Freesurfer July 2009

freesurfer@nmr.mgh.harvard.edu

85 participants
135 discussions

Flipped image talairach correction and missing .dcm extension
by Lena Palaniyappan 31 Jul '09

31 Jul '09

-- Hello group I am new to freesurfer. I have two problems. Please accept my apologies if these queries are bit naïve! Any help will be much appreciated. I am trying to autorecon1 a single image obtained from Philips 3T as dicom output. I use MacOS X11 terminal. 1. I am not able to use mri_convert to change these images to .mgz or niftii format. Is this because these files lack .dcm extension? For some reason all these files don¹t have .dcm extension though my radiology colleagues repeatedl assure me that they are dicoms! 2. I obtained some T1 MPRAGEs in img hdr format (no mat files came with them) and I am trying to recon1 this subject. There is a problem with talairach transforms (z 8) that needs manual correction. But when I try to open the brainmask.mgz on tkmedit for visual inspection I get the following msg Couldn't read the anatomical volume. Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size. Nevertheless when I proceed to open the tkregister2 for manual correction, ( without surf orig), I see the moveable image 180* flipped compared to the target image in sagittal view. Could this be due to some error in conversion of dcms? Or is this due to acquisition differences? Please help. Many thanks in advance Lena This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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Re: [Freesurfer] Processing data with -noaseg flag
by Bruce Fischl 31 Jul '09

31 Jul '09

Hi Falk, can you really not afford the 6 minutes or so of scan time to get a good 1mm dataset? We have analyzed a bunch of 7T data successfully, although it probably isn't as automated as 1.5 and 3T. The error you are getting we only see when you have run out of disk space. It sounds like the surface file is corrupted. As for the cutting planes, you should be able to select a point in the pons above the cerebellar peduncle for the brainstem cutting plane. This should remove the cerebellum, which is required for analysis. We certainly did many cortical thickness studies before the aseg stuff was integrated into the stream, so it should be possible, it just requires more work. cheers, Bruce On Thu, 30 Jul 2009, Falk Lüsebrink wrote: > 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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mghRead error
by leemon albert 31 Jul '09

31 Jul '09

Hi, I am running Ubuntu 8.04 and freesurfer V4.3.0. It worked well once upon a time. However, I get this error about the mghRead as follows. *~$ recon-all -autorecon1 -s liwentao_1 -i /mnt/data2/data/trauma/** liwentao_1.mgz* Subject Stamp: freesurfer-Linux-centos4-stable-pub-v4.3.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v4.3.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer Linux nica 2.6.24-24-generic #1 SMP Tue Jul 7 19:46:39 UTC 2009 i686 GNU/Linux /usr/local/freesurfer/subjects/liwentao_1 mri_convert /mnt/data2/data/trauma/liwentao_1.mgz /usr/local/freesurfer/subjects/liwentao_1/mri/orig/001.mgz mri_convert /mnt/data2/data/trauma/liwentao_1.mgz /usr/local/freesurfer/subjects/liwentao_1/mri/orig/001.mgz mghRead: encountered error executing: 'zcat /mnt/data2/data/trauma/liwentao_1.mgz',frame -1,errno=38 $Id: mri_convert.c,v 1.146.2.4 2009/01/30 02:30:42 nicks Exp $ reading from /mnt/data2/data/trauma/liwentao_1.mgz... Linux nica 2.6.24-24-generic #1 SMP Tue Jul 7 19:46:39 UTC 2009 i686 GNU/Linux recon-all exited with ERRORS at Fri Jul 31 09:20:08 CST 2009 I try to run it step by step: *~$ mri_convert /mnt/data2/data/trauma/**liwentao_1.mgz /usr/local/freesurfer/**subjects/liwentao_1/mri/orig/**001.mgz* mri_convert /mnt/data2/data/trauma/liwentao_1.mgz /usr/local/freesurfer/subjects/liwentao_1/mri/orig/001.mgz $Id: mri_convert.c,v 1.146.2.4 2009/01/30 02:30:42 nicks Exp $ reading from /mnt/data2/data/trauma/liwentao_1.mgz... mghRead: encountered error executing: 'zcat /mnt/data2/data/trauma/liwentao_1.mgz',frame -1,errno=38 There is sufficient disk space for freesurfer running. I searched the mail-archive and noticed the potential solutions. But it doesn't work. Any suggestion is appreciated! -- Albert Lab of Complex System and Artificial Intelligence, Institute of Automation,Chinese Academy of Sciences(CASIA) Beijing, 100190,P.R.CHINA

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[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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Freesurfer July 2009