Freesurfer

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30076 discussions

mri_convert: IMA
by Nurunisa Neyzi 24 Sep '07

24 Sep '07

Hi, I am getting an error message while trying to convert the SIEMENS IMA to MGZ: siemensRead(): file rows (30067) not divisible by image rows (18771) It looks like i managed to do a similar conversion before, so I wonder if there is something I need to add to the command line for this special case that I forget? thanks! On 9/23/07, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > > Hi Martin, > > you can do this with mri_convert using -rl $SUBJECT_ID/mri/orig/001.mgz > (reslice like this volume) and -rt nearest (resample type nearest > neighbor) > I think. Check the help if this is wrong. It will need to resample though. > > cheers, > Bruce > > > On Sun, 23 Sep 2007, Martin Kavec > wrote: > > > Hi, > > > > how can I map the aparc+aseg.mgz back to $SUBJECT_ID/mri/orig/001.mgz, > but > > without suffering from interpolation? > > > > Thanks, > > > > Martin > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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Mapping segmentation to orig
by Martin Kavec 23 Sep '07

23 Sep '07

Hi, how can I map the aparc+aseg.mgz back to $SUBJECT_ID/mri/orig/001.mgz, but without suffering from interpolation? Thanks, Martin

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mean thickness difference maps
by Kirk, Gregory 23 Sep '07

23 Sep '07

Hi All, I wanted to clarify a point. Publications of cortical thickness differences are usually produced with maps called mean thickness difference maps. I dug through the mail archive but did not find an answer (Q1) These statistical parametric maps are I assume produced by computing a mri_glmfit with doss, and a contrast (1 -1 0) i.e. each class is fit to a linear model but both have the same slope and the offsets are different and the inference is on the difference in the intercepts. The resulting maps are the maps commonly referred to as mean thickness difference maps ? (Q2) I seem to remember a conversation about how this is done. First each group is fit to an optimal line, i.e. each group gets a line with the intercept and slope to minimize the data fit error, then the average of the slopes is computed and this average slope is used for each of two new lines, one for each group, then an intercept is computed for each group such that with the nonoptimal slope the data fit error is minimized, am I correct that this is in fact the procedure. (Q3) Does this in fact give an intercept that is the mean of the thickness values for each group , the thought experiments I have cooked say yes but I have not made a proof ? Thanks Greg

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Re: [Freesurfer] recon-all in background
by Pedro Paulo Oliveira Jr 22 Sep '07

22 Sep '07

Notice that usually when ssh disconect for any reason the process stop unless you use nohup in csh or disown -a in bash. Pedro Paulo Oliveira Jr. -- mens. original -- Assunto: Re: [Freesurfer] recon-all in background De: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Data: 23/09/2007 00:59 of course On Sat, 22 Sep 2007, Xiangchuan Chen wrote: > Hi all, > > Can I run recon-all in background? The command line looks like this: > > ssh node11 "recon-all -autorecon1 -subjid XXX" & > > Thanks in advance, > > Xiangchuan Chen > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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recon-all in background
by Xiangchuan Chen 22 Sep '07

22 Sep '07

Hi all, Can I run recon-all in background? The command line looks like this: ssh node11 "recon-all -autorecon1 -subjid XXX" & Thanks in advance, Xiangchuan Chen

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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

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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.

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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

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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 =========

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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

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