Freesurfer

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30132 discussions

Re: [Freesurfer] Freesurfer Digest, Vol 169, Issue 41
by Darko Komnenić 03 Apr '18

03 Apr '18

Hi Bruce, I attached the recon-all.log! Thanks in advance for taking a look! Darko Message: 3 Date: Sat, 31 Mar 2018 06:47:12 -0400 From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_watershed Error: indices out of bounds To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <23B23889-C042-4A04-9316-4C8ED5468428(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=utf-8 Can you send us the recon-all.log? > On Mar 30, 2018, at 11:32 AM, Darko Komneni? <komnenicd(a)gmail.com> wrote: > > Dear experts, > while running recon-all on FreeSurfer 5.1.0 I encountered the following error: > mri_watershed Error: indices out of bounds > > I searched the email archive and found this thread: > https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subj… > My problem seems identical to the one described by initial poster. > The suggestion was to try the following command: > set mdir=$SUBJECTS_DIR/$subject/mri > mri_add_xform_to_header $mdir/transforms/talairach.xfm $mdir/nu.mgz > $mir/nu.mgz > > When I tried it, the message I got was: > mri_add_xform_to_header: could not open source file /nu.mgz > No such file or directory > And indeed such file does not exist in the mri subfolder of my > current subject's folder. > > Any further suggestions on how to fix this? Like the person asking > originally, this is the only participant where it happened, for > others, recon-all finished without error and all the images were > acquired in the same scanner. > Thanks in advance! > Best, > Darko > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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Fwd: Learning Workshop in Bloomington IN (fwd)
by Bruce Fischl 03 Apr '18

03 Apr '18

FYI ---------- Forwarded message ---------- Date: Tue, 3 Apr 2018 11:14:38 -0400 From: Satrajit Ghosh <satra(a)mit.edu> To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>, "Jog, Amod" <AJOG(a)mgh.harvard.edu> Subject: Fwd: Learning Workshop in Bloomington IN hi, this may be of interest. please forward. cheers, satra -- satrajit ghosh | satra.cogitatum.org principal research scientist | mibr @ m i t assistant professor of otolaryngology @ harvard medical school faculty member @ speech and hearing bioscience and technology director, data models and integration | repronim: center for reproducible neuroimaging computation ---------- Forwarded message ---------- From: Franco Pestilli <frakkopesto(a)gmail.com> Date: Tue, Apr 3, 2018 at 10:51 AM Subject: Learning Workshop in Bloomington IN To: Satrajit Ghosh <satrajit.ghosh(a)gmail.com> Dear Satra We are organizing a learning workshop in Bloomington Indiana May 14-15: http://www.indiana.edu/~earbmc/LIHAM/ Would you mind spreading the word please? We have travel scholarships for talented trainees. Best regards, Franco Franco Pestilli, PhD Assistant Professor in Psychology, Neuroscience and Cognitive Science Adjunct Professor in Engineering, Computer Science, and Optometry Indiana Network Science Institute 𝞇 Indiana University, Bloomington francopestilli.com | brainlife.io franpest(a)indiana.edu | +1 (812) 856 9967

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Freesurfer for canine
by Khoi Mai 03 Apr '18

03 Apr '18

Hi, I am interested in the automated volumetric analysis for canine. My question is how can we go about adjusting the pipeline to accommodate canine data. Thank you for your reply Best, Khoi

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Brainhack Ireland 2018 - Brainhack Global
by Chiara Caldinelli 03 Apr '18

03 Apr '18

Join us for Brainhack Ireland 2018 <http://www.brainhackireland.org/>, a 2.5-day event at which you can team up with neuroscience researchers, data scientists, hackers, philosophers and anyone else with an interest in working on innovative projects related to neuroscience. There will be prizes for the winning teams, and the results will be shared with more than 30 institutions across the world through Brainhack <http://www.brainhack.org/global2018>Global <http://www.brainhack.org/global2018>. Our goal is to understand more about the brain and mind, while having fun. It will be held from the evening of May 2 until May 4, at the awesome Huckletree D2 <https://www.huckletree.com/locations/dublin-d2> space on Pearse St., Dublin. To see the program and for more information, go to www.brainhackireland.org . There is a small registration fee, which will cover coffee, snacks and lunch. We thank our sponsors, the Cusacklab <http://www.cusacklab.org/> and the Trinity College Institute of Neuroscience <http://www.tcd.ie/neuroscience>, Trinity College Dublin. Twitter: #BrainhackIreland Meetup: https://www.meetup.com/Brainhack-Ireland-2018/events/249221592/ Looking forward to seeing you! Chiara On behalf of The Brainhack Ireland Team

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Download FreeSurfer for Virtualbox
by Karin Westin 03 Apr '18

03 Apr '18

Hi! I've tried downloading the FreeSurfer Virtualbox-file several times, but when I try to unzip, I get a message that the file is broken and that the file cannot be unzipped. What am I doing wrong? I realise that this message doesn't contain a whole lot of information but this is all I know... Best, Karin

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mirroring fsaverage labels between hemispheres
by Abigail Noyce 02 Apr '18

02 Apr '18

Hi, I have pored over (I think) all of the mailing list postings about cross-hemisphere mapping and I can't quite figure out how to do this. I have a bunch of labels on fsaverage, and I want to be able to check/visualize the relationship between lh and rh versions of the labels. I can do mri_label2label to map from fsaverage to fsaverage_sym, but that doesn't do the right thing, and fsaverage doesn't have the same kind of xhemi registration structure that "normal" subjects get with surfreg --xhemi. I guess I could back-project onto a normal subject and then project to fsaverage_sym, but that seems like an unnecessary step. How can I get mirror-projected labels from fsaverage on fsaverage_sym? Thanks! Abby -- Abigail L. Noyce, Ph.D. Psychological & Brain Sciences Boston University anoyce(a)bu.edu 617-440-3640

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mri_watershed Error: indices out of bounds
by Darko Komnenić 31 Mar '18

31 Mar '18

Dear experts, while running recon-all on FreeSurfer 5.1.0 I encountered the following error: mri_watershed Error: indices out of bounds I searched the email archive and found this thread: https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subj… My problem seems identical to the one described by initial poster. The suggestion was to try the following command: set mdir=$SUBJECTS_DIR/$subject/mri mri_add_xform_to_header $mdir/transforms/talairach.xfm $mdir/nu.mgz $mir/nu.mgz When I tried it, the message I got was: mri_add_xform_to_header: could not open source file /nu.mgz No such file or directory And indeed such file does not exist in the mri subfolder of my current subject's folder. Any further suggestions on how to fix this? Like the person asking originally, this is the only participant where it happened, for others, recon-all finished without error and all the images were acquired in the same scanner. Thanks in advance! Best, Darko

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Re: [Freesurfer] convert labels to volume in MNI?
by gj 30 Mar '18

30 Mar '18

Hi, I loaded the 2mm MNI152 template and the mri_label2vol outputs in mricron, and I saw that the labels are completely outside the template. So, I know now to use freeview rather than the deprecated tkmedit so I can also load the original atlas labels to check against (using the 2mm MNI152 template as background) -- in any case, I don't even see the labels, I guess because the ROIs/masks lie outside the display. I'm also not sure what the equivalent of tkmedit's overlay-reg is for freeview? I assume my not loading one is why I get the error, "Label coordinate out of bound" when I try and load the original atlas labels (in fsaverage space) on the MNI152 template? Thank you! Gina P.S. Can't find a straightforward way to reply with the entire thread when receiving only a digest from the listserv -- reply to the digest takes the freesurfer-request address rather than the list address and the button on the website for archives only gives the option of replying directly to the person who posted)...what am I missing? ------------------------------ Douglas Greve dgreve at mgh.harvard.edu Tue Mar 27 14:01:16 EDT 2018 how are you verifying that it is not in the right place? You should view it on the 2mm MNI152 using freeview. Also, your label should be a label in fsaverage space. On 3/27/18 9:52 AM, gj wrote: > Hi, > > Newbie question....I want to take FreeSurfer labels (from an atlas in > fsaverage space) and convert it into a volumetric NIFTI mask. I ran the > following command, but I must be missing something because the output is > not in the right space (far too posterior): > > $FREESURFER_HOME/bin/mri_label2vol \ > --label $ll \ > --temp $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \ > --reg $FREESURFER_HOME/average/mni152.register.dat \ > --fillthresh .5 \ > --o $wd/${ll}.nii > > Am I perhaps supposed to first create the volumetric file without > mapping into MNI space and then use tkregister2? > > Thanks in advance for any help or advice! > Gina

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error rerunning recon-all (exited with ERRORS)
by Anna Daniels 30 Mar '18

30 Mar '18

Dear FreeSurfer team, after editing the brainmask.mgz (manually or with gcut), brain.finalsurfs.manedit.mgz and/or adding control points, recon-all was rerun in a loop for several subjects with the respective options *-autorecon-pial* (1) or *-autorecon2 -autorecon3* (2), which resulted in the following error for only some of the subjects (while others worked fine): (1) #@# Mask BFS Mo 19. Mär 02:35:22 CET 2018 /scratch/annadan1111/MABT1T2/reruncrosstest_pial/23358_T1_fs_edit/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 mghRead(/scratch/annadan1111/MABT1T2/reruncrosstest_pial/23358_T1_fs_edit/mri/brainmask.mgz, -1): read error mri_mask.bin: could not read mask volume brainmask.mgz Linux node011 2.6.32-696.18.7.el6.x86_64 #1 SMP Wed Jan 3 19:31:16 CST 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 23358_T1_fs_edit exited with ERRORS at Mo 19. Mär 02:35:23 CET 2018 (2) 3d normalization pass 1 of 2 white matter peak found at 110 Cannot allocate memory Linux node098 2.6.32-696.20.1.el6.x86_64 #1 SMP Thu Jan 25 08:47:49 CST 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 44538_T1_fs_edit exited with ERRORS at Do 29. Mär 01:28:15 CEST 2018 Attached are the respective recon-all.log files in case they may be helpful. We also could not detect any similar post in the mailing list. FreeSurfer version 6.0.0 Thank you and Happy Easter greetings from Berlin, Anna

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Building from source -- autoconf error
by Alle Meije Wink 29 Mar '18

29 Mar '18

I'm trying to build FreeSurfer from source on my Debian 8 (jessie) system. (64 bit, using g++ 4.9 for compilation) After $ cvs -d :pserver:anonymous@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot login $ cvs -d :pserver:anonymous@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot checkout -P dev $ cd dev $ cvs update -d # just to make sure $ ./setup_configure I get these messages: rm -rf autom4te.cache libtoolize --force libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, `config'. libtoolize: linking file `config/ltmain.sh' libtoolize: putting macros in `m4'. libtoolize: linking file `m4/libtool.m4' libtoolize: linking file `m4/ltoptions.m4' libtoolize: linking file `m4/ltsugar.m4' libtoolize: linking file `m4/ltversion.m4' libtoolize: linking file `m4/lt~obsolete.m4' libtoolize: Consider adding `AC_CONFIG_MACRO_DIR([m4])' to configure.in and libtoolize: rerunning libtoolize, to keep the correct libtool macros in-tree. aclocal aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in' aclocal: error: configure.in:2045: file 'm4/autotroll.m4' does not exist Which looks like a not-(anymore)supported use of autoconf? I found one previous message on the list about autotroll https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/021854.… that provided another version of configure.in which might solve the issue. And it did in the original case but sadly not for me. I get the same error message also with the new configure.in -- there should probably be a configure.ac? If anyone knows how to make this work (e.g. by modifying the configure script) that would be fantastic.

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