Freesurfer September 2007

freesurfer@nmr.mgh.harvard.edu

69 participants
99 discussions

High-resolution limits of FS4
by Morgan Hough 26 Sep '07

26 Sep '07

Hi there, I just wanted to check on the spatial resolution limits of FS4. Is it possible to process a whole-brain, 0.5mm isotropic voxel size volume without downsampling it? Thanks in advance. Cheers, -Morgan

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tkmedit scripting: control window size?
by Graham Wideman 25 Sep '07

25 Sep '07

Folks: In a tcl script for tkmedit, is there a way to control the size of the graphics window? I see functions for all sorts of other aspects of the view, but not this -- maybe I'm missing something? Thanks, Graham

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what ever happened to spatialsmooth-sess
by Sebastian Moeller 25 Sep '07

25 Sep '07

Dear Doug, dear fsfast experts, now that the shinny new FreeSurfer has its first point release I got around playing with its FSFAST version (befor I forget freesurfer- Linux-centos4_x86_64-stable-pub-v4.0.1-full, on 64 bit SUSE 10.1). I looks like a lot was changed under the hood (and improved I am sure) now my old scripts certainly need some help to keep going. My first stumbling block is spatialsmooth-sess, which complaines about a missing "ip" binary, (and rightly so, since ip got folded into fslmaths, I fathom). 1. Please let me know, what the recommended replacement for spatialsmooth-sess is nowadays. 2. And while I am asking, can I truly switch FSFAST default formats by "export FSF_OUTPUT_FORMAT=whatever" before sourcing SetUpFreeSurfer? 3. I would be happy about a link to a newer tutorial/howto fsf to use as a template to "modernize" my scripts thank you very much for the powerful tools as always & ahoi Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 0 15 77 - 1 90 31 41 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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t-value saved values
by Glenn Lawyer 25 Sep '07

25 Sep '07

Hi, I asked about this last week, and had a nice discussion with Doug, but somehow in that we never got the answer to my original question. When FreeSurfer saves t-values (in F.mgh), what is it actually saving? The numbers in the file do not have a t-distribution (even when the source data for the glm is random noise). Is a transform applied to the t-values before the write, as is done with the p-values?

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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

3 2

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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Freesurfer September 2007