Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30088 discussions

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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DODS/DOSS
by Iris Frankenberg 10 Oct '13

10 Oct '13

Hi mailinglist, I have a question regarding DOSS/DODS. In the mailinglist I read that if you do a group analysis, you have to check for interaction between your continuous variable and categorical variable in DODS, and if there's no interaction, you can use DOSS. This however leaves a few questions regarding my analysis: I want to look at the correlation between cognitive performance and cortical thickness, accounting for gender, age and IQ. In a sense, this is not a 'real' group analysis, since gender is merely a covariate. Do I have to check for interactions, and if so, for which ones? "Does the cogn perf-thickness correlation differ between male and female?" "Does the age-thickness correlation differ between male and female?" (age = demeaned) Last but not least, at which Monte Carlo settings would you usually check for an interaction? As far as I understood from reading the mailinglist, I would think vertexwise threshold at 2, absolute (2 way), clusterwise threshold 1.3. Is this correct? Or would it for example make more sense to test 1 way (positive for cogn perf-thickness, negative for age-thickness)? Thank you very much, Iris

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Processing Freesurfer thickness files in SPM for ANOVA
by Muhammad Naveed Iqbal Qureshi 10 Oct '13

10 Oct '13

Dear Experts, Is it possible to process the FreeSurfer thickness files of T1-MRI data in SPM for ANOVA testing? Waiting for a precise reply. Thank you. Best Regards, Muhammad Naveed Iqbal Qureshi Ph.D. Candidate Bio-Medical Signal & System Analysis Laboratory Department of Medical System Engineering Gwangju Institute of Sciences and Technology 123, Cheomdangwagi-ro, Buk-gu, Gwangju, 500-712, Republic of Korea Tel : +82-62-715-3266 Email : mniqureshi(a)gist.ac.kr URL : http://bmssa.gist.ac.kr P please don't print this e-mail unless you really need to

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suggestion for wiki
by Ruth Carper 10 Oct '13

10 Oct '13

It would be really helpful if your Wiki had a page that collected all of the available commands (e.g. contents of /bin) and listed them with brief descriptions of their functions. Something like part 4 of the page: http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferCommands (Might reduce the number of forum questions you get too). There are other commands listed on that page but without brief descriptions, you're forced to do quite a lot of additional navigation to determine what each command might do or else scan the contents of /bin for something that sounds like it might apply and then check the help output. If you could just collect the descriptions from the individual wiki pages or from the help sections of the code itself that would be great. There also seem to be a number of useful commands that aren't listed anywhere in the Wiki (mni152reg, fslregister, etc) so that a typical user has no idea they exist. --Ruth

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Re: [Freesurfer] V1 Labels (fwd)
by krista kelly 09 Oct '13

09 Oct '13

Thanks Allison, So to be clear, I just need to rename talairach.auto.xfm as talairach.xfm and then rerun recon-all from the normalization step? However, I'm not sure how to run recon starting from the normalization stage. Would you be able to help with that? Also, I've been doing manual edits to the brain extraction as well as adding control points on all of my subjects and I'm wondering if this will negate any edits I've made. So I'm pretty much starting from scratch? Thanks so much for looking into this for me! Best, Krista On Mon, Oct 7, 2013 at 12:19 PM, Allison Stevens < astevens(a)nmr.mgh.harvard.edu> wrote: > Hi Krista, > I took a look at your subject and think I have determined the problem. > Because your input data was high resolution (1.0000 x 0.9375 x 0.9375), the > talairach registration step failed. If you look at the talairach.xfm, > you'll see it is way off: > tkregister2 --mgz --s BV20_2ndrun --fstal --surf orig > > But the talairach.auto.xfm is correct. You can copy the talairach.auto.xfm > to talairach.xfm and rerun from the -normalization step. > > You might also want to look at these instructions: > https://surfer.nmr.mgh.**harvard.edu/fswiki/HiResRecon<https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon> > > They might not all apply to you but could potentially. > Allison > > > > ---------- Forwarded message ---------- >> Date: Thu, 03 Oct 13 22:55:12 -0400 >> From: krista.kelly16(a)gmail.com >> To: fischl(a)nmr.mgh.harvard.edu >> Subject: V1 Labels >> >> Hey! >> >> Krista (krista.kelly16(a)gmail.com) has uploaded some files for you at >> the Martinos Center FileDrop: >> >> -> BV20_2ndrun.zip (167.53 MiB) <http://gate.nmr.mgh.harvard.** >> edu/filedrop2/?u=1079qbdf&f=**dzep9n4<http://gate.nmr.mgh.harvard.edu/filedrop2/?u=1079qbdf&f=dzep9n4> >> > >> >> Also, they left this message for you: >> Hi Bruce, >> >> Here is a zipped file of one of the subjects that I'm having label >> troubles with. The lh.v1.label isn't mapping correctly. I find the same >> goes for the aparc atlas as well (I haven't checked out anything else). If >> you could help me figure out why this is happening, that would be great! >> >> Thanks, >> Krista >> >> Please be aware, your upload will expire on December 31st. If you'd like >> to download these files, feel free to use the link below: >> >> http://gate.nmr.mgh.harvard.**edu/filedrop2/?u=1079qbdf<http://gate.nmr.mgh.harvard.edu/filedrop2/?u=1079qbdf> >> >> Cheers, >> The NMR Team >> >> >> >> >> > > 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<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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