Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

Regarding mri_normalize
by Hae-Jeong Park 21 Sep '07

21 Sep '07

Dear Freesurfer Helpers, I think 'mri_normalize' might play an important step for the cortical thickness measurement. However, I could not find much information regarding 'mri_normalize' except for a brief description as below: "mri_normalize converts orig or nu volume from cortical reconstruction as input into a new volume where white matter image values all range around 110" It only explains the level of white matter but not the intensity level of the gray matter which is also important to segment them. Is the intensity normalized proportionally or just shifted to make white matter level 110? By looking at argument lists for mri_normalize, I could guess the process but I need some confirmation about how it works. Any reference or detailed explanation on procedures for mri_normalize would be greatly appreciated. Hae-Jeong MoNET Yonsei University

2 1

Missing posterior tip of posterior horn of lateral ventricle V4.01 vsV3.05
by Brain Apprentice 20 Sep '07

20 Sep '07

Hello, I was comparing the processing of the "bert" sample data on FreeSurfer V3.05 with V4.01 and I noticed that the posterior tip of posterior horns of lateral ventricles both sides were not counted as part of the lateral ventricles but as cerebral white matter in V4.01. Have I done something wrong or is this just one more thing that needs to be worked on? Thanks.

1 0

Standard deviation map
by Inês Souta 20 Sep '07

20 Sep '07

Hi there, How can I get a standard deviation map of the thickness measurements ina subject? Inês

2 4

Re: [Freesurfer] re-run FreeSurfer with v4
by Xiangchuan Chen 20 Sep '07

20 Sep '07

Hi Bruce, Thank you for your suggestions. I just finished the -autorecon1 step with v4.0.1 for 20 subjects, and checked the talairach registration with tkregister2. I found that most subjects' talairach volume looked smaller than the T1 volume. Suppose this is a "not very good" talairach registration, my questions are: 1. Is a "good" talairach registration critical to the further recon-all steps? 2. If yes, can I use the talairach transformation file generated after I manually modified the talairach registration with v3.05 for the same subject? Thanks for your helps, Xiangchuan ======== Start Of Original Message ======== Date: 2007-09-17 Time: 18:28:46 From: Bruce Fischl (fischl(a)nmr.mgh.harvard.edu) To: Xiangchuan Chen (xiangchuan.chen(a)bme.emory.edu) Subject: Re: [Freesurfer] re-run FreeSurfer with v4 >Hi Xiangchuan > >Avi Snyder's new talairach doesn't seem to fail anymore, and the skullstrip >failures are now extremely rate, so you might just let the whole thing chug >through and only check it at the end to make sure the surfaces are >accurate. > >cheers, >Bruce > >On Mon, 17 Sep 2007, Xiangchuan Chen wrote: > >> Hi all, >> >> I am working on 80 subjects' data with the following work flow: >> >> 1. -autorecon1 >> 2. edit talairach registration >> 3. -autorecon1 >> 4. -autorecon2 >> 5. edit brainmask.mgz >> 6. edit wm.mgz >> 7. -autorecon2-wm >> 8. -autorecon3 >> >> I have already finished this work flow for 30 subjects with FreeSurfer v3.05. I have spent a lot of time on steps 2, 5 and 6. I am not worrying about the other steps because they are my computer's tasks, but not mine. So, if I re-run the same work flow with v4, do I have to go through all these steps? >> >> Any suggestions are greatly appreciated. >> >> Thanks in advance, >> >> Xiangchuan Chen >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> ========= End Of Original Message =========

2 1

centos4_x86_64_V4.0.1 vs. centos4_V4.0.1
by Xiangchuan Chen 20 Sep '07

20 Sep '07

Hi Nick and Kevin, I installed the centos4_x86_64_v4.0.1 on my laptop. The tkmedit could show volume and surface data, the tksurfer could not display surface brain. Then, I changed it to centos4_v4.0.1. In this version, both tkmedit and tksurfer did their jobs. So, the same issue as v4.0 exists on my laptop. In addition, I am not able to enter number in all the boxes with numbers in both tkmedit and tksurfer. Because I have an ATI x1600 video card in the laptop, is it possible that the insufficient linux support for this card caused this issue? Thanks, Xiangchuan

2 1

How to do functional connectivity analysis in fs or fsfast?
by Zhen Zonglei 20 Sep '07

20 Sep '07

Hi, all: I am a naive user of fs and fsfast. Now, I am trying to do functional connectivity analysis with fsfast. But, I actually do not know how to do correlation analysis with a reference time course (a mean time course from a specific ROI) in fs and fsfast? Can someone give me some cues on this issue? Or, can someone tell me how to do regression analysis just with some external regressors rather than the regressors from experiment design? Sincerely Z.L Zhen

1 0

Average surface of mris_register
by Jiefeng Jiang 20 Sep '07

20 Sep '07

Hi, I am using the ?h.sphere.reg files automatically generated by reconall. However, I found that the area distortion compromise the results of my following resample step. I wonder whether replacing the default average surface "$FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif" with the ?h.sphere in the /average/surf directory would reduce the distortion. If so, could anyone tell me how to get a .tif file using files in /average/surf directory? Thank you!

2 3

Alternative Standard Brain
by Dick, Rachel 19 Sep '07

19 Sep '07

Hi there, Is there a "simple" way to plug in and use your own standard brain instead of the mni in the recon-all process? I am using the new 4.0 version. Thanks in advance! Rachel Rachel Marie Dick Research Assistant/Coordinator Brain Research and Imaging Neurosciences Dept. of Psychiatry & Behavioral Neuroscience WSU Medical School brain.wayne.edu <mailto:rcondon@med.wayne.edu> (313)577-6279 CONFIDENTIALITY NOTICE This message is confidential, intended only for the named recipient(s) and may contain information that is privileged, or exempt from disclosure under applicable law. If you are not the intended recipient(s), you are notified that the dissemination, distribution or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the e-mail address. Delete this e-mail from your computer, and destroy any copies in any form immediately. Thank you.

2 1

error: no gl window open
by Xiangchuan Chen 19 Sep '07

19 Sep '07

Hi all, I have got the following error message when running tksurfer to load inflated surface: surfer: ### redraw failed: no gl window open The result is that no surface appears. Any suggestions for solving this issue? My system: HP NC8430 laptop (ATI X1600 video card) Fedora 6 (X86_64) Freesurfer V4.0 Thanks in advance, Xiangchuan Chen

2 1

pictures from the freesurfer digest
by bell0368＠umn.edu 19 Sep '07

19 Sep '07

Hello all, I am subscribed to the freesurfer list in digest format. If someone sends pictures to the list I am not able to see/open them from the digest or from the archives. Is there an option I need to change? Or do I need to switch off digest mode completely? Thanks in advance, Chris Bell

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