Freesurfer November 2019

freesurfer@nmr.mgh.harvard.edu

87 participants
122 discussions

Is -skullstrip set by default?
by Billah, Tashrif 25 Nov '19

25 Nov '19

With recon-all, is [-skullstrip](https://surfer.nmr.mgh.harvard.edu/fswiki/skullstrip) option set by default? I am trying to understand why there is a separate -noskullstrip option. Best, Tashrif ------------------------------------------------------------- Tashrif Billah, MS<https://www.linkedin.com/in/tashrif-billah/> Research Engineer Brigham and Women's Hospital Harvard Medical School tbillah(a)bwh.harvard.edu<mailto:tbillah@bwh.harvard.edu> http://pnl.bwh.harvard.edu/tashrif-billah-m-s/

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Recon-all Error
by Meena M. Makary 22 Nov '19

22 Nov '19

External Email - Use Caution Hi, I have been getting this error with one of my subjects Recon-all. I am attaching the recon-all log file. any help would be appreciated! Meena -- — *Meena M. Makary, Ph.D.* Assistant Professor | Cairo University <http://bmes.cufe.edu.eg/> Postdoctoral Fellow | Radiology, Harvard Medical School <https://connects.catalyst.harvard.edu/Profiles/display/Person/176550> Postdoctoral Fellow | Athinoula A. Martinos Center, MGH <https://www.nmr.mgh.harvard.edu/user/4550386> Career Development and Mentoring Manager | OHBM Student and Postdoc SIG <https://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3449>

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freesurfer linux-ppc build
by Ryan Schneider 22 Nov '19

22 Nov '19

External Email - Use Caution Hello, Is there an available freesurfer linux power pc (Power 9) build? I can not find any information about this online. If not , I have been working on making one and would like to know if anyone else has any progress ... Thanks, Ryan Schneider Boston University

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error in preprocessing
by Muhammad Naveed Iqbal Qureshi 22 Nov '19

22 Nov '19

External Email - Use Caution Hi please see the log below. I do not understand the cause of the failure. [nqureshi@qlogin1 ~]$ recon-all -s /hpf/projects/glongoni/ADHD-200/rest.nii -subject ADHD-1 -all -hippocampal-subfields-T1 -sd /hpf/projects/glongoni/ADHD-200/ -no-isrunning 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 /hpf/projects/glongoni/ADHD-200 Actual FREESURFER_HOME /hpf/tools/centos6/freesurfer/6.0.0 -rw-rw-r-- 1 nqureshi glongoni 57759 Nov 19 16:32 /hpf/projects/glongoni/ADHD-200/ADHD-1/scripts/recon-all.log Linux qlogin1.ccm.sickkids.ca 2.6.32-754.14.2.el6.x86_64 #1 SMP Tue May 14 19:35:42 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux nu_correct: Command not found. `/hpf/tools/centos6/freesurfer/6.0.0/bin/recon-all' -> `/hpf/projects/glongoni/ADHD-200/ADHD-1/scripts/recon-all.local-copy' #-------------------------------------------- #@# MotionCor Tue Nov 19 16:32:47 EST 2019 Found 1 runs /hpf/projects/glongoni/ADHD-200/ADHD-1/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 /hpf/projects/glongoni/ADHD-200/ADHD-1/mri/orig/001.mgz /hpf/projects/glongoni/ADHD-200/ADHD-1/mri/rawavg.mgz /hpf/projects/glongoni/ADHD-200/ADHD-1 mri_convert /hpf/projects/glongoni/ADHD-200/ADHD-1/mri/rawavg.mgz /hpf/projects/glongoni/ADHD-200/ADHD-1/mri/orig.mgz --conform mri_convert.bin /hpf/projects/glongoni/ADHD-200/ADHD-1/mri/rawavg.mgz /hpf/projects/glongoni/ADHD-200/ADHD-1/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /hpf/projects/glongoni/ADHD-200/ADHD-1/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, 1, 0) k_ras = (-0, -0, 1) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /hpf/projects/glongoni/ADHD-200/ADHD-1/mri/orig.mgz... mri_add_xform_to_header -c /hpf/projects/glongoni/ADHD-200/ADHD-1/mri/transforms/talairach.xfm /hpf/projects/glongoni/ADHD-200/ADHD-1/mri/orig.mgz /hpf/projects/glongoni/ADHD-200/ADHD-1/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Tue Nov 19 16:32:54 EST 2019 /hpf/projects/glongoni/ADHD-200/ADHD-1/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /hpf/projects/glongoni/ADHD-200/ADHD-1/mri /hpf/tools/centos6/freesurfer/6.0.0/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 qlogin1.ccm.sickkids.ca 2.6.32-754.14.2.el6.x86_64 #1 SMP Tue May 14 19:35:42 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux Tue Nov 19 16:32:54 EST 2019 nu_correct: Command not found. /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.50153 /hpf/projects/glongoni/ADHD-200/ADHD-1/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.50153/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.50153/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.50153/nu0.mnc... -------------------------------------------------------- Iteration 1 Tue Nov 19 16:32:55 EST 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.50153/nu0.mnc ./tmp.mri_nu_correct.mni.50153/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.50153/0/ -iterations 1000 -distance 50 nu_correct: Command not found. ERROR: nu_correct Linux qlogin1.ccm.sickkids.ca 2.6.32-754.14.2.el6.x86_64 #1 SMP Tue May 14 19:35:42 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ADHD-1 exited with ERRORS at Tue Nov 19 16:32:55 EST 2019 For more details, see the log file /hpf/projects/glongoni/ADHD-200/ADHD-1/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting [nqureshi@qlogin1 ~]$ qsub: job 221779.qtorque2.ccm.sickkids.ca completed Regards, Naveed

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TRACULA: Too many ('s. ERROR: run list is longer than subject list
by Mazzetti, C. (Cecilia) 22 Nov '19

22 Nov '19

External Email - Use Caution Dear all, I keep having problem running -stat function within tracula with 27 subjects. If I remove some of them then the script works (up to 22 subjects). Could you please help me with this? I read in a previous post that it has to do with the FS version but even if I change it the error happens anyway... thanks so much in advance! Best, Cecilia Cecilia Mazzetti - Ph.D. Researcher Donders Centre for Cognitive Neuroimaging, room 2.257 Kapittelweg 29 | 6525 EN Nijmegen

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about to segmentation
by Halil Aziz VELİOĞLU 22 Nov '19

22 Nov '19

External Email - Use Caution Hi Mr/Mrs, I want to segment substantia nigra, nucleus ruber (red nucleus) and subthalamic nucleus in Freesurfer. These regions are not in aseg.stats file. So how can I segment these regions? Is there any pipeline or scripts? Best regard, -- Öğr. Gör. Dr. Halil Aziz Velioğlu Kognitif Sinirbilim Anabilim Dalı

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Post list
by Halil Aziz VELİOĞLU 22 Nov '19

22 Nov '19

External Email - Use Caution Hi, I want to send mail Best Öğr. Gör. Dr. Halil Aziz Velioğlu

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segmentThalamicNuclei.sh exited with error
by Dalton Bermudez 21 Nov '19

21 Nov '19

External Email - Use Caution Dear Freesurfer Support Team, I am trying run the file segmentThalamicNuclei.sh to segment the thalamic nuclei on a subject. I am using the following command line: /usr/local/freesurfer/bin/segmentThalamicNuclei.sh 00_0086 $SUBJECTS_DIR. However, the program exits with the following error message: error while loading shared libraries: libmwmclmcrrt.so.8.4: cannot open shared object file: No such file or directory. What can I do to fix the problem? Thank you, Dalton

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Re: [Freesurfer] Freesurfer 4.5 on Ubuntu 18.04 ?
by fsbuild 21 Nov '19

21 Nov '19

External Email - Use Caution Hello Paulo, I could be wrong, but I don’t see that freesurfer 4 contains or shipped with any ./lib directory with its own copies of needed libraries like libvtk*, libtcl*, etc.   On Ubuntu, those libraries are installed on the system under /usr/lib/x86_64-linux-gnu.   One way to find them is to add a path to search for libraries via the environment variable LD_LIBRARY_PATH, e.g., $ export LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH But even after trying that, it looks like the freesurfer4 binaries cannot find the older versions of the libraries it expects in that system location for libs on Ubuntu 18, e.g.,  libtiff is version 5 but freesurfer4 expects version 3;  on Ubuntu 18 libtcl* is version 8.6 but freesurfer4 expects version 8.4, and so forth for libvtk*, libpango*, and other libs. Another issue (which I did not look at) is that even if the same library revisions that  freesurfer4 expects are installed on Ubuntu 18, the older symbol references compiled into freesurfer4 libraries may no longer exist in the newer Ubuntu 18 versions of those libraries.   If you look at the web page with some freesurfer5 download info, https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall5.3 - the entry for the Xubuntu12 VM I take to mean that freesurfer 5.3 ran on Ubuntu 12.  That was back in 2013, and freesurfer 4 is older than that. So I might expect freesurfer4 to run on Ubuntu 12 or maybe 13, but I would not expect those binaries  to run some 6 iterations (and 6 years) later on Ubuntu 18. - R. On Nov 21, 2019, at 08:49, Baptista, Paulo <paulo_baptista(a)brown.edu> wrote:        External Email - Use Caution        Hello--Good morning.  Thank you very much for your email.Yes we have the license file.  When we didn't have the license file, we would get an error about missing license file.(base) pbaptist@clps-pb1:/var/tmp/freesurfer4$ lsASegStatsLUT.txt  bin              diffusion               FreeSurferEnv.csh  fsfast  mni               SetUpFreeSurfer.csh            subjectsAUTHORS           build-stamp.txt  docs                    FreeSurferEnv.sh   lib     SegmentNoLUT.txt  SetUpFreeSurfer.sh             tkmeditParcColorsCMAaverage           DefectLUT.txt    FreeSurferColorLUT.txt  fsafd              matlab  sessions          Simple_surface_labels2009.txt(base) pbaptist@clps-pb1:/var/tmp/freesurfer4$ ls -la .license-rw-r--r-- 1 root root 49 Nov 18 15:10 .license(base) pbaptist@clps-pb1:/var/tmp/freesurfer4$ cat .licensepb(a)brown.edu41878 *C8f07l/gczz6 FSdMgckdPeGoE(base) pbaptist@clps-pb1:/var/tmp/freesurfer4$(base) root@clps-pb1:/var/tmp/freesurfer4# mv .license license(base) root@clps-pb1:/var/tmp/freesurfer4# cd bin(base) root@clps-pb1:/var/tmp/freesurfer4/bin#  export FREESURFER_HOME=/var/tmp/freesurfer4(base) root@clps-pb1:/var/tmp/freesurfer4/bin# source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /var/tmp/freesurfer4FSFAST_HOME       /var/tmp/freesurfer4/fsfastFSF_OUTPUT_FORMAT niiSUBJECTS_DIR      /var/tmp/freesurfer4/subjectsMNI_DIR           /var/tmp/freesurfer4/mni(base) root@clps-pb1:/var/tmp/freesurfer4/bin# export SUBJECTS_DIR=/var/tmp/f4(base) root@clps-pb1:/var/tmp/freesurfer4/bin# cd  /var/tmp/f4(base) root@clps-pb1:/var/tmp/f4# mri_convert sample-001.mgz sample-001.nii.gzmri_convert sample-001.mgz sample-001.nii.gz$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $reading from sample-001.mgz....--------------------------------------------------------------------------ERROR: FreeSurfer license file /var/tmp/freesurfer4/.license not found.  If you are outside the NMR-Martinos Center,  go to http://surfer.nmr.mgh.harvard.edu to  get a valid license file (it's free).  If you are inside the NMR-Martinos Center,  make sure to source the standard environment.--------------------------------------------------------------------------(base) root@clps-pb1:/var/tmp/f4#(base) root@clps-pb1:/var/tmp/f4# mv /var/tmp/freesurfer4/license /var/tmp/freesurfer4/.license(base) root@clps-pb1:/var/tmp/f4# mri_convert sample-001.mgz sample-001.nii.gzmri_convert sample-001.mgz sample-001.nii.gz$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $reading from sample-001.mgz...Segmentation fault (core dumped)(base) root@clps-pb1:/var/tmp/f4#Ok, will you confirm Ubuntu 18 can not run Freesurfer 4?Thanks,PauloOn Thu, Nov 21, 2019 at 1:14 AM fsbuild <fsbuild(a)contbay.com> wrote:Hello Paulo,What is the location of the freesurfer license file (?), i.e., I would make sure the freesurfer license file is under $FREESURFER_HOME and then see if you get different results running the command.Even with the license file though, I’m not sure all the Freesurfer 4 binaries will run on Ubuntu 18- R.On Nov 19, 2019, at 15:26, Baptista, Paulo <paulo_baptista(a)brown.edu> wrote:        External Email - Use Caution        Hello FreeSurfer Developers,I am helping a researcher in my department run FreeSurfer on a new computer..  They insist that it should run on FreeSurfer 4.5 because their old system ran that version.  Is the following possible?  We can run FreeSurfer 6.0 fine, but they say there are differences between the versions.  1) FreeSurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0-full 2) Platform: Ubuntu 18.04.1 LTS 3) uname -a: Linux clps-pb1 4..15.0-64-generic #73-Ubuntu SMP Thu Sep 12 13:16:13 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: n/a Segmentation Fault - see below(base) root@clps-pb1:/var/tmp# cd freesurfer4(base) root@clps-pb1:/var/tmp/freesurfer4# lsASegStatsLUT.txt  DefectLUT.txt           FreeSurferEnv.sh  mni                  Simple_surface_labels2009.txtAUTHORS           diffusion               fsafd             SegmentNoLUT.txt     subjectsaverage           docs                    fsfast            sessions             tkmeditParcColorsCMAbin               FreeSurferColorLUT.txt  lib               SetUpFreeSurfer.cshbuild-stamp.txt   FreeSurferEnv.csh       matlab            SetUpFreeSurfer.sh(base) root@clps-pb1:/var/tmp/freesurfer4# export FREESURFER_HOME=/var/tmp/freesurfer4(base) root@clps-pb1:/var/tmp/freesurfer4# source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /var/tmp/freesurfer4FSFAST_HOME       /var/tmp/freesurfer4/fsfastFSF_OUTPUT_FORMAT niiSUBJECTS_DIR      /var/tmp/freesurfer4/subjectsMNI_DIR           /var/tmp/freesurfer4/mni(base) root@clps-pb1:/var/tmp/freesurfer4# cd ..(base) root@clps-pb1:/var/tmp# cd f4bash: cd: f4: No such file or directory(base) root@clps-pb1:/var/tmp# mkdir f4(base) root@clps-pb1:/var/tmp# cd f4(base) root@clps-pb1:/var/tmp/f4# ls(base) root@clps-pb1:/var/tmp/f4#  export SUBJECTS_DIR=/var/tmp/f4(base) root@clps-pb1:/var/tmp/f4# cp $FREESURFER_HOME/subjects/sample-001.mgz .(base) root@clps-pb1:/var/tmp/f4# ls -lrttotal 6136-rw-r--r-- 1 root root 6280209 Nov 19 15:13 sample-001.mgz(base) root@clps-pb1:/var/tmp/f4# mri_convert sample-001.mgz sample-001.nii.gzmri_convert sample-001.mgz sample-001.nii.gz$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $reading from sample-001.mgz...Segmentation fault (core dumped)(base) root@clps-pb1:/var/tmp/f4#Thanks,Paulo_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Question about the input for longitudinal processing pipeline
by Darko Komnenić 21 Nov '19

21 Nov '19

External Email - Use Caution Thanks a lot for the reply and the suggestions, Douglas! These scans are at 3T. Best, Darko > ------------------------------ > > Message: 4 > Date: Wed, 20 Nov 2019 22:45:18 +0000 > From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] Question about the input for longitudinal > processing pipeline > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <8be29ed9-8627-d005-fd9b-ca3ec56f8a5b(a)mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > I have not run images with contrast, but I think it should? work. Some > people have tried to use the mp2rage UNI scan, but it often fails > because of very bright voxels outside of the brain. If you can remove > those (eg, skull stripping), then it might work. Alternatively, if you > have a quantitative T1 that comes out of the mp2rage if you have the > license, then you can simulate an mp1rage that will then work in FS (but > it will have bias fields). If you don't have a qT1, it is not too hard > to convert the UNI to qT1. Is this at 3T or 7t? > > On 11/19/19 5:35 AM, Darko Komneni? wrote: > > > > ????????External Email - Use Caution > > > > Hi Douglas, > > thanks for your reply. Indeed, in this particular data set they don't > > all have contrast, which is unfortunate. But my question was also > > general, if we assume that they all have contrast, would it be OK to > > use those images as inputs in the longitudinal pipeline? And the same > > question for mp2rage images, are they OK to use as well, or are they > > not suitable for this pipeline? > > Best, > > Darko > > > > > > ------------------------------ > > > > Message: 11 > > Date: Mon, 18 Nov 2019 18:41:37 +0000 > > From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu > > <mailto:DGREVE@mgh.harvard.edu>> > > Subject: Re: [Freesurfer] Question about the input for longitudinal > > ? ? ? ? processing pipeline > > To: "freesurfer(a)nmr.mgh.harvard.edu > > <mailto:freesurfer@nmr.mgh.harvard.edu>" > > <freesurfer(a)nmr.mgh.harvard.edu > > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > Message-ID: <d5205fe6-329a-f9b4-252a-8f1857aa42e4(a)mgh.harvard.edu > > <mailto:d5205fe6-329a-f9b4-252a-8f1857aa42e4@mgh.harvard.edu>> > > Content-Type: text/plain; charset="utf-8" > > > > Do all images and time points have contrast? If some do and some > > don't, > > then I don't think you can properly do the analysis? > > > > On 11/15/19 10:06 AM, Darko Komneni? wrote: > > > > > > ????????External Email - Use Caution > > > > > > Dear Freesurfer experts, > > > I wanted to run the Freesurfer's longitudinal processing pipeline > > > (described here > > > > > https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing) > > on a > > > series of MRI scans from a single patient. However, after > > looking at > > > the scans, i realized that for most time points, the patient > > doesn't > > > have a "simple/normal" T1 MPRAGE sequence available. Instead, they > > > have a T1 sequence with a contrast agent, as well as T1 mp2rage > > > sequences. > > > > > > Is it possible/advisable to run recon-all in general or this > > pipeline > > > in particular on T1 MPRAGE scans that have a contrast agent, or > > that > > > are mp2rage instead of MPRAGE? > > > > > > Thanks in advance! > > > Best, > > > Darko > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > >

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Freesurfer November 2019