Re: [Freesurfer] recon-all: too many levels of symbolic links
Dear all, I've run into the same error with recon-all -autorecon3. It could be that when I moved my data into the new SUBJECTS_DIR, I missed something out. What files should be in the $FREESURFER_HOME/subjects directory? The error reads as follows: #@# Ex-vivo Entorhinal Cortex Label lh Fri Dec 14 19:07:03 HKT 2012 INFO: lh.EC_average subject does not exist in SUBJECTS_DIR INFO: Creating symlink to lh.EC_average subject... cd /home/virtualuser/freesurfer/lindadata/subjects; ln -s /home/virtualuser/freesurfer/subjects/lh.EC_average; cd - ln: creating symbolic link `./lh.EC_average': File exists mris_spherical_average -erode 1 -orig white -t 0.4 -o ncpoCCW label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject ncpoCCW. processing subject lh.EC_average... MRISread(/home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average/surf/lh.sphere.reg): could not open file eroding label 1 times before writing thresholding label stat at 0.400 before writing No such file or directory mris_spherical_average: could not read surface file /home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average/surf/lh.sphere.reg No such file or directory Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux recon-all -s ncpoCCW exited with ERRORS at Fri Dec 14 19:07:07 HKT 2012 For more details, see the log file /home/virtualuser/freesurfer/lindadata/subjects/ncpoCCW/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Cheers, Linda On 14 November 2012 22:29, Linda Zhang lzhan...@gmail.com wrote: Thanks Bruce. It has 6gb assigned to the virtualbox, I'm running another process alongside it. I'll stop the other one and try again. On 14 Nov 2012 22:14, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: sounds like you are running out of memory. How much ram is in that machine? Are other processes running at the same time? On Wed, 14 Nov 2012, Linda Zhang wrote: Dear all, After moving my data to a different folder, I've come across a different error when running recon-all (autorecon2 and 3). The last few lines are as follows: 0117: dt=32.368000, rms=0.713 (0.122%), neg=0, invalid=766 0118: dt=32.368000, rms=0.713 (0.033%), neg=0, invalid=766 0119: dt=32.368000, rms=0.712 (0.059%), neg=0, invalid=766 0120: dt=32.368000, rms=0.712 (0.081%), neg=0, invalid=766 0121: dt=16.184000, rms=0.712 (0.009%), neg=0, invalid=766 Killed ERROR: mri_ca_register with non-zero status 137 but continuing despite the error #-**- #@# CA Reg Inv Wed Nov 14 15:47:37 HKT 2012 /home/virtualuser/freesurfer/**lindadata/subjects/ncvoCYJ/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux recon-all -s ncvoCYJ exited with ERRORS at Wed Nov 14 15:47:38 HKT 2012 Another set is exiting simply with: #@# EM Registration Mon Nov 12 17:43:05 HKT 2012 /home/virtualuser/freesurfer/**lindadata/subjects/ncvoLML/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /home/virtualuser/freesurfer/**average/RB_all_2008-03-26.gca transforms/talairach.lta Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux recon-all -s ncvoLML exited with ERRORS at Mon Nov 12 17:43:06 HKT 2012 To report a problem, see http://surfer.nmr.mgh.harvard.** edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting What's the problem I should be addressing? Thanks! Cheers, Linda On 2 November 2012 21:40, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Linda it sounds like you put your own subjects into the directory $FREESURFER_HOME/subjects, which is where we store our average data and symlink within your SUBJECTS_DIR. Try putting them somewhere else cheers Bruce On Fri, 2 Nov 2012, Linda Zhang wrote: Dear all, I've been running recon-all on my dataset, but all of them are exiting with the same error. The command line is: recon-all -subjid ncpoCCW -autorecon2 -autorecon3 The error reads: #@# Ex-vivo Entorhinal Cortex Label lh Sat Aug 25 11:54:33 HKT 2012 INFO: lh.EC_average subject does not exist in SUBJECTS_DIR INFO: Creating symlink to lh.EC_average subject... cd /home/virtualuser/freesurfer/**subjects; ln -s /home/virtualuser/freesurfer/**subjects/lh.EC_average; cd - mris_spherical_average -erode 1 -orig white -t 0.4 -o ncpoCCW label lh.entorhinal lh sphere.reg lh.EC_average
[Freesurfer] new atlas
Dear Freesurfers,Sorry for so many and basic questions lately.I'm working with my set of subjects (T1), and I'm looking for a different WM parcellation than the aseg.mgz, I have an atlas (JHU atlas in MNI space, Mori et al 1999, and some other in Colin27 space).I'm guessing I will have to use the FSaverage subject as target space. Since FS has many algorithms to make registrations, and the mris_ca_train requieres the predefined labels into an anootation file. I'm wondering about the best way to translate all the WM labeling from this atlas into FS space. Many thanks in advanced,Gabriel ___ 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] mri_cc segfault
Bruce found that the data had the direction cosine wrong. I have fixed the direction and I'm running it again. I've put the data in the ftp - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Tue, Dec 18, 2012 at 8:41 PM, Nick Schmansky ni...@nmr.mgh.harvard.eduwrote: PPJ, Hi, if you want, you can send me the input files (the two aseg's and the lta) and i can try to replicate the segfault in a debugger. also, if you want, there is a beta of the upcoming v5.2 which is posted here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0-BETA/ which you could try. hopefully that mri_cc doesnt segfault. Nick On Tue, 2012-12-18 at 12:46 -0200, Pedro Paulo de Magalhães Oliveira Junior wrote: I'm having a segfault with mri_cc it's happening sometimes using FreeSurfer 5.1 Searching the mailing list I saw a similar problem in 2008 but with no answers. The relevant portion of recon-all.log: mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /usr/local/freesurfer/subjects/c70eb728-c505-46c2-a2a1-1ed409c36ea1/mri/transforms/cc_up.lta c70eb728-c505-46c2-a2a1-1ed409c36ea1 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /usr/local/freesurfer/subjects/c70eb728-c505-46c2-a2a1-1ed409c36ea1/mri/transforms/cc_up.lta reading aseg from /usr/local/freesurfer/subjects/c70eb728-c505-46c2-a2a1-1ed409c36ea1/mri/aseg.auto_noCCseg.mgz reading norm from /usr/local/freesurfer/subjects/c70eb728-c505-46c2-a2a1-1ed409c36ea1/mri/norm.mgz 2358 voxels in left wm, 13846 in right wm, xrange [122, 136] searching rotation angles z=[-10 4], y=[-31 -17] ^Msearching scale 1 Z rot -9.8 ^Msearching scale 1 Z rot -9.5 ^Msearching scale 1 Z rot -9.3 ^Msearching scale 1 Z rot -9.0 ^Msearching scale 1 Z rot -8.8 ^Msearching scale 1 Z rot -8.5 ^Msearching scale 1 Z rot -8.3 ^Msearching scale 1 Z rot -8.0 ^Msearching scale 1 Z rot -7.8 ^Msearching scale 1 Z rot -7.5 ^Msearching scale 1 Z rot -7.3 ^Msearching scale 1 Z rot -7.0 ^Msearching scale 1 Z rot -6.8 ^Msearching scale 1 Z rot -6.5 ^Msearching scale 1 Z rot -6.3 ^Msearching scale 1 Z rot -6.0 ^Msearching scale 1 Z rot -5.8 ^Msearching scale 1 Z rot -5.5 ^Msearching scale 1 Z rot -5.3 ^Msearching scale 1 Z rot -5.0 ^Msearching scale 1 Z rot -4.8 ^Msearching scale 1 Z rot -4.5 ^Msearching scale 1 Z rot -4.3 ^Msearching scale 1 Z rot -4.0 ^Msearching scale 1 Z rot -3.8 ^Msearching scale 1 Z rot -3.5 ^Msearching scale 1 Z rot -3.3 ^Msearching scale 1 Z rot -3.0 ^Msearching scale 1 Z rot -2.8 ^Msearching scale 1 Z rot -2.5 ^Msearching scale 1 Z rot -2.3 ^Msearching scale 1 Z rot -2.0 ^Msearching scale 1 Z rot -1.8 ^Msearching scale 1 Z rot -1.5 ^Msearching scale 1 Z rot -1.3 ^Msearching scale 1 Z rot -1.0 ^Msearching scale 1 Z rot -0.8 ^Msearching scale 1 Z rot -0.5 ^Msearching scale 1 Z rot -0.3 ^Msearching scale 1 Z rot -0.0 ^Msearching scale 1 Z rot 0.2 ^Msearching scale 1 Z rot 0.5 ^Msearching scale 1 Z rot 0.7 ^Msearching scale 1 Z rot 1.0 ^Msearching scale 1 Z rot 1.2 ^Msearching scale 1 Z rot 1.5 ^Msearching scale 1 Z rot 1.7 ^Msearching scale 1 Z rot 2.0 ^Msearching scale 1 Z rot 2.2 ^Msearching scale 1 Z rot 2.5 ^Msearching scale 1 Z rot 2.7 ^Msearching scale 1 Z rot 3.0 ^Msearching scale 1 Z rot 3.2 ^Msearching scale 1 Z rot 3.5 ^Msearching scale 1 Z rot 3.7 global minimum found at slice 129.0, rotations (-2.52, -3.27) final transformation (x=129.0, yr=-2.521, zr=-3.273): 0.997 0.057 -0.044 -2.975; -0.057 0.998 0.003 -6.742; 0.044 -0.000 0.999 -9.547; 0.000 0.000 0.000 1.000; Segmentation fault Thanks PPJ - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 ___ 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
Re: [Freesurfer] recon-all: too many levels of symbolic links
ls -1 $FREESURFER_HOME/subjects cvs_avg35/ cvs_avg35_inMNI152/ fsaverage/ fsaverage3/ fsaverage4/ fsaverage5/ fsaverage6/ fsaverage_sym/ lh.EC_average/ README rh.EC_average/ sample-001.mgz sample-002.mgz surfer.log V1_average/ not sure why it thinks it doesn't exist. What are the permissions on /home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average can you do an ls on /home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average/surf and post the results? Also do: ls -l /home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average On Wed, 19 Dec 2012, Linda Zhang wrote: Dear all, I've run into the same error with recon-all -autorecon3. It could be that when I moved my data into the new SUBJECTS_DIR, I missed something out. What files should be in the $FREESURFER_HOME/subjects directory? The error reads as follows: #@# Ex-vivo Entorhinal Cortex Label lh Fri Dec 14 19:07:03 HKT 2012 INFO: lh.EC_average subject does not exist in SUBJECTS_DIR INFO: Creating symlink to lh.EC_average subject... cd /home/virtualuser/freesurfer/lindadata/subjects; ln -s /home/virtualuser/freesurfer/subjects/lh.EC_average; cd - ln: creating symbolic link `./lh.EC_average': File exists mris_spherical_average -erode 1 -orig white -t 0.4 -o ncpoCCW label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject ncpoCCW. processing subject lh.EC_average... MRISread(/home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average/surf/lh.sphere.reg): could not open file eroding label 1 times before writing thresholding label stat at 0.400 before writing No such file or directory mris_spherical_average: could not read surface file /home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average/surf/lh.sphere.reg No such file or directory Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux recon-all -s ncpoCCW exited with ERRORS at Fri Dec 14 19:07:07 HKT 2012 For more details, see the log file /home/virtualuser/freesurfer/lindadata/subjects/ncpoCCW/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Cheers, Linda On 14 November 2012 22:29, Linda Zhang lzhan...@gmail.com wrote: Thanks Bruce. It has 6gb assigned to the virtualbox, I'm running another process alongside it. I'll stop the other one and try again. On 14 Nov 2012 22:14, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: sounds like you are running out of memory. How much ram is in that machine? Are other processes running at the same time? On Wed, 14 Nov 2012, Linda Zhang wrote: Dear all, After moving my data to a different folder, I've come across a different error when running recon-all (autorecon2 and 3). The last few lines are as follows: 0117: dt=32.368000, rms=0.713 (0.122%), neg=0, invalid=766 0118: dt=32.368000, rms=0.713 (0.033%), neg=0, invalid=766 0119: dt=32.368000, rms=0.712 (0.059%), neg=0, invalid=766 0120: dt=32.368000, rms=0.712 (0.081%), neg=0, invalid=766 0121: dt=16.184000, rms=0.712 (0.009%), neg=0, invalid=766 Killed ERROR: mri_ca_register with non-zero status 137 but continuing despite the error #-- #@# CA Reg Inv Wed Nov 14 15:47:37 HKT 2012 /home/virtualuser/freesurfer/lindadata/subjects/ncvoCYJ/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux recon-all -s ncvoCYJ exited with ERRORS at Wed Nov 14 15:47:38 HKT 2012 Another set is exiting simply with: #@# EM Registration Mon Nov 12 17:43:05 HKT 2012 /home/virtualuser/freesurfer/lindadata/subjects/ncvoLML/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /home/virtualuser/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux recon-all -s ncvoLML exited with ERRORS at Mon Nov 12 17:43:06 HKT 2012 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting What's the problem I should be addressing? Thanks!
Re: [Freesurfer] space of T1.mgz
Hi there, Sorry, if my question is confusing. This is what I want to do, I have two groups of controls and patients and I've already run recon-all on them. I now want to know the head/body/tail volumes. What I did was: 1. used mri_binarize to get the right and left hippocampal masks from the cortical segmentation (using label numbers 17, 53) 2. used mri_convert to convert left_hippo.mgz, right_hippo.mgz and T1.mgz into .nii files. 3. use itk SNAP to manually segment the total hippocampus (the freesurfer mask) into head, body and tail. now, my questions is regarding the last step. If the individual segmentations are in the native space, I can't be sure that the landmarks I'm using for head/body/tail separation is always the same (since some of the subjects might be in an oblique space). So would you recommend that I first register the T1 and segmentations all into a common space? Also, I was wondering if the segmentation is going to effect the actual volume (since the brain is going to be stretched and transformed while doing the registration). I hope I made my question clear and I would greatly appreciate your advice. Thanks, -Mojdeh On 12/18/2012 12:58 PM, Bruce Fischl wrote: Hi Mojdeh they are not in atlas space and the volumes are for that subject, so you shouldn't have to do anything if I understand you correctly cheers Bruce On Tue, 18 Dec 2012, Mojdeh Zamyadi wrote: Hi Doug, Thanks for the quick reply. I actually saw this link before first posting my question but it doesn't quite answer my question. What I want to know is whether the T1.mgz aseg.mgz files are in an atlas space? if that's the case, it means the segmentation for all my subjects are in the same space and I don't need to convert anything if I want to compare their hippocampal volumes. I'm not quite sure if any sort of registration to an atlas is done in any steps of recon-all or not. I would appreciate if could clarify this for me. Thanks, -Mojdeh On 12/18/2012 12:18 PM, Douglas N Greve wrote: Hi Mojdeh, try looking at this doc http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat doug On 12/18/2012 11:09 AM, Mojdeh Zamyadi wrote: Hi all, I want to segment the hippocampus into head/body/tail in itk SNAP using the hippocampus mask that I create from the result of recon-all segmentation. My question is, are the T1.mgz and aseg.mgz files in the native space of the image or in the atlas space? I know the voxel size is different (1x1x1 mm) from the original voxel size (0.49x0.49x0.45), but I want to know if the original images are registered to a common atlas space or just resampled to a different voxel size. The reason I'm asking this, is because I'm doing a group study and I want to make sure all my subjects are in the same space so that the segmentation I do is accurate for all. Thanks for your help, Mojdeh Zamyadi, MSc Clinical Research Project Assistant The Hospital for Sick Children 555 University Avenue Toronto ON M5G 1X8 ___ 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
Re: [Freesurfer] L-R Volume Flipping
When we added the --spm-nii option, the problem disappears. The following thread is also relevant: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-April/017981.html On Tue, Dec 18, 2012 at 8:26 PM, MCLAREN, Donald mclaren.don...@gmail.com wrote: Thanks, that's what I thought might be happening. I'll check a few different programs to see if I can recover the correct orientation. If we need to reverse the images, would you recommend doing it before or after the bbregister step? Would it be sufficient just to change the header of the image or do we need to physically change the data? Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 = This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. On Tue, Dec 18, 2012 at 11:20 PM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: Hi Donald, it might be the case. If the fmri has an ordering such that the columns increase as you go from left to right, then they will have to be reversed when you map them to the orig.mgz. This is generally not a problem because we always keep track of which side is left and right. If you are using a visualization tool that does not read in and act on the geometry, then things can appear to flip around. doug On 12/18/12 8:47 PM, MCLAREN, Donald wrote: Dear All, I've noticed something strange with some data I'm helping to process: When looking at the L/R asymmetry in the brains (attached), the images seem to flip after bbregister/mri_vol2vol. The exact commands: bbregister --s FS_D011 --mov meanfMRI.nii --reg register.dat --init-spm --t2 mri_vol2vol --s FS_D011 --targ orig.mgz --mov fMRI.nii --reg register.dat --no-resample --o transformed_fMRI.nii I've attached a document that shows the flipping. You'll notice the highest point of the ventricle flips sides after bbregister/mri_vol2vol. Any thoughts on what is going on would be appreciated. The contents of register.dat are as follows: FS_D011 3.00 3.54 0.15 -9.972292184829712e-01 -6.125224381685257e-02 4.221317172050476e-02 1.619825601577759e+00 6.049362570047379e-02 -3.374822735786438e-01 9.393859505653381e-01 -1.230294322967529e+01 4.329330846667290e-02 -9.393369555473328e-01 -3.402525186538696e-01 -1.072110843658447e+01 0 0 0 1 round Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 = This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. ___ 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
Re: [Freesurfer] tracula - posterior density just one-dimensional curve
Hi Andi - I managed to track this down by looking at the complete data set that you sent me. Your bvals file has no b=0, there's only b=2075 with some b=5 interspersed. The b=5 volumes must be your baseline volumes but unfortunately there's no way for the program to know this right now. As a hack for now I'd just set the 5's to 0's in dmri/bvals and rerun the path reconstruction step, it should be a fine approximation for that step. I'll add support to this for the next version. Sorry about that! a.y On Tue, 30 Oct 2012, Andi Heckel wrote: Dear Tracula team, I have noticed in a multisubject tracula analysis, that the posterior density in many if not all paths in the path.pd.nii.gz file is just a bright one-dimensional curve, rather than a true distribution. The path.map.nii.gz is empty. This is true for both flirt and bbreg registered versions in many subjects. Trac-all finished wiithout errors. So did Recon-all. Could it actually be a memory (RAM) problem ? We are running tracula on a cluster with only 2.5 GB per core. thx for any help and kind regards, andi ___ 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] Diffusion Tensor Imaging
Dear Freesurfers, I am not very experienced with Freesurfer and would like to construct a Diffusion Tensor Image. I have the .bvecs, .bvals and .img files which I believe should suffice. I am aware that the format is slightly old but I believe it should still be fine. I attempted to use dt_recon and freeview but could not quite get the results I anticipated. I would really appreciate any help. Many thanks in advance, Yaniv ___ 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] L-R Volume Flipping
Oh, right, that can be a problem. In 5.2, I've changed it to use nii by default. This breaks when spm2 is used, but then the user can spec to use img instead. doug On 12/19/12 5:38 PM, MCLAREN, Donald wrote: When we added the --spm-nii option, the problem disappears. The following thread is also relevant: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-April/017981.html On Tue, Dec 18, 2012 at 8:26 PM, MCLAREN, Donald mclaren.don...@gmail.com wrote: Thanks, that's what I thought might be happening. I'll check a few different programs to see if I can recover the correct orientation. If we need to reverse the images, would you recommend doing it before or after the bbregister step? Would it be sufficient just to change the header of the image or do we need to physically change the data? Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 = This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. On Tue, Dec 18, 2012 at 11:20 PM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: Hi Donald, it might be the case. If the fmri has an ordering such that the columns increase as you go from left to right, then they will have to be reversed when you map them to the orig.mgz. This is generally not a problem because we always keep track of which side is left and right. If you are using a visualization tool that does not read in and act on the geometry, then things can appear to flip around. doug On 12/18/12 8:47 PM, MCLAREN, Donald wrote: Dear All, I've noticed something strange with some data I'm helping to process: When looking at the L/R asymmetry in the brains (attached), the images seem to flip after bbregister/mri_vol2vol. The exact commands: bbregister --s FS_D011 --mov meanfMRI.nii --reg register.dat --init-spm --t2 mri_vol2vol --s FS_D011 --targ orig.mgz --mov fMRI.nii --reg register.dat --no-resample --o transformed_fMRI.nii I've attached a document that shows the flipping. You'll notice the highest point of the ventricle flips sides after bbregister/mri_vol2vol. Any thoughts on what is going on would be appreciated. The contents of register.dat are as follows: FS_D011 3.00 3.54 0.15 -9.972292184829712e-01 -6.125224381685257e-02 4.221317172050476e-02 1.619825601577759e+00 6.049362570047379e-02 -3.374822735786438e-01 9.393859505653381e-01 -1.230294322967529e+01 4.329330846667290e-02 -9.393369555473328e-01 -3.402525186538696e-01 -1.072110843658447e+01 0 0 0 1 round Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 = This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. ___ 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
Re: [Freesurfer] nu_estimate_np_and_em error during recon-all
Hi Tudor, I don't know how to solve this problem. Maybe Nick knows. doug On 12/19/12 6:59 AM, Tudor Popescu wrote: Hi Doug, thanks for replying, here is the file attached. In case the attachment doesn't go through please let me know if I should send it to a different address. Tudor On 18 December 2012 17:34, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Can you send the recon-all.log file (located in the subject/scripts folder). doug On 12/18/2012 11:41 AM, Tudor Popescu wrote: Hello, First of all, apologies for asking for help three times today! THings will hopefully become clearer once I get used to FS a bit; I really do appreciate the amazing support provided by the team behind FreeSurfer! I ran the following command on one of my structurals: /recon-all -subject M01 -i M01.nii.gz -all/ After a few minutes, recon-all ended with the following message: /Assertion failed at line 827 in file templates/CachedArray.cc/ /nu_estimate_np_and_em: crashed while running volume_stats (termination status=256)/ /nu_correct: crashed while running nu_estimate_np_and_em (termination status=256)/ /ERROR: nu_correct/ /Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux/ I apologise for reporting an error that's already been reported in the past, but unfortunately the solutions suggested in those past threads did not work in my case. To address a few of them: * my PATH (listed below) does not seem to include two MNI installations //home/virtualuser/freesurfer/bin:/home/virtualuser/freesurfer/fsfast/bin:/home/virtualuser/freesurfer/tktools:/home/virtualuser/freesurfer/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games/ * the version of FreeSurfer that I installed is the latest disk image available on the website (freesurfer-Virtualbox-linux-x86-stable-pub-v5.1.0-full) - I did not see any dev version that would presumably include any missing libraries presumably implied by the above error * I tried updating the Xubuntu inside my VirtualBox, however it reports an insufficient space problem that from I can see does not have a trivial fix Advance thanks for any help! Tudor ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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.
Re: [Freesurfer] recon-all: too many levels of symbolic links
Hi Bruce, This is what I get: FreeSurfer:~/freesurfer/lindadata ls -l drwxr-sr-x 42 virtualuser virtualuser 4096 2012-11-17 07:38 subjects FreeSurfer:~/freesurfer/lindadata ls /subjects/lh.EC_average/surf ls: cannot access /subjects/lh.EC_average/surf: No such file or directory FreeSurfer:~/freesurfer/lindadata ls -l /subjects/lh.EC_average lrwxrwxrwx 1 virtualuser virtualuser 51 2012-11-17 07:38 /home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average - /home/virtualuser/freesurfer/subjects/lh.EC_average FreeSurfer:~/freesurfer/lindadata ls /home/virtualuser/freesurfer/subjects/ cvs_avg35 fsaverage fsaverage3 fsaverage4 fsaverage5 fsaverage6 README V1_average On 19 December 2012 21:43, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: ls -1 $FREESURFER_HOME/subjects cvs_avg35/ cvs_avg35_inMNI152/ fsaverage/ fsaverage3/ fsaverage4/ fsaverage5/ fsaverage6/ fsaverage_sym/ lh.EC_average/ README rh.EC_average/ sample-001.mgz sample-002.mgz surfer.log V1_average/ not sure why it thinks it doesn't exist. What are the permissions on /home/virtualuser/freesurfer/**lindadata/subjects/lh.EC_**average can you do an ls on /home/virtualuser/freesurfer/**lindadata/subjects/lh.EC_**average/surf and post the results? Also do: ls -l /home/virtualuser/freesurfer/**lindadata/subjects/lh.EC_**average On Wed, 19 Dec 2012, Linda Zhang wrote: Dear all, I've run into the same error with recon-all -autorecon3. It could be that when I moved my data into the new SUBJECTS_DIR, I missed something out. What files should be in the $FREESURFER_HOME/subjects directory? The error reads as follows: #@# Ex-vivo Entorhinal Cortex Label lh Fri Dec 14 19:07:03 HKT 2012 INFO: lh.EC_average subject does not exist in SUBJECTS_DIR INFO: Creating symlink to lh.EC_average subject... cd /home/virtualuser/freesurfer/**lindadata/subjects; ln -s /home/virtualuser/freesurfer/**subjects/lh.EC_average; cd - ln: creating symbolic link `./lh.EC_average': File exists mris_spherical_average -erode 1 -orig white -t 0.4 -o ncpoCCW label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject ncpoCCW. processing subject lh.EC_average... MRISread(/home/virtualuser/**freesurfer/lindadata/subjects/** lh.EC_average/surf/lh.sphere.**reg): could not open file eroding label 1 times before writing thresholding label stat at 0.400 before writing No such file or directory mris_spherical_average: could not read surface file /home/virtualuser/freesurfer/**lindadata/subjects/lh.EC_** average/surf/lh.sphere.reg No such file or directory Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux recon-all -s ncpoCCW exited with ERRORS at Fri Dec 14 19:07:07 HKT 2012 For more details, see the log file /home/virtualuser/freesurfer/** lindadata/subjects/ncpoCCW/**scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.** edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Cheers, Linda On 14 November 2012 22:29, Linda Zhang lzhan...@gmail.com wrote: Thanks Bruce. It has 6gb assigned to the virtualbox, I'm running another process alongside it. I'll stop the other one and try again. On 14 Nov 2012 22:14, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: sounds like you are running out of memory. How much ram is in that machine? Are other processes running at the same time? On Wed, 14 Nov 2012, Linda Zhang wrote: Dear all, After moving my data to a different folder, I've come across a different error when running recon-all (autorecon2 and 3). The last few lines are as follows: 0117: dt=32.368000, rms=0.713 (0.122%), neg=0, invalid=766 0118: dt=32.368000, rms=0.713 (0.033%), neg=0, invalid=766 0119: dt=32.368000, rms=0.712 (0.059%), neg=0, invalid=766 0120: dt=32.368000, rms=0.712 (0.081%), neg=0, invalid=766 0121: dt=16.184000, rms=0.712 (0.009%), neg=0, invalid=766 Killed ERROR: mri_ca_register with non-zero status 137 but continuing despite the error #-**- #@# CA Reg Inv Wed Nov 14 15:47:37 HKT 2012 /home/virtualuser/freesurfer/** lindadata/subjects/ncvoCYJ/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39
