I really like the idea of sites having the ability to utilize advanced imaging methods at the 30 day time point, with ideally a few sites harmonizing methods on a sequence or two so the data can be analyzed together. DTI seems like an obvious one to try for, and I know Fahmeed and Basav have other methods they are interested in.
I agree, this will get unwieldy soon. Let me ask the developers.
Lauren and Cenk: If we are agreeing to a 30day MRI anyway, why not get our standard morphometry sequences, and THEN move on to the fancy schmancy stuff like DTI? Also, from my primitive understanding of DTI, i think the data reducing/bioinformatics part is pretty challenging, no?
From Pat: Lauren and Cenk: If we are agreeing to a 30day MRI anyway, why not get our standard morphometry sequences, and THEN move on to the fancy schmancy stuff like DTI? Also, from my primitive understanding of DTI, i think the data reducing/bioinformatics part is pretty challenging, no?
Reply: I think it's all about scan time. Adding more sequences increases the scan time, which increases animal mortality and cost of the scan. Can someone elaborate on what useful data we did get out of the 30 day morphometry scans? Has anyone done a detailed analysis examining which MRI features at day 30 correlate best with the day 2 lesion volume? Is this in Cenk's MRI paper? If not I will propose this study.
Yes, MRI outcomes paper looked at this. All 3 attributes of atrophy (tissue loss, ventriculomegaly and reverse midline shift) correlated closely with the lesion volume on day 2. It is in the works.
We will discuss day 30 MRI in detail in the MRI group meeting soon. I don't think the readouts we had were helpful for anything so adding the usual 30-45 min scan time would be justified. The time would be better used for more interesting readouts. If they are feasible and can be implemented, of course.
Lauren but not Cenk is attending the lesion analysis paper that Ali is running and already knows this: We have learned that Ryan made a simplifying assumption that is not impactful on Ali's paper, but could make a difference down the road. He segmented the scans first, and then allocated each voxel to CSF, tissue or lesio based on segmentation intensity after labelling CSF. However, when it came to regional topography (e.g., cortex vs caudate vs thalamus vs hippo) he simply mapped in an Atlas without warping the image to fit. In other words, any swelling, atrophy or midline shift that moved any structures outside of the Atlas-defined regions was ignored. It would be nice to re-do the region mapping with a propre correction for distortion.
We have a crude lesion analysis and behavior in control cohort predictors of outcome paper. Ligia and Andreia have been coordinating so we do not have any overlap. I believe Lauren and I have discussed this relatively recently.
You are correct. Regional lesion analysis is not super accurate for the stated reason. Ryan has said it is not trivial to warp and adjust for swelling. So we have not pursued it.
From Huaxin: "Should we reduce the isoflurane concentration to 1.5-2%? 2% isoflurane is enough. It is very important to have the respiratory rate monitored during the procedure ( a sensor is placed under the body). The anesthesia can be adjusted based on the respiratory rate. Hypothermia also may cause animal death so the body should be warmed using a water bath."
Thanks for the comment, Huaxin. All sites are indeed supposed to monitor the respiratory rate and adjust isoflurane accordingly. The %s that reach anesthetic MAC can very depending on the gas delivery at the nose. All sites indeed warm the animal in various ways, but temperature monitoring may not be uniform at each site. We will address this.
We are looking at a lot of the lesion volumes from SPAN 1.0 in the analysis on turning preference. There are (obvious) tradeoffs between thresholds to be able to accurately detect lesion without detecting CSF that I know the MRI and LONI teams grappled with. I think with different coils we may need to think about either a site-specific thresholding or some first stepl of masking to mask CSF so we have improved dynamic range to detect lesion volumes. I know there are any issues for the MRI committee to tackle, but I wanted to add this to your discussions. Thanks!
Also, does the network have a new scientific lead at LONI for MRI analyses since Ryan has moved to a new position?
Yes, Mike Bienkowski at LONI is taking over. We are working on getting him suuport and getting his lab familiar with the pipeline. i have invited him to begin attending MRI meetings.
"Anesthesia: Induce anesthesia with 4% isoflurane in 70:30 N2O:O2 in an appropriate induction chamber with approved scavenging method. Reduce Isoflurane to 2-2.5% in 70:30 N2O:O2. DO NOT use 100% oxygen to deliver isoflurane. Adjust Isoflurane as appropriate based on respiration rate. For day 28 MRI only, if N2O is not available, scan can be performed by using room air mix to deliver isoflurane."
So it is to be reduced and titrated based on respiratory rate.
30 day MRI ideas
I really like the idea of sites having the ability to utilize advanced imaging methods at the 30 day time point, with ideally a few sites harmonizing methods on a sequence or two so the data can be analyzed together. DTI seems like an obvious one to try for, and I know Fahmeed and Basav have other methods they are interested in.
Threads
I agree, this will get unwieldy soon. Let me ask the developers.
Lauren and Cenk: If we are agreeing to a 30day MRI anyway, why not get our standard morphometry sequences, and THEN move on to the fancy schmancy stuff like DTI? Also, from my primitive understanding of DTI, i think the data reducing/bioinformatics part is pretty challenging, no?
From Pat: Lauren and Cenk:…
From Pat: Lauren and Cenk: If we are agreeing to a 30day MRI anyway, why not get our standard morphometry sequences, and THEN move on to the fancy schmancy stuff like DTI? Also, from my primitive understanding of DTI, i think the data reducing/bioinformatics part is pretty challenging, no?
Reply: I think it's all about scan time. Adding more sequences increases the scan time, which increases animal mortality and cost of the scan. Can someone elaborate on what useful data we did get out of the 30 day morphometry scans? Has anyone done a detailed analysis examining which MRI features at day 30 correlate best with the day 2 lesion volume? Is this in Cenk's MRI paper? If not I will propose this study.
Yes, MRI outcomes paper…
Yes, MRI outcomes paper looked at this. All 3 attributes of atrophy (tissue loss, ventriculomegaly and reverse midline shift) correlated closely with the lesion volume on day 2. It is in the works.
We will discuss day 30 MRI in detail in the MRI group meeting soon. I don't think the readouts we had were helpful for anything so adding the usual 30-45 min scan time would be justified. The time would be better used for more interesting readouts. If they are feasible and can be implemented, of course.
Lesion analysis is limited
Lauren but not Cenk is attending the lesion analysis paper that Ali is running and already knows this: We have learned that Ryan made a simplifying assumption that is not impactful on Ali's paper, but could make a difference down the road. He segmented the scans first, and then allocated each voxel to CSF, tissue or lesio based on segmentation intensity after labelling CSF. However, when it came to regional topography (e.g., cortex vs caudate vs thalamus vs hippo) he simply mapped in an Atlas without warping the image to fit. In other words, any swelling, atrophy or midline shift that moved any structures outside of the Atlas-defined regions was ignored. It would be nice to re-do the region mapping with a propre correction for distortion.
We have a crude lesion…
We have a crude lesion analysis and behavior in control cohort predictors of outcome paper. Ligia and Andreia have been coordinating so we do not have any overlap. I believe Lauren and I have discussed this relatively recently.
You are correct. Regional lesion analysis is not super accurate for the stated reason. Ryan has said it is not trivial to warp and adjust for swelling. So we have not pursued it.
From Huaxin: "Should we…
From Huaxin: "Should we reduce the isoflurane concentration to 1.5-2%? 2% isoflurane is enough. It is very important to have the respiratory rate monitored during the procedure ( a sensor is placed under the body). The anesthesia can be adjusted based on the respiratory rate. Hypothermia also may cause animal death so the body should be warmed using a water bath."
Thanks for the comment, Huaxin. All sites are indeed supposed to monitor the respiratory rate and adjust isoflurane accordingly. The %s that reach anesthetic MAC can very depending on the gas delivery at the nose. All sites indeed warm the animal in various ways, but temperature monitoring may not be uniform at each site. We will address this.
yes the current SOP just has…
yes the current SOP just has the anesthesia induction %, needs a statement that then will be reduced for maintenance.
Will do, thanks.
Will do, thanks.
We are looking at a lot of…
We are looking at a lot of the lesion volumes from SPAN 1.0 in the analysis on turning preference. There are (obvious) tradeoffs between thresholds to be able to accurately detect lesion without detecting CSF that I know the MRI and LONI teams grappled with. I think with different coils we may need to think about either a site-specific thresholding or some first stepl of masking to mask CSF so we have improved dynamic range to detect lesion volumes. I know there are any issues for the MRI committee to tackle, but I wanted to add this to your discussions. Thanks!
Also, does the network have…
Also, does the network have a new scientific lead at LONI for MRI analyses since Ryan has moved to a new position?
LONI MRI leadership
Also, does the network have a new scientific lead at LONI for MRI analyses since Ryan has moved to a new position?
Yes, Mike Bienkowski at LONI is taking over. We are working on getting him suuport and getting his lab familiar with the pipeline. i have invited him to begin attending MRI meetings.
Unfortunately, I was not…
Unfortunately, I was not made aware, so he missed the last meeting.
The MRI SOP has the…
The MRI SOP has the following language:
"Anesthesia: Induce anesthesia with 4% isoflurane in 70:30 N2O:O2 in an appropriate induction chamber with approved scavenging method. Reduce Isoflurane to 2-2.5% in 70:30 N2O:O2. DO NOT use 100% oxygen to deliver isoflurane. Adjust Isoflurane as appropriate based on respiration rate. For day 28 MRI only, if N2O is not available, scan can be performed by using room air mix to deliver isoflurane."
So it is to be reduced and titrated based on respiratory rate.