Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

11 Aug '08

Hello: I am a new to FreeSurfer, and i run the following command : recon-all -autorecon1 -s temp , and it exit with some errors: Mon Aug 11 15:49:56 CST 2008 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Mon Aug 11 15:49:57 CST 2008 /home/liri/liri/freesurfer/subjects/temp/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Linux liri-desktop 2.6.24-19-generic #1 SMP Fri Jul 11 23:41:49 UTC 2008 i686 GNU/Linux recon-all exited with ERRORS at Mon Aug 11 15:49:57 CST 2008 I have seen that it might be caused by the direction cosines in the input file were all wrong (coronal, saggital, horizontal wrong). so I checked the nu.mgz, and it displays different from the bert subject, if this is the reason , how can i correct it. thanks tim

1 0

recon error
by Ilana Hairston 10 Aug '08

10 Aug '08

Hi there, I am new to free surfer, and am trying to analyse brains of kids ages 8-11. running recon1 i get the following error message: ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Looking at past mailings seems you recommended checking the registry. However, during recon no file called ???.dat was created as far as i can tell, and without specifying --reg i get the error: ___$ tkregister2 --s C2647 --mov C2647_070809cv.img INFO: no target volume specified, assuming FreeSurfer orig volume. ERROR: no registration file specified thanks, ilana -- You must believe in free will; there is no choice.

2 1

Watershed Error
by Vina Goghari 09 Aug '08

09 Aug '08

Hi all, I get this error for one subject: mri_watershed Error: GLOBAL region of the brain empty ! I check the talairach transformation and it looked good. I also tried just scripting the orig.mgz and I get a wonderful strip. How can I move forward with the recon-all process? Thanks, Vina

4 3

longitudinal stuff
by Bruce Fischl 08 Aug '08

08 Aug '08

Hi All, we have just been alerted to a bug in the longitudinal processing stream that will require re-analysis of any longitudinal data. Sorry, we'll have a fix sometime in the next couple of weeks, but for the moment you should hold off analyzing any longitudinal data. We'll keep you posted. Bruce

1 0

Permissions change
by John Kuster 08 Aug '08

08 Aug '08

Hi, I was wondering if anyone can tell me how to make permissions read out as group executable, basically I would like to make it so my data files can be worked with by others in my group. Thanks for your help, Jake

3 2

Fwd: [Freesurfer] editing masks
by Daniel H Choi 08 Aug '08

08 Aug '08

---------- Forwarded message ---------- From: Daniel H Choi <dhchoi(a)u.northwestern.edu> Date: Fri, Aug 8, 2008 at 11:10 AM Subject: Re: [Freesurfer] editing masks To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Hi all, I was wondering how to edit the voxels of a mask (the name of which is "lh.stg.mask.mgz") so that each voxel would be a value of 1 (if I try adding voxels in tkmedit, their values are 255). Additionally, we use this mask to isolate STG. But instead of a simple binary mask, this mask keeps the white matter values within STG intact (and anything outside is 0). Would adding voxels to the mask in tkmedit change this function? Thanks Dan On Tue, Aug 5, 2008 at 7:40 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > I see. You should be able to manually edit it in tkmedit, or you can try > using mri_morphology to close small holes. > > cheers, > Bruce > > On Tue, 5 Aug 2008, Daniel H Choi wrote: > > The mask was obtained from a friend, who had actually inquired earlier to >> freesurfer about using a binary mask to extract everything except the roi. >> (He wanted to include white matter in the roi, while everything outside >> remained a value of 0). The mask is in an .mgz format and we apply >> mri_mask >> to the individual brainmask.mgz. Upon using this mask, we noticed that >> there >> were some voxels missing in the mask itself (it was not an entirely smooth >> surface). This might be attributing to some problems we are having later >> on. >> Thanks >> >> Dan >> >> On Tue, Aug 5, 2008 at 5:47 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu >> >wrote: >> >> Sorry, I don't understand. Where did you get the mask? Or are you trying >>> to >>> create it from scratch? >>> >>> On Tue, 5 Aug 2008, Daniel H Choi wrote: >>> >>> Hi, >>> >>>> >>>> I have a binary mask that I apply to my .mgz files. It allows me to >>>> block >>>> everything outside of the STG as 0 and everything inside the way it is. >>>> I >>>> was wondering though how I might go about editing the mask? I see that >>>> there >>>> are random voxels that have been left out and I would like to fill those >>>> in. >>>> Thanks >>>> >>>> Dan >>>> >>>> >>>> >>>> >> >> >> -- Daniel Horim Choi Northwestern University Class of 2009 dhchoi(a)u.northwestern.edu or dchoi1024(a)gmail.com -- Daniel Horim Choi Northwestern University Class of 2009 dhchoi(a)u.northwestern.edu or dchoi1024(a)gmail.com

1 0

Compute individual Statistics
by Balaji Goparaju 08 Aug '08

08 Aug '08

Hi Doug, When i run selxavg3-sess -analysis LD-analysis -s LD-functional i seem to get errors in some other files, The output is as follows: [balaji-goparajus-computer:~/Desktop/subjectdata] balajigo% selxavg3-sess -analysis LD-analysis -s LD-functional -------------------------------------------------------------- selxavg3-sess logfile is /Users/balajigoparaju/Desktop/subjectdata/log/selxavg3-sess-bold-LD-analysis-080728180123.log -------------------------------------------------------------- ------------------------------------------- /Users/balajigoparaju/Desktop/subjectdata/LD-functional Mon Jul 28 18:01:23 EDT 2008 anadir = /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold/LD-analysis ------------------------------------------ ------- matlab output -------------------- Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. < M A T L A B (R) > Copyright 1984-2008 The MathWorks, Inc. Version 7.6.0.324 (R2008a) February 10, 2008 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> >> >> >> /Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> $Id: fast_selxavg3.m,v 1.55.2.2 2007/11/27 18:42:09 greve Exp $ outtop = /Users/balajigoparaju/Desktop/subjectdata Extension format = nii UseFloat = 0 INFO: acfbins is not set, setting to 10 INFO: mask is not set, setting to brain 1 LD-contrast.mat Loaded /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold/006/emotion.par as a par2 file. ERROR: empty nonpar matrix for mcextreg ??? Attempt to reference field of non-structure array. Error in ==> flac_taskregind at 37 nev = length(flac.ev); Error in ==> flac_customize at 267 flacnew.indtask = flac_taskregind(flacnew); Error in ==> fast_selxavg3 at 97 flac0 = flac_customize(flac0); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n Thank you for the help you have been providing!

1 0

RE: extending the pial surface and scuba
by 류철형 07 Aug '08

07 Aug '08

Dear freesurfer I’m one of the neurologists in South Korea and having an interest in the functional neuroimaging studies in neurodegenerative diseases. Recently, I’m planning to study the cortical thickness of various degenerative disorders and trying to learn the freesurfer (version 4.0.5), which is running on the brand new MacBook Pro (leopard) with core2duo intel CPU of 2.5GHz speed and 4MB internal RAM. Now, I am facing with some troubles. First, how can I edit or correct the underestimated pial surface. The MR signals (GE 3.0T, T1 axial SPGR sequence, 1mm slice thickness) acquired in the vertex gray matter and lower part of cerebellum were rather attenuated than the center of brain. Therefore, the freesurfer would classify upper part of the vertex gray matter into the extra-cerebral tissue. In other words, the thickness of the vertex was underestimated. How can I manually expand the boundary of vertex gray matter with tkmedit ? Second, the scuba did not work. When I type the scuba in the terminal, the ‘bus error’ come out and it do not work at all. Alternatively, I tried the scuba1 and it worked with some errors (stopping of scuba program and I have to force quit the X11 application). How can I correct the bus errors and use more advanced viewing and editing software in the freesurfer ? Thank you for reading my questions and I’m waiting for your kind answer. Chul Hyoung Lyoo, MD, PhD Instructor Department of Neurology Youngdong Severance Hospital Yonsei University College of Medicine 612 Eonjuro, Gangnam-gu Seoul, Korea Phone: +82-2-2019-3327 Fax: +82-2-3462-5904 E-mail: lyoochel(a)yuhs.ac

2 1

SNR maps
by Christian Battista 07 Aug '08

07 Aug '08

Hi freesurfers, I am using FSFAST on a group of 29 subjects...having run isxconcat-sess I am now doing the final quality control (Volume) step outlined in the FSFAST tutorial, which is to inspect the SNR maps. Inspecting the signal to noise ratio maps I am seeing 3 outliers (see attached), suggesting there is something strange going on with 3 participants' trials. I assume this means I should be excluding these participants from the analysis...but I am also wondering what the cause of the outliers might be, and whether it might be the result of a failed step earlier in the analysis. Is there anywhere else in the processing stream that I would be able to notice something is wrong? Take it easy, -Christian

2 1

Re-processing
by p.s.bjerkan＠studmed.uio.no 07 Aug '08

07 Aug '08

Hi! Have some subjects processed with 3.0. This version turned out to do wrong ICV-calculations. We therefore want to re-run with 3.0.2. (That version is chosen because the results will be compared with other subjects run with 3.0.2). Just asking this to be sure: If I re-run them now, it´s ok to run from autorecon2 (with 3.0.2) and further? That will include every manual edit and make new valid calculations in the aseg (including ICV)? Or is it necessary to think autorecon1, T1´s and legacy? Thanks! Petr Szulc Bjerkan

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