Freesurfer

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Re: [Freesurfer] Recon-all Error in output - ERROR: nu_correct
by Gregory Mierzwinski 05 Aug '19

05 Aug '19

External Email - Use Caution Hello, Even though this is an old post, the entire solution to this has not been posted and I couldn’t find it anywhere. I hit this error, and I had to (1) make sure the SUBJECT_DIR environment variable was pointing to a directory that is not on the shared Neurodebian folder, and (2) that the data given as input through `-i` was not on the shared folder. Greg

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mri_vol2label with fs v5.3
by Alshelh, Zeynab 05 Aug '19

05 Aug '19

Hi freesurfers, I am currently using freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 and I need to run $mri_vol2label which I have been informed works with fs v6.0. Is there any way I can use this command or a is there a similar command on v5.3? Thanks in advance, ---- Zeynab Alshelh, PhD | Postdoctoral Research Fellow Pain and Neuroinflammation Imaging Laboratory Harvard Medical School | A. A. Martinos Center for Biomedical Imaging | Massachusetts General Hospital | 149 Thirteenth Street, Room 1101 | Charlestown, MA 02129 +1 (617) 794 6838 zalshelh(a)mgh.harvard.edu | www.nmr.mgh.harvard.edu

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A Question Regarding Topology Correction
by Maedeh Khalilian 05 Aug '19

05 Aug '19

External Email - Use Caution Dear Bruce, The other day I asked you about doing topology correction on my own segmentation(I have put my first e-mail and you response in the following so u can track easier). according to what you suggested, I have created a synthetic T1 volume based on my own segmentation. Now I wonder what to do exactly as the second step. Should I use "mris_fix_topology"? I would be grateful if you could help me with that. Best, Maedeh "Dear FreeSurfer experts, I know that FreeSurfer does segmentation, surface reconstruction and topology correction through its routine pipeline using "recon-all" . However, I have some T2w brain MR images and I have done the segmentation and extracted WM, GM, and CSF with my own algorithm. Now I need to remove back to back (i.e. a part of topology correction) which is caused in sulci due to the segmentation. In other word, after doing my segmentation, I wanna open the closed concavities in CSF that were open originally. Now I wanna know if I can do the topology correction using FreeSurfer while I have done the segmentation by myself? I would be grateful if you could help me with that. Best, Maedeh Hi Maedeh in principle you can, although it would be a lot easier if you just had a reasonable quality T1. If not, you will need to create all the files that recon-all expects to exist prior to the topology correction step (wm.mgz, norm.mgz, orig.mgz, ....). Maybe the easiest thing to do would be to use your gray/white/csf segmentation to create a synthetic T1 volume? Set all the wm voxels to 110, all the gray to 70 and all the csf to 20, or something like that? cheers Bruce"

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Re: [Freesurfer] [External] Re: mri_deface fails on pediatric brain
by Soichi Hayashi 04 Aug '19

04 Aug '19

External Email - Use Caution Bruce, I've uploaded one of the failed subject to surfer.nmr.mgh.harvard.edu ftp server (named t1.nii.gz).Thank you for looking into this problem. Soichi On Sun, Aug 4, 2019 at 10:35 AM Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > This message was sent from a non-IU address. Please exercise caution when > clicking links or opening attachments from external sources. > ------- > > Hi Soichi > > mri_deface isn't really supported anymore, but if you upload a subject > that fails I'll take a look. I would have thought in the ABCD subject age > range it would work > > cheers > Bruce > On Sat, 3 Aug 2019, Soichi Hayashi wrote: > > > > > External Email - Use Caution > > > > Hello. > > > > We are running mri_deface on subjects from ABCD (Adolescent Brain > Cognitive > > Development) study and many of the subjects are failing on mri_deface. > > > > $ mri_deface t1.nii.gz > > $FREESURFER_HOME/average/talairach_mixed_with_skull.gca > > $FREESURFER_HOME/average/face.gca defaced.nii.gz > > logging results to defaced.nii.log > > reading > > '/usr/local/freesurfer/average/talairach_mixed_with_skull.gca'... > > reading 't1.nii.gz'... > > changing type of input volume to 8 bits/voxel... > > MRIchangeType: Building histogram > > bounding unknown intensity as < 10.3 or > 1461.6 > > total sample mean = 111.8 (0 zeros) > > spacing=8, using 2055 sample points, tol=1.00e-03... > > resetting wm mean[0]: 143 --> 144 > > resetting gm mean[0]: 89 --> 89 > > input volume #1 is the most T1-like > > using real data threshold=11.0 > > skull bounding box = (54, 38, 18) --> (205, 255, 220) > > using (104, 110, 119) as brain centroid... > > mean wm in atlas = 144, using box (85,83,94) --> (122, 136,143) > > to find MRI wm > > before smoothing, mri peak at 79 > > robust fit to distribution - 80 +- 8.7 > > distribution too broad for accurate scaling - disabling > > WARNING2: gca.c::GCAhistoScaleImageIntensities: > > h_mri->nbins=111, mri_peak=140 > > after smoothing, mri peak at 0, scaling input intensities by > > inf > > GCAhistoScaleImageIntensities: could not find wm peak > > Numerical result out of range > > > > > > Should talairach_mixed_with_skull.gca template work with pediatric > > subjects? Or is there a different template we must choose? Or maybe any > > parameters that we could tweak to get it work better? > > > > Thanks! > > Soichi > > > >

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segmentHA_T1.sh error
by Daniel Callow 04 Aug '19

04 Aug '19

External Email - Use Caution Hello, When trying to run segmentHA_T1.sh I keep getting the following error log that I am having a lot of trouble debugging. Matlab 2014b is installed. Any help or guidance would be greatly appreciated! ------------------------------ USER dcallow HOST compute-4-9.bswift.umd.edu PROCESSID 8771 PROCESSOR x86_64 OS Linux ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS 1 Linux compute-4-9.bswift.umd.edu 2.6.32-754.15.3.el6.x86_64 #1 SMP Thu Jun 13 22:49:44 EDT 2019 x86_64 x86_64 x86_64 GNU/Linux ------------------------------ freesurfer-darwin-OSX-ElCapitan-dev-20190326-01e71dc setenv SUBJECTS_DIR /homes/dcallow/freesurfer_Tracy cd /a/ha-nfs-1-ib/export/home/bswift/dcallow /homes/dcallow/freesurfer_dev/bin/segmentHA_T1.sh HMN002 #-------------------------------------------- #@# Hippocampal Subfields processing (T1) left Sun Aug 4 15:08:35 EDT 2019 ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/homes/dcallow/freesurfer_dev/MCRv84//runtime/maci64:/homes/dcallow/freesurfer_dev/MCRv84//bin/maci64:/homes/dcallow/freesurfer_dev/MCRv84//sys/os/maci64:/hom$ /homes/dcallow/freesurfer_dev/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 33: /homes/dcallow/freesurfer_dev/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/s$ @#@FSTIME 2019:08:04:15:08:35 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e 0.07 S 0.00 U 0.00 P 15% M 1360 F 0 R 2250 W 0 c 13 w 171 I 40 O 0 L 0.12 0.68 0.88 @#@FSLOADPOST 2019:08:04:15:08:35 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 0.12 0.68 0.88 Linux compute-4-9.bswift.umd.edu 2.6.32-754.15.3.el6.x86_64 #1 SMP Thu Jun 13 22:49:44 EDT 2019 x86_64 x86_64 x86_64 GNU/Linux T1 hippocampal subfields exited with ERRORS at Sun Aug 4 15:08:36 EDT 2019 *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

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Estimation of surface based smoothing
by Matthieu Vanhoutte 04 Aug '19

04 Aug '19

External Email - Use Caution Dear experts, Knowing the size of the effects on volume-based data, does anyone would know a way to estimate the size of the effects on surface data? Best, Matthieu

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Issues about freeview
by 曾冉 04 Aug '19

04 Aug '19

External Email - Use Caution Dear everyone I have a problem about freeview.After runned sample-001.mgz,I will see freeview via code from official website of freesurfer,but it has a error that don't open the file about libpng12.so.0.I had take photos and uploading as attachment.Can you help me resolve this issue?any help would be much appreciated. Kind regards, Zero [cid:image002.jpg@01D549DA.C9CC8660] [cid:image006.jpg@01D549DA.C9CC8660] 发送自 Windows 10 版邮件<https://go.microsoft.com/fwlink/?LinkId=550986>应用

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mri_deface fails on pediatric brain
by Soichi Hayashi 04 Aug '19

04 Aug '19

External Email - Use Caution Hello. We are running mri_deface on subjects from ABCD (Adolescent Brain Cognitive Development) study and many of the subjects are failing on mri_deface. $ mri_deface t1.nii.gz > $FREESURFER_HOME/average/talairach_mixed_with_skull.gca > $FREESURFER_HOME/average/face.gca defaced.nii.gz > logging results to defaced.nii.log > reading '/usr/local/freesurfer/average/talairach_mixed_with_skull.gca'... > reading 't1.nii.gz'... > changing type of input volume to 8 bits/voxel... > MRIchangeType: Building histogram > bounding unknown intensity as < 10.3 or > 1461.6 > total sample mean = 111.8 (0 zeros) > spacing=8, using 2055 sample points, tol=1.00e-03... > resetting wm mean[0]: 143 --> 144 > resetting gm mean[0]: 89 --> 89 > input volume #1 is the most T1-like > using real data threshold=11.0 > skull bounding box = (54, 38, 18) --> (205, 255, 220) > using (104, 110, 119) as brain centroid... > mean wm in atlas = 144, using box (85,83,94) --> (122, 136,143) to find > MRI wm > before smoothing, mri peak at 79 > robust fit to distribution - 80 +- 8.7 > distribution too broad for accurate scaling - disabling > WARNING2: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=111, > mri_peak=140 > after smoothing, mri peak at 0, scaling input intensities by inf > GCAhistoScaleImageIntensities: could not find wm peak > Numerical result out of range Should talairach_mixed_with_skull.gca template work with pediatric subjects? Or is there a different template we must choose? Or maybe any parameters that we could tweak to get it work better? Thanks! Soichi

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recon-all exited with ERRORS
by Kuo Li 03 Aug '19

03 Aug '19

External Email - Use Caution Dear FreeSurfer Developers, I'm attempting to do cortical reconstruction, but for some of my subjects I get the following error when I run the recon-all command: #-------------------------------------------- #@# Curv .H and .K lh Wed Jul 17 04:03:21 PDT 2019 /mnt/hgfs/ShareFolder/output/sample01/surf mris_curvature -w lh.white.preaparc total integrated curvature = 0.838*4pi (10.527) --> 0 handles ICI = 216.7, FI = 1989.1, variation=32373.324 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H Linux ubuntu 4.18.0-25-generic #26~18.04.1-Ubuntu SMP Thu Jun 27 07:28:31 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sample01 exited with ERRORS at Wed Jul 17 04:03:23 PDT 2019 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I've searched google and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, I've 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 18.04.2 LTS 3) recon-all -i sample-001.nii.gz -s sample01 -all 4) recon-all.log: see attached

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Re: [Freesurfer] Issues about freeview
by fsbuild 02 Aug '19

02 Aug '19

External Email - Use Caution Hello Zero, It’s not clear from the photo what linux OS and version you are running, but on CentOS to get the libpng12 system library, you will need root or sudo privileges to install the packages, $ sudu yum install libpng12.x86_64 libpng12-devel.x86_64 If you are on Ubuntu then depending upon what version you are running, you may need to download the libpng package as I think it may longer be directly available via the install tools on Ubuntu 18. You can check the freeview binary, freeview.bin, to see what libraries it uses are not being found.  So if the following command works to find freeview.bin,$ which freeview.bin - then you can do$ ldd `which freeview.bin` - and it will probably tell you that libpng12.so is not found - along with any other libraries it cannot find.   Some package installs will probably need to be done depending upon what is missing, but it would help to know your linux OS and version. - R. On Aug 2, 2019, at 21:06, 曾冉 <> wrote:        External Email - Use Caution        Dear everyoneI have a problem about freeview.After runned sample-001.mgz,I will see freeview via code from official website of freesurfer,but it has a error that don't open the file about libpng12.so.0.I had take photos and uploading as attachment.Can you help me resolve this issue?any help would be much appreciated.Kind regards,Zero<0BA6AC6859524FEFAA1490278261578B.jpg><A48C0D6BA65D42C2BA379369FEA7B123.jpg> 发送自 Windows 10 版邮件应用 _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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