[Freesurfer] make_average_subject error: could not load norm volume from (null)
External Email - Use Caution HI FreeSurfer Developers, I'm attempting to create an average subject make_average_subject but I get the error message the following error when I run the make_average_command: Loading aseg from REMOVED-PATH/avg_elder/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: --- -1.0 0.0 0.0 128.0; 0.0 0.0 1.0 -128.0; 0.0 -1.0 0.0 128.0; 0.0 0.0 0.0 1.0; mghRead(mri/norm.mgz, -1): could not open file - Labeling Slice relabeling unlikely voxels in interior of white matter mri/norm.mgz: could not load norm volume from (null) Linux 4.4.0-130-generic #156-Ubuntu SMP Thu Jun 14 08:53:28 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux I cannot find anything similar on the mailing list. I hope anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: Ubuntu 16.04.4 LTS 3) uname -a: Linux hyades02 4.4.0-130-generic #156-Ubuntu SMP Thu Jun 14 08:53:28 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached recon-all.log Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all error on ubuntu 16.04
Hi Zeke, Thank you for clarifying this, it did help. You are right the perl version is 5.22 I will give the development version a try. best, mads On 05/11/2016 04:51 PM, Z K wrote: > Hello Mads, > > This is a recently discovered issue with the mni tools that ship with > freesurfer v5.3 and the latest version of perl (which probably comes > with Ubuntu 16). I know the issue exists with perl version 5.22 but I > dont know with what version the issue started. > > This has been fixed in the dev version of freesurfer and thus will be > fixed in the upcoming release of freesurfer version 6.0. Unfortunately, > you only have 2 options if you want to use freesurfer v5.3 on your > Ubuntu 16 machine: > > 1) Update to the newest Development Version of freesurfer: > >https://surfer.nmr.mgh.harvard.edu/fswiki/Download > > 2) Use the "sudo apt-get" tools to install a pre 5.22 version of perl on > your machine. > > Hope this helps. > > -Zeke > > > > > > On 05/11/2016 10:06 AM, Mads Jensen wrote: >> Hi Martin, >> >> Thanks for your reply. >> >> rawavg.mgz and orig.mgz does exist. When I run the command I get the >> following error: >> >> mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale >> --i orig.mgz --o orig_nu.mgz >> /home/XYZ/Projects/tmp/fs_test/test/mri >> /home/XYZ/Toolboxes/freesurfer/bin/mri_nu_correct.mni >> --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o >> orig_nu.mgz >> nIters 1 >> $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ >> Linux comp_name 4.4.0-22-generic #39-Ubuntu SMP Thu May 5 16:53:32 UTC >> 2016 x86_64 x86_64 x86_64 GNU/Linux >> Wed May 11 16:03:55 CEST 2016 >> Program nu_correct, built from: >> Package MNI N3, version 1.10, compiled by nicks@minerva >> (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 >> tmpdir is ./tmp.mri_nu_correct.mni.3509 >> /home/XYZ/Projects/tmp/fs_test/test/mri >> mri_convert orig.mgz ./tmp.mri_nu_correct.mni.3509/nu0.mnc -odt float >> mri_convert orig.mgz ./tmp.mri_nu_correct.mni.3509/nu0.mnc -odt float >> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 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.3509/nu0.mnc... >> >> >> Iteration 1 Wed May 11 16:03:57 CEST 2016 >> nu_correct -clobber ./tmp.mri_nu_correct.mni.3509/nu0.mnc >> ./tmp.mri_nu_correct.mni.3509/nu1.mnc -tmpdir >> ./tmp.mri_nu_correct.mni.3509/0/ -iterations 1000 -distance 50 >> Can't use 'defined(@array)' (Maybe you should just omit the defined()?) >> at /home/XYZ/Toolboxes/freesurfer/mni/bin/nu_estimate_np_and_em line 165. >> nu_correct: crashed while running nu_estimate_np_and_em (termination >> status=65280) >> ERROR: nu_correct >> >> >> best, >> mads >> >> On 05/11/2016 03:32 PM, Martin Reuter wrote: >>> Hi Mads, >>> >>> is the file being copied (does >>> /home/XYZ/Projects/tmp/fs_test/test/mri/rawavg.mgz and orig.mgz exist)? >>> If not, maybe some disk space / IO problem. >>> Also what happens when you run >>> >>> mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 >>> --no-rescale --i orig.mgz --o orig_nu.mgz >>> >>> directly? Maybe something is wrong with the MNI tools. >>> >>> Best, Martin >>> >>> On 05/11/2016 07:43 AM, Mads Jensen wrote: >>>> Dear FreeSurfer group, >>>> >>>> I get an error trying to run basic recon-all on a ubuntu 16.04 system. >>>> >>>> It finish with errors after a few minutes and I cannot find any help in >>>> the recon-all.log (pasted below). >>>> >>>> I have made the symbolic links from the installation notes. >>>> >>>> Any ideas or thoughts on what the problem might be or how to track it >>>> down would be very welcome. >>>> >>>> best regards, >>>> mads >>>> >>>> >>>> >>>> >>>> from bugr: >>>> FREESURFER_HOME: /home/XYZ/Toolboxes/freesurfer >>>> >>>> Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 >>>> >>>> Debian version: stretch/sid >>>> >>>> Kernel info: Linux 4.4.0-22-generic x86_
Re: [Freesurfer] recon-all error on ubuntu 16.04
Hi Martin, Thanks for your reply. rawavg.mgz and orig.mgz does exist. When I run the command I get the following error: mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz /home/XYZ/Projects/tmp/fs_test/test/mri /home/XYZ/Toolboxes/freesurfer/bin/mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz nIters 1 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux comp_name 4.4.0-22-generic #39-Ubuntu SMP Thu May 5 16:53:32 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Wed May 11 16:03:55 CEST 2016 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.3509 /home/XYZ/Projects/tmp/fs_test/test/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.3509/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.3509/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 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.3509/nu0.mnc... Iteration 1 Wed May 11 16:03:57 CEST 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.3509/nu0.mnc ./tmp.mri_nu_correct.mni.3509/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.3509/0/ -iterations 1000 -distance 50 Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at /home/XYZ/Toolboxes/freesurfer/mni/bin/nu_estimate_np_and_em line 165. nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280) ERROR: nu_correct best, mads On 05/11/2016 03:32 PM, Martin Reuter wrote: > Hi Mads, > > is the file being copied (does > /home/XYZ/Projects/tmp/fs_test/test/mri/rawavg.mgz and orig.mgz exist)? > If not, maybe some disk space / IO problem. > Also what happens when you run > >mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale > --i orig.mgz --o orig_nu.mgz > > directly? Maybe something is wrong with the MNI tools. > > Best, Martin > > On 05/11/2016 07:43 AM, Mads Jensen wrote: >> Dear FreeSurfer group, >> >> I get an error trying to run basic recon-all on a ubuntu 16.04 system. >> >> It finish with errors after a few minutes and I cannot find any help in >> the recon-all.log (pasted below). >> >> I have made the symbolic links from the installation notes. >> >> Any ideas or thoughts on what the problem might be or how to track it >> down would be very welcome. >> >> best regards, >> mads >> >> >> >> >> from bugr: >> FREESURFER_HOME: /home/XYZ/Toolboxes/freesurfer >> >> Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 >> >> Debian version: stretch/sid >> >> Kernel info: Linux 4.4.0-22-generic x86_64 >> >> >> recon-all.log: >> >> Mon May 9 11:12:07 CEST 2016 >> /home/XYZ/Projects/tmp/fs_test/test >> /home/XYZ/Toolboxes/freesurfer/bin/recon-all >> -all -subjid test -i T1.mgz >> subjid test >> setenv SUBJECTS_DIR /home/XYZ/Projects/tmp/fs_test >> FREESURFER_HOME /home/XYZ/Toolboxes/freesurfer >> Actual FREESURFER_HOME /home/XYZ/Toolboxes/freesurfer >> build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 >> Linux comp_name 4.4.0-22-generic #39-Ubuntu SMP Thu May 5 16:53:32 UTC >> 2016 x86_64 x86_64 x86_64 GNU/Linux >> cputime unlimited >> filesize unlimited >> datasize unlimited >> stacksize8192 kbytes >> coredumpsize 0 kbytes >> memoryuseunlimited >> vmemoryuse unlimited >> descriptors 1024 >> memorylocked 64 kbytes >> maxproc 62044 >> maxlocks unlimited >> maxsignal62044 >> maxmessage 819200 >> maxnice 0 >> maxrtprio0 >> maxrttimeunlimited >> >> totalusedfree shared buff/cache >> available >> Mem: 15924580 3455984 375968 32364812092628 11975092 >> Swap: 16616956 25422016362736 >> >> >> program versions used >> $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ >> $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ >> mri_convert -all-info >> ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: >> $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: >> May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 &
[Freesurfer] recon-all error on ubuntu 16.04
Dear FreeSurfer group, I get an error trying to run basic recon-all on a ubuntu 16.04 system. It finish with errors after a few minutes and I cannot find any help in the recon-all.log (pasted below). I have made the symbolic links from the installation notes. Any ideas or thoughts on what the problem might be or how to track it down would be very welcome. best regards, mads from bugr: FREESURFER_HOME: /home/XYZ/Toolboxes/freesurfer Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Debian version: stretch/sid Kernel info: Linux 4.4.0-22-generic x86_64 recon-all.log: Mon May 9 11:12:07 CEST 2016 /home/XYZ/Projects/tmp/fs_test/test /home/XYZ/Toolboxes/freesurfer/bin/recon-all -all -subjid test -i T1.mgz subjid test setenv SUBJECTS_DIR /home/XYZ/Projects/tmp/fs_test FREESURFER_HOME /home/XYZ/Toolboxes/freesurfer Actual FREESURFER_HOME /home/XYZ/Toolboxes/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux comp_name 4.4.0-22-generic #39-Ubuntu SMP Thu May 5 16:53:32 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize8192 kbytes coredumpsize 0 kbytes memoryuseunlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 62044 maxlocks unlimited maxsignal62044 maxmessage 819200 maxnice 0 maxrtprio0 maxrttimeunlimited totalusedfree shared buff/cache available Mem: 15924580 3455984 375968 32364812092628 11975092 Swap: 16616956 25422016362736 program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: XYZ Machine: comp_name Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 === NUMBER OF OPENMP
Re: [Freesurfer] Problem with recon-all
I got a skullstrippen mask from another pipeline to remove the noise in the MP2RAGE. Is it possible to give that to the recon-all? it is either a mnc or nii thanks, mads On 5 October 2015 at 23:11, Andre van der Kouwe <an...@nmr.mgh.harvard.edu> wrote: > I think the standard MP2RAGE only generates the T1 image on the scanner. > With the Bloch simulation you can also figure out PD but the online > image analysis doesn't do it. > > On 10/05/2015 04:21 PM, Bruce Fischl wrote: >> I thought mp2rage lets you derive a proton-density (PD) weighted image, >> but I could be wrong. I'll cc Andre van der Kouwe who will know >> >> >> On Mon, 5 Oct 2015, Mads Jensen wrote: >> >>> Hi and thanks for the fast reply. >>> >>> Pardon my ignorance, but I am not sure that the PD images are? >>> >>> thanks, >>> mads >>> >>> On 5 October 2015 at 21:59, Bruce Fischl <fis...@nmr.mgh.harvard.edu> >>> wrote: >>>> Hi Mads >>>> >>>> my guess is that this is a problem with the MP2RAGE. We don't see >>>> this in >>>> the mprage or memprage. Can you look at the PD images in that region? Is >>>> the PD close to 0? Maybe you can threshold it out? That region is >>>> usually >>>> very dark on an mprage >>>> >>>> cheers >>>> Bruce >>>> >>>> >>>> On Mon, 5 Oct 2015, Mads Jensen wrote: >>>> >>>>> Hi, >>>>> >>>>> I got a problem with recon-all of T1's. The problem is that the >>>>> surfaces extent into what is essential noise, see linked images. The >>>>> problem is reoccurring in all the subjects I have ran so far, so I was >>>>> wondering if there could be a generic fix or if it will be necessary >>>>> to fix each recon individually. >>>>> >>>>> The sequence is a MP2RAGE recorded from a Siemens Skyra. >>>>> >>>>> thanks, >>>>> mads >>>>> >>>>> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0005_coronal.jpg >>>>> >>>>> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0005_sagittal.jpg >>>>> >>>>> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0006_coronal.jpg >>>>> >>>>> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0006_sagittal.jpg >>>>> >>>>> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0007_coronal.jpg >>>>> >>>>> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0007_sagittal.jpg >>>>> >>>>> ___ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> >>>> ___ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> The information in this e-mail is intended only for the person to >>>> whom it is >>>> addressed. If you believe this e-mail was sent to you in error and >>>> the e-mail >>>> contains patient information, please contact the Partners Compliance >>>> HelpLine at >>>> http://www.partners.org/complianceline . If the e-mail was sent to >>>> you in error >>>> but does not contain patient information, please contact the sender >>>> and properly >>>> dispose of the e-mail. >>>> >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Problem with recon-all
Hi and thanks for the fast reply. Pardon my ignorance, but I am not sure that the PD images are? thanks, mads On 5 October 2015 at 21:59, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Mads > > my guess is that this is a problem with the MP2RAGE. We don't see this in > the mprage or memprage. Can you look at the PD images in that region? Is > the PD close to 0? Maybe you can threshold it out? That region is usually > very dark on an mprage > > cheers > Bruce > > > On Mon, 5 Oct 2015, Mads Jensen wrote: > >> Hi, >> >> I got a problem with recon-all of T1's. The problem is that the >> surfaces extent into what is essential noise, see linked images. The >> problem is reoccurring in all the subjects I have ran so far, so I was >> wondering if there could be a generic fix or if it will be necessary >> to fix each recon individually. >> >> The sequence is a MP2RAGE recorded from a Siemens Skyra. >> >> thanks, >> mads >> >> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0005_coronal.jpg >> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0005_sagittal.jpg >> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0006_coronal.jpg >> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0006_sagittal.jpg >> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0007_coronal.jpg >> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0007_sagittal.jpg >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Problem with recon-all
Hi, I got a problem with recon-all of T1's. The problem is that the surfaces extent into what is essential noise, see linked images. The problem is reoccurring in all the subjects I have ran so far, so I was wondering if there could be a generic fix or if it will be necessary to fix each recon individually. The sequence is a MP2RAGE recorded from a Siemens Skyra. thanks, mads https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0005_coronal.jpg https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0005_sagittal.jpg https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0006_coronal.jpg https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0006_sagittal.jpg https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0007_coronal.jpg https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0007_sagittal.jpg ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] brainmask error
Hi Bruce (and the rest of the list), It looks better (see attached) but it still look like it removed too much. cheers for the point though, Mads On 21/08/14 16:22, Bruce Fischl wrote: Hi Mads what does it look like if you move off the mideline? Or check a coronal view? Sagittal views of the midline are notoriously bad for judging skull stripping accuracy cheers Bruce On Tue, 19 Aug 2014, Mads Jensen wrote: Dear list, I have problem with the brainmask from a subject where there is removed to much of the gray matter. So, I would like to hear if someone has a good idea where I should start to fix this issue? I have attached a jpgs of the brainmask and orig, and a link to the recon-all.log best regards, mads https://dl.dropboxusercontent.com/u/915037/recon-all.log ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
