Freesurfer

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Open lab manager position in Perception & Brain Dynamics Laboratory at NYU Medical Center
by Wu, Yuan hao 06 Mar '20

06 Mar '20

External Email - Use Caution The Perception & Brain Dynamics Laboratory (http://www.med.nyu.edu/helab/) at New York University School of Medicine is looking for a lab manager to start in spring/summer 2020. The Laboratory is within the Neuroscience Institute at NYU Langone Health(http://www.med.nyu.edu/neuroscience), affiliated with Departments of Neurology, Neuroscience and Physiology, and Radiology. Our research focus is on understanding the neural bases of perceptual awareness using multimodal imaging (fMRI, MEG, EEG, ECoG) and stimulation (tDCS, TMS) techniques in humans, combined with computational neuroscience approaches. We are looking for a bright and driven candidate with a Bachelor's or Master's degree who is dedicated to neuroscience research. A variety of backgrounds, including neuroscience, biology, psychology, and computer science is possible, and experience with programming is highly desirable. In addition, the ideal candidate has high responsibility and dependability, as well as excellent critical thinking, organizational and leadership skills. Performing independent research is an important aspect of the position, in addition to lab management duties. A minimal commitment of 2 years is required. Interested candidates please send a cover letter, a CV, undergraduate and/or graduate transcript, and names and contacts of two to three referees, to Prof. Biyu J. He at biyu.jade.he(a)gmail.com, with the subject line "Lab manager application 2020". The application is rolling, so please submit your materials as soon as possible.

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Fwd: FreeSurfer Course @ Caltech information - FOLLOW UP
by Paul Wighton 06 Mar '20

06 Mar '20

External Email - Use Caution Hi FreeSurfer friends, Does anybody have experience getting FreeView to run on Windows 10? Any suggestions on how to resolve this issue below? Or, are there any other installation notes you could pass along? Thanks, -Paul I’ve installed FreeSurfer on a Windows 10 machine with a WSL (Ubuntu 18.04 LTS) and Xming for graphical display. It generally works. However, when testing the installation using the examples on the website it fails to display the output volumes from Example 4 (see screenshot below). Do you have any idea what the problem might be? Thank you! Tessa

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some basic questions regarding longitudinal analyses in Freesurfer
by Lara Foland-Ross 06 Mar '20

06 Mar '20

External Email - Use Caution Hello, I'm analyzing a large dataset using an LME model to examine longitudinal changes in brain structure that vary as a function of group (patients vs controls). Because some participants were scanned several years apart in early childhood, the intra-subject registration failed in the longitudinal processing stream. For this reason, my data were not initially processed using the longitudinal processing stream within Freesurfer. However, per this thread - https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg55847.html - I still plan to use the LME model. As I understand it, this model assumes that the longitudinal processing stream was conducted. Therefore, I have the following questions: 1. would the "base" (aka within-subject template) for each subject be = time point 1? 2. would the "long run" for each subject be = each subject's individual time points? 3. assuming #1 and 2 are correct, would I need to set my directory structure to match that used in the longitudinal processing stream? For example, if I have 2 time points for subject 1234, and they are initially labeled "1234.time1" and "1234.time2", then in order to run the LME model, I would create a copy of "1234.time1" and rename the copy as "1234" to indicate to the software that this should be used as the base. And, I would also need to rename "1234.time1" and "1234.time2" as "1234.time1.long.1234" and "1234.time2.long.1234" to indicate that these folders should be used as the longitudinal time points. Does this seem appropriate? Thanks in advance for your help, Lara Lara Foland-Ross, Ph.D. Senior Research Associate and Imaging Lab Manager Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795

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Could not login in "https://mail.nmr.mgh.harvard.edu/NMRAuth/GLOBAL/LOGIN"
by ZhangBo 06 Mar '20

06 Mar '20

External Email - Use Caution Hi teams, I could not login in "Could not login in "https://mail.nmr.mgh.harvard.edu/NMRAuth/GLOBAL/LOGIN"". Thanks.

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recon-all with errors
by Laboratorio de Neurociencia Funcional 05 Mar '20

05 Mar '20

External Email - Use Caution Dear Freesurfer experts, After running the recon-all in one of my subjets, part of the temporal lobe was partially excluded. Then, I tried to use the watershed algorithm to be less agressive in the skull stripping as follows: recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgcaatlas -subjid sub_001 The problem was solved in the brainmask.mgz but not in the cortical surfaces. To handle this issue, I edited the white matter and run the recon-all (-autorecon2-wm -autorecon3) without success. I also placed control points but the following error appeared after running the recon-all -autorecon2-cp -autorecon3: recon-all -s sub_001 existed with errors I noted that white matter of this part of the temporal lobe has high values (up to 132). What can I do to solve the problem with this subject? Thank you in advance. Best regards, Marina

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8 Gb of ram
by Ian 05 Mar '20

05 Mar '20

External Email - Use Caution Hey guys. I'm running Freesurfer on an AWS EC2 instance, in a docker container (t3.large specifically.) Would you expect 8Gb of ram to *always* be enough to run recon-all on a 280x280x240 T1 image? The instance is running Ubuntu; the container image is based on Ubuntu; and nothing else is being explicitly run on the instance while recon-all is running. Thanks, Ian -- *Ian Hardingham*

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ubuntu: run freesurfer in two terminal
by ZhangBo 05 Mar '20

05 Mar '20

External Email - Use Caution Hello FreeSurfer Developers, My computer doesn't support cuda. To speed up data processing, could I open two terminal, and in each of them, I first runing: $> export FREESURFER_HOME=/usr/local/freesurfer $> export FREESURFER_HOME=/SetUpFreeSurfer.sh $> export SUBJECTS_DIR=/usr/local/freesurfer/subjects/ then running: recon-all -s sub-01 -i sub-01_T1w.nii.gz -all (for terminal 1) recon-all -s sub-02 -i sub-02_T1w.nii.gz -all (for terminal 2) Thanks.

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mri_vol2surf produces invalid surface
by Shuntaro Aoki 05 Mar '20

05 Mar '20

External Email - Use Caution Dear mailing list, I was trying to convert a volume image to a freesurfer surface (as gii) with `mri_vol2surf` for visualization, but ended up with invalid surface data (i.e., a file not loadable by freeview). What I did was: --- % mri_vol2surf --version stable5 % mri_vol2surf --src ./sample_volume.nii.gz --regheader sample-sub --hemi lh --out ./sample_vol2surf_lh.gii --- Here, `sample_volume.nii.gz` is a volume image (such as a statistical map) registered to an individual reference T1w image of subject `sample-sub`, which was the input of recon-all for the subject. The command completed without errors: --- srcvol = ./sample_volume.nii.gz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /home/share/data/fmri/freesurfer/subjects/sample-sub/mri/orig.mgz as target reference. Reading surface /home/share/data/fmri/freesurfer/subjects/sample-sub/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 0 0 0 using old Done mapping volume to surface Number of source voxels hit = 31055 Writing to ./sample_vol2surf_lh.gii Dim: 155685 1 1 --- Then I tried to open the resulting surface `sample_vol2surf_lh.gii` with freeview (ver 1.0 build 2013-05-13) but it failed, saying "Failed to load Surface". I also got the following shell output: --- mriseadGIFTIfile: mris is NULL! found when parsing file /home/mu/aoki/work/surf_sphere/sample_vol2surf_lh.gii MRISread failed mriseadGIFTIfile: mris is NULL! found when parsing file /home/mu/aoki/work/surf_sphere/sample_vol2surf_lh.gii --- The output of `mris_info` is: --- % mris_info sample_vol2surf_lh.gii ================================================== gifti_image struct version = 1.0 numDA = 1 gim->meta nvpairs struct, len = 3 : nvpair: 'UserName' = 'aoki' nvpair: 'Date' = 'Thu Feb 27 17:32:40 2020' nvpair: 'gifticlib-version' = 'gifti library version 1.09, 28 June, 2010' gim->labeltable giiLabelTable struct, len = 0 : -------------------------------------------------- gim->darray[0] giiDataArray struct intent 0 = NIFTI_INTENT_NONE datatype 16 = NIFTI_TYPE_FLOAT32 ind_ord 1 = RowMajorOrder num_dim = 1 dims = 155685, 0, 0, 0, 0, 0 encoding 3 = GZipBase64Binary endian 2 = LittleEndian ext_fname = ext_offset = 0 darray->meta nvpairs struct, len = 0 : data = <set> nvals = 155685 nbyper = 4 numCS = 0 darray->ex_atrs nvpairs struct, len = 0 : -------------------------------------------------- gifti_image struct swapped = 0 compressed = 1 -- darray totals: 1 MB gim->ex_atrs nvpairs struct, len = 0 : ================================================== --- I checked matching between voxels in the input volume and the surface with the output of --srchit option and found the registration was fine. I also tried mgh output but got another invalid file. --- % mris_info sample_vol2surf_lh.mgh ERROR: MRISread: file 'sample_vol2surf_lh.mgh' has 0 vertices! Probably trying to use a scalar data file as a surface! No such file or directory --- I would appreciate any advice on this. Regards, Shuntaro -- ---------------------------------------- Shuntaro C. Aoki, Ph.D. Program-specific Researcher Neuroinformatics group Graduate School of Informatics Kyoto University s_aoki(a)i.kyoto-u.ac.jp ----------------------------------------

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(no subject)
by Laboratorio de Neurociencia Funcional 04 Mar '20

04 Mar '20

External Email - Use Caution Dear Freesurfeer experts, After running the recon-all in one of my subjets, part of the temporal lobe was partially excluded. Then, I tried to use the watershed algorithm to be less agressive in the skull stripping as follows: recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgcaatlas -subjid sub_001 The problem was solved in the brainmask.mgz but not in the cortical surfaces. To handle this issue, I edited the white matter and run the recon-all -autorecon2-wm -autorecon3 without success. I also placed control points but the following error appeared after running the recon-all -autorecon2-cp -autorecon3: recon-all -s sub_001 existed with errors I noted that white matter of this part of the temporal lobe has high values (up to 132). What can I do to solve the problem with this subject? Thank you in advance. Best regards, Marina

2 1

CBF data for mri_glmfit processing
by Beata Brzeska 04 Mar '20

04 Mar '20

External Email - Use Caution Hello everyone, I am using Freesurfer 6.0 on linux cluster. We are analyzing CBF data (ASL derived) coupled with fMRI task in longitudinal design. The fMRI data was analyzed in FS-FAST (with paired-diff) and now we want to repeat the group analyses on CBF maps. So far I registered the ASL data to individual anatomy and successfully transformed into fsaverage surface space (and smoothed afterwards). The data looks good so far - I can overlay it on inflated fsaverage surface. My question is: how to stack the data for further mri_glmfit processing? I suppose I should use mris_preproc for this purpose, but I am at loss with which flags are appropriate and hoe to use CBF maps as an input here. So far I did as follows for all the subjects, timepoints and hemispheres: bbregister --s Sub01_I --mov Sub01_I_CBF.nii.gz --t2 --reg Sub01_I_reg.dat ; mri_vol2surf --src Sub01_I_CBF.nii.gz --trgsubject fsaverage --out Sub01_I_CBF_to_surf_lh.nii.gz --srcreg Sub01_I_reg.dat --hemi lh mris_fwhm --s fsaverage --hemi lh --fwhm 5 --smooth-only --i Sub01_I_CBF_to_surf_lh.nii.gz --o Sub01_I_CBF_to_surf_lh_smooth.nii.gz; I would really appreciate your help. Thanks, Beata -- Beata Brzeska Medical University of Gdansk, Poland Radiology Department -- Beata Brzeska Zakład Radiologii Uniwersyteckie Centrum Kliniczne w Gdańsku

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