Freesurfer

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30097 discussions

FSFAST- Cerebellum
by sabin khadka 16 Jun '16

16 Jun '16

Hi all, I am trying to extract mean time series BOLD data using FSFAST from Cortical ROIs + sub cortical ROIs and cerebellum. preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305 -fwhm 6 -per-run -stc odd mri_segstats --annot fsaverage lh aparc --i rest210/bold/001/fmcpr.odd.sm6.fsaverage.lh.nii.gz --excludeid 1000 --excludeid 1004 --avgwf CorticalTimeSeries_lh.txt mri_segstats --annot fsaverage rh aparc --i rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz --excludeid 2000 --excludeid 2004 --avgwf CorticalTimeSeries_rh.txt and for cortical time series mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab /opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id 12 --id 13 --id 17 --id 18 --id 26 --id 49 --id 50 --id 51 --id 52 --id 53 --id 54 --id 58 --i rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz --avgwf subCorticalTimeSeries.txt But I am not sure on how exactly to extract time series from cerebellar regions. So if I want to extract time series from regions as described in Buckner et.al 2011. Could I just use mri_segstats for the labels 601-628 in FreeSurferCololLUT.txt? If not could you please direct me to processes that I can use. Cheers, Sabin Khadka

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Hippocampal subfields error
by Greenberg, Jonathan 16 Jun '16

16 Jun '16

Hi all I ran recon-all on data from about 60 participants pre and post an intervention, with the hippocampal subfields flag (e.g. "recon-all -all -subjid SPS01-1910_pre_lazar -hippocampal-subfields-T1"). The recon-all.log file states that the process finished without errors. However, the hippocampal-subfieldsT1.log indicated the following: "Error:Cannot find CTF archive /autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf" (see below for the full content of hippocampal-subfieldsT1.log). I tried to run only the hippocampal subfield recon-all again (e.g. "recon-all -s recon-all -all -subjid SPS01-1910_pre_lazar hippocampal-subfields-T1") and received the same error message. I tried to look in the indicated folder ("/autofs/cluster/freesurfer/centos6_x86_64/dev/bin") and found a file named segmentSubjectT1_autoEstimateAlveusML (without the ctf extension). I do not know if this is the source of the problem. My FREESURFER_HOME directory is /autofs/cluster/freesurfer/centos6_x86_64/stable6/. My SUBJECTS_DIR is /autofs/cluster/lazar/Projects/jonathan-miracle/unpacking-dicoms/SUBJECTS_DIR/. Any suggestions? (full hippocampal-subfieldsT1.log below) Thank you! Jonathan hippocampal-subfieldsT1.log content: #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) left Thu Jun 16 09:58:23 EDT 2016 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/usr/local/freesurfer/stable6/MCRv80/runtime/glnxa64:/usr/local/freesurfer/stable6/MCRv80/bin/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64: Error:Cannot find CTF archive /autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) right Thu Jun 16 09:58:26 EDT 2016 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/usr/local/freesurfer/stable6/MCRv80/runtime/glnxa64:/usr/local/freesurfer/stable6/MCRv80/bin/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64: Error:Cannot find CTF archive /autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf

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Job opening: Computational Neuroscience Faculty
by Kendrick Kay 16 Jun '16

16 Jun '16

Computational Neuroscience Faculty University of Minnesota, Minneapolis, MN, USA The University of Minnesota seeks 2 scientists with documented backgrounds and interests in using brain imaging and computational neuroscience to understand brain function in health and disease. The University of Minnesota seeks to fill two newly-created positions at the level of Assistant Professor, Associate Professor and/or Professor. For each position, rank and tenure status will be commensurate with experience. The research emphasis can be basic, translational or disease-focused neuroscience using innovative modeling and data analysis techniques. Appropriate tenure home departments would depend on the expertise, background and interest and could include: Neuroscience, Radiology, Psychiatry, Neurology, Psychology, Computer Science and Engineering, Biomedical Engineering, or Electrical and Computer Engineering. Irrespective of tenure home department, the successful candidate will be housed at the CMRR, which is an interdepartmental and interdisciplinary research laboratory that provides state-of-the-art instrumentation, expertise, and infrastructure for high field MRI research. CMRR plays a key role in the NIH’s Human Connectome Project and is equipped with magnets ranging in field strength from 3 to 10.5 Tesla for human imaging and up to 16.4 T for small animal model studies. To apply, please see http://neurojobs.sfn.org/jobs/8170600 The University of Minnesota is an Affirmative Action/Equal Opportunity Employer Candidates will have a Ph.D., M.D./Ph.D. or similar degree in neuroscience, biophysics, psychology, biomedical engineering or a related discipline. Background and training should include research experience in a combination of the following domains: cognitive neurosciences, computational neuroscience, and brain imaging technology, in particular Magnetic Resonance Imaging (MRI). The demonstrated ability to work in a collaborative, transdisciplinary and interactive environment is a requirement. The successful candidate will be expected to complement and exploit the unique capabilities that exist in the Center for Magnetic Resonance Research (CMRR, www.cmrr.umn.edu) in high field MRI. -- Kendrick Kay, PhD Assistant Professor Center for Magnetic Resonance Research, Room 2-116 University of Minnesota, Twin Cities Web: http://cvnlab.net E-mail: kay(a)umn.edu

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unit for hippocampus segmentation results
by Fengji Geng 16 Jun '16

16 Jun '16

Hi freesurfer experts, We used the development version of freesurfer 6.0 to segment hippocampus. We are wondering what the unit is for the segmentation results. Thanks, -- Fengji Geng

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Found 0 unique series
by Raney, Talia L. 15 Jun '16

15 Jun '16

Hi FreeSurfer users, I've been running dcmunpack and I get an error that said Found 0 unique series, even though it has dicom files. What does this mean and what could I do to fix the problem? Best, Talia

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wm.mgz edits
by marco mcsweeney 15 Jun '16

15 Jun '16

Dear all, I have a few questions regarding wm.mgz edits. I am very new to this area and have only recently started using Freesurfer so please excuse me if my questions appear naive or misinformed. I have managed to make most of the necessary edits needed to fix skullstrip errors, intensity normalization errors and pial errors, but I am a bit stuck when it comes to fixing topological defects. My question relates to what should or should not be included in the wm.mgz. Apart from the optic chiasm, which I have removed, is it normal to have, what appear to be, multiple specs included in the wm.mgz which when the aseg is loaded turn out to be parts of the amygdala and hippocampus. When I view the smoothwm.nofix these appear as jagged shard like shapes protruding out from the surface. In one publication I saw recently it was suggested that these should be removed but should this be done if they are parts of the amygdala and hippocampus. I am worried about this as these are the 2 main subcortical areas I will be focusing on. Also, is it normal for the wm.mgz to include parts of the cerebral cortex (labelled as such in the aseg). Also, most of the scans I am working with have numerous holes and handles and this is taking a very long time to fix. I have tried to run the automatic topology fixer again. This has helped a bit but the scans still require a lot of edits. Could this be down to the quality of the scans or could it be that I have edited too much - control points for example. I have followed the advice given and have tried not to make too many edits, but having said that it has taken me a very long time. Any advice in relation to any of these questions would be very very very much appreciated. Best wishes Marco

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selxavg3-sess error
by Francesca Strappini 15 Jun '16

15 Jun '16

Hi Freesurfer experts, I'm re-posting this message because I think it got lost. I'm trying to analyze some phase-encoded data with the eccentricity protocol for retinotopic data and I'm having troubles with selxavg3-sess. I run the following commands: mkanalysis-sess -analysis OrderDisorder.idsubj.lh -surface idsubj lh -TR 2 -retinotopy 24 -paradigm rtopy.par -fwhm 0 -per-run -nskip 5 -fsd bold selxavg3-sess -a OrderDisorder.idsubj.lh -s idsubj_OrderDisorder_continous and I got this error message: Found 122573/130829 (93.7) voxels in mask Creating Design Matrix ... creation time = 0.019 sec DoMCFit = 1 ntptot = 875, nX = 80, DOF = 795 Saving X matrix to /usr/local/freesurfer/fsfast/OrderDisorder_new/MK_OrderDisorder_continous/bold/OrderDisorder.MishaK.lh/Xtmp.mat Error using svd Input to SVD must not contain NaN or Inf. Error in cond (line 35) s = svd(A); Error in fast_selxavg3 (line 279) XCond = cond(XtX); Thanks! Best Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini(a)weizmann.ac.il

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Fwd: Getting the pial surface to cover the entire medial temporal lobe structures
by David Groppe 15 Jun '16

15 Jun '16

Dear Free Surfers, I am using FreeSurfer's pial surface to map ECoG electrodes onto the FreeSurfer average brain for group analyses via these two methods: Dykstra, A. R., Chan, A. M., Quinn, B. T., Zepeda, R., Keller, C. J., Cormier, J., et al. (2011). Individualized localization and cortical surface-based registration of intracranial electrodes. *NeuroImage*, 1–42. http://doi.org/10.1016/j.neuroimage.2011.11.046 Yang, A. I., Wang, X., Doyle, W. K., Halgren, E., Carlson, C., Belcher, T. L., et al. (2012). Localization of dense intracranial electrode arrays using magnetic resonance imaging. *NeuroImage*, *63*(1), 157–165. http://doi.org/10.1016/j.neuroimage.2012.06.039 The methods work great. However, we've noticed that the pial surface typically underestimates the extent of the amygdala and hippocampus (see attached example images from FreeSurfer's demo Bert subject) where we often have electrodes. I understand that FreeSurfer does this by design, since the amygdala and hippocampus are not neocortex. However, is there a way to force the pial surface to include those medial temporal lobe structures for our purposes? I tried "mris_make_surfaces -fix_mtl" but that did the opposite of what we need (i.e., it withdrew the pial surface so that it included none of the amygdala or hippocampus). much appreciated, -David P.S. Thanks for creating and maintaining such an amazing suite of freeware.

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Convert ascii to .mgh
by Robby De Pauw 15 Jun '16

15 Jun '16

Dear Doug Thank you for your answer. I however encounter an error: >> F.vol = fast_mat2vol(lfdr,F.volsize) ERROR: szvol inconsistent with mat2d I have attached the final output (.mgh) and the .asc file. (As the files are too large, I added them here: https://we.tl/MKhhmeT5Zn) Thank you Robby From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Douglas Greve <greve(a)nmr.mgh.harvard.edu> Reply-To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Date: Wednesday 15 June 2016 at 17:43 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Convert ascii to .mgh I would do it in matlab, eg, F = MRIread('F.mgh'); % This is to get the proper header information lfdr = load('lfdr.asc'); F.vol = fast_mat2vol(lfdr,F.volsize); MRIwrite(F,'lfdr.mgh'); On 6/15/16 4:45 AM, Robby De Pauw wrote: Dear FreeSurfer users, To address the problem of multiple comparison, I wanted to apply the localfdr-method. For this purpose, I need the F-statistic (which I can extract from the F.mgh scalar overlay I presume?). I converted this to an ascii-file, which I was able to load into R, using the following chink of code: mris_convert -c /Users/robbydepauw/Desktop/FreeSurfer/GLM/lh.Group.volume.glmdir/Groupeffect/F.mgh $SUBJECTS_DIR/fsaverage/surf/lh.white F.asc After performing an local fdr analysis in R, I want to create a scalar overlay “lfdr.mgh”, but I fail at converting the asci file into an “.mgh”-overlay file. Any idea how I could approach this conversion (from asci back to .mgh)? Many thanks, Greetings Robby Robby De Pauw, PT, MT, drs. T +32 09 332 12 19 | Email Robby.DePauw(a)Ugent.be<mailto:Robby.DePauw@ugent.be> Ghent University | Rehabilitation Sciences and Physiotherapy Campus Heymans 3B3 (022) De Pintelaan 185 BE-9000 Ghent Route to my office<https://soleway.ugent.be/routes/1090> _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] SIENAX
by Hassan bakhshi 15 Jun '16

15 Jun '16

We have some cases which we want to process , I searched about SIENAX and as you are more expert in this area, I wanted to know Freesurfer preferences on SIENAX!!!! ??? The other thing is process time in these two software. Kind Regards,

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