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30132 discussions

Hippocampal subfield segmentations
by newfei＠nmr.mgh.harvard.edu 27 Jun '11

27 Jun '11

Hi, I have a couple of questions about hippocampal subfield segmentations generated using the kvlQuantifyHippocampalSubfieldSegmentations.sh script (recons performed using version 5.1). The volumes obtained for each individual subfield are systematically larger than the total hippocampal segmentation volume generated by the recon-all. These volumes are also larger than the volumes in the paper (van Leemput, 2009) where CA1: 537-935 mm^3 and CA4/DG: 526 mm^3. For example in the dataset that I am working on , a typical subfield volume in the right hippocampus would be 2270 mm^3; CA2-3: 6477 mm^3; CA4-DG: 3796 mm^3.The sum of all subfields is 24437 mm^3. c.f. hippocampal volume obtained from aseg.stats:3688 mm^3 First, are my values correct? Second, are the discrete subfield volumes supposed to match up with the hippocampal volume from aseg.stats? Thanks, New Fei

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Freeview Overlay
by iacono＠nmr.mgh.harvard.edu 27 Jun '11

27 Jun '11

Hi all, I haven't had any answer to my post, so I give another try. Hope it doesn't bother you. I am trying to overlay a map on a specific subcortical structure (the caudate). -I obtained the surface of the structure using the command: mri_tessellate structure.nii.gz 1 lh.structure.surf -then I projected my map on the surface using: mri_vol2surf --mov map.nii --regheader structure --hemi lh --surf structure.surf --projdist 0 --fwhm 5 --out projected_map.mgz --interp trilinear Everything seems to work properly. I am able to see the result using tksurfer. However, when I try to overlay projected_map.mgz on lh.structure.surf using freeview I experience a segmentation fault issue. It seems that the software looks for the WM, the pial, the curv, etc surfaces. Obviously I don't have these information, since I am projecting the map only on the caudate nucleus. Is it mandatory to have these inputs? Could you give me an advice about that? Thanks Maria

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Help with tkmedit
by Sandy Goncalves 27 Jun '11

27 Jun '11

Hello, I am brand new to this software (and command for that matter) and need some help. After installing all the software, when I enter tkmedit in the xterminal, I receive an error message that looks like this: X Error of failed request: BadRequest (invalid request code or no such operation) Major opcode of failed request: 128 (Apple-DRI) Minor opcode of failed request: 1 () Serial number of failed request: 16 Current serial number in output stream: 16 Interestingly, when I type in tksurfer, this works. So I'm not sure what I should do in order to get tkmedit to work! Any help would be great! Thanks, Sandy

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Error while loading shared libraries: libXmu.so.6
by Antonella Kis 27 Jun '11

27 Jun '11

Dear Freesurfer experts, 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! Antonella

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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!

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