Freesurfer

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30084 discussions

[Fwd: A Question]
by Nick Schmansky 30 Jul '09

30 Jul '09

Luis, I'm forwarding this to the freesurfer list, as that is the forum for freesurfer related questions. Also, posting questions in text format with attached pictures if necessary is preferred over .pptx files. To try to answer the first question, mri_glmfit will produce a file (or files) called sig.mgh which store the significance map. That file can be loaded as an overlay in tksurfer (typically after loading the fsaverage inflated surface). A Brodmann atlas is not available yet, although there are label files in the fsaverage/label directory of some, which you can use to limit your stats to particular labels (with mri_segstats), although i dont know if anybody has tried this yet. Nick -------- Forwarded Message -------- From: Dr. Luis Guillermo Almeida Montes <almeidal(a)prodigy.net.mx> To: nicks(a)nmr.mgh.harvard.edu Subject: A Question Date: Mon, 27 Jul 2009 12:55:21 -0500 Hi, Nick. I would like to solve a doubt I have when I realized the GLM analysis. I detailed my questions in a powerpoint presentation. I hope you can help me with this. Thanks a lot. Luis G. Almeida

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Fwd: Re: clusterwise correction for multiple comparison
by Rosa Steimke 30 Jul '09

30 Jul '09

HI Nick! I generated and ran the scribt, but it gives me following error message: ERROR: dimension mismatch between X and contrast /Users/steimke/Rosa_MRTs/qdec/Untitled/tmp.mri_glmfit-sim-77641/lh-Avg-thickness-Age-Cor.mtx X has 2 cols, C has 12 cols I have to admitt that I did not really understand wether I had to change anything in the scribt or whether i ould leave it like it is? thanks for your help! Rosa -------- Original-Nachricht -------- > Datum: Fri, 24 Jul 2009 17:16:27 -0400 > Von: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> > An: Rosa Steimke <rosasteimke(a)gmx.de> > CC: freesurfer(a)nmr.mgh.harvard.edu > Betreff: Re: [Freesurfer] clusterwise correction for multiple comparison > Rosa, > > If you have the newest version of qdec, it has a button to generate the > mri_glmfit-sim script for you, with the proper directory input and > output generated for you. > > You'll still have to load the results on your own in tksurfer by > following these instructions: > > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#Clusterwi… > > Nick > > > On Fri, 2009-07-24 at 13:48 +0200, Rosa Steimke wrote: > > HI! > > i have a question regarding multiple comparion correction in qdec. can i > use a clusterwise correction? > > > > i found the following script for glm: > > > > mri_glmfit-sim \ > > --glmdir lh.gender_age.glmdir \ > > --sim mc-z 5 4 mc-z.negative \ > > --sim-sign neg \ > > --overwrite > > > > but i dont understand how i should apply it in qdec. what shoudl i use > as input directory? > > rosa > > > > -- GRATIS für alle GMX-Mitglieder: Die maxdome Movie-FLAT! Jetzt freischalten unter http://portal.gmx.net/de/go/maxdome01 -- Jetzt kostenlos herunterladen: Internet Explorer 8 und Mozilla Firefox 3 - sicherer, schneller und einfacher! http://portal.gmx.net/de/go/chbrowser

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manually continue surfcluster on unfinished sim?
by Victoria Williams 30 Jul '09

30 Jul '09

Hi, I am processing several multiple comparison jobs on launchpad: 'mri_glmfit-sim --glmdir lh.physio2_chol_final.cvram.115.thickness.07092009.doss.30.glmdir --sim mc-z 5000 1.3 mc-z.pos.1.3 --sim-sign pos --bg 6' and I believe that the job is almost finished running the simulation (it has been running for a few days). However, launchpad, the batch system, is shutting down in a few hours and I am dissappointed that I may lose all the progress it's made. If interrupted, I probably need to create the "glmdir/csd/poll/StopSim" file since I used the --bg flag, correct? Question: Even though the simulation might not be completely finished, would there be a reason NOT to manually finish the corrections procedure by picking up with the mri_glmfit-sim script at the "now run clustering" section? In other words running the mri_surfcluster command? Thank You! Tori

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Help In VBM processing.
by Orsi Gergely 30 Jul '09

30 Jul '09

Dear All! First of all, I'm completely newbie to freesurfer. So far I only used FSL (mainly), rarely SPM and NordicICE. I need to do a VBM study to compare 2 groups each containing 50 subjects for GM density (already done with FSL), volumetry (not yet done), and cortical thickness and surface area. I'd like to do the last two with Freesurfer. Just a single Unpaired Two-Group difference, to answer the question: Is there a significant difference between the two groups in cortical thickness or surface area. My only problem, that I havent found any tutorials or guides (step-by-step, along with the commands) to do this. Could anyone help me in this? I'd really appreciate it. Best Regards: Gergely Orsi Diagnostic Center of Pecs Hungary

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RES: tksurfer error in ubuntu...
by Pedro Paulo de Magalhaes Oliveira Jr 30 Jul '09

30 Jul '09

setenv doublebufferflag 1 And then run tksurfer Enviado do meu celular Nokia -----Msg original----- De: Gonzalo Rojas Enviada: 30/07/2009 10:48:45 Para: freesurfer(a)nmr.mgh.harvard.edu Assunto: [Freesurfer] tksurfer error in ubuntu... Hi: How can I solve the following error ? ubuntu:~> tksurfer rezende rh pial surfer: current subjects dir: /home/image/bin/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/image surfer: Reading header info from /home/image/bin/freesurfer/subjects/rezende/mri/T1.mgz surfer: vertices=119258, faces=238512 Loading /home/image/bin/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(rezende) Window type not found! surfer: failed, trying double buffered window surfer: using interface /home/image/bin/freesurfer/lib/tcl/tksurfer.tcl Reading /home/image/bin/freesurfer/lib/tcl/tkm_common.tcl Reading /home/image/bin/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /home/image/bin/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /home/image/bin/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... Sincerely, -- Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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tksurfer error in ubuntu...
by Gonzalo Rojas 30 Jul '09

30 Jul '09

Hi: How can I solve the following error ? ubuntu:~> tksurfer rezende rh pial surfer: current subjects dir: /home/image/bin/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/image surfer: Reading header info from /home/image/bin/freesurfer/subjects/rezende/mri/T1.mgz surfer: vertices=119258, faces=238512 Loading /home/image/bin/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(rezende) Window type not found! surfer: failed, trying double buffered window surfer: using interface /home/image/bin/freesurfer/lib/tcl/tksurfer.tcl Reading /home/image/bin/freesurfer/lib/tcl/tkm_common.tcl Reading /home/image/bin/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /home/image/bin/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /home/image/bin/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... Sincerely, -- Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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exiting freesurfer
by William Sohn 30 Jul '09

30 Jul '09

Hi freesurfer community I installed freesurfer on my mac however after I installed it FSL stopped working. When i typed in "fsl" in the terminal it says the command is not recognized. This is a bit embarassing but I think my problem is that I am stuck in the freesurfer environment. I was wondering if someone could tell me how do i get out or close freesurfer. I've tried ctrl-z, exit, logout and non of those seem to work Thank you, -William Sohn

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RES: Help In VBM processing.
by Pedro Paulo de Magalhaes Oliveira Jr 30 Jul '09

30 Jul '09

Gergo Take a look in the Tutorial section of the wiki. Probably you'll find out that you can do the whole study using FreeSurfer. Cheers PPJ Enviado do meu celular Nokia -----Msg original----- De: Orsi Gergely Enviada: 30/07/2009 05:53:47 Para: freesurfer(a)nmr.mgh.harvard.edu Assunto: [Freesurfer] Help In VBM processing. Dear All! First of all, I'm completely newbie to freesurfer. So far I only used FSL (mainly), rarely SPM and NordicICE. I need to do a VBM study to compare 2 groups each containing 50 subjects for GM density (already done with FSL), volumetry (not yet done), and cortical thickness and surface area. I'd like to do the last two with Freesurfer. Just a single Unpaired Two-Group difference, to answer the question: Is there a significant difference between the two groups in cortical thickness or surface area. My only problem, that I havent found any tutorials or guides (step-by-step, along with the commands) to do this. Could anyone help me in this? I'd really appreciate it. Best Regards: Gergely Orsi Diagnostic Center of Pecs Hungary _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Processing data with -noaseg flag
by Falk Lüsebrink 30 Jul '09

30 Jul '09

Hi FreeSurfers, As the subcortical segmentation fails fairly often on my high resolution data I want to skip it by using the noaseg flag, but Im currently encountering another issue. 1.) During the fix stage of autorecon2 I receive following error during mris_euler_numbers (also if I want to view the lh.orig or rh.orig in tksurfer): rh.orig: face[233615].v[2] = 119048, but face 233615 not in vertex 119048 face list lh.orig: face[196300].v[1] = 100366, but face 196300 not in vertex 100366 face list 2.) Normally the subcortical segmentation is also used to cut both hemisphere and to remove the cerebellum. The cutting plane between the hemispheres is done very well, but I have never been able to remove the cerebellum. Do I need to remove it manually or are there some ways to remove it automatically? Is it required to be removed? 3.) Im interested in measuring cortical thickness only. But do I need to keep something else in mind while not using the subcortical segmentation to process my data? Thanks in advance, Regards, Falk

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mri_convert with old GE-LX data
by Chris Watson 29 Jul '09

29 Jul '09

Hello, I'm trying to use mri_convert to convert old (~1999) functional data that was acquired on a GE LX scanner. However, nothing seems to work. I'm running version 4.4.0 on RHEL4 x86_64. Here's my command line: (results are similar if I omit the -in_type flag) [matlab7@occipital functional]$ mri_convert I.001.s01 -it lx -ot spm "image" mri_convert I.001.s01 -it lx -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.001.s01... genesisRead(): can't determine file name format for /raid2/fmri5/LDProj/BOSEN/functional/I.001.s01 [matlab7@occipital functional]$ mri_convert I.001.s01 -it ge -ot spm "image" mri_convert I.001.s01 -it ge -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.001.s01... fname_format : /raid2/fmri5/LDProj/BOSEN/functional/I.%03d genesisRead(): error opening file /raid2/fmri5/LDProj/BOSEN/functional/I.001 [matlab7@occipital functional]$ mri_convert I.001.s01 -it dicom -ot spm "image" mri_convert I.001.s01 -it dicom -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.001.s01... Starting DICOMRead2() dcmfile = /raid2/fmri5/LDProj/BOSEN/functional/I.001.s01 dcmdir = /raid2/fmri5/LDProj/BOSEN/functional ERROR: /raid2/fmri5/LDProj/BOSEN/functional/I.001.s01 is not a dicom file

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