Freesurfer June 2016

freesurfer@nmr.mgh.harvard.edu

152 participants
213 discussions

Stuck on “CORRECTING DEFECT”
by Dan Loewenherz 27 Jun '16

27 Jun '16

Hi freeserver folks, First time poster here. First off, thanks so much to the folks who work on and make this software available to the public. It seems like pretty incredible tech, from what little I understand of it. :) My problem is that the freesurfer process appears to be stuck on the recon-all command. It’s been sitting at ”CORRECTING DEFECT 0 (vertices=96285, convex hull=13916)” for about 10 hours now. Any way to cut that number down or should I just let it keep doing its thing? I’ve pasted all of the output pasted at end of the message. Thanks so much! Dan ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-684 (nv=141228, nf=283824, ne=425736, g=343) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 14 iterations marking ambiguous vertices... 190731 ambiguous faces found in tessellation segmenting defects... 40 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 2 into 0 -merging segment 5 into 0 -merging segment 8 into 0 -merging segment 14 into 0 -merging segment 25 into 0 -merging segment 28 into 0 -merging segment 20 into 17 -merging segment 29 into 17 -merging segment 36 into 35 31 defects to be corrected 0 vertices coincident reading input surface /Applications/freesurfer/subjects/Dan/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.8790 (-4.4395) -vertex loglikelihood: -7.4039 (-3.7020) -normal dot loglikelihood: -3.5029 (-3.5029) -quad curv loglikelihood: -6.1567 (-3.0783) Total Loglikelihood : -25.9425 CORRECTING DEFECT 0 (vertices=96285, convex hull=13916)

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Freeview nightly / dev / beta
by Vincent Koppelmans 27 Jun '16

27 Jun '16

Hello Freesurfer developers, I am looking for a version of Freeview that recognizes the -noquit flag. V 1.0 Build Aug 24 2015 14:50:08 allows this, but is no longer available from "ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev <ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev>”. I am particularly interested in a Linux version. Would it be possible to open up access to the beta versions of Freeview to us endusers again? Thanks! - Vincent

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Re: [Freesurfer] visualizing statistical maps in FreeView
by Bruce Fischl 27 Jun '16

27 Jun '16

Hi Lars I'll leave this for Ruopeng. cheers Bruce On Mon, 27 Jun 2016, Lars Morten Rimol wrote: > > Hi Bruce, > > > > Yes, now it works (my guess is I loaded a single subject surface as template > before…) but I don’t find an FDR correction button in the Configure Overlay > interface. The fdr threshold can of course be calculated in Matlab but then > why not use tksurfer, which provides that functionality it in the > interface. Also: Unlike in tksurfer, the color bar doesn’t seem to reflect > the thresholding of the overlay…. > > > > > > Thanks! > > > > LMR > > >

2 2

Qdec-correction for multiple comparison
by John Anderson 25 Jun '16

25 Jun '16

1 0

License for data file?
by Matthew Brett 24 Jun '16

24 Jun '16

Hi, Over at our nibabel Python package, we've got stuck trying to work out what license we should give to a file we got from Freesurfer version 3.0.3: https://github.com/nipy/nibabel/pull/461 The file is `subjects/bert/surf/lh.inflated.nofix` from Freesurfer 3.0.3. It looks like this is a modified version of the original files from the tutorial dataset - which I think derive from here: https://web.archive.org/web/20070711224104/http://www.fmridc.org/f/fmridc/7… Is that right? What license should we give when we are distributing the `subjects/bert/surf/lh.inflated.nofix` in an archive we are using to test our software? Thanks a lot, Matthew

2 4

ReconAll error
by Hao wen 24 Jun '16

24 Jun '16

Hi, FS experts: I run the reconAlll command with two nii file, and I got some error here, can you help me to check it out, cuz I think I use the command correctly... here is the info for the error: I think the problem is for the mri_convert command, I checked thr orig folder, there is no T1.mgz file! can you tell me why? crash-20160624-204118-guest-_recon_all0.pklz File: crash-20160624-204118-guest-_recon_all0.pklz Node: _recon_all0 Working directory: /tmp/tmpzZyfB0/reconall_workflow/recon_all/mapflow/_recon_all0 Node inputs: T1_files = ['/home/guest/HAO/Clinica/clinica/examples/data/Recon-all/example2/struct.nii'] T2_file = <undefined> args = -qcache directive = all environ = {} flags = <undefined> hemi = <undefined> ignore_exception = False openmp = <undefined> subject_id = example2 subjects_dir = /tmp/tmpzZyfB0 terminal_output = stream Traceback: Traceback (most recent call last): File "/home/guest/Downloads/ENTER/lib/python2.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 18, in run_node result['result'] = node.run(updatehash=updatehash) File "/home/guest/Downloads/ENTER/lib/python2.7/site-packages/nipype/pipeline/engine.py", line 1428, in run self._run_interface() File "/home/guest/Downloads/ENTER/lib/python2.7/site-packages/nipype/pipeline/engine.py", line 1538, in _run_interface self._result = self._run_command(execute) File "/home/guest/Downloads/ENTER/lib/python2.7/site-packages/nipype/pipeline/engine.py", line 1664, in _run_command result = self._interface.run() File "/home/guest/Downloads/ENTER/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1033, in run runtime = self._run_wrapper(runtime) File "/home/guest/Downloads/ENTER/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1457, in _run_wrapper runtime = self._run_interface(runtime) File "/home/guest/Downloads/ENTER/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1491, in _run_interface self.raise_exception(runtime) File "/home/guest/Downloads/ENTER/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1415, in raise_exception raise RuntimeError(message) RuntimeError: Command: recon-all -all -i /home/guest/HAO/Clinica/clinica/examples/data/Recon-all/example2/struct.nii -qcache -subjid example2 -sd /tmp/tmpzZyfB0 Standard output: Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /tmp/tmpzZyfB0 Actual FREESURFER_HOME /usr/local/freesurfer Linux guest-Latitude-E6220 3.19.0-49-generic #55~14.04.1-Ubuntu SMP Fri Jan 22 11:24:31 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux /tmp/tmpzZyfB0/example2 mri_convert /home/guest/HAO/Clinica/clinica/examples/data/Recon-all/example2/struct.nii /tmp/tmpzZyfB0/example2/mri/orig/001.mgz Linux guest-Latitude-E6220 3.19.0-49-generic #55~14.04.1-Ubuntu SMP Fri Jan 22 11:24:31 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s example2 exited with ERRORS at vendredi 24 juin 2016, 20:40:29 (UTC+0200) For more details, see the log file /tmp/tmpzZyfB0/example2/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Standard error: Return code: 1 Interface ReconAll failed to run. Thanks in advance

1 0

reconall error
by Hao wen 24 Jun '16

24 Jun '16

1 0

visualizing statistical maps in FreeView
by Lars M. Rimol 24 Jun '16

24 Jun '16

Hi, Is it possible to overlay .mgh files with statistics (e.g. p-maps) directly in FreeView, for purposes of visualizing the results, the same way you can in tksurfer? When I try load an overlay in FreeView, it seems to be expecting a volume file. Thank you! sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway

2 1

Creating spheres in the volume
by Afzal, Afsana 24 Jun '16

24 Jun '16

Hi, This question might have already been answered before but is there a way to take a coordinate in MNI space and create, say, a 5mm sphere in the volume? My goal is to take the sphere in the volume and convert it to a label using something like mri_vol2surf. Thanks for your help, Afsana ______________________________ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078

1 0

Qdec-correction for multiple comparison
by John Anderson 23 Jun '16

23 Jun '16

1 0

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Freesurfer June 2016