Freesurfer August 2010

freesurfer@nmr.mgh.harvard.edu

102 participants
152 discussions

hippocampus volume
by Zhangyuanchao 09 Aug '10

09 Aug '10

hi, expert, In a paper named "MRI of hippocampal volume loss in early Alzheimer's disease", I can see the average volume of hippocampus is 2133mm^3 for 279 normal controls with std=25 as well as 1631mm^3 for 330 AD subjects with std=34. However, in the aseg.stats, the volume of a normal subject is roughly 4000mm^3 or so, why the hippocampus volume of two samples differ so greatly due to age effect ( nearly about two times as much as the volume of the study). Thanks!

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Artifact
by Lena Palaniyappan 09 Aug '10

09 Aug '10

I am getting a consistent artifact in a set of images that went through autorecon-1. The original T1 also has the same artifact. It does not seem like a movement artifact as it is consistent across the whole set of images, and seems to leave other areas unperturbed. Any ideas what this might be will further processing be affected due to this localised defect? (it is seen in slices 142 to 152) Cheers Lena _______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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mapping surface file??
by Gennan Chen 06 Aug '10

06 Aug '10

Hi! I was able to use mri_convert to reslice aprc+aseg.mgz to the original dicom coordinates/space. However, I wonder if I need to do the same for all surface files, i.e. mapping vertex coordinate to different one. If I need to do that, which utility should I use? Gen ________________________________ This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator

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Normalization of wmparc.stats?
by Jason Reed 06 Aug '10

06 Aug '10

Hi all, Regarding the white matter parcellations in the wmparc.stats file, is it necessary to normalize these values by eTIV or by another factor? Or should this step be skipped as with the cortical thickness measures (?h.aparc, etc.)? Thanks! -Jason

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hippocampus volume
by Zhangyuanchao 06 Aug '10

06 Aug '10

Hi, expert, I would like to measure the volume of hippocampus, is there any way i can obtain the raw volume of hippocampus for each subject? How can I obtain it? In fact, in the folder stats, there is a file named aseg.stat, where I can find a line which contains "ColHeaders Index SegId NVoxels Volume_mm3 StructName normMean normStdDev normMin normMax normRange", I wonder whether the corresponding volume of the Left-hippocampus is what I want. I mean the volume of the left hippocampus. Thanks a lot ! Yuanchao Zhang

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eTIV and aseg.stats
by Yolanda Vives 06 Aug '10

06 Aug '10

Hi all, I have read about the eTIV and how to obtain it in the paper from Buckner et al. but I have a question related to the implementation of it in Freesurfer, just to be sure that I have correctly understood it. Regarding the volumes of the subcortical structures presented in "aseg.stats", are these volumes measured in atlas space and therefore, it is not necessary to normalize them to the TIV or should we apply a normalization method (i.e. covariance method) using the eTIV (ICV from aseg.stats)? Thank you for your time, Yolanda

2 1

Command line to map volume data to surface data
by Xinian Zuo 06 Aug '10

06 Aug '10

Dear surfers, Hi, I used freeesurfer to visualize my volume from FEAT outputs on the surface in the way: tksurfer fsaverage rh inflated_pre -overlay data.nii.gz -mni152reg , then save surface overlay as a mgh file. My question is, how can I get the identical mgh data by using a command line without launching the tksurfer gui? I found there is a command mri_vol2surf, but not sure about these default settings in tksurfer gui. Really appreciate it if some know and like to give your suggestions. -- Xinian Zuo, Ph.D Associate Research Scientist Institute for Pediatric Neuroscience NYU Child Study Center 215 Lexington Ave., 14th Floor New York, NY 10016 Phone: (212) 263 2485

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Sulci
by Oya, Hiroyuki 05 Aug '10

05 Aug '10

Dear All, Looking at pial surface, sulci looks wider than those of the actual brain. Is there any parameter to be tuned? Does watershed threshold have any effect on the pial surface estimation ? Hiroyuki

2 1

skull strip on raw data
by Zhang, Yuning 05 Aug '10

05 Aug '10

hi,experts, is there a way to use -skullstrip of freesurfer on my raw data (.mgz format) without any correction,i.e , intensity correction , normalization ? thanks a lot yuning

2 1

aparc.anot of average contains 35 ROIs
by wanlin 05 Aug '10

05 Aug '10

HI, I am using freesurfer4.5.0. After processed using recon-all, the ?aparc.annot of each subject contains 36 ROIs (including insula), However the ?aparc.annot of average subject ( make_average_subject) only has 35 ROIs(without insula). Did i do anything wrong or it is a bug? Thanks.

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Freesurfer August 2010