Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

freeview and complex values
by shahin＠nmr.mgh.harvard.edu 22 Apr '19

22 Apr '19

Hi Surfers, I am trying to use freeview to present retinotopy mapping in subcortical regions. I need to show complex (real and imag) values generated by a retinotopy analysis in a 'color wheel' format (similar to what tksurfer does). Any hint? _____________________________________ Shahin Nasr Assistant Prof. in Radiology Harvard Medical School Martinos Imaging Center, MGH Bldg 149, 13th street, Charlestown, MA 02129

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mri_surf2surf help
by Larson, Kathleen E 22 Apr '19

22 Apr '19

External Email - Use Caution Hello FreeSurfer developers, I'm having trouble running the command mri_surf2surf, and I haven't been able to find a fix in the message archives (a similar question has been asked, but I couldn't find the answer). I am trying to convert the pial and white matter surfaces for a series of subjects back to the anatomical space. I have computed the registration matrix to transform the surfaces, but am having trouble with the mri_surf2surf syntax. This is the command I am trying to run: mri_surf2surf --hemi lh --sval-xyz pial --reg register.native.dat rawavg.mgz --tval lh.pial.native --tval-xyz --s <subjectID> and I get an error saying that --tval-xyz requires an input volume. (The syntax described on the website (https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat) is out of date.) I have tried to use rawavg.mgz as the input volume, but then I get an output that can only be read as a scalar overlay, and I need an actual surface. When I try to use a surface as the input, I get an error saying that the file type cannot identified. Do you have any suggestions for what I am doing wrong? Thank you, Kathleen Larson Department of Biomedical Engineering Vanderbilt University 304 Featheringill-Jacobs Hall (425)-894-2005

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mri_vol2surf error
by Nillo, Ryan Michael R 22 Apr '19

22 Apr '19

External Email - Use Caution Hello FS users, I am having a problem with mri_vol2surf. I want to project subcortical voxels onto the cortical surface. I found out that I can do this with the mri_vol2surf command. I am following the example given on the documentation, but I am getting this error: mri_vol2surf: could not read surface /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc//surf/lh.white. I am trying to project to the surface of the fsaverage. Does this error mean that FS is unable to find the fsaverage surface? Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging

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thresholded cluster output data
by Peters, Douglas G 22 Apr '19

22 Apr '19

External Email - Use Caution Hi Everyone, I'm new to freesurfer, and I was wondering if there is a way to output clusterwise threshold from Freeview (or any other tool) to illustrate cluster size, location, and significance? I understand that mri_glmfit-sim outputs cluster data after multiple cluster correction, but I was wondering if there is a way to get a similar cluster output prior to running multiple cluster correction. Thank you, DP

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Problems with recon-all -s soft and hard fallures
by Camerino, .I.L. (Ileana) 22 Apr '19

22 Apr '19

External Email - Use Caution Dear Freesurfer experts, I am running recon all from the terminal of a linux machine: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c. I tried recon all on an image dataset of small vessel disease patients. I tried the command on several subjects and I got the same outcome: a soft fallure. Please, find the recon all log in the attachment. Even though in the "recon all.log": it says: recon-all -s sub025 finished without errors, after checking the pial and white matter segmentations, very clear misplacement failures and part of dura mater are present (see attachment: segmenation misplacement and dura). I am also wandering how to avoid that white matter lesions are taken into the aseg segmentation? I checked the documentation and this kind of errors is not mentioned anywhere. Can be the case, that this error is due to the fact that these are clinical images? Can this problem be fixed? For sake of curiosity, I tried the recon all command on another dataset (stroke) and with these data I got an hard failure. recon all exited with errors: ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0573, pval=0.0034 < threshold=0.0050). (see second recon all o35403143 with errors) Please, can anyone give me some ideas how to fix both errors? Thank you in advance Ileana

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Re: [Freesurfer] Lazy binding problem {Disarmed}
by fsbuild 21 Apr '19

21 Apr '19

External Email - Use Caution Hello Lingyan, You can download an updated Mac freesurfer distribution from the following link,https://drive.google.com/file/d/1v2WwPg68id42NqfMeBTI3zijjto69_C1/view… After the download, you can uncompress the freesurfer_Mac.zip archive and put the freesurfer tree anywhere as long as you change the FREESURFER_HOME environment variable to point to it.  Then you would run the freesurfer script to setup the environment using that location.  For example, you can put the ../freesurfer tree under your home directory which you always have privileges to read/write to. $ cd $HOME$ pwd/Users/lwang  <— I am making up this path for this example ... then uncompress the zip archive in to your home directory, here assuming the archive was downloaded into your Downloads folder, $ unzip -d $HOME  $HOME/Downloads/freesurfer_Mac.zip … then in Bourne shell or bash shell you could do….  $ export FREESURFER_HOME=$HOME/Mac/freesurfer … and then to setup the environment… $ source $FREESURFER_HOME/SetUpFreeSurfer.sh Then you should no longer see the lazy evaluation error or be concerned with doing an install that needs admin privileges or whether or not SIP is on/off..(Setup instructions for the environment are also here, https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall) - R. On Apr 19, 2019, at 15:17, Wang, Lingyan <Lingyan.Wang(a)bcm.edu> wrote:        External Email - Use Caution        Hi,I had this lazy binding problem described in the FS6 releasenotes and couldn't solve it. This is the error message I got when using @SUMA_Make_Spec_Fs:dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib  Expected in: /usr/lib/libSystem.B.dylibdyld: Symbol not found: ___emutls_get_address  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib  Expected in: /usr/lib/libSystem.B.dylibdyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib  Expected in: /usr/lib/libSystem.B.dylibdyld: Symbol not found: ___emutls_get_address  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib  Expected in: /usr/lib/libSystem.B.dylibAnd I've disabled SIP.When I tried use sudo -E fs_update, here is the message I got:Build is freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c   Running this will update some of your freesurfer binaries. Shall I proceed? [y/n/Abort]: yrsync -zbrlv --progress --suffix=.1555625828_bak rsync://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c/* /Applications/freesurferreceiving file list ... rsync: change_dir "/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c" (in pub) failed: No such file or directory (2)0 files to considersent 4 bytes  received 9 bytes  26.00 bytes/sectotal size is 0  speedup is 0.00rsync error: some files could not be transferred (code 23) at /BuildRoot/Library/Caches/com.apple.xbs/Sources/rsync/rsync-51/rsync/main.c(1404) [receiver=2.6.9]The MacOS system is macOS Sierra 10.12.5 and freesurfer is freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96cI was wondering if you have any suggestions to fix this problem. Many thanks!Wang, Lingyan Yau LabDepartment of NeuroscienceBaylor College of Medicine_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Extracting mean of values within a lable
by Sims, Sara A (Campus) 21 Apr '19

21 Apr '19

External Email - Use Caution Hello! I have a surface overlay that I want to extract the mean of the values within a label and export to a text file. How can I do that? I was looking into mris_anatomical_stats, but does mris_anatomical_stats let you tell it what file to pull the data from instead of just doing the standard extractions? Alternatively, I would be fine with just extracting all the values within the label and then finding the mean on my own. How could I extract all the values within the label and exporting to a text file? Thanks, Sara Sims

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epidewarp.fsl error in trac-all script
by Daniel Callow 20 Apr '19

20 Apr '19

External Email - Use Caution Hello freesurfer developers, When running trac-all the script seems to be getting tripped up on the epidewarp.fsl portion of the script and throwing a weird error about the fsl version? I am running trac-all -prep with bo homogeneity correction included in the configuration file. I get the following error. writing to /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0pha.nii.gz... orientLAS /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0pha.nii.gz /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0pha.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 10 mri_convert -oni 96 -onj 96 -onk 53 -oid -0.998405 -0.0247418 0.0507528 -ojd 4.61648e-10 0.898878 0.438199 -okd 0.0564624 -0.4375 0.897444 -oc 2.21634 10.523 31.9495 -rt nearest /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0pha.nii.gz /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0pha.nii.gz mri_convert.bin -oni 96 -onj 96 -onk 53 -oid -0.998405 -0.0247418 0.0507528 -ojd 4.61648e-10 0.898878 0.438199 -okd 0.0564624 -0.4375 0.897444 -oc 2.21634 10.523 31.9495 -rt nearest /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0pha.nii.gz /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0pha.nii.gz normalizing out_i_direction: (-0.998405, -0.0247418, 0.0507528) -> (-0.998405, -0.0247418, 0.0507528) $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0pha.nii.gz... TR=560.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998405, -0.0247418, 0.0507528) j_ras = (-4.61648e-10, -0.898878, -0.438199) k_ras = (0.0564624, -0.4375, 0.897444) Reslicing using nearest writing to /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0pha.nii.gz... mri_probedicom --i /Volumes/DANIEL/dti_freesurf/diffusion_recons//AES101.Rest/phase/TE7.38_image000001.dcm > /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0info.dat fslroi /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_eddy.nii.gz /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/lowb.nii.gz 0 1 epidewarp.fsl --mag /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0mag.nii.gz --dph /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0pha.nii.gz --exf /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/lowb.nii.gz --epi /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_eddy.nii.gz --tediff 2.46000000000000000000 --esp 0.7 --vsm /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/vsm.nii.gz --epidw /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi.nii.gz FSLVersion 6.0.1 FSLVerMaj 6 FSL Version is 6.0.1, must be 3.X or 4.X or 5.X Darwin 255a-280.umd.edu 18.2.0 Darwin Kernel Version 18.2.0: Thu Dec 20 20:46:53 PST 2018; root:xnu-4903.241.1~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Sat Apr 20 14:56:02 EDT 2019 Does this mean there is an issue with the trac-all script that makes it incompatable with fsl? I notice the --vsm /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/vsm.nii.gz portion of the epidewarp.fsl script was not created. Everything else that should go into it was created. Can anyone give me some guidance on why this might be happening? Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

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fsgd creation
by Amrita Bedi 20 Apr '19

20 Apr '19

External Email - Use Caution Hi Freesurfer developers, My question is related to creation of an fsgd file for glm analysis. I have approximately 500 subjects and 10 variables. I was wondering whats the most time efficient way of creating an fsgd file given my data currently resides in an excel file. Best Amrita

2 1

Senior Research Scientist position at Penn
by Satterthwaite, Theodore 20 Apr '19

20 Apr '19

External Email - Use Caution Hi All, We have an open Senior Research Scientist position; see info below. Feel free to email me directly. Thanks!! Ted Full post: https://jobs.hr.upenn.edu/postings/45503 Ted Satterthwaite and the Lifespan Brain Institute at Penn are seeking to recruit a Senior Research Scientist to lead the analytic efforts of a multi-institution initiative in developmental data science. This initiative will create a large-scale public resource for developmental human neuroscience. In collaboration with collaborators at Child Mind Institute (Mike Milham) we will aggregate, process, harmonize, and publicly share >10,000 structural and functional images for youth ages 5-22. Using this massive data resource, we will seek to develop normative patterns of brain network development, and identify how abnormal network development is associated with specific patterns of psychopathology. This position will involve working as part of a highly-interdisciplinary research team that includes experts in diverse fields such as network science (Danielle S. Bassett), multivariate pattern analysis (Christos Davatzikos), and imaging statistics (Taki Shinohara). To work effectively in this highly collaborative environment, the applicant must have superior communication, language, and writing skills. The applicant must have completed their Ph.D. in neuroscience, engineering, psychology, or statistics with an established record of high productivity; post-doctoral training is desirable. Expertise in using neuroimaging software (e.g., FSL, FreeSurfer, ANTs, AFNI), statistical packages (e.g., R), and scripting languages (e.g., nipype , python, bash) are required. Flexible salary, based upon experience. Theodore D. Satterthwaite, M.D. Assistant Professor of Psychiatry University of Pennsylvania Perelman School of Medicine **NOTE NEW EMAIL: sattertt(a)pennmedicine.upenn.edu<mailto:sattertt@pennmedicine.upenn.edu> ** www.satterthwaitelab.com<http://www.satterthwaitelab.com>

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