Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

DWI EPI correction
by Adam Rytina 06 Feb '20

06 Feb '20

External Email - Use Caution Hello all, I have an input DWI dataset and wanna perform the diffusion data correction (mg susceptibility induced distortion correction, geometric correction...). Does Freesurfer enable to perform the diffusion correction? Does recon-all include this option? Thanks a lot Regards Adam

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Retinotopy analysis results interpretation
by Marco Ninghetto 06 Feb '20

06 Feb '20

External Email - Use Caution Dear FREESURFERs, I'm performing retinotopy analysis. I preprocessed data and made 1st level analysis. Stimuli definition is: 6 cycles of rotating wedge (counter-clockwise rotation) and 6 cycles of expanding ring. One cycle lasts ~41 seconds. Scan TR = 2.5 sec. I followed the pipeline below (after recon-all): preproc-sess -sf sessid -fsd bold -fwhm 5 -surface self lhrh -per-run mkanalysis-sess -a ret_?h -surface self ?h -fwhm 5 -retinotopy 41 -paradigm > rtopy.par -TR 2.5 -fsd bold -per-run selxavg3-sess -a ret_?h -s SUBJ01 (let's say first subject) I created an occipital flat patch and then: fieldsign-sess -a ret_?l -patch lh.occip.patch.flat -s SUBJ01 > Then, I visualize results using tksurfer-sess -a ret_?h -s SUBJ01 -map angle -tksurfer tksurfer-sess -a ret_?h -s SUBJ01 -map angle.masked -tksurfer tksurfer-sess -a ret_?h -s SUBJ01 -tksurfer tksurfer-sess -a ret_?h -s SUBJ01 -fieldsign -tksurfer I'm not sure about the activations I get and I'm not sure how to interpret these data. What are the colors in the colorbar telling me? What is fieldsign img showing? what's the difference between raw angle and angle.masked (is this the mask created during preprocessing?)? In angle.masked result, the red part is the center of population receptive fields deducted from eccentricity or from polar? Here the link to the folder with images <https://drive.google.com/open?id=1ers6Cq9uYEEZnCUHZyFlqtzevV7d-xyg> Any help on interpreting these results would be much appreciated. Thank you, Marco -- --------------------------------------------------- Marco Ninghetto, PhD candidate Laboratory of Neuroplasticity Nencki Institute of Experimental Biology Polish Academy of Sciences 3 Pasteur Street, 02-093 Warsaw, Poland

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Highlighting single atlas structures in freeview
by Francesco Puccettone 05 Feb '20

05 Feb '20

External Email - Use Caution Dear all, I would like to show several structures from the DKT (or the Desikan-Killiany) atlas alone on a "blank" fsaverage brain, rather than have all structures displayed in different colors (as happens by default). For instance, I'd like to just show "medialorbitofrontal" on its own, then "middletemporal" on its own, etc. After I open the parcellation, freeview -v /FS/fsaverage/mri/aparc+aseg.mgz:colormap=lut:opacity=0.4 -f /FS/fsaverage/surf/lh.white:annot=aparc.annot , I expected to be able to turn each label in the list on and off like a layer, but this does not work. [image: 21-01-2019 14.48.54.jpg] I hoped I could use Alt+F to hide/show each atlas label at a time (cf freeview tutorial <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData_freeview>), but this instead toggles the entire external surface of the brain on and off. Can anyone help? Thank you! --Francesco

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Error in segmentSubjectT1_autoEstimateAlveusML
by Pascale Patenaude 05 Feb '20

05 Feb '20

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to produce an automated segmentation of the hippocampal substructures and the nuclei of the amygdala (see hippocampal module https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm…) When I try to run the segmentHA_T1.sh SUBJECT_ID [SUBJECTS_DIR] command with the dev version of freesurfer, I keep getting this error: Open file failed because file '/tmp/MCR_1572363005/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2/bin/kvlWriteImage.m' has invalid content. Details: 'file is closed.failbit is set.' Attempt to execute SCRIPT kvlWriteImage as a function: /tmp/MCR_1572363005/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2/bin/kvlWriteImage.m Error in segmentSubjectT1_autoEstimateAlveusML (line 1547) MATLAB:scriptNotAFunction Does anyone have any suggestions on how this can be fixed? Thank you in advance, Pascale

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Cannot load overlay through GUI
by Fengdan Ye 04 Feb '20

04 Feb '20

External Email - Use Caution Dear FreeSurfer experts: I encountered a weird problem when trying to load overlay through the Freeview GUI. I opened a surface file through terminal command “freeview -f lh.pial”, and then in the GUI I clicked Overlay -> load generic -> Select overlay file. After I selected the overlay file Freeview stopped responding. The following messages showed up in terminal: 2020-01-29 16:13:31.469 Freeview[1067:24667] warning: <NSRemoteView: 0x7fee5240bf70 com.apple.appkit.xpc.openAndSavePanelService ((null)) NSServiceViewControllerForTouchBarItem> determined it was necessary to configure <_NSFunctionRowPanel: 0x7fee49fe2c70> to support remote view vibrancy 2020-01-29 16:13:31.491 Freeview[1067:24667] warning: <NSRemoteView: 0x7fee5240ddd0 com.apple.appkit.xpc.openAndSavePanelService ((null)) NSServiceViewControllerForTouchBarItem> determined it was necessary to configure <_NSFunctionRowPanel: 0x7fee49fe2c70> to support remote view vibrancy The first message showed up when I clicked on the folder icon to select overlay file, and the second message showed up when I clicked “Open” after I selected overlay file. However, if I just ran “freeview -f rh.pial:overlay=<some_overlay_file>”, the viewer could open the overlay file without problem. Is there any fix for this GUI problem? I am on macOS Catalina Version 10.15.2. Thank you, Fengdan

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activation timeseries
by Nasiriavanaki, Zahra 04 Feb '20

04 Feb '20

Dear Freesurfer experts I want to extract "activation timeseries (BOLD signal changes in each time point) " from a predefined ROI in a single subject task fMRI data. Previously, I extracted these values from fmcpr.sm0.self.lh.nii.gz by using mri_segstats, but the data seems to be too noisy. I searched the forum and found this solution (mri_glmfit --y fmc.nii --qa --glmdir qa.glm --save-yhat This will detrend the time series (removing mean, linear, and quadratic trends). With --save-yhat, one of the outputs will be yhat.mgh (the detrended time series). If you have a task, the task will still be in there.https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18901.… I ran this command: mri_glmfit --y fmcpr.nii.gz --qa --glmdir qa.glm --save-yhat and then this command to extract the timeseries: mri_segstats --i yhat.mgh --slabel arap_7T_all lh $SUBJECTS_DIR/arap_7T_all/lh.label --id 1 --avgwf-remove-mean --avgwf ./lh.01.txt I got this error: ERROR: dimension mismatch between input volume and seg input 174 174 51 seg 148565 1 1 I would like to know if this is the right way to extract timeseries from a task data. and if yes, how can I fix the error. Thanks a lot Mona Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

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mri_deface error: could not find wm peak
by Tim Schäfer 04 Feb '20

04 Feb '20

External Email - Use Caution Dear FreeSurfer experts, I am running mri_deface for all relevant volume files of more than 700 subjects (~3500 MGZ files in total). For roughly 10% of the files, the command fails, i.e., it stops with non-zero exit code and does not produce a result file. The relevant part of the mri_deface output is: after smoothing, mri peak at 0, scaling input intensities by inf GCAhistoScaleImageIntensities: could not find wm peak The full command line, an example file and the full output can be found in the footer of this email. Is there anything I can try to fix this? Some more information/observations: I noticed that for the subjects with errors, there are almost *always* the same 3 files affected: * mri/orig.mgz * mri/rawavg.mgz * mri/orig/001.mgz The file mri/T1.mgz is never affected. The file mri/orig_nu.mgz is only affected 2 times in total, and in these cases the image quality is extremely bad, so they can be ignored. Therefore, I suspect that the problems with the orig/rawavg/001 files are related to intensity inhomogeneity, which may lead to issues with the registration to the skull/face templates. Tim -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany * Demo file: rawavg.mgz uploaded via FTP to /transfer/incoming/rawavg.mgz on surfer.nmr.mgh.harvard.edu * System info: FreeSurfer v6 stable, MacOS * Full mri_deface command and output for the demo file: $ SKULL_TEMPLATE="${FREESURFER_HOME}/average/talairach_mixed_with_skull.gca" $ FACE_TEMPLATE="${FREESURFER_HOME}/average/face.gca" $ mri_deface /path/to/subject/mri/rawavg.mgz "${SKULL_TEMPLATE}" "${FACE_TEMPLATE}" ~/defaced.mgz logging results to defaced.log reading '/Applications/freesurfer/average/talairach_mixed_with_skull.gca'... reading '/path/to/subject/mri/rawavg.mgz'... changing type of input volume to 8 bits/voxel... MRIchangeType: Building histogram bounding unknown intensity as < 10.3 or > 1461.6 total sample mean = 111.8 (0 zeros) spacing=8, using 2055 sample points, tol=1.00e-03... resetting wm mean[0]: 143 --> 144 resetting gm mean[0]: 89 --> 89 input volume #1 is the most T1-like using real data threshold=6.0 skull bounding box = (40, 39, 17) --> (213, 255, 225) using (98, 111, 121) as brain centroid... mean wm in atlas = 144, using box (77,84,95) --> (119, 137,146) to find MRI wm before smoothing, mri peak at 89 robust fit to distribution - 89 +- 6.7 distribution too broad for accurate scaling - disabling WARNING2: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=109, mri_peak=141 after smoothing, mri peak at 0, scaling input intensities by inf GCAhistoScaleImageIntensities: could not find wm peak

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Post Doctoral Position: Neuroimaging
by Keedy, Sarah [PSY] 03 Feb '20

03 Feb '20

External Email - Use Caution Post Doctoral Position: Neuroimaging The Human Behavioral Pharmacology Laboratory in the Department of Psychiatry and Behavioral Neuroscience at the University of Chicago is seeking a post-doctoral fellow with expertise in fMRI study design and analysis, as well as human behavioral research. Join an active and collaborative lab http://hbpl.uchicago.edu/ to investigate behavioral and brain effects of psychoactive drugs (stimulants and other drugs) in healthy volunteers. Requirements: PhD and experience with fMRI design and analysis (e.g., SPM, AFNI); experience with programming or script-driven data analyses; experience with human subjects behavioral testing preferred. Publications and good writing skills essential. Send cv and letter to H. de Wit hdew(a)uchicago.edu<mailto:hdew@uchicago.edu>

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surfaceRAS to vertex coordinates
by Noah Markowitz 03 Feb '20

03 Feb '20

External Email - Use Caution Hi all, I’m trying to get the coordinates for specifice vertices of an inflated surface. I noticed there’s a difference between surfaceRAS and vertex coordinates (though I don’t understand it much). After getting the index of the specific vertex of interest I load the inflated surface through matlab with `vert = read_surf(‘lh.inflated’);` but notice that the coordinates it outputs is in surfaceRAS. ex: For fsaverage vertex 34686 SurfaceRAS = -17.53, -15.27, 48.87 Vertex = -46.54,-28.5,56.26 Is there a way I can get the vertex coordinates from those surfaceRAS coordinates? Please let me know when you get the chance. Have a good day, Noah

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New UCSF Cross-Sectional FreeSurfer (6.0) data
by Hasan Al Marzouqi 03 Feb '20

03 Feb '20

External Email - Use Caution I'm trying to access the ADNI/FreeSurfer dataset mentioned in the link below. How can I download it the directions are not clear. How can I get to the DOWNLOAD | Imaging | MR Image Analysis section of the ADNI archive? http://adni.loni.usc.edu/new-ucsf-cross-sectional-freesurfer-6-0-data-avail… Hasan Al Marzouqi Assistant Professor Electrical and Computer Engineering [cid:image001_5b9d5da2-5226-498c-8efe-a7084a62646b.png] P O Box 127788, , UAE T +971 2 6075090 F +971 2 447 2442 hasan.almarzouqi(a)ku.ac.ae ku.ac.ae<http://www.ku.ac.ae/> [cid:social_logos_bc6725d5-148a-4909-ae81-760d8b1c3dc4.png] [cid:MBZIRC_4cc4c5e3-e83d-4eb1-a48f-3e36e61af982.jpg]<http://bit.ly/mbzirc> <http://bit.ly/KUranking16> <http://bit.ly/KUranking16>

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