Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Surface failure in centos7 dev freesurfer
by Baxter P. Rogers 13 Nov '18

13 Nov '18

External Email - Use Caution Hi all - I'm having a problem with recon-all in the current dev version of Freesurfer. It is failing somewhere in the surface creation steps. I get an error during mris_extract_main_component: ERROR: MRISalloc: nvertices=-1879047998 < 0 No such file or directory The filled left and right white matter images look reasonable but I can't load the lh.orig.nofix surface in Freeview. More info below. Thanks much for any help, Baxter ----------------------------------------------------------------------------- FREESURFER VERSION: https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-linux… Downloaded 2018-11-12 SHA256 792a0e90ec6b4cfd3a530c3e5b4c9aead575dbb45217756e66931bb5d118e89d ----------------------------------------------------------------------------- SYSTEM INFORMATION: CentOS 7.5.1804 Running in Docker on OS X El Capitan with 1 CPU, 6.5 GB RAM # df -h Filesystem Size Used Avail Use% Mounted on overlay 74G 30G 40G 43% / tmpfs 64M 0 64M 0% /dev tmpfs 3.2G 0 3.2G 0% /sys/fs/cgroup osxfs 465G 438G 27G 95% /wkdir /dev/sda1 74G 30G 40G 43% /etc/hosts shm 3.0G 0 3.0G 0% /dev/shm # cat /proc/meminfo MemTotal: 6616764 kB MemFree: 4934288 kB MemAvailable: 6134084 kB ... ----------------------------------------------------------------------------- ATTEMPT TO VIEW SURFACE IN FREEVIEW: Failed to load Surface .../surf/lh.orig.nofix # ls -l lh.orig.nofix -rw-rw-r-- 1 root root 4320024 Nov 11 23:02 lh.orig.nofix ----------------------------------------------------------------------------- LATER PORTIONS OF recon-all.log mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 49 found - 49 modified | TOTAL: 49 ... pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 1264 (out of 703656: 0.179633) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.presurf.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... ... Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 ... pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 15 (out of 347364: 0.004318) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.39 2016/07/20 21:05:04 zkaufman Exp $ $Id$ slice 30: 1553 vertices, 1720 faces ... slice 250: 179904 vertices, 180024 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix ERROR: MRISalloc: nvertices=-1879047998 < 0 No such file or directory

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QA_tools do not find v.mgz
by Simon Jones 13 Nov '18

13 Nov '18

External Email - Use Caution I have run some Freesurfer 6 recon-all processed data through the Freesurfer QA analysis QA_tools_v1.2. The output looks mostly good but I repeatedly see these errors. ERROR: Subject a1 missing output file ../mri/v.mgz ERROR: Subject a1 missing output file ../stats/wmsnr.e3.dat I do actually find 100% of wmsnr.e3.dat files so that may not be a problem. But only 41% of my subjects have a file called v.mgz. This looks like ventricles prior to aseg processing. I do not find the file v.mgz referenced in any of the recon-all log files or help pages. I don’t think I have been aware of this file previously. Why are many subjects missing this file and should I worry about it. Thanks for your help, Simon

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From .nii.gz
by Rosalia Dacosta Aguayo 13 Nov '18

13 Nov '18

External Email - Use Caution Dear Free Surfer team, I wonder how I could pass from .nii.gz format to .mgz format in order to change the brainmask.mgz generated by FreeSurfer for my bet image from FSL. I have noticed that lot of brainmask images have optic radiations and part of the skull. Best regards, Rosalia

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Medial prefrontal cortex mPFC in Destrieux Atlas
by Daya P 13 Nov '18

13 Nov '18

External Email - Use Caution Hi all, I am trying to find out which regions in Destrieux atlas would correspond to mPFC? Any ideas ? Also for lateral parietal cortex .. Than you, Daiana

1 0

Fwd: Manually fix FreeSurder ICV value when talairach.xfm registration is incorrect
by Gamaliz 13 Nov '18

13 Nov '18

External Email - Use Caution I have a few T1 scans that have obvious incorrect registration to mni_average_305. I opened tkregister2 --s subjid --fstal --surfs and I am able to fix the registration, but I wonder how to use the ew registration to recalculate the new ICV. I am interested in doing it with Freesurfer (as I know I could get the matrix and calculate the determinant. I guess I will have to save the transform and rerun some of Freesurfer command to overwrite the old icv value? Thanks Gabriel

2 4

Editing errors
by Rosalia Dacosta Aguayo 13 Nov '18

13 Nov '18

External Email - Use Caution Dear Free Surfer team, I am visually checking for errors in every step of the recon-all process. In the skull stripping stage, some participants have left skull behind, but the grey matter (gm) and white matter (wm) separation is right. Should I edit the brainmask image in order to make that no skull is left behind even when the gm and wm are fine? Best regards, Rosalia

1 0

freesurfer selxavg3-sess error
by Francesca Strappini 12 Nov '18

12 Nov '18

External Email - Use Caution Dear FreeSurfer experts, I'm trying to analyze some monkey functional data. I got this error message with selxavg3-sess. I run the following commands: mkcontrast-sess -analysis FF-MonkeyCassis.sm03.lh -contrast ON-vs-OFF -a 1 -c 0 mkcontrast-sess -analysis FF-MonkeyCassis.sm03.rh -contrast ON-vs-OFF -a 1 -c 0 preproc-sess -surface MonkeyCassis lhrh -fwhm 3 -s MonkeyCassis-FF -fsd bold -per-session selxavg3-sess -a FF-MonkeyCassis.sm03.lh -s MonkeyCassis-FF ------- matlab output -------------------- MATLAB is selecting SOFTWARE OPENGL rendering. < M A T L A B (R) > Copyright 1984-2016 The MathWorks, Inc. R2016b (9.1.0.441655) 64-bit (glnxa64) September 7, 2016 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m >> /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m >> /usr/local/freesurfer/matlab/MRIread.m >> >> >> starting fast_selxavg3b #@# MonkeyCassis-FF ############################### /usr/local/freesurfer/fsfast/Monkeys/MonkeyCassis-FF ------------------------- $Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $ ------------------------- outtop = /usr/local/freesurfer/fsfast/Monkeys Extension format = nii.gz INFO: key nSliceGroups unrecognized, line 11, skipping 1 ON-vs-OFF.mat Subscripted assignment dimension mismatch. Error in fast_ldpar4 (line 97) par4(nthrow,1) = tonset; Error in flac_customize (line 121) [par partype] = fast_ldpar4(parpath); Error in fast_selxavg3b (line 129) flac0 = flac_customize(flac0); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n Thank you! 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

4 8

Transformation from original dicom to skull striped output
by Min Zhang 12 Nov '18

12 Nov '18

External Email - Use Caution Dear Freesufer team: I have marked bounding box in the original DICOM File, and applied autorecon1 to do the skull striping for the images. I want to transfer the bounding box to the skull stripped output. How can I get the coordinates transformation matrix between the input and skull stripped output. Many Thanks! Best Min

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Re: [Freesurfer] Consistent volume increases for some regions when using longitudinal stream
by Pagliaccio, David (NYSPI) 11 Nov '18

11 Nov '18

External Email - Use Caution Hello, Our lab has been running a set of data from a pre/post-treatment study through the FreeSurfer v6 pipeline. I was comparing the pre-treatment structural values initially run through the cross-sectional pipeline with the same pre-treatment data later run through the longitudinal pipeline and was seeing the same issue as has been previously posted about (msg52994). Particularly, one cortical region of interest shows on average 0.24mm (8.8%) larger cortical thickness values processed in the longitudinal pipeline vs. the cross-sectional pipeline. While all participant’s data showed increased thickness in this area with the longitudinal vs. cross-sectional pipeline, this was not at all consistent across participants (ranging from 0.08 to 0.47mm differences [3-18%]). While the longitudinal pipeline would increase reliability and sensitivity comparing the pre to post-scans, we are just very concerned about these major and inconsistent differences analyzing the same baseline data with the different pipelines. Particularly, we have some attrition so most participants have 2 but some have only 1 scan and thus this feels like it could introduce systematic bias in overall thickness. Any input would be appreciated! David

2 1

Nonsensical Vertex Coordinates, please help with interpretation
by Bruss, Joel E 11 Nov '18

11 Nov '18

External Email - Use Caution I'm trying to make a surface file from a subject's head and to map coordinates to that surface. If I run: mri_seghead --invol $SUBJECTS_DIR/$sub/mri/T1.mgz --outvol $SUBJECTS_DIR/$sub/mri/seghead.mgz --fill 255 --thresh1 20 --thresh2 20 --nhitsmin 2 mri_tessellate $SUBJECTS_DIR/$sub/mri/seghead.mgz 255 $SUBJECTS_DIR/$sub/surf/lh.seghead and then load lh.seghead in FreeView, it looks as I would expect. Clicking anywhere near a vertex gives the typical output, showing the closest vertex. All fine and well. However, if I load the file in Matlab: vCoord=read_surf('$SUBJECTS_DIR/$sub/surf/lh.seghead'); my values are nothing near what I'm seeing in Freeview. For example, FreeView reports: vertex 234741 [-78.50,14.50,26.50] read_surf reports: vertex 234740 0 168.980000000000 0 Of note, an error log tells me that: MRISreadNewCurvature: incompatible vertex number in file $SUBJECTS_DIR/$sub/surf/lh.curv How do I edit, update or create a curv file to play with the new surface file, or what can I do to get sensical surface coordinates from this data? Thanks, Joel ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of the individual or entity to which it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete or destroy all copies of the original message and attachments thereto. Email sent to or from UI Health Care may be retained as required by law or regulation. Thank you. ________________________________

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