Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30128 discussions

Error running recon from command line
by Harshad Shanbhag 23 Feb '05

23 Feb '05

Hello, I installed FreeSurfer according to instructions on the website. To overlay FSL data, I used the following instructions from the FMRIB website. avwswapdim TEST x -z y TEST_reorient slices TEST_reorient bet TEST_reorient TEST_brain -f 0.4 mri_convert /home/bbernal/freesurfer/subjects/TEST/mri/orig/001/TEST_brain.img . recon-all -stage1 -subjid TEST However, the program gives me errors at this stage. I saved the error messages to the file that I have attached. Could you please have a look at it and help me with this. Thank you. Sincerely, Harshad.

2 1

Cortical thickness correlated with age
by Claus Tempelmann 23 Feb '05

23 Feb '05

Hi everybody, for quite a while we have been comparing the cortical thickness between groups of patients and I hope we did everything as we should. Now, we have been trying to look for the correlation between cortical thickness and age and somewhere we seem to make a mistake. I know that it's difficult for you to find this mistake as there are many possible sources. Nevertheless, I hope that somebody has an idea ;-) Let me describe what we did: 1. We have a group of subjects, for all of the subjects we went through the steps of segementation, inflating, sphering, morphing ... 2. We edited a simple mtx-file named PatBas-Alter1.mtx (this is not the complete group, we just started with a few subjects to check the method). This file has only two columns, column 1 is the name of the subject in the SUBJECTS_DIR, column 2 is the age of the subject: Patient_2_Baseline 33 Patient_4_Baseline 42 Patient_5_Baseline 27 Patient_6_Baseline 40 Patient_7_Baseline 35 Patient_9_Baseline 48 Patient_10_Baseline 31 Patient_12_Baseline 29 Patient_13_Baseline 33 Patient_14_Baseline 37 Patient_15_Baseline 36 Patient_16_Baseline 41 Patient_17_Baseline 41 Patient_18_Baseline 26 Patient_21_Baseline 30 Patient_22_Baseline 37 3. We run mris_glm with a script or directly from the command line: (we are using version 1.18, 2003/06/30 20:40:38 greve) mris_glm --design $mtxfile.mtx --surfmeas thickness --hemi lh --trgsubj average7 --nsmooth 50 --gcv 0 0 1 --sigt sigt_$outputname-lh.w paint 4. We render sigt_$outputname-lh.w on the inflated surface of average 7. The result is surprising. Everywhere in the brain the cortical thickness shows a high positive correlation (t-values between 9 and 12) with age. Obviuosly, that's nonsense but I haven't seen any error message. 5. To check what may have happened we edited the mtx-file according to the motto the last will be the first, high age is assigned to young subjects and viceversa. 6. The resulting t-maps look very similar. They are not identical but again the cortical thickness shows a high correlation with (now faked) age, again we get t-values between 9 and 12. Any ideas what might have happened? I'm sure that we made something very stupid but what can that be?? Our mtx-file has only two columns. Can that be a problem?? Thanks in advance for all suggestions Claus ----------------------------------------------------------------------- Claus Tempelmann email: Claus.Tempelmann(a)medizin.uni-magdeburg.de Clinic for Neurology II MR department Tel.: +49-(0)391-6117183 OvG University Magdeburg +49-(0)391-6117177 Leipziger Strasse 44 39120 Magdeburg Fax: +49-(0)391-6117178 Germany

1 0

Workstation Spec
by maryfitz＠indigo.ie 22 Feb '05

22 Feb '05

I am about to purchase a workstation which will be used to run Freesurfer. Can you tell me the recommended specification for suitable hardware and OS. Many thanks Mary Fitzsimons Epilepsy Programme Beaumont Hospital Dublin -------------------------------------------------------------------- mail2web - Check your email from the web at http://mail2web.com/ .

2 1

Cluster version of FreeSurfer
by Satrajit Ghosh 21 Feb '05

21 Feb '05

Is there a cluster/parallel version of freesurfer available? Thanks, Satra -- Satrajit S. Ghosh Postdoctoral Associate Speech Communication Group Research Laboratory of Electronics, MIT

2 1

new tkmedit and tksurfer
by Wan Park 17 Feb '05

17 Feb '05

I am supposed to have libtiff, glut, tclkt, tix and blt installed, but I still receive this message: for volume: Command Finished /usr/local/freesurfer_package/freesurfer/bin/Darwin/tkmedit 22970 T1 -csurf dyld: /usr/local/freesurfer_package/freesurfer/bin/Darwin/tkmedit can't open library: /sw/lib/libtix8.1.8.4.dylib (No such file or directory, errno = 2) Command Finished for surface: Command Finished /usr/local/freesurfer_package/freesurfer/bin/Darwin/tkmedit 22970 T1 -csurf dyld: /usr/local/freesurfer_package/freesurfer/bin/Darwin/tkmedit can't open library: /sw/lib/libtix8.1.8.4.dylib (No such file or directory, errno = 2) Command Finished Curiously, I did not have this problems before the new binaries. Do you think that may be a line or it is more about env? thanks! wan

2 1

surface atlas
by Nguyen, Thang Q 16 Feb '05

16 Feb '05

Hello all, I have a question: What atlas freesurfer uses when it parcellates the final surface? If I were using a different atlas for my functional volumes, can I warp the data to the proper atlas? Thank you, Thang Nguyen

2 1

Re: [Freesurfer] new binaries for tkmedit and tksurfer
by Wan Park 16 Feb '05

16 Feb '05

hi kevin, i reinstalled fink and installed the blt package. then i copied the new binaries. now i cannot open the tkedit nor the tksurfer. these are the messages i receive: when i press volume: Command Finished /usr/local/freesurfer_package/freesurfer/bin/Darwin/tkmedit 22970 T1 -csurf dyld: /usr/local/freesurfer_package/freesurfer/bin/Darwin/tkmedit can't open library: /sw/lib/libtix8.1.8.4.dylib (No such file or directory, errno = 2) Command Finished when i press surface: Command Finished env tksurferinterface=csurf patchname= /usr/local/freesurfer_package/freesurfer/bin/Darwin/tksurfer -22970 rh white -tcl /tmp/TmpTclSurf.20719 dyld: /usr/local/freesurfer_package/freesurfer/bin/Darwin/tksurfer can't open library: /sw/lib/libtix8.1.8.4.dylib (No such file or directory, errno = 2) Command Finished any suggestion? thanks a lot, wan On Feb 14, 2005, at 2:15 PM, Kevin Teich wrote: > > Do you have BLT installed via Fink or FinkCommander? > > > On Sun, 13 Feb 2005, Wan Park wrote: > >> hi teich, >> >> i went to this place: >> >> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/ >> tkmedit_tksurfer-20050211-Darwin.tar.gz >> >> and I Unziped it in a temp directory, then move bin/tkmedit and >> bin/tksurfer into your freesurfer/bin/Darwin directory, and the >> lib/tcl/* files into freesurfer/lib/tcl. >> >> now when i put: >> >> $tksurfer >> >> i receive this new message: >> >> dyld: tksurfer can't open library: /sw/lib/libBLT.2.dylib (No such >> file or directory, errno = 2) >> Trace/BPT trap >> [ogden:freesurfer_package/freesurfer/subjects] wpark% >> >> how can i solve this problem? >> >> thanks >> >> wan > > -- > Kevin Teich >

2 1

Preparing cortical surface for EEG source localization
by Alex Wade 14 Feb '05

14 Feb '05

I have recently started to use FS to generate cortical surfaces for boundary element modelling in EEG source localization. In particular I would like to use the pial surface generated by FS. I have three problems: 1: I can only get FS to generate individual hemispheres. For the BEM, I need a single, connected, mesh for the entire brain. Is there a way to get this (perhaps by fooling FS into not disconnecting the hemispheres early in the segmentation process)? 2: The white/gray boundary mesh is topologically correct (no bridges / handles / holes etc..). Is the pial surface mesh also correct? 3: Is there a way to generate the volume inside the pial surface? That is - can I flood fill the pial surface in some way to extract the voxels that lie inside it as 3d volume? Many thanks Alex A.R. Wade Ph.D. Associate Scientist The Smith-Kettlewell Eye Research Institute 2318 Fillmore Street San Francisco, CA 94115 tel. 415 345 2083 fax. 309 416 6533

4 3

new binaries for tkmedit and tksurfer
by Wan Park 14 Feb '05

14 Feb '05

hi teich, i went to this place: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/ tkmedit_tksurfer-20050211-Darwin.tar.gz and I Unziped it in a temp directory, then move bin/tkmedit and bin/tksurfer into your freesurfer/bin/Darwin directory, and the lib/tcl/* files into freesurfer/lib/tcl. now when i put: $tksurfer i receive this new message: dyld: tksurfer can't open library: /sw/lib/libBLT.2.dylib (No such file or directory, errno = 2) Trace/BPT trap [ogden:freesurfer_package/freesurfer/subjects] wpark% how can i solve this problem? thanks wan

2 1

Freesurfer MAC OSX Installlation
by willcott＠pop.ruf.rice.edu 11 Feb '05

11 Feb '05

I have downloaded and installed freesurfer-20040218-Darwin.tar.gz with no seeming problems. I modified my .tcshrc file, checked directories and think all is in order. I operate in X11 windows. I still can not find csurf or any work-around. Does anyone have any ideas about my problem? -- M. Robert Willcott 1807 Orchard Country Lane Houston, TX 77062 713.302.5148

4 3

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer