way that you would recommend?
Thanks in advance for any advice!
Best,
Panos
Panagiotis Fotiadis Senior Imaging Research Technologist J. P. Kistler Stroke Research Center, Department of Neurology Massachusetts General Hospital, Boston, MA T: (617) 643-3869
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
On 8/10/18 3:26 PM, Fotiadis, Panagiotis wrote:
Hi Doug,
Thanks for your response! I had a couple follow-up questions:
- If I used mri_fit_parms to calculate the T1 maps, then created a
surface mid-cortex (with mris_expand) with that T1 map as a reference, and uploaded that file into MATLAB through MRIread, would the resulting values represent absolute "pure" T1 values?
If by "pure" you mean quantitative (ie, values in milisec), then yes.
- Even though we are scanning on a Siemens scanner we have been
acquiring a tfl_mgh_multiecho_4E_P2_1MM_ISO sequence. Do you think I could do T1 mapping based on that sequence (with the same method as the one described in the previous question)?
Multiecho does not help for measuring T1. But if you have multiple flip angles or multiple inversions with you rmultiecho, then you can use the multiecho data to compute T1
Thanks again, and I apologize for the potential triviality of the questions!
Best,
Panos
Panagiotis Fotiadis Senior Imaging Research Technologist J. P. Kistler Stroke Research Center, Department of Neurology Massachusetts General Hospital, Boston, MA T: (617) 643-3869
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve dgreve@mgh.harvard.edu *Sent:* Friday, August 10, 2018 1:59:47 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] T1 mapping mri_fit_parms should do it. BTW, if you are using a siemens scanner, you should just collect an MP2RAGE. That automatically outputs a quantitative T1 map using the two inversion technique. The results are much more accurate than using multiple flip angles
On 8/8/18 5:00 PM, Fotiadis, Panagiotis wrote:
Hello,
I am interested in doing some T1-mapping analyses on some ex vivo brains. We have collected flash sequences under multiple flip angles (5, 10, 15, 20, 25 and 30). How would you suggest that I proceed? Should I use the mri_ms_fitparms to come up with the T1 maps for each subject and then maybe calculate the signal intensity 1mm into the cortex, or is there another way that you would recommend?
Thanks in advance for any advice!
Best,
Panos
Panagiotis Fotiadis Senior Imaging Research Technologist J. P. Kistler Stroke Research Center, Department of Neurology Massachusetts General Hospital, Boston, MA T: (617) 643-3869
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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
-
Douglas Greve -
Fotiadis, Panagiotis