Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Error in Reconstruction of bert samples.
by IPL Neurosurgery 20 Mar '17

20 Mar '17

IPL Neurosurgery has shared a OneDrive file with you. To view it, click the link below. <https://1drv.ms/u/s!AiMzXSfGawBBdqVKAa4rOGRiPGw> [https://r1.res.office365.com/owa/prem/images/dc-generic_20.png]<https://1drv.ms/u/s!AiMzXSfGawBBdqVKAa4rOGRiPGw> recon-all 1.log<https://1drv.ms/u/s!AiMzXSfGawBBdqVKAa4rOGRiPGw> Hi, We have encountered a error in skull stripping process in bert sample. We are a novice. We attached the log. Command : recon-all -s bert -all #@# Skull Stripping Sat Mar 18 14:58:05 IST 2017 /home/iplneurosurgery/Documents/freesurfer/subjects/bert/mri mri_watershed -rusage /home/iplneurosurgery/Documents/freesurfer/subjects/bert/touch/rusage.mri_watershed.dat -keep brainmask.auto.mgz brainmask.mgz brainmask.mgz -T1 -brain_atlas /home/iplneurosurgery/Documents/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Keeping brain edits brainmask.auto.mgz brainmask.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) mghRead(/home/iplneurosurgery/Documents/freesurfer/subjects/bert/mri/brainmask.mgz, -1): read error ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz No such file or directory Linux localhost.localdomain 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18 13:06:36 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s bert exited with ERRORS at Sat Mar 18 14:58:06 IST 2017 freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Platform: Cent OS 7 uname -a : 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18 13:06:36 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Any Suggestion will be appreciated. Thanking you, IPL Neurosurgery. Sent from Outlook<http://aka.ms/weboutlook>

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T1 error
by Manuel Delgado 20 Mar '17

20 Mar '17

Dear list, After recon-all the T1 seems to have an error. Has anybody had this problem before? Please find attached the image. I guess I have to recon-all again. I am using v 6.0 with Ubuntu 16.04. Thank you. -- *Manuel Delgado Alvarado, MD* Neurology Department Neuroimaging Unit Valdecilla Biomedical Research Institute, IDIVAL Santander, SPAIN

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Re: [Freesurfer] Tracula: anatomical priors
by Jacobs H (NP) 19 Mar '17

19 Mar '17

Ok,thank you for the clarification! Best Heidi From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of "Yendiki, Anastasia" <AYENDIKI(a)mgh.harvard.edu<mailto:AYENDIKI@mgh.harvard.edu>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Thursday, March 16, 2017 at 10:32 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Tracula: anatomical priors Hi Heidi - TRACULA does not use deterministic constraints like pre-defined ROIs to reconstruct the tracts. For each point along a tract (and not just the end points), it has a prior probability (that it has computed from the atlas subjects) that a tract goes through each of the aparc+aseg labels, or goes next to (in the L, R, A, P, etc direction) each of the aparc+aseg labels. Best, a.y ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Jacobs H (NP) [h.jacobs(a)maastrichtuniversity.nl<mailto:h.jacobs@maastrichtuniversity.nl>] Sent: Wednesday, March 15, 2017 12:47 AM To: Freesurfer support list Subject: [Freesurfer] Tracula: anatomical priors Dear FreeSurfers, Where can I find the anatomical ROIs from the aparc/aseg (end and begin points) that are being used to reconstruct the tracts in Tracula? Many thanks Heidi

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Re: [Freesurfer] Repost: tracula stats including NAs?
by Jacobs H (NP) 19 Mar '17

19 Mar '17

Thanks! From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of "Yendiki, Anastasia" <AYENDIKI(a)mgh.harvard.edu<mailto:AYENDIKI@mgh.harvard.edu>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Thursday, March 16, 2017 at 10:29 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Repost: tracula stats including NAs? Hi Heidi - It's up to you. As long as the N of subjects at each point is included in the statistical test, this will adjust the corresponding p-value accordingly. Best, a.y ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Jacobs H (NP) [h.jacobs(a)maastrichtuniversity.nl<mailto:h.jacobs@maastrichtuniversity.nl>] Sent: Friday, March 10, 2017 5:39 PM To: Freesurfer support list Subject: [Freesurfer] Repost: tracula stats including NAs? Hi FreeSurfer, I have analyzed my diffusion data using Tracula and combined the voxelwise diffusion measures across all subjects in one file (following the guidelines on the wiki). In this text file, I saw that for some of these voxels some people have NAs, so their tract is most likely shorter. I now would like to do t-tests for each voxel and plot these in freeview (as also suggested in the wiki). Would you recommend to only take those voxels that have a value in each subject to keep the number of subjects consistent at each voxel ? Look forward to your thoughts on this. Best wishes Heidi

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Re: [Freesurfer] A Bug in Monte-Carlo Simulation.
by June Kang 19 Mar '17

19 Mar '17

The version downloaded in offical page. 6.0 stable for OS X. On Mar 20, 2017, at 11:02 AM, Douglas Greve <greve(a)nmr.mgh.harvard.edu> wrote:what version of FS are you running? On 3/18/17 11:41 AM, June Kang wrote:Dear Freesurfer Developers, 6.0 Stable in OS X seems to have some bugs. Monte-Carlo simulation works fine in 10mm FWMH, but error shows up in 5mm or 0mm as below. ###Error Code### ERROR: CSDread(): could not open /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm4/abs/th13/mc-z.csd ERROR! Error in Monte Carlo simulation: Error running mri_surfcluster! ###Error Code### I found that the actual directory contains cud file is fwhm04, and not fwhm4, so after I copied fwhm04 to fwhm4 in cortex directory, the simulation works.I think it’s small bug, but can make many people (like me) confused. Bests,J. _______________________________________________ Freesurfer mailing list Freesurfer(a)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 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.

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Error while attempting Segmentation
by IPL Neurosurgery 18 Mar '17

18 Mar '17

Hi, We have newly installed Freesurfer. We are a novice. We were trying to segment our data set. We used the following command. We attached the log. Command: recon-all -s testsample -all Output: [iplneurosurgery@localhost /]$ recon-all -s testsample -all 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 /home/iplneurosurgery/Documents/freesurfer/subjects Actual FREESURFER_HOME /home/iplneurosurgery/Documents/freesurfer -rw-rw-r--. 1 iplneurosurgery iplneurosurgery 18906 Mar 11 12:15 /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/scripts/recon-all.log Linux localhost.localdomain 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18 13:06:36 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux /home/iplneurosurgery/Documents/freesurfer/mni/bin/nu_correct: Permission denied. '/usr/local/freesurfer/bin/recon-all' -> '/home/iplneurosurgery/Documents/freesurfer/subjects/testsample/scripts/recon-all.local-copy' #-------------------------------------------- #@# MotionCor Sat Mar 11 14:48:00 IST 2017 Found 1 runs /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/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 /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig/001.mgz /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/rawavg.mgz /home/iplneurosurgery/Documents/freesurfer/subjects/testsample mri_convert /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/rawavg.mgz /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig.mgz --conform mri_convert.bin /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/rawavg.mgz /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/rawavg.mgz... TR=483.49, TE=12.00, TI=0.00, flip angle=73.00 i_ras = (-0.989525, -0.140773, -0.0319737) j_ras = (0.144349, -0.962296, -0.230541) k_ras = (0.00168578, -0.232741, 0.972537) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig.mgz... mri_add_xform_to_header -c /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/transforms/talairach.xfm /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig.mgz /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Sat Mar 11 14:48:05 IST 2017 /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri /usr/local/freesurfer/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 localhost.localdomain 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18 13:06:36 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Sat Mar 11 14:48:05 IST 2017 /home/iplneurosurgery/Documents/freesurfer/mni/bin/nu_correct: Permission denied. /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.10571 /home/iplneurosurgery/Documents/freesurfer/subjects/testsample/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.10571/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.10571/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=483.49, TE=12.00, TI=0.00, flip angle=73.00 i_ras = (-1, 9.77889e-09, 1.16415e-09) j_ras = (5.82077e-09, 0, -1) k_ras = (1.21945e-08, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.10571/nu0.mnc... -------------------------------------------------------- Iteration 1 Sat Mar 11 14:48:07 IST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.10571/nu0.mnc ./tmp.mri_nu_correct.mni.10571/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.10571/0/ -iterations 1000 -distance 50 /home/iplneurosurgery/Documents/freesurfer/mni/bin/nu_correct: Permission denied. ERROR: nu_correct Linux localhost.localdomain 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18 13:06:36 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s testsample exited with ERRORS at Sat Mar 11 14:48:07 IST 2017 freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Platform: Cent OS 7 uname -a : 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18 13:06:36 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Sent from Outlook<http://aka.ms/weboutlook>

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bbregister problem with --init-best
by Feilong Ma 17 Mar '17

17 Mar '17

Hi FreeSurfer Developers, I'm having trouble using bbregister with the `--init-best` flag, a minimal example and error message is like this: $> bbregister --s ag00 --mov data/ag00/align/raiders/run00_ref.nii.gz --init-best --bold --lta data/ag00/align/raiders/run00_ref_to_anat.lta ERROR: cannot spec an init method with --init-best It seems `InitCoreg` is set to 1 by default in the code of bbregister. Therefore, when `--init-best` is also set, it would always trigger the conflict detection and exit with the error message. Here are some related version information: - FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c - bbregister version: $Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $ - OS: CentOS Linux release 7.3.1611 (Core) Best, Feilong

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subject directory
by Limachia, Gaurang (NIH/NINDS) [F] 17 Mar '17

17 Mar '17

Dear Freesurfer Experts, I want to customize the directory so I can run the following command mris_preproc --fsgd gender_age.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.gender_age.thickness.10.mgh However, after running this command it keeps checking in the wrong directory for the files. How do I change the directory, do I change it in the FSGD file I made or somewhere else? I ran the recon-all qcache, but I need to run this on the previously cached data. I would greatly appreciate it if you can assist me with this problem. Best Regards, Gaurang Shyam LImachia

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need help clean up pial and wm surfaces
by padma 17 Mar '17

17 Mar '17

Hi, I’m trying to get pial and wm surfaces for a subject (who has some clinical wm related problems). They were imaged (T1-MPRAGE at 3T) at their imaging center not here at Martinos Center. The gray-white contrast doesn’t look as good as the healthy volunteers that I imaged in the 3T at the Martinos Center. My question is — I can’t figure out where to start repairing the subject’s pial and wm surfaces. I wonder if someone could suggest how to proceed. I’ve ftp/uploaded the freesurfer output to surfer.nmr (PT001_from_padma.tar.gz) Thanks for your help, Cheers, —Padma

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registration for AD, MD and RD images
by Su, Shiran 16 Mar '17

16 Mar '17

Hi, FreeSurfer developers, I am trying to use the command 'bbregister' to register the axial diffusivity, mean diffusivity, radial diffusivity and FA maps to the segmentation result (get from the 'recon-all' command). The registration works well for the FA map. But for AD, MD and RD maps, the registration is a little off (as can be seen in the example). Although we could use the 'transform volume' tool (tkregister tool) to move the diffusion maps to make the map fit better with the segmentation surface, I am wondering whether this is a normal issue and we could only use 'transform volume' tool to modify them? Because our AD, MD, RD and FA maps are all masked and have good location correspondence with each other. If not, is there any method we could use to get a better registration result for the AD, MD and RD maps? i.e. [cid:3d37426c-cd99-4a42-a61b-d88da1cab2f9] [cid:599ee7ae-47c2-4675-99c5-b0c82ee7d8df] The registration works well for the FA map (left) but not for the AD map (right). Thank you! Best, Shiran Su

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