[Freesurfer] Brain Volume
Hi, I've been working with Freesurfer and FSL in order to compare the two softwares. However the last one has a tool called "Brain Extraction Tool" (BET) that provides all the brain volume including cerebellum. Is there any option in Freesurfer that makes the same as *BET*? Thank you for your attention, Ana Arruda ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] Brain Volume
Thank you. But in the last message I forgot to say my final aim. After the skull stripping, how can I measure the volume? Ana Arruda ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] Brain Volume
I've just seen the output from mri_watershed. And from the file aseg.stats, is there any measure that provide the brain volume? Thank you once again, Ana Arruda ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] Freesurfer and FSL
Dear experts, About the differences between FSL and Freesurfer, I've noticed that the left-hippocampus volumes measured by Freesurfer are always bigger than the left-hippocampus volumes measured by FSL. Is there any reason that can explain that? According to the literature, the percent volume difference between Freesurfer and manual tracing for left-hippocampus is always smaller than the percent volume difference between FSL and manual tracing and in my case, it happens exactly the opposite. Would you mind helping me? Thank you for your attention, Ana Arruda ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] Freesurfer and FSL
The manual protocol was made by doctors.They traced the hippocampus segmentation based on their knowledge of anatomical structures. For automatic segmentation I've used the following command: recon-all -i input_suject_name -autorecon1 -autorecon2 -s output_subject_name and after this simulation I've been working with the values given in the terminal X11 for left-hippocampus and right-hippocampus. Am I doing anything wrong? Or am I missing something? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] Freesurfer and FSL
That fact can explain the differences between manual and automatic segmentations. But how can I explain the differences just for the left-hippocampus values in Freesurfer? Comparing percent volume difference between Freesurfer-Manual and FSL-Manual, the percent is bigger in left-hippocampus for Freesurfer-Manual. And according to the literature (Morey et al.) the percent volume difference for Freesurfer-Manual is always smaller than FSL-Manual as you can see in Fig. 5 of that article. FSL Manual FreesurferHDHEHDHEHDHE3810.7416983382.601803 3355.53007.537053721 3409.8294672860.18722428682653.533823331 3306.4098913381.8851563025.5 3001.5335835753794.7671472907.55911628802769365134744521.4508974587.515346 36423468404941133794.6383173841.1113483042306640614242 4772.5126714028.94992435703496.548124801 4025.0371153833.112593772.5 351340944224 ??3196.52704.5?? 2900.8389382705.713765252624663184 28203607.9960483061.210132749.5258938523591 3694.4012053343.9468022682 2559353035074562.1957574484.21525131563286.541144599 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] Freesurfer and FSL
I'm not sure about this, but probably the doctors use the same methods for left-hippocampus and right-hippocampus. The softwares, FSL and Freesurfer, don't have a different away to operate in either hippocampus. Do you agree? That way of operating confuses me on how to interpret the differences found only for the left hippocampus. Anyway, thank you for your help. Another thing, in my thesis I'll have to describe what I've done in Freesurfer to obtain the hippocampus segmentation. Is there any article that describes in a general and brief way all the steps to be followed towards the final goal? Thank you all, again. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] Freesurfer and FSL
Thank you very much! About the previous question, do the softwares use the same criteria for each hippocampus? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] Freesurfer and FSL
I haven't gone so far. I've just done the simplest way. I've search the proper commands just to do the hippocampus segmentation, but not its subfields. All my analysis was made with the left and right-hippocampus volumes from the *aseg.stats *file. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] Freesurfer and FSL
Yes, you're right. But in that case, these changes would be quite similar for right-hippocampus too. Based on my analysis and literature, Freesurfer has more accurate measures than FSL. The doctors are quite conservative about boundaries so that measures are the smallest between Freesurfer and FSL. In other words, the measures obtained by Freesurfer are in the middle, they are bigger than manual and smaller than FSL. However, for left-hippocampus the volumes measured by Freesurfer are always bigger than FSL and Manual segmentation. The only reason I can find, once the softwares use the same criteria for left and right-hippocampus, is related with the doctor responsible for the manual segmentation. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] Normalization
Hello, I'm working on hippocampus segmentations obtained by Freesurfer to compare with manual and FSL segmentations. Do I have to normalize to make these comparisons more accurate? If so, what volume do I have to use? I've read about eTIV but I would like to confirm if there is any value for normalization purpose in the aseg.stats file. What does ICV include? Does it include the CSF between the brain and the skull? Best regards, Ana Arruda ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] Normalization
Thanks a lot Martin. I really get confused about normalization. I've already done the comparisons and the values between methods, as you said, are different. Although I haven't understood why, in this case, I don't have to normalize. My advisor told me to normalize all the brain values from the patients. Do you have any idea what did he mean with that? I thought that this suggestion would be related to hippocampus volume. Ana Arruda ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] Normalization
It's clear now. Thank you very much. And you're right about manual ICV, I have only two images for each patient with the area of the biggest plan in the brain, commissural area. Best regards, Ana Arruda ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] Freesurfer and FSL
Dear experts, About the previous subject I have one more question. Based on Morey, et al. article we can say that there is better results for the right hippocampus. Generally, it is known that right hippocampus volume is often bigger than left hippocampus. So, is there any possible explanation for my volumes, measured by Freesurfer, for left-hippocampus be often bigger than the right hippocampus? Best regards, Ana Arruda ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] Freesurfer and FSL
Can you please take a look to my previous posted hippocampi values? What do you think about them? Thank you for your prompt help. Best regards, Ana Arruda ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] Freesurfer and FSL
Hello again, I'm sorry about all these questions. My analysis is being based on Morey et al. and I would like to know why do they not divide the study in left hippocampus and right hippocampus? Is it related with the type of comparison, once they are only worried about the comparison between methods? Thank you for your attention. Ana Arruda ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] Freesurfer and FSL
Dear experts, I'm an MSc student and part of my final project is related to the measurement of the volume of the hippocampus. The last thing I have to do is to compare two softwares, FSL and Freesurfer. On Freesurfer, I've used the following commands: recon-all -i where_my_subject_is -autorecon1 -s output_name then, related to the same subject recon-all -autorecon2 -s output_name After approximately 12 hours, and after comparing the results of Freesurfer and FSL, I found that those obtained with Freesurfer are bigger than those obtained with FSL. According to the literature the results are the reverse. Do you know any idea what I'm doing wrong? Thank you for your attention, Ana Arruda ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] Freesurfer and FSL
Thanks for your help Martin. However I don't have just a single subject with that discrepancy. My data has 18 subjects and most of the results obtained with Freesurfer are bigger than FSL. Thank you again, Ana ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] Freesurfer and FSL
I really appreciate your help. Thank you. Has anyone on the list ever compared FSL and Freesurfer? Thanks, Ana ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
