Freesurfer May 2013

freesurfer@nmr.mgh.harvard.edu

174 participants
299 discussions

Cortical thickness
by Joshua deSouza 03 Jun '13

03 Jun '13

Hello everyone, Please pardon my rather simple question I have done a GLM fit anlysis and have obtained a file sig.mgh alonf with a few others after the analysis.As I know, I do not have to create ROIs in order to do this. I also understand that doing a multiple comparison analysis just compares the regions of importance and evaluates them giving the most resilient cluster depending on the threshold. So, this does not give a thickness estimate. I would like to know how do I get the cortical thickness values from the results? If so, can I do it after glmfit? And thanks Doug for your help in the other questions that I had prior to this! Thank you

3 7

mris_resample: Command not found.
by Barron, Daniel S 03 Jun '13

03 Jun '13

Hello, I am trying to perform an inter-subject registration using mri_cvs_register on version 5.3. When I ran mri_cvs_check, my feedback was I needed to find "mri_cvs_register.settings.txt" but I didn't worry about this per Lilla's post: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-April/023445.ht… mri_cvs_register kicks off well, but eventually it ends with: "mris_resample: Command not found." I go into my $FREESURFER_HOME/bin directory and note that mris_resample is truly not there. Did I not install 5.3 properly? I have attached a log file in case this helps. Cheers, Daniel

4 7

REPOST: NFS v4 on CentOS 5.4 or Red Hat 6.2
by Garikoitz Lerma-Usabiaga 01 Jun '13

01 Jun '13

Hi, Has anybody got problems using FS with NFS v4? We cannot write subjects if the SUBJECTS_DIR is in a NFS v4 system. Many thanks, Gari ---------- Forwarded message ---------- From: Garikoitz Lerma-Usabiaga <garikoitz(a)gmail.com> Date: Tue, May 7, 2013 at 5:25 PM Subject: NFS v4 on CentOS 5.4 or Red Hat 6.2 To: Freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Hi FS experts, we have changed our file systems to NFS v4 and we found that FS cannot write to it (I mean, FS installed in an app server and subjects in the file system is not working). Last new I have is that FS in CentOS could read but not write and in Red Hat could not write or read. Is it a known problem? Is it something going on with FS or the problem is in our end? (the rest of the programs are working fine: FSL, Matlab...) Many thanks, Gari

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CVS crashing consistently: update
by Graham Wideman 31 May '13

31 May '13

Hi MGH folks, Update to previous report: Review: Both of my attempts from scratch to CVS the 5.3.0 source failed after about 760 files, directory trctrain. CVS quit with fatal signal 9 error. Previously when I tried to restart either of these, CVS would quickly run through all the up-to-date directories, then hang at trctrain, with no terminal, disk or network activity (as judged by router lights). I have since let it sit there for probably 20 minutes, and suddenly the process came to life... downloading trctraindata.tar.gz (over 500 Meg). So, I don't know if or why that large file was resulting in signal 9 error, but progress is now unjammed. -- Graham

1 0

CVS crashing consistently
by Graham Wideman 31 May '13

31 May '13

Hi MGH folks, I am attempting to download the source via CVS as described here: http://freesurfer.net/fswiki/ReadOnlyCVS using: cvs -d :pserver:anonymous@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot checkout -P -r release_5_3_0 dev (ie: 5.3.0 source) The CVS process is consistently stopping about 760 files into the process, with the final lines of output being: ------------------------------------------------ cvs checkout: Updating dev/distribution/trctrain U dev/distribution/trctrain/Makefile.am Terminated with fatal signal 9 ------------------------------------------------ After the first attempt got stuck here, I attempted to run the checkout command again. CVS quickly displays a bunch of "Updating xxxxx" where xxxxx is all the directories already downloaded, then gets to trctrain and stops indefinitely. (I then killed it using Ctl-C) I then created a new local directory and restarted from scratch. The checkout proceeded apace, and then got stuck at the same place (trctrain), with same failure message. So... I'm thinking it might be something at your end, maybe disk problems in whatever files come next after the last one above? FWIW, I'm using cvs as installed with Mint 15, which is 1.12.13-MirDebian-9 (client/server) -- Graham

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Re: [Freesurfer] mprage flag in recon-all
by Caspar M. Schwiedrzik 31 May '13

31 May '13

yes, but recon-all just calls mri_segment with -mprage and mri_normalize with -mprage. I would like to know what -mprage does in these two functions, but i cannot search them because they are executables, not scripts. Caspar 2013/5/31 Harms, Michael <mharms(a)wustl.edu> > > Use any editor (even Word) with a search capacity, and search for the > string 'mprage'. > That will lead to you the variable internal to recon-all called > "IsMPRAGE". Searching for "IsMPRAGE" will then show you all in the stages > that the -mprage flag affects. > > cheers, > -MH > > -- > Michael Harms, Ph.D. > ----------------------------------------------------------- > Conte Center for the Neuroscience of Mental Disorders > Washington University School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave. Tel: 314-747-6173 > St. Louis, MO 63110 Email: mharms(a)wustl.edu > > From: "Caspar M. Schwiedrzik" <cschwiedrz(a)mail.rockefeller.edu> > Date: Friday, May 31, 2013 2:14 PM > To: "Freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] mprage flag in recon-all > > I only find flags for mri_normalize and mri_segment in recon-all, and I > have trouble reading the contents mri_normalize with a regular text editor. > caspar > > > 2013/5/31 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > >> Hi Caspar >> >> it changes some parameters to the intensity normalization and >> segmentation to account for the lower SNR and increased CNR in the mprage. >> You'll need to look in the recon-all script for the details >> >> cheers >> Bruce >> >> >> >> On Thu, 30 May 2013, Caspar M. Schwiedrzik wrote: >> >> Hi! >>> Is there more documentation on what settings the mprage flag enables in >>> recon-all? >>> Specifically, I would be interested which individual steps it affects and >>> what the parameters are for each of the steps. >>> Thanks! >>> Caspar >>> >>> >>> >>> >> >> The information in this e-mail is intended only for the person to whom >> it is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. If the e-mail was sent to you in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> > > > ------------------------------ > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. >

3 3

Difference between Original and Main surfaces?
by Jonathan Holt 31 May '13

31 May '13

Always wondered, was never quite sure. I'm wondering why sometimes they mirror each other and other times they shift away. jon

2 1

Group Analysis
by Fotiadis, Panagiotis 31 May '13

31 May '13

Hey Doug, Sorry for the overwhelming amount of questions. I wanted to confirm something. Suppose you want to do group analysis between two groups say a healthy cohort vs a diseased cohort. Each cohort has ~40 and ~30 subjects each (different people), and you want to compare how for instance the cortical thickness decreases over age in the one group versus the other. Do you still set the contrast vector as [0 0 1 -1] ([intercept 1 intercept 2 slope 1 slope 2]) and follow the analysis described in https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis or do you go on a different way since there are different subjects instead of one with 40 (or 30) different longitudinal data for each cohort? Don't we need to correct the age slopes for the fact that we have 40 (and 30) different subjects in each cohort? Thanks, Panos

2 7

ventral DC
by Yang, Daniel 31 May '13

31 May '13

Dear all, in the aseg.volume, there is a term called 'ventral DC' and I am wondering what it is. I looked up the previous posts and know DC = diencephalon, and it's a grab bag of stuff that cannot be resolved. However, does anyone know what exactly ventral DC is? Thanks! Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

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Freeview automation
by Garikoitz Lerma-Usabiaga 31 May '13

31 May '13

Hi list, is it possible to automate Freeview automation from the command line? I want to automatically render 3D images of the hippocampus (I have a separate volume, based on hippo-subfields) and have an image for all subjects for quality checking. thanks! Gari

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Freesurfer May 2013