Re: [Freesurfer] Freesurfer and FSL

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

Re: [Freesurfer] Freesurfer and FSL

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

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

[Freesurfer] Normalization

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

Re: [Freesurfer] Normalization

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

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

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

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

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. ___

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

Re: [Freesurfer] Freesurfer and FSL

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

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

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] Brain Volume

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

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

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

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

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] Freesurfer and FSL

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