Freesurfer June 2012

freesurfer@nmr.mgh.harvard.edu

124 participants
195 discussions

Use of separate manual segmentation for hippocampus formation
by Dhinakaran Chinappen 17 Jun '12

17 Jun '12

Hi Freesurfer Experts and Advisors, Would it be possible to use different manually segmented images (of the hippocampus formation only) as a-priori maps and then use Freesurfer to automatically segment the hippocampus formation only, based on the furnished manually segmented images? This would be relevant if the hippcampus formation needed to be automatically segmented for subjects over an age range, whereby those different manually segmented images would also be over an age range. Thanks, Dhinakaran.

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Rejoindre mon réseau sur LinkedIn
by Luisa Leo via LinkedIn 17 Jun '12

17 Jun '12

LinkedIn ------------ Luisa Leo a indiqué que vous êtes un(e) ami(e) ------------------------------------------ Vorrei aggiungerti alla mia rete professionale. - Luisa Leo Accepter l'invitation de Luisa Leo http://www.linkedin.com/e/-qq80um-h3jz1ttz-53/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… Voir l'invitation de Luisa Leo http://www.linkedin.com/e/-qq80um-h3jz1ttz-53/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… ------------------------------------------ Quel est l'intérêt de faire partie du réseau de Luisa Leo ? Le réseau de Luisa Leo développera votre propre réseau : Si vous acceptez l'invitation de Luisa Leo, vous pourrez voir qui vous connaissez dans son réseau et demander à Luisa Leo de vous présenter. Appartenir à un réseau est toujours un plus pour votre carrière. -- (c) 2012, LinkedIn Corporation

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mri_register memory error
by Shantanu Ghosh 15 Jun '12

15 Jun '12

Hi Freesurfer experts, I am receiving an error message while processing registration to fsaverage using mri_register. Please tell me why it is happening and how to get this going. Here is the terminal output: glia:shantanu[219] mri_register /autofs/space/calvin_001/marvin/1/users/MRI/WMA/recons/AC058/mri/brainmask.mgz /autofs/space/glia_001/users/shantanu/tutcc/ddd/fsaverage/mri/brainmask.mgz AC058.reg.mgz reading 1 input volumes... logging results to AC058.reg.log reading input volume '/autofs/space/calvin_001/marvin/1/users/MRI/WMA/recons/AC058/mri/brainmask.mgz'... reading GCA '/autofs/space/glia_001/users/shantanu/tutcc/ddd/fsaverage/mri/brainmask.mgz'... gcaAllocMax: node dims 15 15 15 gcaAllocMax: prior dims 15 15 15 gcaAllocMax: max_labels 0 GCAread(/autofs/space/glia_001/users/shantanu/tutcc/ddd/fsaverage/mri/brainmask.mgz): could not allocate -136441340 labels @ (0,0,0) Cannot allocate memory Thanks in advance, Shantanu -- Shantanu Ghosh, Ph.D. Martinos Center for Biomedical Imaging Harvard-MIT Program in Health Sciences & Technology

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Re: [Freesurfer] [Fwd: Re: TRACULA dpath problem]
by Priti Srinivasan 15 Jun '12

15 Jun '12

Hi XJ, I'm just starting to look at your log files. Just curious, did you decide to not do eddy current correction and b0 inhomogenity correction or accidentally left it out? When I look at the configuration file, you've given all the parameters for b0 inhomogenity correction, but it is set to '0' (set dob0 = 0) and the same is the case for eddy current correction too (set doeddy = 0). Just wanted to make sure you did not set that '0' accidentally. Eddy current correction is definitely one of the recommended preprocessing steps, so you might want to consider doing that. Also looks like your original input dwi file (with NaNs) may be the root cause of the problem. If you do have the original dicoms, you can give that as an input. I'm not sure if you can give a series of 3D Nifti DWI files as an input in the configurations file...Anastasia (cc'd) might be able to answer that question. Hope that helps, Priti > > ---------------------------- Original Message ---------------------------- > Subject: Re: [Freesurfer] TRACULA dpath problem > From: "XJ Kang" <xkang(a)ucdavis.edu> > Date: Fri, June 15, 2012 2:22 pm > To: "Priti Srinivasan" <rspriti(a)nmr.mgh.harvard.edu> > -------------------------------------------------------------------------- > > Hi Priti, > > Attached are the tracula conf file and log files from two subjects. > > I ran the two subjects. The results are almost the same. Here are what I > found so far: > > 1. There are NaN values in the 4D image. I created it from 3D images > using "fslmerge -a", and the 3G images have no NaNs. > 2. The image "dlabel/diff/White-Matter++.flt" was not found. Probably > this is the origin of all the problems? > > Do you want me to send the email to you or to the mailing list? Probably > many people are not interested in my email if I post on the whole list. > > Thank you. > > XJ > > On 6/15/2012 11:02 AM, Priti Srinivasan wrote: >> Can you send us your configuration file (mytracula.conf) and log file >> (it >> should be under scripts/trac-all.log). I can take a look. >> >> Priti >> >>> Hi, >>> >>> I am trying to run the last step of TRACULA. I used the command line: >>> >>> % trac-all -path -c mytracula.conf >>> >>> Here is all the info I got on the screen: >>> >>> INFO: SUBJECTS_DIR is /home/sata2/FreeSurfer/Subjects.Verio >>> INFO: Diffusion root is /home/xkang/DTI/ >>> Actual FREESURFER_HOME /home/local/freesurfer-v510 >>> trac-paths -c /home/xkang/DTI//S0006/scripts/dmrirc.local -log >>> /home/xkang/DTI//S0006/scripts/trac-all.log -cmd >>> /home/xkang/DTI//S0006/scripts/trac-all.cmd >>> #------------------------------------- >>> /usr/local/freesurfer/bin/trac-paths >>> #------------------------------------- >>> #@# Path reconstruction Fri Jun 15 10:47:44 PDT 2012 >>> #------------------------------------- >>> trac-paths finished without error at Fri Jun 15 10:47:44 PDT 2012 >>> >>> >>> >>> I didn't see "dpath" under the subject's directory. Seems nothing has >>> been done. I already ran the "trac-all -prep" and "trac-all -bedp". I >>> have the directories dlable, dmri and dmir.bedpostX, but not dpath. Can >>> any body help where the problems are? >>> >>> I use DTI images in NIFTI format and the resolution is 2x2x2, which is >>> not the same as that of the FreeSurfer orig.mgz. Probably this is fine. >>> >>> Thanks. >>> >>> XJ Kang >>> _______________________________________________ >>> 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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precoloring - adjusted errors
by Caspar M. Schwiedrzik 15 Jun '12

15 Jun '12

Hi! I am processing a resting state data set, which I would like to low pass filter to get rid of some artifacts. The sample will be very small, so I won't run a RFX GLM, but an FFX GLM and/or single subject analyses. Since the low pass filter introduces high autocorrelations, it does not make sense to whiten the data before the GLM. However, in order not to violate the assumptions of the OLS, I would like to use the precoloring approach described in Worsley & Friston 1995. Is that by any chance implemented in FSFAST, and if not, where would be the right place to add it? Thanks in advance, Caspar

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recon error- too many arguments?
by Borzello, Mia 15 Jun '12

15 Jun '12

Hi, I'm trying to run a recon, but I keep getting the error: too many arguments for the following command: econ-all -autorecon1 -autorecon2 -autorecon3 -subject XXXX_SurferOutput -i [path to dicom] Any help on this would be excellent! Thanks, M

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TRACULA dpath problem
by XJ Kang 15 Jun '12

15 Jun '12

Hi, I am trying to run the last step of TRACULA. I used the command line: % trac-all -path -c mytracula.conf Here is all the info I got on the screen: INFO: SUBJECTS_DIR is /home/sata2/FreeSurfer/Subjects.Verio INFO: Diffusion root is /home/xkang/DTI/ Actual FREESURFER_HOME /home/local/freesurfer-v510 trac-paths -c /home/xkang/DTI//S0006/scripts/dmrirc.local -log /home/xkang/DTI//S0006/scripts/trac-all.log -cmd /home/xkang/DTI//S0006/scripts/trac-all.cmd #------------------------------------- /usr/local/freesurfer/bin/trac-paths #------------------------------------- #@# Path reconstruction Fri Jun 15 10:47:44 PDT 2012 #------------------------------------- trac-paths finished without error at Fri Jun 15 10:47:44 PDT 2012 I didn't see "dpath" under the subject's directory. Seems nothing has been done. I already ran the "trac-all -prep" and "trac-all -bedp". I have the directories dlable, dmri and dmir.bedpostX, but not dpath. Can any body help where the problems are? I use DTI images in NIFTI format and the resolution is 2x2x2, which is not the same as that of the FreeSurfer orig.mgz. Probably this is fine. Thanks. XJ Kang

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qdec
by Richter, Julia 15 Jun '12

15 Jun '12

Dear all, after comparing two groups in qdec and hitting the question "Does the average thickness differ between group 1 and group 2?", do yellow areas mean that group 1 has a thicker cortex in that area than group 2? Thanks, Julia

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1 Group (2 Levels) 2 Covariates
by Jeff Sadino 15 Jun '12

15 Jun '12

Hello, I want to do an analysis with 1 Group (Control and HIV) with two covariates (Age and ICV). Qdec only lets me choose one covariate. So instead I choose two nuisance variables. No matter how many different permutations I run on this, I can not get it to duplicate my SAS results, and the Qdec results look suspiciously wrong. Also, when I do it manually with the mri_glmfit command, I still can not duplicate the SAS results. I have tried both demeaning and not demeaning. This should be pretty straight forward? Am I missing something obvious? How would one do a 1 Group (2 levels) 2 Covariate analysis in QDEC? Thank you, Jeff

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Scripting with fs 5.1 vs 5.0
by Nicole Senecal 14 Jun '12

14 Jun '12

Hi all, I'm having trouble getting anything through on 5.1 using scripts, although I can run recon-all at the commandline. I'm running freesurfer on a remote cluster, not locally. Specifics of the cluster itself aside, with 5, I could run: *vbbatch -c * *"PATH=$PATH:/usr/local/freesurfer_64bit_5; export PATH; * *FREESURFER_HOME=/usr/local/freesurfer_64bit_5; export FREESURFER_HOME; * *SUBJECTS_DIR=/jet/kable/CorticalThickness/Subjects; export SUBJECTS_DIR;** * *recon-all -i SW419_Day1.mgz -subject SW419Day1_fullrecon -all" -d1 -r* With 5.1, I have to specify MINC_BIN_DIR within this command (get an error if I don't, saying that it's not defined) and I still get stuck in the talairach transform, with: mritotal -verbose -debug -clobber -modeldir /../share/mni_autoreg -protocol icbm transforms/tmp.talairach.22637/src.mnc transforms/talairach.auto.xfm mritotal: Command not found. Clearly mritotal is working if recon-all at the commandline works. Do I need to specify more environmental variables somewhere for 5.1? I've tried specifying MINC_BIN_DIR, MINC_LIB_DIR, and MNI_DIR in the command as well, with no luck. My bash profile includes: PATH=$PATH:/usr/local/freesurfer5-1/bin FREESURFER_HOME=/usr/local/freesurfer5-1 SUBJECTS_DIR=/jet/kable/CorticalThickness/Subjects MINC_BIN_DIR=/usr/local/freesurfer5-1/mni/bin MINC_LIB_DIR=/usr/local/freesurfer5-1/mni/lib PERL5LIB=/usr/local/freesurfer5-1/mni/lib/perl5/5.8.5 MNI_DIR=/usr/local/freesurfer5-1/mni FSFAST_HOME=/usr/local/freesurfer5-1/fsfast FSF_OUTPUT_FORMAT=nii And on startup I see: -------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer5-1 FSFAST_HOME /usr/local/freesurfer5-1/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /jet/kable/CorticalThickness/Subjects MNI_DIR /usr/local/freesurfer5-1/mni FSL_DIR /usr/local/fsl thanks, Nicole -- Nicole Senecal Neuroscience Graduate Group Kable Lab 3720 Walnut St., Room C37 Philadelphia, PA 19104 Lab phone: 215-746-4371

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Freesurfer June 2012