Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available
by Nolan Nichols 18 Nov '11

18 Nov '11

Thanks, Pedro! I am glad to see that you posted a public AMI for freesurfer. And thanks to Thomas for producin documentation on how to use it. This thread inspired me share a StarCluster AMI (ami-27f1384e in the us-east-1 region) that I built for batch FS jobs, which includes the initial setup for installing tools from the NeuroDebian repository. I've also been playing around with using s3fs, which allows Amazon's S3 to be mounted as a drive and accessed directly as the "subjects_dir". The AMI can be launched here: https://console.aws.amazon.com/ec2/home?region=us-east-1#launchAmi=ami-27f1… I did not include the .license for FS as I wasn't sure about licensing issues, but I would be happy to publish an AMI with a built-in license if I get the go ahead. For now you will need to start a cluster and your license to each instance. A few details: Ubuntu 10.04 x86 built from StarClusters ami-8cf913e5 us-east-1 region See the StarCluster details at http://web.mit.edu/stardev/cluster/ Customizing StarCluster (http://web.mit.edu/stardev/cluster/docs/latest/manual/create_new_ami.html) s3fs (http://code.google.com/p/s3fs/) Freesurfer 5.1 32-bit NeuroDebian ready (so you can apt-get install mricron, fsl, nipype, etc.) Thanks again for starting this thread, and let me know if I can help in any way. It would be great to see "cloud" resources be readily accessibly to the community with minimal effort to get a cluster with freesurfer and tools available via neurodebian up and running. Cheers, Nolan

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Cerebellum Edits
by Jordan Pierce 18 Nov '11

18 Nov '11

We've been manually editing brainmask.mgz to remove voxels that are included in the pial surface that shouldn't be, and recently found on the wiki that to remove cerebellum voxels we should be editing brain.finalsurfs.manedit.mgz instead. What is the reason for this difference? Do we need to redo edits that we've done only on brainmask.mgz? We are going to be looking at cortical thickness. Thanks, Jordan Pierce Graduate Student Behavioral and Brain Sciences Program Psychology Department The University of Georgia

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Re: [Freesurfer] Cerebellum Edits
by Allison Player 18 Nov '11

18 Nov '11

You can copy your edited brainmask.mgz to brain.finalsurfs.manedit.mgz then rerun the case from the beginning using: recon-all -all -clean-bm -s subjid This will recreate the brainmask.mgz so no chunks of cerebellum are missing (and therefore cerebellum volume estimates won't be off). If you don't care about cerebellum and the aseg is still accurate everywhere else despite the missing cerebellum, you don't have to do this. Make a backup copy of brain.finalsurfs.manedit.mgz somewhere else just in case it gets written over when you rerun. Allison > Date: Fri, 18 Nov 2011 11:55:49 -0800 (PST) > From: Jordan Pierce <jepierce87(a)yahoo.com> > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Subject: [Freesurfer] Cerebellum Edits > > We've been manually editing brainmask.mgz to remove voxels that are included > in the pial surface that shouldn't be, and recently found on the wiki that > to remove cerebellum voxels we should be editing > brain.finalsurfs.manedit.mgz instead. What is the reason for this > difference? Do we need to redo edits that we've done only on brainmask.mgz? > We are going to be looking at cortical thickness. > > Thanks, > > Jordan Pierce > Graduate Student > Behavioral and Brain Sciences Program > Psychology Department > The University of Georgia _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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trac-all "Error: bvecs and bvals don't have the same number of entries"
by Peter J. Molfese 18 Nov '11

18 Nov '11

Hello, I'm running trac-all (trac-preproc) on some DTI data and receive the following error: dtifit -k /Users/pete/Documents/dti/pete/run7/peter/dmri/dwi.nii.gz -m /Users/pete/Documents/dti/pete/run7/peter/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -r /Users/pete/Documents/dti/pete/run7/peter/dmri/bvecs -b /Users/pete/Documents/dti/pete/run7/peter/dmri/bvals -o /Users/pete/Documents/dti/pete/run7/peter/dmri/dtifit Error: bvecs and bvals don't have the same number of entries I found the following thread http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19747.html but when I attempted to add "export LC_ALL=en_US", the problem persists. I have looked in the files and found that they do indeed have different numbers of entries. The scans were performed on a Siemens TimTrio 3T scanner. Is there something else I should set? Peter J. Molfese, Ph.D. Postdoctoral Associate Haskins Laboratories 300 George Street, Suite 900 New Haven, CT 06511 peter.molfese(a)yale.edu CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intende d recipient, please contact the sender immediately by reply e-mail and destroy all copies of the original message.

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data files fsfast-functional missing
by Verena Gramse 18 Nov '11

18 Nov '11

Hi, I'd like to follow the fsfast tutorial but I can't find the data for it: ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-functional.tar.gz & ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-tutorial.subjects.tar.gz & Were they renamed or displaced? Thanks, Verena

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kvlSegmentHippocampalSubfields.sh seg fault
by Spencer Bowen 18 Nov '11

18 Nov '11

To whom it may concern, When running the hippocamapal subfield segmentation routine on the left hippocampus for a normal subject (early Parkinson) I get the following segmentation fault error: kvlSegmentHippocampalSubfields.sh: line 18: 29522 Segmentation fault kvlSegmentWithoutGUI configurationFileSegmentationWithoutPartialVolumingButAfterUpsampling.txt After looking at the recon-all.error log file, this appears to be the only error occurring. Any suggestions would be greatly appreciated. Thanks, Spencer -- Spencer L. Bowen, Ph.D. Research Fellow Department of Radiology, MGH Building 149 Room 2301, 13th St. Charlestown, MA 02129 Phone: (617) 643-6751 Email: slbowen(a)nmr.mgh.harvard.edu

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Rejoindre mon réseau sur LinkedIn
by Nikolas Borrel-Jensen via LinkedIn 18 Nov '11

18 Nov '11

LinkedIn ------------ Nikolas Borrel-Jensen souhaite se connecter à vous sur LinkedIn : ------------------------------------------ Freesurfer, Je vous invite à faire partie de mon réseau professionnel en ligne sur le site LinkedIn. Accepter l'invitation de Nikolas Borrel-Jensen http://www.linkedin.com/e/-qq80um-gv4xga12-28/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… Voir l'invitation de Nikolas Borrel-Jensen http://www.linkedin.com/e/-qq80um-gv4xga12-28/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… ------------------------------------------ Quel est l'intérêt de faire partie du réseau de Nikolas Borrel-Jensen ? Le réseau de Nikolas Borrel-Jensen développera votre propre réseau : Si vous acceptez l'invitation de Nikolas Borrel-Jensen, vous pourrez voir qui vous connaissez dans son réseau et demander à Nikolas Borrel-Jensen de vous présenter. Appartenir à un réseau est toujours un plus pour votre carrière. -- (c) 2011, LinkedIn Corporation

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error creating template (base) for longitudinal analysis
by bbruijn＠bidmc.harvard.edu 17 Nov '11

17 Nov '11

Dear FS-experts, I'm doing a longitudinal comparison of cortical thickness and am therefore following the steps of the longitudinal stream on the freesurfer wiki. I've created templates for all of my subjects but one, for which I received an error message trying to create the template (or base). This is the command: recon-all -base subjectname_template -tp subjectname_pre_nii -tp subjectname_post_dicom -all This is the error message I receive: recon-all -s subjectname_template exited with ERRORS at Wed Nov 16 18:19:57 EST 2011 When I look in the logfile, I read this line (repeated): mhtVoxelList_Add(139, 172, 245, 85437): complete list too big! etc. Is this something I can fix? Are my pre and post files not compatible? I hope you can help me, thanks in advance! Bente

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Fixing Talairach.lta
by Jeff Sadino 17 Nov '11

17 Nov '11

Hello, I have several subjects with bad surfaces in fs 5.0.0. After checking their talairach.lta file, these transforms are all bad. I tried using tkregister2 to create a good talairach.lta file, but it just wasn't working. I tried rerunning these subjects in fs 5.1.0, and their talairach.lta files are all good. Can I just copy the fs510 talairach.lta file to the fs500 subject folder, or will that cause other issues that are not obvious? As a side note, what would the tkregister2 command be to create the lta file? Thank you, Jeff Sadino

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Re: [Freesurfer] cvs_avg35
by Antonella Kis 17 Nov '11

17 Nov '11

Hi Lilla, Many thanks again for your help. In the mean time I checked with echo $FREESURFER_HOME and as I knew my $FREESURFER_HOME is /usr/local/freesurfer Under this directory I have the subjects directory but here unfortunately I am having the cvs_avg35/mri/norm.mgz. 1) Can you please help me find or get the the cvs_avg35/mri/norm.mgz? I saw online the same question was posted on June 2011 but there is no answer for the question online: http://www.opensubscriber.com/message/freesurfer@nmr.mgh.harvard.edu/155066… 2) Since for my TBSS TBSS study was used by the TBSS the nonlinear registration FNIRT (is about 15 times faster than IRTK on FA data and possibly a little more 'accurate') I would like to use for a Tal space a non-linear talairach registration. Can you please give me some directions on how I can do this? What is the default Tal registration (linear or non-linear) for dt_recon? 3) When dt_recon is aligning the diffusion data in the Tal space is in fact aligning the register.dat data (difussion data already aligned to the structural data) and the output is the fa-tal.nii.gz? If not why I need the register.dat file? 4) So by my understanding each subject will have a file called fa-tal.nii which in fact represents the subject's registration on the Tal-space? How about the mean diffusivity? I don't have only one file for this adc.nii. What if I want to do a non_FA values study on the tal space? 5) I understood that the 'registration.dat' file describes a rigid-body transformation from the diffusion to the structural space and in order to resample the structural volume in the diffusion space, I will need to apply the inverse of this transformation to my input volumes and to use for this the 'mri_vol2vol': mri_vol2vol --mov $TUTORIAL_DIR/$subj/dtrecon/lowb.nii \ --targ $SUBJECTS_DIR/$subj/mri/wmparc.mgz \ --inv --interp nearest --o $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz \ --reg $TUTORIAL_DIR/$subj/dtrecon/register.dat --no-save-reg Is the register.dat file created by this function mri_vol2vol? I believe the registration between the diffusion and structural space (so the register.dat file) has already been computed as part of the previous pre-processing step so while using the mri_vol2vol as above do I need to use the '--no-save-reg' flag as in the above example or the '--save-reg' flag? 6) To resample the diffusion data of one subject in the CVS space do I need to run after dt_recon the mri_vol2vol as below? mri_vol2vol --targ $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \ --m3z $SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \ --noDefM3zPath --reg $TUTORIAL_DIR/$subj/dtrecon/register.dat \ --mov $TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgz \ --o $TUTORIAL_DIR/$subj/dtrecon/fa-masked.ANAT+CVS-to-avg35.mgz \ --interp trilin --no-save-reg Do I need to run the mri_cvs_registration on the structural data in order to get the above .m3z file 'combined_tocvs_avg35_elreg_afteraseg-norm.m3z' before I run the mri_vol2vol? If I want to have my second registration step done in the Tal space not CVS space since after running dt_recon I am getting the fa-tal.nii.gz and the fa-masked.mgz is this the equivalent file to fa-masked.ANAT+CVS-to-avg35.mgz (if I use the CVS space)? In this case I don't need to run the last mri_vol2vol command? Sorry for asking so many questions but it is very confusing the online material. Many thanks! Antonella From: Lilla Zollei <lzollei(a)nmr.mgh.harvard.edu> To: Antonella Kis <atorok9(a)yahoo.com> Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Sent: Tuesday, November 15, 2011 5:11 PM Subject: RE:[Freesurfer] dt_recon registration Hi Antonella, > 1) Why I don't have in my $FREESURFER_HOME/subjects the cvs_avg35/mri/norm.mgz? In my subjects directory I only have my subjects and nothing else. How can I get the cvs_avg35/mri/norm.mgz? $FREESURFER_HOME is different from your $SUBJECTS_DIR. Could you double check? > 2) Do you believe that for my subjects-all children ages 6-13 the results are gone be OK if I use the talairach registration and re-sampling? As I mentioned in my previous email I would like to do > a two-group study similar with TBSS so to do a statistical analysis on the FA and non_FA data such as mean diffusivity, to see if there are any clusters that may survive by multiple comparisons without any covariant. Are you referring to a linear or a non-linear talairach registration? It will be you who needs to decide which space to use for analysis. You would want all your data to be well aligned in that space in order to achieve a meaningful group comparison. The decision might also depend on in which space you want to report your final results in. > 3) Do you have any suggestion regarding which registration is better to be used for this study? I am not familiar with your study, so it would be hard to say. > 4) How I can check for each individual subject if the registration worked out well if for example I choose the talairach space? > Do I run: > > tkregister2 --mov lowb.nii --reg register.dat --surf > or which file is in fact the registered data file? Is the fa-tal.nii.gz or the lowb.nii.gz? You mentioned that the default registration is on talairch space and the I see on dt_recon tutorial > that is also doing a registration of lowb to same-subject anatomical so I have two registration done when I run the dt_recon? dt_recon has two registration steps. One aligns the diffusion data (lowb) to the structural (registration.dat is the default name of the registration file) and the other aligns the diffusion data in the Tal space (the resampled fa file in that space is fa-tal). You can use both freeview and thregister to check the alignment of your volumes. Lilla > ___________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ > From: Lilla Zollei <lzollei(a)nmr.mgh.harvard.edu> > To: Antonella Kis <atorok9(a)yahoo.com> > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Sent: Monday, November 14, 2011 4:13 PM > Subject: Re: [Freesurfer] dt_recon registration > > > Hi Antonella, > > > 1) I will be very grateful if you can confirm if my coding is write. First can you please let me know if by default dt_recon is re-sample FA to talairch space? In this case because I want to register on CVS should I add the --no-tal flag? I am asking this > question > > because after I ran the following command I see in my output directory called P07_dti a file called fa_tal.nii as well as fa_tal.nii.reg. > > The talairach registration and re-sampling does take place by default, but that should not affect your further processing as the fa.nii file (in the native space) is not deleted from the directory. So you can either leave the default settings or you can also use > --no-tal. > > > 2) Do I need this files if I want to do a group study for my FA and mean diffusivity, similar to TBSS in FSL? > > Are you referring to the tal registration files? If you want to do the group study in the CVS spacem then you will not need the tal registration files. > > > 3) Can I use the talairch registration or should I use the CVS? > > Depends on where you want to do your analysis. > > > 4) Should I add the flag --no-tal? > > You can. If you don't you just end up with two additional files. > > > This is what I was running: > > > > setenv FREESURFER_HOME /usr/local/freesurfer > > setenv SUBJECTS_DIR $FREESURFER_HOME/subjects/DTI_FS/dtrecon > > > > dt_recon --i P07_dti.nii.gz -- b P07.bvals P07.bvects --s P07 --o P07_dti where > > > > P07_dti.nii.gz is my DTI volume > > P07.bvals P07.bvects are the bvals and bvects for my subject > > P07 is my structural recons data for my P07 subject > > > > > > > > 5) From the dt_recon --help I understand that dt_recon is doing the registration of lowb to same-subject anatomical using > > FSLs flirt (creates mask.nii and register.dat). > > > > mri_vol2vol --mov /usr/local/freesurfer/subjects/DTI_FS/dtrecon/P07_dti/lowb.nii \ > > --targ $SUBJECTS_DIR/P07/mri/wmparc.mgz \ > > --inv --interp nearest --o $SUBJECTS_DIR/P07/mri/wmparc2diff.mgz \ > > --reg /usr/local/freesurfer/subjects/DTI_FS/dtrecon/P07_dti/register.dat --no-save-reg > > Actually dt-recon now uses bbregister, but the output of this step is still register.dat. With the above you move the wmparc into the diffusion space. > > > 6) Should I run mri_vol2vol to re-sample the structural volume in the diffusion space and register in the CVS space: > > > > > > mri_vol2vol --targ $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \ > > --m3z $SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \ > > --noDefM3zPath --reg $TUTORIAL_DIR/$subj/dtrecon/register.dat \ > > --mov /usr/local/freesurfer/subjects/DTI_FS/dtrecon/dti_15_p7/fa-masked.mgz \ > > --o /usr/local/freesurfer/subjects/DTI_FS/dtrecon/dti_15_p7/fa-masked.ANAT+CVS-to-avg35.mgz \ > > --interp trilin --no-save-reg > > With the above you are going to move your diffusion file (fa) into the CVS space (by implicitely combining a moprh moving the diffusion file to the structural space and then to the CVS space) and not resampling the structural volume in the diffusion space. > > > 7) I found online that the default CVS template is cvs_avg35 which is supplied with my FreeSurfer distribution. Can you please tell me in which directory is located or how I can obtain > > the cvs_avg35? > > It should be in $FREESURFER_HOME/subjects (as indicated above in your command --targ). > > --Lilla > _______________________________________________ > 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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