Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Novice have a problem
by shilin18 05 Mar '18

05 Mar '18

Hi all, very nice to find a place to ask all the fs giants a question. I run recon-all …-all -localGI, which always return this at the end. Can anyone help me find out what I need to do to evade this error? Every time I delete the shortcut folder created during the process and copy the fsaverage folder to the SUBJECT_DIR folder and run recon-all … -qcache it will go through. But I think something is missing because in the surf folder, there are no *h.pial.outer_smoothed files created. I really need the files to go forward. Thanks. Reporting on 70 segmentations Using PrintSegStat mri_segstats done /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR/SHICEP_S15_84_KG/label INFO: fsaverage subject does not have uptodate *rhinal labels! \n cd /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR; rm -Rf fsaverage; cd - \n INFO: Creating symlink to fsaverage subject... \n cd /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR; ln -s /Applications/freesurfer/subjects/fsaverage; cd - \n #-------------------------------------------- #@# BA_exvivo Labels lh Tue Feb 27 02:44:34 PST 2018 \n mri_label2label --srcsubject fsaverage --srclabel /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR/fsaverage/label/lh.BA1_exvivo.label --trgsubject SHICEP_S15_84_KG --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface \n No such file or directory mri_label2label.bin: could not open label file /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR/fsaverage/label/lh.BA1_exvivo.label srclabel = /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = SHICEP_S15_84_KG trglabel = ./lh.BA1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR FREESURFER_HOME /Applications/freesurfer Loading source label. No such file or directory ERROR reading /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR/fsaverage/label/lh.BA1_exvivo.label Darwin Lin.local 17.4.0 Darwin Kernel Version 17.4.0: Sun Dec 17 09:19:54 PST 2017; root:xnu-4570.41.2~1/RELEASE_X86_64 x86_64 recon-all -s SHICEP_S15_84_KG exited with ERRORS at Tue Feb 27 02:44:34 PST 2018 For more details, see the log file /Users/istone/MATLAB_SOFTWARE/data/SUBJECT_DIR/SHICEP_S15_84_KG/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

3 2

analysing scans other than brain
by Matyas Varga 05 Mar '18

05 Mar '18

Dear Free Surfer, I was wondering if it was possible to analyse (surface-based morphometry and SPM) NOT brain scans. I am doing my PhD looking at how the shape of children's feet change as they get older (2-7 years old). I will use a 3D scanner which will provide me with a mesh of triangles of the foot and I am considering to create average age group foot shapes and compare them using surface based morphometry and SPM. I will obviously have to create my own foot "atlas". I was wondering if this was possible in Free Surfer? Please let me know if it is possible or if you have any suggestions if it is not. Thank you. Best Regards Matyas Varga PhD student School of Health Sciences Research University of Brighton Aldro Building, 49 Darley Road Eastbourne, BN20 7UR Tel: 01273 644189 ___________________________________________________________ This email has been scanned by MessageLabs' Email Security System on behalf of the University of Brighton. For more information see: https://staff.brighton.ac.uk/is/computing/Pages/Email/spam.aspx

2 3

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

3 3

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

2 1

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

1 0

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

1 0

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

2 1

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

1 0

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.

1 0

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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