Freesurfer October 2012

freesurfer@nmr.mgh.harvard.edu

119 participants
191 discussions

WM/GM boundary changes and control points
by EK Kim 10 Oct '12

10 Oct '12

I already uploaded this problem 2 days ago, reprocessing the subject to make sure about control points. However when I added the control points to the left hemisphere, the right hemisphere surface was changed severely. I used the command line, recon-all -autorecon2-cp -s subjectID. Could you tell me why does it occur and how to deal with it? Best, EK

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assembling data
by Gregory Kirk 10 Oct '12

10 Oct '12

a have a bunch of data stored in the subj_id directories of the subjects for convieniance but it is already in the average surface space, but i want to assemble it into one file so i can run the glm. mris_preproc --fsgd subset.fsgd --target subset_average --hemi lh --meas winkler.mgh --out lh.surf.mgh does not work obviously as the subjects # verticies does not agree ERROR: number of vertices in /study5/aa-scratch/UTAH/freesurfer_subjects/AD33112_2/surf/lh.winkler.mgh does not match surface (163842,149346) because it thinks the surf is on the subj_id surface. how can i accomplish ? cheers greg

2 1

volumes per lobe
by Carolina Valencia 10 Oct '12

10 Oct '12

Hi FS users and developers, I need to obtain the volume per lobe (occipital, parietal, temporal, frontal) in a particular subjects and if it is possible divided by gray and white matter. I found similar topics in the mailing list, but I don't succeed to get this values. I follow the instructions for the FSv5.1 Using mri_annotation2label and mris_anatomical_stats but I got values for each hemisphere instead of lobes. mri_annotation2label --subject vol17 --hemi rh --lobesStrict rhlobesfile mri_annotation2label --subject vol17 --hemi lh --lobesStrict lhlobesfile then: mris_anatomical_stats vol17 rh mris_anatomical_stats vol17 lh I got values number of vertices = 115348 total surface area = 76188 mm^2 total gray matter volume = 282811 mm^3 average cortical thickness = 3.071 mm +- 1.034 mm average integrated rectified mean curvature = 0.149 average integrated rectified Gaussian curvature = 0.106 folding index = 4797 intrinsic curvature index = 391.1 Can somebody guide me? Thank you in advance, -- -- *Carolina Valencia * The information contained in this message and its attachments is confidential and intended for exclusive use of the recipients. If you received this email by error please notify the sender and delete it. The use, retention or distribution for any purpose is prohibited. Link is not responsible for damage caused by the contents of this message. The recipient should check for any presence of viruses or other defects.

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(Ir?)Regular durations for recon-all -all
by Denis-Alexander Engemann 10 Oct '12

10 Oct '12

Dear Freesurfers, presumably this is quite a newbie's question but I was wondering whether my recon-all times can be plausible if it takes less then 10 or 12 hours to perform the entire routine on a local machine. I'm using freesurfer 64 bit on Debian testing equipped with 16GB of RAM and Intel Core i7 CPUs (3.4Ghz), build-stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0. On superficial inspection, the results seem ok but I fear I'm overlooking something important. Any pointers would be of great help. Cheers, Denis ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Kennen Sie schon unsere app? http://www.fz-juelich.de/app

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Freesurfer and FSL
by Ana Arruda 10 Oct '12

10 Oct '12

Dear experts, I'm an MSc student and part of my final project is related to the measurement of the volume of the hippocampus. The last thing I have to do is to compare two softwares, FSL and Freesurfer. On Freesurfer, I've used the following commands: recon-all -i where_my_subject_is -autorecon1 -s output_name then, related to the same subject recon-all -autorecon2 -s output_name After approximately 12 hours, and after comparing the results of Freesurfer and FSL, I found that those obtained with Freesurfer are bigger than those obtained with FSL. According to the literature the results are the reverse. Do you know any idea what I'm doing wrong? Thank you for your attention, Ana Arruda

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Dimension Issues with mri_surf2surf
by Aimi Watanabe 10 Oct '12

10 Oct '12

Hello, My input to freesurfer is: mri_surf2surf --cortex --fwhm-src 5 --noreshape --hemi rh --tval [$output file] --sval [$input file] --srcsubject [$subject id] --trgsubject fsaverage --tfmt nii When I reopen the resulting image with Nibabel, the dimensions are 27307 x 1 x 6 x 296. While 296 is the time axis, I was hoping to get 27307*6 = 163842 vertices. I have replaced '--noreshape' with '--reshape', '--reshape_factor=6' and the bash output looks proper: 121010-16:49:28,430 interface INFO: stdout 2012-10-10T16:49:28.429912:Saving target data 121010-16:49:28,430 interface INFO: stdout 2012-10-10T16:49:28.429912:Reshaping 6 (nvertices = 163842) 121010-16:49:28,430 interface INFO: stdout 2012-10-10T16:49:28.429912:Saving to [$output file] However, it does not change the resulting image. I have also tried other file types that are not 'nii', like 'mgh', but this does not help either. Please advise? Also, I could easily make a work-around, and reshape the image from a(27307, 1, 6, 296) to b(163842, 1, 296) in FORTRAN (column-major) order. I.E.: 0~27306 then add the next set 27307~54613. If I do this, would the original vertex map be preserved? Thank you!

2 1

hippocampal segmentation
by Hugh Pemberton 10 Oct '12

10 Oct '12

Dear freesurfer crew, I'm having a few issues with segmentation around the hippocampus, I have included a few screenshots of main and aux vol where the hippocampus has been excluded even with the addition of control points. Have you got any tips for rectifying this? It's happened a fair few times with my subjects. Thanks very much in advance and all the best, Hugh

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PhD position available – Cognitive Neuroimaging of Language and Audition
by Narly GOLESTANI 10 Oct '12

10 Oct '12

Dear all, Applications are invited for a PhD in the newly established ‘Brain and Language Lab’ at the University of Geneva in Switzerland, under the supervision of Narly Golestani. Projects will include using functional MRI (fMRI), structural MRI (sMRI), diffusion tensor imaging (DTI) and electroencephalography (EEG) to better understand brain functional and structural plasticity arising from auditory training. The laboratory is affiliated with the Department of Clinical Neuroscience of the Faculty of Medicine at the University of Geneva, and is a member of the Geneva University Neuroscience Center (http://neurocenter.unige.ch/) Geneva offers a thriving international environment, with extensive cultural and outdoor activities, and a high quality of living. Applicants should have strong interest and a background in neuroscience and ideally also in language and/or auditory research. Prior experience with fMRI, sMRI, DTI and/or EEG is required. Salary will start at 45,540 CHF per year and will increase by about 2,200 CHF annually. Applications will be considered until the position is filled. Informal inquiries can be addressed to Narly Golestani (Narly.Golestani(a)unige.ch) Applications including a CV including list of publications, a statement of research interests, and the names and full contact details of two referees should be sent to: Narly.Golestani(a)unige.ch.

1 0

motion cut off
by Mürner-Lavanchy, Ines 10 Oct '12

10 Oct '12

Dear FreeSurfers, Due to motion I have to exclude participants from my analysis. Is there an objective measure which could serve as a cut off value concerning motion in the scanner? Can I find it in one of the FreeSurfer files generated through the recon-all process? Subjectively, one can see which images are good or good enough for segmentation. But I'd rather like to include or exclude participants based on an objective threshold. Thank you very much in advance, Best regards, Ines

1 0

Error with updated freeview.bin
by Irwin, William 09 Oct '12

09 Oct '12

Hello- I just downloaded the updated freeview.bin (8/23/2012) file (from: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86…) I am running Linux 64-bit (2.6.32-279.5.1.el6.x86_64 #1 SMP Tue Aug 14 16:11:42 CDT 2012 x86_64 x86_64 x86_64 GNU/Linux). When I tried to execute freeview, I got the following error: freeview.bin: symbol lookup error: freeview.bin: undefined symbol: _ZN9QListData11detach_growEPii I'm assuming there are updates, improvements to the newer version, which I what motivated me to update. Please advise. Thanks, Wil

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Freesurfer October 2012