Freesurfer

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30132 discussions

mri_glmfit-sim without talairach.xfm, orig.mgz and aparc
by Caspar M. Schwiedrzik 10 Oct '13

10 Oct '13

Hi Freesurfer experts, I am running a group analysis of functional data on a custom template/average subject for which I do not have a talairach.xfm file, an orig.mgz nor aparc data (it is a primate dataset). I ran into some error messages when trying to use mri_glmfit-sim. 1) I get an error message that the flag --no-cortex is not recognized. I am using --no-cortex in mri_glmfit because I do not have a cortex label file for my template subject. This error does not crash the program, but may be worth a minor bug fix in future releases. 2) For the primate data, I did not make an average volume yet, but only an average surface. Hence, I do not have an orig.mgz file for the average subject. All analyses I currently run are surface based. Can I just copy any orig.mgz into the mri folder without negatively affecting mri_glmfit-sim? 3) I do not have a Talairach.xfm file for the average subject either. Can I copy an identity matrix into mri/transforms without negatively affecting mri_glmfit-sim? Again, all analyses are surface-based. 4) I removed the --annot flag where mri_glmfit-sim where mri_surfclusters is being called. Is that expected to result in any problems? 5) Anything else I should observer? Thanks, Caspar

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Re: [Freesurfer] brain.mgz and control.dat attached
by Francesco Siciliano 10 Oct '13

10 Oct '13

Thank you for your help! I will re-run this brain and see if it reads all 53 control points and then let you know the outcome. However, the last time I ran this brain with this control point set, it only read 22 control points. ________________________________________ From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] Sent: Monday, October 07, 2013 3:28 PM To: Francesco Siciliano Subject: RE: brain.mgz and control.dat attached but it should say "reading 53 control points". Can you verify whether this is or is not the case? And also please cc the list so that others can answer! On Mon, 7 Oct 2013, Francesco Siciliano wrote: > I can run it again - but it has already been run with the current control point set (apparently with 53 points) and some of the points have not been successful for some reason. > ________________________________________ > From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] > Sent: Monday, October 07, 2013 2:55 PM > To: Francesco Siciliano > Subject: Re: brain.mgz and control.dat attached > > hmmm, and you reran after this? There are 53 points in it. Can you run > autorecon2-cp and see if it now reads 53 control points? > On Mon, 7 Oct 2013, > Francesco Siciliano wrote: > >> >> ________________________________________ >> From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] >> Sent: Monday, October 07, 2013 2:48 PM >> To: Francesco Siciliano >> Subject: RE: [Freesurfer] [FreeSurfer] control points >> >> can you email me the control.dat and the brain.mgz? >> >> On Mon, 7 Oct 2013, Francesco Siciliano >> wrote: >> >>> In the control.dat file it says numpoints 53. Is that referring to control points? Because I certainly don't have that many! I counted about 28 when I loaded the control.dat file onto the brainmask volume. >>> ________________________________________ >>> From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] >>> Sent: Monday, October 07, 2013 2:14 PM >>> To: Francesco Siciliano >>> Cc: freesurfer(a)nmr.mgh.harvard.edu >>> Subject: RE: [Freesurfer] [FreeSurfer] control points >>> >>> and how many do you see in the control.dat file? Sounds like they aren't >>> getting saved to disk somehow.... >>> On Mon, 7 Oct 2013, Francesco Siciliano >>> wrote: >>> >>>> I counted at least 28 control points on the brainmask when I loaded the set and my log indicates that freesurfer read 22 control points. I've attached part of the log below. >>>> >>>> >>>> #@# Intensity Normalization2 Mon Sep 16 19:44:17 EDT 2013 >>>> /Users/jonathanposner/Desktop/AdultControls/diffusion_recon/6156/Subject1/mri >>>> \n mri_normalize -f /Users/jonathanposner/Desktop/AdultControls/diffusion_recon/6156/Subject1/tmp/control.dat -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz \n >>>> using control points from file /Users/jonathanposner/Desktop/AdultControls/diffusion_recon/6156/Subject1/tmp/control.dat... >>>> using segmentation for initial intensity normalization >>>> reading from norm.mgz... >>>> normalizing image... >>>> Reading 22 control points... >>>> only using 22 control points from file, mean 84.1, scaling by 1.31... >>>> building Voronoi diagram... >>>> performing soap bubble smoothing... >>>> removing outliers in the aseg WM... >>>> 4899 control points removed >>>> building Voronoi diagram... >>>> performing soap bubble smoothing... >>>> building Voronoi diagram... >>>> performing soap bubble smoothing... >>>> 3d normalization pass 1 of 2 >>>> building Voronoi diagram... >>>> performing soap bubble smoothing... >>>> 3d normalization pass 2 of 2 >>>> building Voronoi diagram... >>>> performing soap bubble smoothing... >>>> writing output to brain.mgz >>>> 3D bias adjustment took 4 minutes and 46 seconds. >>>> using MR volume brainmask.mgz to mask input volume... >>>> white matter peak found at 111 >>>> white matter peak found at 102 >>>> gm peak at 66 (66), valley at 25 (25) >>>> csf peak at 33, setting threshold to 55 >>>> white matter peak found at 111 >>>> white matter peak found at 110 >>>> gm peak at 66 (66), valley at 24 (24) >>>> csf peak at 33, setting threshold to 55 >>>> >>>> >>>> >>> >>> >>> 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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Re: [Freesurfer] TRACULA question
by Anastasia Yendiki 10 Oct '13

10 Oct '13

Hi Lars - Just like you have to do before you run any freesurfer programs, you'll have to run a script that comes with freesurfer and sets up all the necessary environment variables. See: http://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration Hope this helps, a.y PS: Please send emails about tracula usage to the freesurfer list (cc'd here) and not to me personally. This makes sure the answers get archived so that people can search for answers to common questions. Thanks! On Thu, 10 Oct 2013, Lars M. Rimol wrote: > Dear Dr. Yendiki, > > I am trying to learn how to do Tracula analyses and was wondering about one > thing: > > According to the tutorial, all I need to do is set up the various > configuration files. However, when I try to run the example data set, with > > trac-all -prep -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial > > it complains: "FSLDIR: Undefined variable." > > FSL dir doesn't seem to be defined in any of the configuration files > provided in the tutorial. Is it necessary to install FSL in order to use > Tracula? And where do I set the FSLDIR variable? > > > > > Thank you! > > > > yours, > > Dr. Lars M. Rimol > >

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Problem with DWI and structural coregistration
by stdp82＠virgilio.it 10 Oct '13

10 Oct '13

Hi list, I'm performing trac-all but I'm noting some coregistration error.I have try to run separately each step. When -masks was finished, cortex masks and other file were wrongly coregistared on DTI. In the next step also the dti_FA and other maps are wrong becouse some parts are lacking. Please see also the attachments. Thanks, Stefano

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trac-all -tensor error
by Jennifer Segawa 10 Oct '13

10 Oct '13

Hello! I'm having problems running the trac-all -tensor step. dtifit appears to run correctly; the problem seems to be in mapping the output files to the template space. The command I run is: trac-all -tensor -c /cluster/manoach/dod/BU_pipeline/data/DOD_DODCON004/tracula.cfg ----------------------------------------------- And the error I get is (the move file doesn't exist, but dtifit_FA.nii.gz does exist): mri_vol2vol --mov /cluster/manoach/dod/BU_pipeline/data/DODCON004/dmri/anatorig/dtifit_FA.flt.nii.gz --targ /autofs/cluster/manoach/dod/subjects/cvs_avg35/mri/norm.mgz --o /cluster/manoach/dod/BU_pipeline/data/DODCON004/dmri/cvs/dtifit_FA.flt.nii.gz --m3z /cluster/manoach/dod/BU_pipeline/data/DODCON004/dmri/xfms/cvs/final_CVSmorph_tocvs_avg35.m3z --noDefM3zPath --interp trilin --no-save-reg niiRead(): error opening file /cluster/manoach/dod/BU_pipeline/data/DODCON004/dmri/anatorig/dtifit_FA.flt.nii.gz Using the m3z file as it is; no assumed location. movvol /cluster/manoach/dod/BU_pipeline/data/DODCON004/dmri/anatorig/dtifit_FA.flt.nii.gz targvol /autofs/cluster/manoach/dod/subjects/cvs_avg35/mri/norm.mgz outvol /cluster/manoach/dod/BU_pipeline/data/DODCON004/dmri/cvs/dtifit_FA.flt.nii.gz invert 0 tal 0 talres 2 regheader 0 noresample 0 interp trilin (1) precision float (3) Gdiag_no -1 Morphing InvertMorph 0 Synth 0 SynthSeed 1381542765 Linux huygens 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Sun Oct 6 12:04:16 EDT 2013 --------------------------------------------------------------------- And here is the output of bugr: FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0 Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 RedHat release: CentOS release 6.4 (Final) Kernel info: Linux 2.6.32-358.2.1.el6.x86_64 x86_64 NMR Center info (/space/freesurfer exists): machine: huygens SUBJECTS_DIR: /cluster/manoach/dod/subjects PWD: /cluster/manoach/dod/BU_pipeline/dti_scripts ssh huygens setenv SUBJECTS_DIR /cluster/manoach/dod/subjects cd /cluster/manoach/dod/BU_pipeline/dti_scripts --------------------------------------------------------------------- Additionally, the subject is DODCON004 and the script directory can be found at /cluster/manoach/dod/BU_pipeline/data/DODCON004/scripts Thanks for your help! Any advice would be appreciated. Jenn Segawa

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Gender as a nuisance factor
by Eduard Vilaplana Martinez 10 Oct '13

10 Oct '13

Dear Freesurfer experts, I'm performing a group analysis in Qdec correlating a biological marker and the CTh, and I would like to covariate the gender and age effect, i.e. ideally get rid of both effects and isolate the biological marker effect. So, I understand that the age effect is (at least partially) removed when I select it as a Nuisance variable in the Design Tab. I've treated the Gender both as a continous and as a discrete variable. When treating it as a continous variable, I can select it as a Nuisance Factor in the design tab, so I understand that the Gender effect is theoretically removed. However, the gender is not actually a continous variable. So, when treating the Gender as a discrete variable, I can't select it in the nuisance factors. The only option I have is to select it as a Discrete (Fixed Factors) in the Design tab and then select the Option "Does the correlation between thickness and the biological parameter, accounting for GENDER, differ from zero?". Is that one the correct option in order to covariate (get rid off) the gender effect? In other words, is this the correct option to treat a discrete variable as a "Nuisance Factor"? Any comments would be greatly appreciated, Thanks in advance for your attention, Eduard

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New Atlas Creation
by Liv Wroblewski 10 Oct '13

10 Oct '13

Hi Freesurfers, I am interested in creating new atlas for Freesurfer reconstruction, and I am having some trouble figuring out where to start and where to edit my labels though I have been researching it for some time. I have emailed Mark Plantz, who has been asking you similar questions with UNC's 1yr AAL atlas, but I am not sure if he has gotten it to work yet. I have looked at the documentation, but it is unclear to me. I have the following materials: 100 or so age-specific infant brains that do not segment, reconstruct, nor brain extract very well in Freesurfer due to the immature nature of the brains. I have a nice average diffeomorphically warped template, 116-region version of the AAL atlas which applies to this template we made, and segmentation information, all in NIFTI format and RAS coordinates. I want to do the following two things: 1. Make preliminary GCA non-probabilistic atlas using 116-region AAL atlas. 2. Make GCA probablistic edits using manual edits of the individual brains. 3. Set freesurfer to use these atlases for recon, infant brain size information for future brain extraction, infant segmentation information for future. Have freesurfer perform the most accurate possible WM segs on all our infants in the future for purposes of MEG localization. My questions are: 1. What exact steps do I need to do to my original AAL.mgz volumteric atlas to get it ready to be converted to surface format and gca and mr_ca_train? combined with my new Lookuptable I created? I have looked at all documentation and this remains elusive to me. 2. Do I need to Freesurfer all brains I want probability information from, or can I hand segment in another program, and then use these segmentations as a training set? 3. What are all these atlases, such as RB_all_2008-03-26.gca RB_all_withskull_2008-03-26.gca etc in the pipeline and can I change them to be my own infant information to improve skull stripping with the --atlas, etc? Thanks in advance, Liv Wroblewski -- Liv Wroblewski Research Assistant UW Institute for Learning & Brain Sciences CHDD 369, Box 357988 206-616-9725

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QDEC issues
by Gautam, Prapti 10 Oct '13

10 Oct '13

Dear FreeSurfers, While running analyses in QDEC, it only allows me to select one continuous variable at a time instead of the usual two –so running analyses in QDEC is extremely limited. I have used QDEC before, and this is a new issue. Has anyone else encountered this problem? Thanks, Prapti

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T1 data on 1yr-old subjects
by Alexopoulos, Dimitrios 10 Oct '13

10 Oct '13

Just wondering if anyone has attempted to process T1-mpr data for a 1yr-old subject or if this is possible with FS. Our data is of reasonable spatial resolution (1mm isotropic), however the flip in gm/wm intensities is still occurring at this age. I presume these data would also be problematic due to registration issues to existing FS atlases. Jim The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email.

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DOSS in FS 5.3 QDEC
by amirhossein manzouri 10 Oct '13

10 Oct '13

Dear Experts, Hi, I have already done my data analysis having group as fixed factor and age as nuisance factor in QDEC FS 5.3. I also need to run it with DOSS. Would you please advise how to run the same analysis with DOSS from terminal and if it is possible to look at the results in QDEC Display again. -- Best regards, Amirhossein Manzouri

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