Freesurfer July 2013

freesurfer@nmr.mgh.harvard.edu

165 participants
332 discussions

Is this an example of pial surface extending into cerebellum?
by ye tian 09 Jul '13

09 Jul '13

Dear Freesurfers, Is the attached file an example of pial surface extending into cerebellum? Thank you very much! Sincerely, Ye

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qdec control variable limitation
by Jiang Jiyang 09 Jul '13

09 Jul '13

Dear all, I am using qdec to do a shape analysis with 16 control variables. I was wondering if there is a limit on how many covariates can be used in qdec? Because it seems that I cannot select all my covariates in "nuisance factors". Thanks and regards, Jiyang

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average/RB_all_2008-03-26.gca not found error
by Salil Soman 09 Jul '13

09 Jul '13

Hi, *Am running this command:* $FREESURFER_HOME/bin/recon-all -i 3DSPGR.nii.gz -s WCA_248_T1Q_FS -nuintensitycor-3T -nocanorm -openmp 50 -hippo-subfields -use-cuda -all *And am get this out put / error:* Testing for CUDA device: nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2012 NVIDIA Corporation Built on Fri_Sep_21_17:28:58_PDT_2012 Cuda compilation tools, release 5.0, V0.2.1221 Driver : 5.50 Runtime : 5.0 Acquiring CUDA device Using default device CUDA device: GeForce GTX 660 ======= NUMBER OF OPENMP THREADS = 50 ======= stable5 NVIDIA driver version info: NVRM version: NVIDIA UNIX x86_64 Kernel Module 319.32 Wed Jun 19 15:51:20 PDT 2013 ERROR: cannot find /usr/local/freesurfer/average/RB_all_2008-03-26.gca Any suggestions what I am doing incorrectly? Thank you, Sal

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mri_cvs_register std:: bad_alloc
by Marcel Falkiewicz 09 Jul '13

09 Jul '13

Dear FreeSurfers, I'm trying to use mri_cvs_register, however the process can't complete and I get the following error: [...] loading transform id string = data size = 18728074 uilen = 6 loading transform id string = data size = 19845421 uilen = 6 loading transform id string = data size = 19120776 uilen = 6 loading transform id string = data size = 71 uilen = 7 loading transform id string = saveTransform code writing transform size = 117019458 saveTransform code writing transform size = 117019458 saveTransform code writing transform size = 16 saveTransform code writing transform size = 21339696 saveTransform code writing transform size = 21092930 saveTransform code writing transform size = 20795616 saveTransform code writing transform size = 20591898 saveTransform code requested buffer size = 436643894 Exception caught while saving morph ZlibStringCompressor::setBufferSize - Caught std::bad_alloc My command line was: mri_cvs_register --mov subject01 --mni --openmp 8 --m3d At the time of crash all RAM is consumed by createMorph process (10 GB). Is this crash related to the ammount of RAM on my machine (12 GB)? If so, how much RAM is needed to complete mri_cvs_register? Best regards, Marcel

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custom fill function for matlab
by Catarina Rua 09 Jul '13

09 Jul '13

Dear freesurfer admin, I'm writing a piece of code in matlab based on freesurfer reconstructed brains generating series of labels to an annotation file. However, I wanted to include a process similar to the existing in tksurfer options in the 'custom fill' where you can fill in all vertices up to a label border/up to included paths. I have searched on the web for a piece of matlab code that would process this, but I coulnt seem to find it. Is there any quick way to do this? The basic idea is that I have a group of non-labeled vertices enclosed within a label, and I just want to 'fill" them with the same label as the label that surrounds it. Thank you very much in advance. I really do hope this can be possible! Cheers! Catarina Rua

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how to use mris_register?
by fatma zribi 09 Jul '13

09 Jul '13

Dear Mr, When I execute mris_register to register one subject to a template., I have this message of error: mris_register -1 s000/surf/lh.sphere avg_all_subjects_SD/lh.reg.template.tif sphere_reg treating target as a single subject's surface... $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere... MRISread(s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere): could not open file No such file or directory mris_register: could not read surface file s000/surf/lh.sphere No such file or directory note that the file exist in the specifeid SUBJECT_DIR Thank you for your help Fatma

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Re: [Freesurfer] Artefactual skull stripping for some subjects
by Tudor Popescu 09 Jul '13

09 Jul '13

Dear FSers, Still haven't got to the bottom of this, any suggestions would be much appreciated, thanks in advance! Tudor On 5 July 2013 17:26, Tudor Popescu <tudor3(a)gmail.com> wrote: > Hi everyone > > The skull-stripping step of recon-all must have gone bad for my sample, > because I noticed that there are artefacts (chips) in the brain-extracted > structurals of several of my subjects. Since I ran recon-all on all my > sample without having noticed this initially, this of course also lead to > the surfaces being created wrongly, i.e. following the wrong volumetric > information. > > I attach screenshots showing some of the more obvious artefactual skull > extractions, corresponding to subjects 04, 06 and 17, and also the > brain.mgz and T1.mgz for subject 17. > > FSL's BET extracted the skull with no problems from the same original > structurals, so I'm guessing it's maybe the case that I need to override > some parameters in recon-all in order for the initial recon-all to produce > good brain extractions? > > And by the way, I noticed that, in any one subject's folder, the images > /mri/T1.mgz, /mri/orig.mgz and /mri/orig/001.mgz all seem to contain the > subject's original structural scan. Why does this exist in 3 separate > copies, which also seem to be of different file sizes? The only difference > I can see between them is in terms of brightness correction... > > Many thanks! > > Tudor >

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likelihood of identical subcortical volumes
by Satrajit Ghosh 08 Jul '13

08 Jul '13

2 4

Re: [Freesurfer] importing from nifti
by Martin Reuter 08 Jul '13

08 Jul '13

Yes that is done that way. I thought you wanted to rerun the cross sectional data from scratch. But you can use your existing setup and run base and long on top of it. But avoid mixing freesurfer versions if posdible. Best martin Sent via the Samsung Galaxy S™ III, an AT&T 4G LTE smartphone -------- Original message -------- From: Jonathan Holt <whatsdac(a)umich.edu> Date: To: Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: importing from nifti would it be possible to use volumes generated from recon-all -s <subjID> into the second and third steps of the longitudinal processing workflow? On Tue, Jul 2, 2013 at 2:24 PM, Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> wrote: In the meantime you can check how the mri/orig/001.mgz and the mri/orig.mgz and mri/orig_nu.mgz look. Best, Martin On 07/02/2013 02:16 PM, Jonathan Holt wrote: Thanks Martin, I have attached recon-all.log. I tried to run the process several times, I clearly forgot to pass -all that time but I know for certain the first time I tried I passed -all and it provided the same issue. I can pass the dicom images but I'll have to wait for my PI to return in lab. On Tue, Jul 2, 2013 at 2:05 PM, Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> wrote: Hi Jonathan, I changed the subject of the thread, to better reflect this problem, it (so far) has nothing to do with longitudinal processing. Next time, can you send the log file, it is in /net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/tpNdt/scripts/recon-all.log not the output on the screen. But first lets check these: - your command in the email below seems to be missing "-all"? Probably you passed it? - and from your screen output it looks like there is a problem importing the nifit: WARNING: neither NIfTI-1 qform or sform are valid WARNING: your volume will probably be incorrectly oriented $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /net/data4/ALSSCI/FreeSurfer201211/Subjects/DT/100922dt/anatomy/ht1spgr.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 WARNING: it does not appear that there was sufficient information in the input to assign orientation to the volume... So you need to check the orientation of your /net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/tpNdt/mri/orig/001.mgz... Not sure why your nifti files are incomplete. Can you point -i to the original dicom? Best, Martin On 07/02/2013 01:13 PM, Jonathan Holt wrote: and the command nohup recon-all -s 100922dt_01 -i 100922dt_nifti_revised.nii On Tue, Jul 2, 2013 at 12:40 PM, Jonathan Holt <whatsdac(a)umich.edu> wrote: Here ya go (to list) On Tue, Jul 2, 2013 at 12:38 PM, Jonathan Holt <whatsdac(a)umich.edu> wrote: Here ya go. On Mon, Jul 1, 2013 at 3:31 PM, Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> wrote: No, it's not nifti, that should work. Can you send me your log file and the command you issued. Thanks, Martin On 07/01/2013 03:13 PM, Jonathan Holt wrote: Martin, definitely passing my images and naming time points appropriately. I have been passing nifti as opposed to dicom and it's entirely possible that may be the issue? jon On Jul 1, 2013, at 2:32 PM, Martin Reuter wrote: Hi Jon, are you passing your images? <tpNid> is a placeholder for the id of your subject+time point, for example it could be jon_01 the "path_to_tpN_dcm" needs to specify the path to the dicom files, point it to the first file in the MPRAGE series (or multi echo mprage or what you are using). This is the full path on your file system to that file. Best, Martin On 07/01/2013 02:29 PM, Jonathan Holt wrote: I have tried to inspect the tal xfms that were created in the brief time this string was running recon-all -all -s <tpNid> -i path_to_tpN_dcm while viewing orig.mgz in tkmedit. they were talairach.xfm and talairach.auto.xfm, both were empty and the tkmedit window was empty. upon further inspection the log file is complaining about my nifty. WARNING: neither NIfTI-1 qform or sform are valid WARNING: your volume will probably be incorrectly oriented $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /net/data4/ALSSCI/FreeSurfer201211/Subjects/DT/100922dt/anatomy/ht1spgr.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 WARNING: it does not appear that there was sufficient information On Mon, Jul 1, 2013 at 1:46 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: can you cc the list so that others can answer? On Mon, 1 Jul 2013, Jonathan Holt wrote: I have not and I am not certain how to do so On Jul 1, 2013, at 1:03 PM, Bruce Fischl wrote: Hi Jon have you visually inspected the results of the tal xform? Bruce On Mon, 1 Jul 2013, Jonathan Holt wrote: Log file indicates manual talairach alignment may be necessary. ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0079, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary Can anyone provide direction. Alternatively, the error indicates talairach alignment can be skipped with -notal-check flag. Is this step completely necessary? jon 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(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.edu Web : http://reuter.mit.edu -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.edu Web : http://reuter.mit.edu _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.edu Web : http://reuter.mit.edu -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.edu Web : http://reuter.mit.edu

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Cutting into a surface of grey matter
by ye tian 08 Jul '13

08 Jul '13

Dear Freesurfers, When an image cuts through a surface of grey matter (e.g. attached Freesurfer.png), will freesurfer overestimate cortical thickness? If so, how do you go about editing the image? Thank you very much! Sincerely, Ye

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Freesurfer July 2013