Freesurfer March 2018

freesurfer@nmr.mgh.harvard.edu

115 participants
161 discussions

tksurfer/freeview vertex coordinates difference?
by Yagmur Ozdemir 19 05 Mar '18

05 Mar '18

Hello FS experts, I am wondering if anyone knows why the same vertices' coordinates are shown slightly different when opened in freesurfer and tksurfer. I was checking some annotation files for each subject across the two on inflated surface, and noticed slight coordinate differences in RAS. ex. freesurfer vertex 2407 [-18.23, -78.84, 27.92] ----- tksurfer vertex 2407 [-18.48, -78.82, 28.23] Best Idil

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gcut error
by Anna Daniels 05 Mar '18

05 Mar '18

Dear FreeSurfer team, we are trying to remove dura from the brainmask automatically as described in the SkullStrip tutorial: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix_freeview This however resulted in the following error when starting this command: *recon-all-skullstrip -clean-bm -gcut -subjid 15689_T1_fs* Killed Linux ubuntu recon-all -skullstrip -clean-bm -gcut -subjid 15689_T1_fs4.13.0-36-generic #40~16.04.1-Ubuntu SMP Fri Feb 16 23:25:58 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 15689_T1_fs exited with ERRORS at Mon Mar 5 03:47:39 PST 2018 Attached is the recon-all.log in case it may be helpful. We also could not detect any similar post in the mailing list. FreeSurfer version 6.0.0 Thank you and best, Anna

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Recon-all Error in output - ERROR: nu_correct
by Jordi Muchart Lopez 05 Mar '18

05 Mar '18

Hello everybody, I have searched the mailing list and I have found the same error I am facing but unfortunately I haven't been able fo find the correct answer. I am running Freesurfer 6.0 on Debian 8.0 (Neurodebian). When I run recon-all I get the following output, which I also attach in a text file (recon-all.log) I am new to Freesurfer, sorry for the inconvenience, I would appreciate very much if someone could point me in the right direction, Thank you, Jordi ---------------------------- Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c INFO: SUBJECTS_DIR is /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer Actual FREESURFER_HOME /usr/local/freesurfer Linux neurodebian 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt9-3~deb8u1 (2015-04-24) x86_64 GNU/Linux '/usr/local/freesurfer/bin/recon-all' -> '/media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018/scripts/recon-all.local-copy' /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018 mri_convert /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/20180305_081619SAGT1SENSE14RECON1s1201a1012.nii.gz /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018/mri/orig/001.mgz mri_convert.bin /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/20180305_081619SAGT1SENSE14RECON1s1201a1012.nii.gz /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/20180305_081619SAGT1SENSE14RECON1s1201a1012.nii.gz... TR=9.90, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0917001, -0.930202, 0.355409) j_ras = (0.0349643, 0.3597, 0.932413) k_ras = (0.995173, 0.0730758, -0.0655084) writing to /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Mon Mar 5 04:07:23 EST 2018 Found 1 runs /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018/mri/orig/001.mgz /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018/mri/rawavg.mgz /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018 mri_convert /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018/mri/rawavg.mgz /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018/mri/orig.mgz --conform mri_convert.bin /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018/mri/rawavg.mgz /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018/mri/rawavg.mgz... TR=9.90, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0917001, -0.930202, 0.355409) j_ras = (0.0349643, 0.3597, 0.932413) k_ras = (0.995173, 0.0730758, -0.0655084) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018/mri/orig.mgz... mri_add_xform_to_header -c /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018/mri/transforms/talairach.xfm /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018/mri/orig.mgz /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon Mar 5 04:07:32 EST 2018 /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux neurodebian 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt9-3~deb8u1 (2015-04-24) x86_64 GNU/Linux Mon Mar 5 04:07:32 EST 2018 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.1538 /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1538/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.1538/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=9.90, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 7.45058e-09) j_ras = (0, -1.21072e-08, -1) k_ras = (7.45058e-09, 1, 1.16415e-08) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.1538/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon Mar 5 04:07:37 EST 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.1538/nu0.mnc ./tmp.mri_nu_correct.mni.1538/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1538/0/ -iterations 1000 -distance 50 [root@neurodebian:/media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018/mri/] [2018-03-05 04:07:37] running: /usr/local/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.1538/0/ ./tmp.mri_nu_correct.mni.1538/nu0.mnc ./tmp.mri_nu_correct.mni.1538/nu1.imp Processing:.................................................................Done ncvarput: ncid 5: Protocol error miicv_put: 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 Linux neurodebian 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt9-3~deb8u1 (2015-04-24) x86_64 GNU/Linux recon-all -s 2018 exited with ERRORS at Mon Mar 5 04:07:39 EST 2018 For more details, see the log file /media/sf_NDb_1/2018_5_3_1390019/FreeSurfer/2018/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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is untar existing runtime2012b.tar.gz sufficient?
by Schumman Resonance 05 Mar '18

05 Mar '18

Hi, I was following the steps on the wiki to run the hipposubfields stream and it mentioned runtime needs to be downloaded. However, I noticed in my free surfer home the tar file runtime2012b.tar.gz. Would untaring this existing file in fresurfer homer put the libraries required in the MCR folder, I do I still need to download runtime? Thanks and best regards, Kev

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Region in Yeo_17Network_16 as seed in FS-FAST
by stdp82＠virgilio.it 04 Mar '18

04 Mar '18

Hi list, I should use the the region describing the mPFC in Yeo_17Network_16 (DMN) as a seed in FS-FAST (FC analysis) How can I do to isolated this regions? Thanks Stefano

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Hippocampus subfields {Disarmed}
by 郑凤莲 03 Mar '18

03 Mar '18

Hi Experts, I ran the segmentation of hippocampus in Freesurfer dev version. The left or right whole volume isn't equal to the sum of 12 subfields. But it is equal to the sum of the volume of tail, whole head and body. Why? I am looking forward to your reply. Thank you very much. Sincerely, Zheng | | 13181786167 邮箱：13181786167(a)163.com | 签名由网易邮箱大师定制

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error ruining bedpost (-bedp)
by Alexopoulos, Dimitrios 02 Mar '18

02 Mar '18

Hi, I'm running tracula and having some issues. Using FS5.3, I have run successfully (without errors) 'recon-all -all', then 'trac-all -prep -c dmrirc'. I then get an error (below) running 'trac-all -bep -c dmrirc'. The 'dmri' directory is generated from the -prop step above. [jimalex@login01 freesurfer]$ trac-all -bedp -c dmrirc INFO: SUBJECTS_DIR is /scratch/jimalex/freesurfer INFO: Diffusion root is /scratch/jimalex/freesurfer Actual FREESURFER_HOME /act/freesurfer-5.3.0-HCP INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-HCP INFO: current FREESURFER_HOME does not match that of previous processing. Current: /act/freesurfer-5.3.0-HCP Previous: /data/gizmo/data1/freesurfer5.3 WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 /scratch/jimalex/freesurfer/neo321e_chpc/dmri subjectdir is /scratch/jimalex/freesurfer/neo321e_chpc/dmri /scratch/jimalex/freesurfer/neo321e_chpc/dmri/data not found [jimalex@login01 freesurfer]$ ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Possible mri_cc error - process failed
by Matthew Grecsek 02 Mar '18

02 Mar '18

My recon-all ended prematurely with the following message: final transformation (x=136.0, yr=-10.054, zr=-0.114): 0.98464 0.00200 -0.17457 15.51372; -0.00197 1.00000 0.00035 17.22442; 0.17457 0.00000 0.98464 -17.83761; 0.00000 0.00000 0.00000 1.00000; mri_cc: no WM voxels found with norm > 40 -- check skull stripping No such file or directory Linux centos-7-1 3.10.0-693.17.1.el7.x86_64 #1 SMP Thu Jan 25 20:13:58 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s matt2 exited with ERRORS at Thu Mar 1 04:35:09 UTC 2018 I am running: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c My full log file is attached. Please let me know suggestions for correcting and continuing the process. Thanks, -Matt

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QA tools
by Micah Rhodes 01 Mar '18

01 Mar '18

Dear Freesurfer list, As I have used the QA tools on a couple recon-all jobs, I have run into an error when running recon_checker QA tools. The QA tools are not able to read many of the output files from recon-all, in the "label" directory. As I look back into the label directory, this is because many of my files after running recon have an "_exvivo" stem. For example, the QA tools cannot read the "../label/lh.BA1.label" file because in my subject directory, as it is named "../label/lh.BA1_exvivo.label". And the same is true for many other files. After searching online for solutions to this problem I have not found any way to eliminate the _exvivio stem, but I understand that exvivo data has been used to increase the quality of images for FS v6. Is there a way to fix this when running recon-all? Or, is this problem occurring because I'm using QAtools1.2 with FS v6.0? Best, Micah

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bad aseg but WM and pial surfaces look good
by C.P.E. Rollins 01 Mar '18

01 Mar '18

Hi Freesurfer developers, I've processed my sample of T1 scans through recon-all and have corrected the pial and WM surfaces. The surfaces look mostly good, though when I checked the aseg segmentations they are pretty poor and there is huge variability in the volumes I get from asegstats2table (for instance, Left-Lateral-Ventricle is anywhere from 3773.1 to 22575.9). I was wondering if there's any way to improve the subcortical segmentations? Moreover, if the subcortical segmentations are poor, should I worry that there might also be errors in my cortical thickness or local gyrification index calculations (though the values for these show much less variability). Many thanks, Colleen -- Colleen Rollins, PhD Candidate Department of Psychiatry University of Cambridge Herchel Smith Building, Robinson Way, Cambridge CB2 0SZ

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Freesurfer March 2018