Freesurfer

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30088 discussions

recon-all could not read surface file error
by Daniel Callow 22 Mar '19

22 Mar '19

External Email - Use Caution Hello, During recon-all I keep running into the same error for one of my subjects. #@# Make White Surf rh Fri Mar 22 00:57:11 EDT 2019 /Volumes/DANIEL/freesurfer/Rest.AES118/scripts \n mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs Rest.AES118 rh \n using white.preaparc as white matter name... only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /Volumes/DANIEL/freesurfer/Rest.AES118/mri/filled.mgz... reading volume /Volumes/DANIEL/freesurfer/Rest.AES118/mri/brain.finalsurfs.mgz... reading volume /Volumes/DANIEL/freesurfer/Rest.AES118/mri/../mri/aseg.presurf.mgz... reading volume /Volumes/DANIEL/freesurfer/Rest.AES118/mri/wm.mgz... 25155 bright wm thresholded. 1843 bright non-wm voxels segmented. reading original surface position from /Volumes/DANIEL/freesurfer/Rest.AES118/surf/rh.orig... mris_make_surfaces: could not read surface file /Volumes/DANIEL/freesurfer/Rest.AES118/surf/rh.orig ERROR: reading /Volumes/DANIEL/freesurfer/Rest.AES118/surf/rh.orig Read 0 bytes, expected 1 Argument list too long Darwin hlhp-105.umd.edu 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 10 20:06:00 PDT 2018; root:xnu-3789.73.24~1/RELEASE_X86_64 x86_64 recon-all -s Rest.AES118 exited with ERRORS at Fri Mar 22 00:57:16 EDT 2019 For more details, see the log file /Volumes/DANIEL/freesurfer/Rest.AES118/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Thanks for any help you can provide with debugging! *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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help
by Lance 22 Mar '19

22 Mar '19

External Email - Use Caution Hi there, I want to calculate the significance of grayvol between two groups, but the data i noticed in the 'lh.aparc.stats' file shew some problem.The pic below shows the grayvol of entorhinal of some subjects,but one of them appears to be 136,far more lower than the others, what's the problem? is it a normal systematic error or is there something wrong with my operation while calculating? The same situation is also found in CurvInd and FoldInd. Thank you for your help!

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recon-all error
by Daniel Callow 21 Mar '19

21 Mar '19

External Email - Use Caution Hello, I am trying to run recon-all on a dataset and am running into errors with one of my subjects. I get an error at the following point -------------------------------------------------------- Iteration 1 Tue Mar 19 10:11:08 EDT 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.40972/nu0.mnc ./tmp.mri_nu_correct.mni.40972/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.40972/0/ -iterations 1000 -distance 50 [administrator@hlhp-105.umd.edu:/Volumes/DANIEL/freesurfer/Ex.AES118/mri/] [2019-03-19 10:11:09] running: /Applications/freesurfer//mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.40972/0/ ./tmp.mri_nu_correct.mni.40972/nu0.mnc ./tmp.mri_nu_correct.mni.40972/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done ncvarget: ncid 4; varid 6: Argument list too long miicv_get: MINC package entry point nu_estimate_np_and_em: crashed while running mincmath (termination status=768) nu_correct: crashed while running nu_estimate_np_and_em (termination status=768) ERROR: nu_correct Darwin hlhp-105.umd.edu 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 10 20:06:00 PDT 2018; root:xnu-3789.73.24~1/RELEASE_X86_64 x86_64 recon-all -s Ex.AES118 exited with ERRORS at Tue Mar 19 10:11:18 EDT 2019 For more details, see the log file /Volumes/DANIEL/freesurfer/Ex.AES118/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Any help you can provide for troubleshooting would be greatly appreciated. *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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Build stamp missing in current dev release
by Baxter P. Rogers 21 Mar '19

21 Mar '19

External Email - Use Caution This one: https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-linux… The build-stamp.txt file currently contains "freesurfer" with no version info. It used to be something like "freesurfer-linux-centos7_x86_64-dev-20181114-4f05c76" which is considerably more helpful :) Thanks much, Baxter

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Strange annotations in Freeview?
by Funk, Quentin 21 Mar '19

21 Mar '19

External Email - Use Caution See the link here: https://imgur.com/a/ACsG73A [https://i.imgur.com/1zEaYUT.jpg?fb]<https://imgur.com/a/ACsG73A> Annotations?<https://imgur.com/a/ACsG73A> imgur.com Post with 0 views. Annotations? There's not actually any voxel values in those regions. The labels go away if I load in other images and shuffle the order in the window, so at least easy to eliminate. But any ideas what's causing this? Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas for patient care. Houston Methodist is nationally ranked in 8 specialties and is designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Talairach failed
by Alexander Greiner 21 Mar '19

21 Mar '19

External Email - Use Caution Hello Freesurfer Developers, I am new to Freesurfer and I am currently only using it to reconstruct the surface structure from MRI data in order to make 3D prints. That means that I only need the files lh.pial and rh.pial in the end. This works fine as long as I am using data from fully developed brains. But for my studies it would be more important to reconstruct the surface from brains beginning from gestational week 21. If I do so, I am running into errors with recon-all: 1. Talairach failed If I skip this test using -notal-check flag I get 2. Watershed error If I add -no-wsgcaatlas I get a 3. Segmentation fault The log files are attached to the email. The general question is: Can Freesurfer also be used for not fully developed brains or even animal brains if only the both surface files mentioned above are necessary? If yes, how can this be done? If not, do you know any other (free) software that might be suited for this task? I am grateful for any suggestions! If you need further information please ask. FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Platform: macOS Mojave 10.14.3 Kind regards Alexander Greiner

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Extracting anatomical locations for a set of RAS coordinates
by Sparsh Jain 20 Mar '19

20 Mar '19

External Email - Use Caution Good afternoon Is there is way to automatically extract the anatomical locations corresponding to a set of RAS coordinates using Freesurfer's atlas? I have a set of 200 points and I am trying to get their anatomical labels automatically. Thank you Sparsh

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Re. TRACULA configuration file
by Yuwen Hung 20 Mar '19

20 Mar '19

External Email - Use Caution Dear TRACULA expert: I wonder if it is recommended to turn on performing of registeration-based B0-inhomogeneity compensation (set dob0 = 1) and utilise the field map magnitude and phase dicom files? The default is set to not to use these functions, but I wonder whether using them may result in better outcomes? Thank you, Yuwen

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mri_glmfit in custom ROI
by Williamson, Brady 20 Mar '19

20 Mar '19

External Email - Use Caution Hi, I have a couple of specific questions about mri_glmfit that I could not quite find the answers to in the tutorials or message boards. 1. How would I run mri_glmfit in a custom ROI (or set of ROIs) and then correct for multiple comparisons? I have found information on how to use the freesurfer predefined labels but not a custom regions. Just for some background, I have a set of 50 regions that make up our network of interest and I would like to limit the glm to these regions. 2. How do I extract and use the results from a whole-brain glm, above a specified corrected threshold, and use those in subsequent analyses? I am doing a whole-brain, between groups analysis and then trying to use the significant results from that in within-subjects analyses. Thank you very much for your time, Brady

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[how to highlight a known ROI in original MR Image]
by Yi Li 20 Mar '19

20 Mar '19

External Email - Use Caution Hi, I want to highlight one known ROI (eg left caudate) in a MR image. I understand known ROIs are already in aseg or aparc and there is a color look up table, but I want to highlight one ROI at a time. I searched the website, and found the following instructions, but it highlighted the region of lh.BA45 which has label file at $sub/label/lh.BA45.label. I couldn't find label file at $sub/label/lh.caudate.label. Is there any way to get a known ROI to be highlighted as in the fig below? Thank you so much for the help. Best Regards Yi ============================================ https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI cd $SUBJECTS_DIR mri_label2label \ --srcsubject fsaverage \ --srclabel fsaverage/label/lh.BA45.label \ --trgsubject 004 \ --trglabel 004/label/lh.BA45.label \ --hemi lh \ --regmethod surface freeview -v 004/mri/orig.mgz Then on the menu bar click File > Load ROI [loadroi.jpeg] choose lh.BA45.label and hit 'Open'. The label is visible in coronal slice 153. To jump to that slice, double click on the coordinates [127,127,128] next to where it says 'orig' in the Cursor window pane. The last number is the slice number. Change it to 153 and hit enter. [cid:image003.jpg@01D4DF30.6DED4EC0] --- The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

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