Hello, I am finding differences in hippocampus voulme of same subject when scanned at different times . Our study requires our subjects to be scanned 3-4 times (T0-T3) within a period of 1 month. We have performed MRI Scanning on all our subjects with same sequence using 3T GE scanner. Please suggest the reason behind this difference and how would I go about correcting it. For example following are the hippocampal values for two subjects ( A and AA ) calculated by freesurfer from different scans. Surprisingly for these two subjects T3 and T2 Hipp-values for A and AA respectively that are differing from the other timepoints are same.
Left-Hippocampus Right-Hippocampus A.T0 3537 3632 A.T1 3629 3796 A.T2 3536 3782 A.T3 3096 3671 AA.T1 4245 4667 AA.T2 3096 3671 AA.T3 4341 4491
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Hi Rashmi
what version of FS are you using? And what sequence are you using? There will of course be noise-induced variation across scans, which in the best case is around 2%. But that only occurs if you use multi-echo (high bandwidth sequence) and are careful about subject positioning to minimize differential gradient nonlinearity distortions. You should also make sure that your outlier measurements aren't significantly more motion corrupted than your other scans. Finally, it can also help to control for hydration status and time-of-day.
cheers Bruce
On Thu, 1 Mar 2012, Rashmi Singh wrote:
Hello, I am finding differences in hippocampus voulme of same subject when scanned at different times . Our study requires our subjects to be scanned 3-4 times (T0-T3) within a period of 1 month. We have performed MRI Scanning on all our subjects with same sequence using 3T GE scanner. Please suggest the reason behind this difference and how would I go about correcting it. For example following are the hippocampal values for two subjects ( A and AA ) calculated by freesurfer from different scans. Surprisingly for these two subjects T3 and T2 Hipp-values for A and AA respectively that are differing from the other timepoints are same.
Left-Hippocampus Right-Hippocampus A.T0 3537 3632 A.T1 3629 3796 A.T2 3536 3782 A.T3 3096 3671 AA.T1 4245 4667 AA.T2 3096 3671 AA.T3 4341 4491
This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made.
Hello FreeSurfer expets, Our study requires our subjects to be scanned 3-4 times and then I use FreeSurfer Tool to generate their voulumetrics. Since I do several time points on a subjects also perform the longitudinal runs and then take the volumetrics information from longitudinal run output for each time point subject wise. To do the ccros sectional time point runs I performed run recon all on my subjects T1 Mparge data as follows: recon-all -s SUBjid -use-mritotal -all </dev/null&> outFSSubjid &
I examined the output data for skull stripping and I am finding errors. What do you suggest: shall I try to correct the skull stripping on the cross sectional out put before performing the base and longitudinal run or shall I complete all the runs and do skull strip editing in the output of the longitudinal run data. Please advise. Thanks, Rashmi.
I am
On 3/2/12 8:02 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Rashmi
what version of FS are you using? And what sequence are you using? There will of course be noise-induced variation across scans, which in the best case is around 2%. But that only occurs if you use multi-echo (high bandwidth sequence) and are careful about subject positioning to minimize differential gradient nonlinearity distortions. You should also make sure that your outlier measurements aren't significantly more motion corrupted than your other scans. Finally, it can also help to control for hydration status and time-of-day.
cheers Bruce
On Thu, 1 Mar 2012, Rashmi Singh wrote:
Hello, I am finding differences in hippocampus voulme of same subject when scanned at different times . Our study requires our subjects to be scanned 3-4 times (T0-T3) within a period of 1 month. We have performed MRI Scanning on all our subjects with same sequence using 3T GE scanner. Please suggest the reason behind this difference and how would I go about correcting it. For example following are the hippocampal values for two subjects ( A and AA ) calculated by freesurfer from different scans. Surprisingly for these two subjects T3 and T2 Hipp-values for A and AA respectively that are differing from the other timepoints are same.
Left-Hippocampus Right-Hippocampus A.T0 3537 3632 A.T1 3629 3796 A.T2 3536 3782 A.T3 3096 3671 AA.T1 4245 4667 AA.T2 3096 3671 AA.T3 4341 4491
This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made.
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.
Hi Rashimi,
please read http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits it should explain everything.
The clean way would be to edit the brainmask in the cross sectional runs, complete them, run the base and the longs. Optimally no edits should be necessary in the base and longs if cross are correct.
A potential short cut (depending on how bad the skull strips are) would be to run cross and base, then edit only the base. This can work if the skull strip is not too bad and if the asegs in the cross are good.
Best, Martin.
On Thu, 2012-09-27 at 16:04 +0000, Rashmi Singh wrote:
Hello FreeSurfer expets, Our study requires our subjects to be scanned 3-4 times and then I use FreeSurfer Tool to generate their voulumetrics. Since I do several time points on a subjects also perform the longitudinal runs and then take the volumetrics information from longitudinal run output for each time point subject wise. To do the ccros sectional time point runs I performed run recon all on my subjects T1 Mparge data as follows: recon-all -s SUBjid -use-mritotal -all </dev/null&> outFSSubjid &
I examined the output data for skull stripping and I am finding errors. What do you suggest: shall I try to correct the skull stripping on the cross sectional out put before performing the base and longitudinal run or shall I complete all the runs and do skull strip editing in the output of the longitudinal run data. Please advise. Thanks, Rashmi.
I am
On 3/2/12 8:02 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Rashmi
what version of FS are you using? And what sequence are you using? There will of course be noise-induced variation across scans, which in the best case is around 2%. But that only occurs if you use multi-echo (high bandwidth sequence) and are careful about subject positioning to minimize differential gradient nonlinearity distortions. You should also make sure that your outlier measurements aren't significantly more motion corrupted than your other scans. Finally, it can also help to control for hydration status and time-of-day.
cheers Bruce
On Thu, 1 Mar 2012, Rashmi Singh wrote:
Hello, I am finding differences in hippocampus voulme of same subject when scanned at different times . Our study requires our subjects to be scanned 3-4 times (T0-T3) within a period of 1 month. We have performed MRI Scanning on all our subjects with same sequence using 3T GE scanner. Please suggest the reason behind this difference and how would I go about correcting it. For example following are the hippocampal values for two subjects ( A and AA ) calculated by freesurfer from different scans. Surprisingly for these two subjects T3 and T2 Hipp-values for A and AA respectively that are differing from the other timepoints are same.
Left-Hippocampus Right-Hippocampus A.T0 3537 3632 A.T1 3629 3796 A.T2 3536 3782 A.T3 3096 3671 AA.T1 4245 4667 AA.T2 3096 3671 AA.T3 4341 4491
This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made.
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.
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Hi Rashimi,
1. there can be large differences, often they indicate a problem with the scan (e.g. motion artifacts etc). Or a problem with the processing (you should quality check the aseg and surfaces). 2. you should use FreeSurfer 5.1 and the longitudinal processing stream as is designed exactly for this and reduces variability significantly. A paper about the longitudinal stream has been accepted to NeuroImage, let me know if you want a pre-print. 3. Something is wrong with your table. It is extremely unlikely that both subjects have exactly the same numbers A.T3 and AA.T2. Something got mixed up.
Best, Martin
On Thu, 2012-03-01 at 21:13 +0000, Rashmi Singh wrote:
Hello, I am finding differences in hippocampus voulme of same subject when scanned at different times . Our study requires our subjects to be scanned 3-4 times (T0-T3) within a period of 1 month. We have performed MRI Scanning on all our subjects with same sequence using 3T GE scanner. Please suggest the reason behind this difference and how would I go about correcting it. For example following are the hippocampal values for two subjects ( A and AA ) calculated by freesurfer from different scans. Surprisingly for these two subjects T3 and T2 Hipp-values for A and AA respectively that are differing from the other timepoints are same.
Left-Hippocampus Right-Hippocampus A.T0 3537 3632 A.T1 3629 3796 A.T2 3536 3782 A.T3 3096 3671 AA.T1 4245 4667 AA.T2 3096 3671 AA.T3 4341 4491
This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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