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30088 discussions

Problems with hippocampal subfield segmentation
by Jürgen Hänggi 27 Jun '11

27 Jun '11

Dear FS experts We have some problems with the segmentation of hippocampal subfields. The recon-all finished without problems, but when using GEMS the following error occured: nan nan nan nan nan nan nan nan nan Singular: 0 m_BoundingBoxSize: [94, 66,144] minimalMappedCoordinate: [3.40282e+38, 3.40282e+38,3.40282e+38] maximalMappedCoordinate: [1.17549e-38, 1.17549e-38,1.17549e-38] Cropping with min [-1932735280 -1932735280 -1932735280] and max [-214748367 -214748367 -214748367] /Applications/freesurfer/bin/kvlSegmentHippocampalSubfields.sh: line 18: 58718 Segmentation fault kvlSegmentWithoutGUI configurationFileDeformableRegistration.txt failed to do kvlSegmentWithoutGUI configurationFileDeformableRegistration.txt Darwin Reinhard-Drobetzs-iMac.local 10.7.0 Darwin Kernel Version 10.7.0: Sat Jan 29 15:17:16 PST 2011; root:xnu-1504.9.37~1/RELEASE_I386 i386 recon-all -s 13716099 exited with ERRORS at Fri Jun 24 00:12:30 CEST 2011 I guess the problem occurred due to the NANs in the matrix, isn't it? Thanks in advance Regards Jürgen ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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Difference in hippocampal volume between scanners
by Jessica Liu 24 Jun '11

24 Jun '11

Hi everyone! I'm currently a summer student working at a lab which uses Freesurfer to measure hippocampal volumes. I noticed that scanning the same patient first on a GE 3T (Multi-channel head coil) and then a GE 1.5T (single-channel head coil) 24 hours later resulted in a 30% increase in the left hippocampus volume and a 18% increase for the right hippocampus based on the values in aseg.stats. Can anyone please comment on this and explain the large discrepancies? Thanks! Jessica Liu

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Error with tkmedit
by Antonella Kis 24 Jun '11

24 Jun '11

Dear Freesurfer experts, I am still a beginer in using Freesurfer v.5.1.0 I finished running the recon-all and I am trying to visualize the volumes and surfaces but I got an error wile using tkmedit. I will appreciate any help, suggestions. This is from bugr: FREESURFER_HOME: /usr/local/freesurfer/ Build stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 RedHat release: Fedora release 12 (Constantine) Kernel info: Linux 2.6.32.23-170.fc12.x86_64 x86_64 Here is what I was running. It also shows the error: [root@EW-LNX3 elysa]# tcsh setenv FREESURFER_HOME /usr/local/freesurfer/ setenv SUBJECTS_DIR $FREESURFER_HOME/subjects/june2011/_orig_/ tkmedit NPI002 brainmask.mgz \-aux T1.mgz -surfs \-segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt /usr/local/freesurfer//tktools/tkmedit.bin: error while loading shared libraries: libXmu.so.6: cannot open shared object file: No such file or directory Is this because I use a licence from the same version but installed on another computer? Thank you very much!

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Not label correctly on Longitudinal Procees on FS5.1
by Yiyu Chou 24 Jun '11

24 Jun '11

Dear Freesurfer users, I was running the longitudinal process using FS 5.1, but I noticed that the segmentation doesn't label voxels correctly on part of the cerebral-cortrex. Please have a look at the attached snapshot: Left: cross-sectionally process - looks good Right: longitudinal process - labels were not correct on cerebral-cortex (dash-line region). I wonder why the cross-sectionally process does a better job than the longitudinal one. Is there a way to fix it ? Or I have to manually edit aseg.mgz ? I would appreciate it if you can give me some suggestions. Thanks !! Yi-Yu Chou

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PhD position in structural imaging of the vulnerability to develop schizophrenia
by Marie Schaer 24 Jun '11

24 Jun '11

PhD position in structural imaging of the vulnerability to develop schizophrenia We are seeking a highly motivated student for a doctoral position in the Behavioral Psychiatry and Neuroimaging laboratory in Geneva. This group, headed by Prof. Stephan Eliez, provides a multidisciplinary approach to the study of the prodroms of psychosis in a population at risk for schizophrenia for genetic reasons (22q11.2 deletion syndrome). The cohort of patients with 22q11 deletion syndrome recruited in Geneva since 2001 constitutes one of the largest and more extensively assessed worldwide to date, including longitudinal psychiatric and cognitive evaluations, as well as structural (T1-weighted and DTI) and functional (task-related and resting state) brain imaging data. In the first part of the PhD, the candidate will learn a critical and independent application of image analysis techniques. A specifically emphasis will be put on the identification of predictors of the emergence of psychosis or schizophrenia based on the longitudinal data analysis. He / she will benefit from the large amount of already collected MRI data as well as participate in the ongoing data recruitment (accompany the participants to the scanner). From the beginning, the candidate will be required to actively write first author articles. Through the participation at the structured PhD program offered by the lemanic neuroscience school of the Geneva and Lausanne Universities (http://www.unil.ch/ln/page56876.html) the candidate will have the opportunity to build a larger neuroscience network of high quality. The candidate should hold a Master’s degree in medicine, biology, psychology, neuroscience or a related field. Experience with brain imaging is an advantage. Salary is provided according to the scale of the Swiss National Science Foundation. The starting date is October 1st, 2011. The candidates’ applications will be reviewed from July 15th, 2011. Later applications will be considered only if the position was not filled. Interested candidates should send their CV along with a letter of motivation and their detailed marks during their Master (or latest achieved degree) to Dr. Marie Schaer, marie.schaer(a)unige.ch.

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Does the order of subjects need to match in .fsgd and isxconcat?
by John Richey 23 Jun '11

23 Jun '11

Dear freesurfer experts, I have a simple question about the use of isxconcat-sess. I plan to conduct a between-groups analysis later (using mri_glmfit), but as I am creating my osgm using isxconcat-sess, is it is necessary for the text file list of subjects (indicated by -sf) to match the order of subjects in my .fsgd file? Of course the .fsgd file will contain information about the group membership, but I wasn't sure if the order of subj had to line up in both files, nevertheless. Many thanks!

2 1

(no subject)
by leonardo kay 23 Jun '11

23 Jun '11

Hi all Do anyone have experience doing parcellations using AXIAL T2 FLAIR acquisitions? What sequence do you recomend most for parcellation/labelling under freesurfer? Best regards, -- Leo Kay.

2 1

How to obtain volume of specific structure
by ZhiLiangLong 23 Jun '11

23 Jun '11

Hi all: After all "recon-all -all" processing has been completed for all subjects ,I want to obtain volume of specific structure of each subject(e.g., the volume of Caudate Nucleus). But i have no idea about it,Are there some tools or commands that can help? I hope you can give me some suggestions . Thanks!

3 2

mri_convert & PD
by G. William Chapman IV 23 Jun '11

23 Jun '11

Hello all, I'm attempting to use mri_convert in order to match the slice size and thickness of T2 and PD images to the Freesurfer T1 images, after converting the norm.mgz and the T2/PD images to .nii.gz. For the T2 I'm using: mri_convert ${SUBJECT}/T2/T2.nii.gz -rl ${SUBJECT}/mri/norm.nii.gz --like ${SUBJECT}/mri/norm.nii.gz ${SUBJECT}/T2/T2_like_norm.nii.gz And having no problems. However, using the same code for the PD images I'm arriving at a bus error each time (output below). Is there any possible work around for this? (freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0) --- bash-3.2$ mri_convert ${SUBJECT}/PD/PD.nii.gz -rl ${SUBJECT}/mri/norm.nii.gz --like ${SUBJECT}/mri/norm.nii.gz ${SUBJECT}/PD/PD_like_norm.nii.gz mri_convert 003_S_0907_M00/PD/PD.nii.gz -rl 003_S_0907_M00/mri/norm.nii.gz --like 003_S_0907_M00/mri/norm.nii.gz 003_S_0907_M00/PD/PD_like_norm.nii.gz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from 003_S_0907_M00/PD/PD.nii.gz... TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 2.05103e-10, 0) j_ras = (-2.05103e-10, -1, 0) k_ras = (-0, -0, 1) reading template info from volume 003_S_0907_M00/mri/norm.nii.gz... INFO: transform src into the like-volume: 003_S_0907_M00/mri/norm.nii.gz Bus error

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Re: [Freesurfer] error while loading shared libraries:libtiff.so.3
by Daniel Ferreira Padilla 23 Jun '11

23 Jun '11

Thanks Jordi, thanks Krish, The problem goes on. I have checked my libtiff files ($ sudo apt-cache search libtiff) and have got exactly the same as you, Jordi. The problem is that libtiff.so.3 is not between them. I also managed to do the symbolic link with sudo ln -sf usr/lib/libtiff.so.4 /usr/lib/libtiff.so.3. So, as I have 6 different lib folders I have created this libtiff.so.3 link in each one of them, cause I do not know where recon-all is pointing to. So, these are my lib folders: /lib /lib32 /lib64 /usr//lib /usr//lib32 /usr/ /lib64 Only in those three folders inside /usr/ have got the following files: pngtools - series of tools for PNG (Portable Network Graphics) images libtiff-doc - TIFF manipulation and conversion documentation libtiff-tools - TIFF manipulation and conversion tools libtiff4 - Tag Image File Format (TIFF) library libtiff4-dev - Tag Image File Format library (TIFF), development files libtiffxx0c2 - Tag Image File Format (TIFF) library -- C++ interface libtiff-opengl - TIFF manipulation and conversion tools So, perhaps recon-all is pointing to libs outside /usr/, where I do not have these files. Should I paste them on it? And how can I do it by command line? Please, any other idea? Thank you very much Daniel 2011/6/20 Krish Subramaniam < <mailto:krish@nmr.mgh.harvard.edu> krish(a)nmr.mgh.harvard.edu> Hi Daniel You get permission denied because you need write permissions for /usr/lib ( wherever libtiff.so.3 is ). If you think you have the permissions, prefix your "ln" command with a "sudo" and it'll ask for your password, and that should work successfully. If you don't have permissions, you need to ask your system administrator to do so. -Krish On Jun 20, 2011, at 5:44 AM, Daniel Ferreira Padilla wrote: Dear all, I'm using Ubuntu 10.10 and have the same problem only when working with 4.5 version (I also use 5.1 version without any problem). I have followed previous suggestions making a symbolic link named libtiff.so.3, but it gives me back the message "denied permission". Also tried to install it with "sudo aptitude install ia32-libs" but it did not recognize "aptitude" command. So I tried with "sudo apt-get install ia32-libs" instead and it was ok, but I am still having the same problem. So, what could I do? Can I download libtiff.so.3 from somewhere? How can I avoid that "denied permission"? Thank you very much for your help. Daniel Ferreira #-------------------------------------------- #@# Cortical ribbon mask Sat Jun 18 17:57:36 WEST 2011 /home/neuroimagen/DANI/subjects/uu0148_36_1/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance uu0148_36_1 mris_volmask.bin: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory Linux neuroimagen 2.6.35-28-generic #50-Ubuntu SMP Fri Mar 18 18:42:20 UTC 2011 x86_64 GNU/Linux recon-all exited with ERRORS at Sat Jun 18 17:57:36 WEST 2011 _______________________________________________ Freesurfer mailing list <mailto:Freesurfer@nmr.mgh.harvard.edu> Freesurfer(a)nmr.mgh.harvard.edu <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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