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30088 discussions

multiple frames error message for recon-all
by Chan, Noel Yan-Ki,Ph.D. 10 Dec '13

10 Dec '13

Hi, I'm trying to do recon-all for a file, and it gave me this multiple frame error message: #@# MotionCor Mon Nov 25 13:11:40 EST 2013 Found 1 runs /autofs/cluster/lazar/projects/Noel/SUBJECTS_DIR/BHI_BJU-345_pre_lazar/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /autofs/cluster/lazar/projects/Noel/SUBJECTS_DIR/BHI_BJU-345_pre_lazar/mri/orig/001.mgz has 4 frames If this is a multi-frame MEMPRAGE image, use mri_concat --rms to combine echo frames. Linux compute-0-73 2.6.32-358.23.2.el6.x86_64 #1 SMP Wed Oct 16 18:37:12 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s BHI_BJU-345_pre_lazar exited with ERRORS at Mon Nov 25 13:11:47 EST 2013 For more details, see the log file /autofs/cluster/lazar/projects/Noel/SUBJECTS_DIR/BHI_BJU-345_pre_lazar/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting May I ask what should I do to solve this problem? There are actually two files which give me the same error message: BHI_BJU-345_pre_lazar (pbsjob_30) and BHI_JJA-329_pre_lazar (pbsjob_33) Thanks, Noel --- Noel Yanki Chan, PhD Department of Psychiatry Neuroscience Laboratory of Sara Lazar, PhD Harvard Medical School Massachusetts General Hospital Building 120, 2nd avenue, Suite 103 Charlestown, MA 02129 Tel: 617-643-5078 (lab) 607-229-7096 (cell)

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Cortical thickness values of significant clusters
by Sinead Kelly 10 Dec '13

10 Dec '13

Dear Freesurfer users, I have just ran mri-glmfit on cortical thickness data and corrected for multiple comparisons using Monte Carlo Simulation. I have significant clusters (cwp < .05), however, when I analyse the average thickness measures from the xxx.y.ocn.dat file in SPSS, there are no significant differences between my groups. I'm not sure if I am using the correct approach to extract thickness values for the significant clusters. Thank you for your help, Sinead -- Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8

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after PialEdit_tktools
by Rujing Zha 10 Dec '13

10 Dec '13

Dear all, I run "recon-all -autorecon-pial -s subjects" after editing the pial by PialEdit_tktools. However I only find "-autorecon2-pial" option in recon-all manual. So I donot know whether I should run the "recon-all -s subjects -autorecon3" to complete all the 31 stages? Thanks. All the best. 2013-12-10 Rujing Zha School of Life Science University of Science and Technology of China E-mail: zharj(a)mail.ustc.edu.cn charujing(a)gmail.com charujing123(a)163.com

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Occipital cortex segmentation
by Megha K. 10 Dec '13

10 Dec '13

Dear Sir/Madam, I am using freesurfer for 3T MRI analysis of visual cortical thickness in elderly patients with ophthalmic disease. We are having a bit of trouble with the accuracy of cortical segmentation in the visual cortex (namely the pericalcarine region) as the cortex is quite thin in our patients (compared to controls). You can see in the attached image that whilst there is smooth cortical segmentation in the peri-calcarine region, the cortex is not visible to the naked eye. If you have any ideas on improving accuracy, I would be very grateful. Thanks Megha

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viewing the atlas?
by Gregg, Brian E. 09 Dec '13

09 Dec '13

Hello, I'm looking for a way to view the Desikan-Killiany atlas. I'd like to open the file $FREESURFER_HOME/average/?h.curvature.buckner40.filled.desikan_killiany.gcs in Freeview (or Tkmedit, or similar) and be able to see the segmentations and segmentation names, as well as pan through all of the slices. I've searched the archives and the wiki, but I haven't found anything. Can anyone point me in the right direction please? Thanks, Brian

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qdec analysis with 2 covariates
by Jon Wieser 09 Dec '13

09 Dec '13

HI freesurfer experts I want to do an analysis in qdec with 2 groups(ADHD, and Marijuana usage) and 2 covariates(age and gender) to study the effect of these factors on cortical thickness. I can only select a covariate in the qdec gui. is there a way to select both covariates in the qdec GUI? Thanks Jon -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219

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mris_anatomical_stats error
by krista kelly 09 Dec '13

09 Dec '13

Hi, I'm trying to run mris_anatomical_stats to get cortical thickness from labels for each participant but I keep getting the following error: MRISread: file '/Applications/freesurfer/subjects/MB19/surf/lh.thickness' has many more faces than vertices! Probably trying to use a scalar data file as a surface! Here is the command I'm using: mris_anatomical_stats -l MB07/label/lh.V1.thresh.label -b -f MB07/stats/lh.V1.thresh.thickness.stats MB07 lh thickness I wasn't able to find a suitable solution from the archives. I used the same command to get area.pial stats without any problems. Any help is appreciated! Krista

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Paired analysis: use of covariates
by Aldo Cordova 09 Dec '13

09 Dec '13

Dear FreeSurfer experts, I'm trying to implement the steps you indicate in the Paired Analysis' wiki site, but I still don't get something: In this site, you show the next FSGD file: GroupDescriptorFile 1 Class Main Variables Age Input subject1pair Main 30 Input subject2pair Main 40 Input subject3pair Main 50 Input subject4pair Main 60 Accordingly, "Age" is a variable whose value is the same for each pair of subjects (i.e., it is a measure of between-pair differences, but does not contain information about differences found in subjects of the same pair). Nevertheless, I need to introduce some covariates of interest whose value would indicate within-pair differences (i.e., the difference between "subjectN" and "subjectNmatch", where "N" is the arbitrarily assigned pair number). I made the next FSGD, but I'm wondering it's not correct (is it?): GroupDescriptorFile 1 Title trait1_trait2_paired MeasurementName thickness Class male Class female Variables Age trait1_diff trait2_diff Input subject1pair female 24 150 1850 Input subject2pair male 41 -200 -2090 Input subject3pair female 48 50 -6508 Input subjec4tpair male 53 -100 -7100 Input subject5pair female 36 150 1950 . . . In this FSGD, the last two variables ("trait1_diff" and "trait2_diff") would represent within-pair differences. As you can see, there are both positive and negative values, depending on the random order of individuals within a pair. Afterwards, contrast files such as "0 0 0 0 0.5 0.5 0 0" or "0 0 0 0 0 0 0.5 0.5" would be used to check whether "trait1_diff" or "trait2_diff" have an effect on cortical thickness, regressing out the effects of "gender", "Age" and either "trait2_diff" or "trait1_diff". Could you please tell me if the FSGD table is correct? If it isn't, how to implement such an approach? (I.e., how to use both between-pair and within-pair variables?) Also, are the contrast files mentioned above correct? Thank you in advance, Aldo

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New features in TRACULA
by Anastasia Yendiki 09 Dec '13

09 Dec '13

Hi all - I have just posted a tracula software update. This update adds some new functionality without any changes to any existing functionality, so you can use it with any analyses you have already done in 5.3. What's new: 1. Compute measures of head motion, as in our recent paper: http://www.sciencedirect.com/science/article/pii/S1053811913011312 2. Makes it easier to perform "along-the-tract" type analyses by combining the FA/MD/etc values from multiple subjects by position along each tract. 3. Gradient vector tables can now be different for each scan, they can be formatted in columns or rows, and blank lines at the end of the table should not pose a problem. 4. Fixed a small scripting bug that was causing the longitudinal stream not to run at all on certain platforms. You can get the update here: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates Download the file for the appropriate platform (same as your freesurfer 5.3 distribution), unzip it, and copy the files directly into your $FREESURFER_HOME/bin. The trac-all wiki page has been updated, with the new command-line options shown in red: http://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Arguments The tracula tutorials have also been updated with info on how to use these new features. Specifically: 1. For measures of head motion, see "Outputs from quality assessment" in: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaOutputs 2. For along-the-tract analyses, see "Anisotropy and diffusivity along the trajectory of a pathway" in: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics 3. For new options for specifying gradient tables, see "Specify the diffusion-encoding gradient table" in: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula Enjoy and thank you for your feedback, a.y

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Research Fellow Positions on Imaging Genetics of Infant Brain
by Anqi Qiu 09 Dec '13

09 Dec '13

Postdoctoral Fellow Position on Imaging Genetics of Infants Job description: Computation functional anatomy laboratory at National University of Singapore (http://www.bioeng.nus.edu.sg/cfa) focuses on brain and cognition studies using neuroimaging techniques. Our group is leading a large-scale longitudinal neurodevelopmental project from birth onwards in Singapore. The project examines neurocognition using EEG and eye trackers, brain development using diffusion tensor imaging (DTI), resting-state fMRI, and structural MRI, genetic and epigenetic influences on cognition and brain. Thus far, we have collected both functional and anatomical imaging as well as genetic and epigenetic data of 200 newborns and their follow-up at six months. The follow-up scanning at 4, 6, and 8 years will start soon. We are looking for a research fellow who is interested in developing and (or) employing pattern recognition approaches to understand the relationship of the brain with psychopathology in early life and how environmental factors and genetics influence such relationship. Or the candidate is interested in developing spatial-temporal analysis tools for this longitudinal datasets. Requirements: Ph. D or MD Neuroimaging Research background is preferable but necessary Knowledge in multivariate statistical analysis is necessary Good communication and writing skills in English language If you are interested in the jobs listed above, please send your CV to Associate Prof. Anqi QIU Department of Biomedical Engineering National University of Singapore Email: bieqa(a)nus.edu.sg Phone: +(65) 6516 7002

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