Freesurfer April 2010

freesurfer@nmr.mgh.harvard.edu

102 participants
147 discussions

scripting get label form talirach point
by Ben Hamida Cammoun Leila Faiza 07 Apr '10

07 Apr '10

Hello, I am trying to check if some talairach coordinates of AI (auditory primary) (from paper) are in the transverstamporal label, on am subjects. To do this, and thanks to your answers I used the commands line in tksurfer: select_talairach_coordinate x y z mark_vertex $select 1 and I can read: the vertex number and the label but I have to get the vertex number and the label for 5 points and 40 subjects, do you know how to get the vertex number and the label in a script? I tried func_select_label which gives me the label in the command line but I don't know how to get it in a file. Thanks a lot for this help

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Using own atlas - file conversion
by Pernille Iversen 07 Apr '10

07 Apr '10

Dear all, We have created our own atlas based on several subjects. We have the atlas in analyze volume files and would like to know if we can somehow convert these files into the .gcs format without having to go through all the manual steps of creating a template and labels. Thanks, Pernille Iversen

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Is this longitudinal result correct
by Guang Zeng 06 Apr '10

06 Apr '10

Hi, there, I ran the freesurfer longitudinal stream to analysis scans from two tps. I attached the segmentation results of one time-point to its orig.mgz and the longitudinal brainmask, I can see part of the brainmask are not labeled, I understood that it is because of the brainmask is the mean or median of the norm.mgz from different time points. Just wanna double check that the results is ok. Thanks! Guang _________________________________________________________________ The New Busy is not the too busy. Combine all your e-mail accounts with Hotmail. http://www.windowslive.com/campaign/thenewbusy?tile=multiaccount&ocid=PID28…

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How to convert a cortical thickness map to a NIFTY file
by Xiaojing Long 06 Apr '10

06 Apr '10

Hi, I have a question regarding how to convert a cortical thickness map (i.e. lh.thickness) to a NIFTY file. I have a subject called 'subjid' and I run recon-all on it. So I got the ?h.thickness files. Does freesurfer provide a tool to convert the surface file to a nifty file? I tried using the command 'mri_surf2vol' as follows: mri_surf2vol --surfval lh.thickness --hemi lh --template orig.mgz --volregidentity subjid \ --outvol /path/to/lh.thickness.nii The thickness values of the output lh.thickness.nii are integers between 1 and 3. But the original thickness values are between 0~5 and not all of them are integers. Could someone know what's wrong or suggest another tool? Thanks in advance. Best, Xiaojing

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radiologic convention ?
by ridatta＠mail.med.upenn.edu 06 Apr '10

06 Apr '10

Hello All, If my input images are in Analyze format in Radiologic convention, does FreeSurfer "know" that the MPRAGE images are in radiologic convention (right side of the brain on the left side of the image)? How do we confirm this? Thanks Rito

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why same structure has two different volume in aseg.stats and wmparc.stats, for example: amygdala.
by liyari5018 06 Apr '10

06 Apr '10

Hi freesurfer experts, why same structure has two different volume in aseg.stats and wmparc.stats , for example: amygdala. thanks for your reply! LJ

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dt_recon failed
by movado 03 Apr '10

03 Apr '10

Hi all, I use dt_recon on DTI scans from Siemens machine. The command I used is > dt_recon --i k1/ep2d/81678191 --s k1 --o k1_DTI The error message is as follows sysname Linux hostname movado-laptop machine x86_64 user movado FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /usr/local/freesurfer/subjects/k1_DTI/dwi-ec.nii logyflag 1 X /usr/local/freesurfer/subjects/k1_DTI/dwi-infodump.dat usedti 1 glmdir /usr/local/freesurfer/subjects/k1_DTI IllCondOK 0 DoFFx 0 Creating output directory /usr/local/freesurfer/subjects/k1_DTI Loading y from /usr/local/freesurfer/subjects/k1_DTI/dwi-ec.nii Using DTI ERROR: cannot extract sDiffusion.alBValue[1] from /usr/local/freesurfer/subjects/k1_DTI/dwi-infodump.dat What can I do to solve this problem? Thank you advance for the help. movado

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Retinotopy analysis ERROR: selfreqavg failed
by Yuhong Jiang 02 Apr '10

02 Apr '10

Hi, I want to provide more information about the retinotopy analysis error in case someone has insight about the problem. Using the same exact commands (mkanalysis-sess.new, then sfa-sess), I was able to successfully run the retinotopy commands in my old Linux box (the version of sfa-sess was from 2005, and we used matlab 6.5). However, the program hang using the newest version of freesurfer on Linux (the version of sfa-sess was from 2007, MATLAB 7.8). The program hang almost immediately. On Mac OS 10.6 using MATLAB 7.6, the command sfa-sess also hang with an error message of "ERROR: selfreqavg failed". I tried to replace the new sfa-sess with the old sfa-sess, and the new selfreqavg with the old selfreqavg, but the problems were not fixed. Is there a bug in the binary files that makes them incompatible with higher versions of MATLAB, or Mac OS 10.6, or Linux 2.6.9-89.0.15.ELsmp? Thanks for your insight. --Yuhong -- ---------------------------------------------------------- Yuhong Vanessa Jiang, PhD, Associate Professor & McKnight Presidential Fellow Department of Psychology, Univ of Minnesota jiang166(a)umn.edu, 612-625-7003 http://jianglab.psych.umn.edu/ ----------------------------------------------------------

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Correcting subcortical segmentation
by John Fredy 01 Apr '10

01 Apr '10

Hello all, I'm trying to obtain a set of statistics of subcortical segmentation from a pacient with Huntington's disease. The tutorial of freesurfer shows six possible case of error in freesurfer: correcting white/gray surfaces, topological errors, skull removing, talairach transformation, among others. But, how I can correct subcortical segmentation error? Thanks in advance

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Recon-all problem (with talairach)
by Janani Dhinakaran 01 Apr '10

01 Apr '10

Hello everyone, I wanted to know what I can do to fix this error- it occurs when I'm running recon-all -all -s Subject Tue Mar 30 11:27:20 BST 2010 talairach_avi done #-------------------------------------------- #@# Talairach Failure Detection Tue Mar 30 11:27:20 BST 2010 /home/s0964091/Desktop/Newdata/JS/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 CRIC-0012 2.6.31-20-generic #58-Ubuntu SMP Fri Mar 12 04:38:19 UTC 2010 x86_64 GNU/Linux recon-all exited with ERRORS at Tue Mar 30 11:27:20 BST 2010 Thank you for your help Jan -- I am the Sun, I know no darkness.

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Freesurfer April 2010