Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30096 discussions

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. >

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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

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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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Importance of Segmentation/Parcellation edits with respect to cortical thickness
by Jonathan Holt 31 May '13

31 May '13

Hi all, We are using the parcellation of Desikan-Killiany https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation and creating labels for each structure in each hemisphere with: mri_annotation2label --subject ${SUBJ} --hemi ${HEMI} --outdir ${SUBJ}/${SUBJ}_annotate and making matlab text readable (via matlab load command) thickness files with: mris_convert -c ${HEMI}.thickkness ${HEMI}.white ${HEMI}.thickness.asc Then we are reading in the ascii thickness files and the labels and creating histograms (unit area) for each structure for each participant, essentially following: https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.HowcanIma keahistogramofcorticalthickness.3F We've dropped the zeros but also dropping values of thickness identically = 5mm. The question is: How important are parcellation edits, that is how accurate are the generated segmentation labels, and should we be dedicating effort to ensuring they're accurate and possibly editing them if not (if so, what should be used as a guide/template?) jon

2 1

Average for each voxel across all conditions
by Katie Bettencourt 31 May '13

31 May '13

Hi, I have an experiment where I have 3 conditions in a FIR event related analysis (running FS 4.5). I need to get the mean activity level for each voxel across all conditions across the run, so that I can calculate percent signal change for each individual voxel. Is this available (I have analyzed each run separately) somewhere? Katie

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recon-all errors: v5.0.0; dataset 4
by Sudhin A. Shah 31 May '13

31 May '13

CORRECTING DEFECT 1 (vertices=33, convex hull=57) After retessellation of defect 1, euler #=-41 (88676,260208,171491) : difference with theory (-61) = -20 CORRECTING DEFECT 2 (vertices=30163, convex hull=6211) error in the retessellation normal vector of length zero at vertex 88778 with 0 faces vertex 88778 has 0 face No such file or directory Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux recon-all -s IN387G exited with ERRORS at Thu May 16 05:11:49 EDT 2013

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Editing after reconstruction
by Cristian Paz 31 May '13

31 May '13

Hello FS-ers, I have a beginner question. I am wondering about editing. Since I have no superior of me in my lab to inspect or guide me in my freesurfer analyses - I get a bit worried that I might oversee some important errors from recon-all. If there is nothing that is strikingly wrong in the output from recon-all - should I then expect my results to be good enough for group analyses? If there is no error messages, and nothing that looks strange when I open rsults in tkmedit (for a beginner)? How often does a reconstruction from Freesurfer need to be edited,(roughfly, on average) if you have a group of lets say 32 subjects ? thank you so much for your help! best regards, Cris

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