Freesurfer

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30132 discussions

mri_fill failure in macaque
by Soyoung Park 17 Oct '13

17 Oct '13

Dear FreeSurfer experts, I'm attempting to make cortical surfaces for a macaque brain, and am having trouble getting mri_fill to work. The command has worked without any errors for a different macaque dataset in the past, and I can't seem to figure out why it isn't working this time. I am using v. 5.3 for Mac Snow Leopard, and I used the command (I have confirmed on tkmedit that the CC and pons seed coordinates are correct): *mri_fill -CV 125 119 147 -PV 125 103 65 wm.mgz fill.mgz* The log from running the command is as follows: -------------------------------------------------------------------------------------------------------- using voxel position (125, 119, 147) as corpus callosum seed point using voxel position (125, 103, 65) as pons seed point reading input volume...done. searching for cutting planes...INFO: volume does not have linear_transform set nor lta is given by option.-xform. INFO: use identity matrix as the talairach transform. INFO: use src volume parameters for the talairach volume. voxel to talairach voxel transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Calculated talairach cc position (125.00, 119.00, 147.00) Using the seed to calculate the cutting plane find_cutting_plane:seed point not in structure! Searching neighborhood... Looking for area (min, max) = (350, 1400) area[0] = 1 (min = 350, max = 1400), aspect = 1.00 (min = 0.10, max = 0.75) need search nearby using seed (125, 119, 147), TAL = (125.0, 119.0, 147.0) talairach voxel to voxel transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; talairach cc position changed to (125.00, 119.00, 147.00) Using voxel pons seed point, calculated talairach pons position (125.00, 103.00, 65.00) find_cutting_plane:seed point not in structure! Searching neighborhood... Looking for area (min, max) = (350, 790) area[0] = 1 (min = 350, max = 790), aspect = 1.00 (min = 0.60, max = 1.20) need search nearby using seed (125, 103, 65), TAL = (125.0, 103.0, 65.0) talairach voxel to voxel transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(143.00, 119.00, 147.00) SRC: (143.00, 119.00, 147.00) could not find rh seed point around (143, 119, 147) ------------------------------------------------------------------------------------------------------------ Any help with this would be greatly appreciated. Best, Soyoung

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inferior horn of lateral ventricle
by Nawaf Yassi 17 Oct '13

17 Oct '13

Hi I would like to ask a question about the segmentation of the inferior horn of the lateral ventricle using freesurfer. I have noticed that the inferior horn is usually not filled in the wm.mgz file and excluded from the surface reconstruction (as demonstrated in the attachment). However, it is correctly labelled in the aseg file. Will I need to correct the wm.mgz manually and rerun recon-all or is this expected? Regards Nawaf freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

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Re: [Freesurfer] Tracula configuration error
by Anastasia Yendiki 17 Oct '13

17 Oct '13

Hi Mike - Good to know. This would make perfect sense b/c in 5.1 trac-all required a variable to be defined that isn't used any more in 5.3. a.y On Tue, 15 Oct 2013, Michael Datko wrote: > Hi Anastasia,I updated freesurfer from 5.1 to 5.3 and that fixed the > problem! Thanks for taking a look at my file. > > Mike > > > > On Tue, Oct 15, 2013 at 1:49 PM, Michael Datko <mikedatko(a)gmail.com> wrote: > I tried making the subjects directory line in the configuration > file point to somewhere that didn't actually exist. I got the > same error as you, where it says that SUBJECTS_DIR doesn't > exist. Then I changed it to point to the real folder, and I am > back at the "set: variable name must begin with a letter" error. > I have now tried this on two different computers with similar > but not identical setups, and get the same error. I am using > freesurfer 5.1 now, but the original data was processed with > version 5.0, if that makes a difference. > Mike > > > > On Mon, Oct 14, 2013 at 6:04 PM, Michael Datko <mikedatko(a)gmail.com> > wrote: > Very strange...I'm running this on a 2009 macbook pro, > with OSX 10.6.8 (Snow Leopard). I've never had this sort > of problem with command-line programs like AFNI or > freesurfer. > > > On Mon, Oct 14, 2013 at 2:37 PM, Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi Michael - It doesn't look like the configuration > file is the problem, or at least I cannot replicate > it. I ran "trac-all -c dmrirc.txt -prep" on a mac > and a linux machine and the only error I got was > that the SUBJECTS_DIR doesn't exist (as expected > since I don't have your directory structure). What > system are you running this on? > > a.y > > On Mon, 14 Oct 2013, Michael Datko wrote: > > Hi Anastasia,No log files were created, > it seems like the program does not even > begin to run. I get that > error immediately upon calling trac-all. > I pasted the entire configuration file > into the original > message, but I attach it here as well. > > Thanks, > Mike > > > > > On Mon, Oct 14, 2013 at 1:55 PM, > Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi Michael - It's hard to tell at > which point it fails. Is there any > output, is there a > trac-all.log? If so, can you > please attach the entire file, as well > as the entire > configuration file? > > Thanks, > a.y > > On Sat, 12 Oct 2013, Michael Datko > wrote: > > Hello,I have been trying to > set up a working Tracula configuration > file and I keep > getting an error: > > set: Variable name must > begin with a letter > I have searched previous > message board questions and it seems > that others have > seen this same error. I > have tried implementing some > of their solutions, as well as searching > my code for > a problem, but I cannot > find the source. Any > advice? I am trying to get this working > for a single > subject for now. I used the > dmrirc.example file as a > template. I am calling trac-all from > the tcsh command > line with the following: > trac-all -c dmrirc.example > -prep > > The contents of my dmrirc > file are below, I have deleted most of > the options for > which I am just using the > default, to make things > simpler. > > Thank you, > Mike > > # FreeSurfer SUBJECTS_DIR > # T1 images and FreeSurfer > segmentations are expected to be found > here > # > setenv SUBJECTS_DIR > /Users/mdatko/Desktop/tracula_tutorial/data/freesurfer > > # Output directory where > trac-all results will be saved > # Default: Same as > SUBJECTS_DIR > # > set dtroot = > /Users/mdatko/Desktop/tracula_tutorial/data/freesurfer > > # Subject IDs > # > set subjlist = (a226A) > > # In case you want to > analyze only Huey and Louie > # Default: Run analysis on > all subjects > # > set runlist = (1) > > # Input diffusion DICOMs > (file names relative to dcmroot) > # If original DICOMs don't > exist, these can be in other image > format > # but then bvecfile and > bvalfile must be specified (see below) > # > set dcmroot = > /Users/mdatko/Desktop/tracula_tutorial/data/dti > set dcmlist = > (a226A/226A/data.nii.gz) > > # Diffusion gradient table > # Must be specified if > inputs are not MGH DICOMs > # Three-column format, one > row for each volume in the diffusion > data set > # Default: Read from DICOM > header > # > set bvecfile = > > /Users/mdatko/Desktop/tracula_tutorial/data/dti/a226A/226A/bvecs.txt > > # Diffusion b-value table > # Must be specified if > inputs are not MGH DICOMs > # Single-column format, one > value for each volume in the diffusion > data set > # Default: Read from DICOM > header > # > set bvalfile = > > /Users/mdatko/Desktop/tracula_tutorial/data/dti/a226A/226A/bvals.txt > > # Perform registration-based > eddy-current compensation? > # Default: 1 (yes) > # > set doeddy = 0 > > # Perform diffusion-to-T1 > registration by bbregister? > # Default: 1 (yes) > # > set doregbbr = 1 > > # Perform registration of T1 > to MNI template? > # Default: 1 (yes) > # > set doregmni = 1 > > # Use brain mask extracted > from T1 image instead of low-b diffusion > image? > # Has no effect if there is > no T1 data > # Default: 1 (yes) > # > set usemaskanat = 1 > > # Paths to reconstruct > # Default: All paths in the > atlas > # > set pathlist = ( lh.cst_AS > rh.cst_AS \ > lh.unc_AS > rh.unc_AS \ > lh.ilf_AS > rh.ilf_AS \ > fmajor_PP > fminor_PP \ > lh.atr_PP > rh.atr_PP \ > lh.ccg_PP > rh.ccg_PP \ > lh.cab_PP > rh.cab_PP \ > lh.slfp_PP > rh.slfp_PP \ > lh.slft_PP > rh.slft_PP ) > > # Number of path control > points > # It can be a single number > for all paths or a different number for > each of the > # paths specified in > pathlist > # Default: 7 for the forceps > major, 6 for the corticospinal tract, > # 4 for the angular > bundle, and 5 for all other paths > # > set ncpts = ( 6 6 5 5 5 5 7 > 5 5 5 5 5 4 4 5 5 5 5 ) > > # List of training subjects > # This text file lists the > locations of training subject > directories > # Default: > $FREESURFER_HOME/trctrain/trainlist.txt > # > set trainfile = > $FREESURFER_HOME/trctrain/trainlist.txt > > # Number of "sticks" > (anisotropic diffusion compartments) in > the bedpostx > # ball-and-stick model > # Default: 2 > # > set nstick = 2 > > # Number of MCMC burn-in > iterations > # (Path samples drawn > initially by MCMC algorithm and > discarded) > # Default: 200 > # > set nburnin = 200 > > # Number of MCMC iterations > # (Path samples drawn by > MCMC algorithm and used to estimate path > distribution) > # Default: 7500 > # > set nsample = 7500 > > # Frequency with which MCMC > path samples are retained for path > distribution > # Default: 5 (keep every 5th > sample) > # > set nkeep = 5 > > > > > > 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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mri_binarize to mask and include only positively activated voxels
by Maya Rosen 17 Oct '13

17 Oct '13

Hi Doug/freesurfers, I am now trying to make a mask that includes only positively activated voxels for one conditon versus passive viewing (ConditionAvspassive). Using the inputs that you suggested, I ran the following command: mri_binarize --i ./output_23subjects/fsavg_lh_sm3_nopace_exoltm/ConditionAvpassive/ces.nii.gz --o ./output_23subjects/fsavg_lh_sm3_nopace_exoltm/ConditionAvpassive_mask.ces.nii.gz --mask-thresh 0.00001 --min 0.00001 So my understanding of what this should be doing is making a mask that only includes positively activated voxels compared to passive viewing. However, if you see the attached images of both the mask that this command creates, and the activation maps of ConditionAvpassive (set at a very low threshold for visualization purposes), you can see that there are several regions that are included in the mask that are in fact deactivated compared to passive viewing. Is there something wrong with the command that I'm running that is causing this to happen? Thank you for any insight! Maya

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Extract Cortical Thickness from my data based on ROIs from Qdec
by amirhossein manzouri 17 Oct '13

17 Oct '13

DEar FS experts, I need to extract the CTh from my whole data (90 subjects) based on generated ROI from Qdec(mc-z.neg.th13.sig.ocn.mgh). Would you please advise if I can do it in the same way you have mentioned in this post : http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg22973.html -- Best regards, Amirhossein Manzouri

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Freeview Volume & Surface alignment
by Kambiz Tavabi 17 Oct '13

17 Oct '13

I would like to inspect the results of my surface boundary on the volume as per the approach in tkmedit. However in freeview the surface boundary and volume are not aligned in a common space. Why is that? How does one go about aligning the tkregRAS with the RAS? (those are apparently the two different coordinate systems according to the information panel). Thanks in advance. [image: Inline image 1] ------------------------------------------------------------ Kambiz Tavabi PhD Institute for Learning & Brain Sciences 1715 Columbia Road N Portage Bay Building Box 357988 University of Washington Seattle, WA 98195-7988 Tel: 206-685-6173 ------------------------------------------------------------

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tkmedit error message
by Elissa McIntosh 17 Oct '13

17 Oct '13

Hello, I am a new freesurfer user. I tried to view subject data with tkmedit for the first time after the recon-all process finished without errors. Here is what I typed and the message I got: [ariana:~/Desktop/ELISSA_ THESIS/ATO] cmurphy% tkmedit ATO brainmask.mgz -aux T1.mgz -surfs -aseg Wed Oct 16 14:35:57 ariana.local tkmedit.bin[66069] <Error>: kCGErrorFailure: Set a breakpoint @ CGErrorBreakpoint() to catch errors as they are logged. xp_init: error: not initialized error: invalid CoreGraphics connection Abort Can someone explain this error message? Despite that the recon-all log said that the subject was completed without error, there were several places in the log that read invalid. Is this normal? Also, I realized that I have an older version of freesurfer and should upgrade. Should I delete the former version and re-install with new version? Thank you for your help, E

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DOSS FS 5.3
by amirhossein manzouri 17 Oct '13

17 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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Postdoc position available - Alzheimer's Disease
by Juan Domingo Gispert López 17 Oct '13

17 Oct '13

Postdoctoral Position in Neuroimaging - Pasqual Maragall Foundation, Barcelonabeta Brain Research Center, Barcelona, Spain. Job Summary: Pasqual Maragall Foundation invites applications for a full-time postdoctoral position to conduct post-processing and analyzing of MRI neuroimaging data (e.g. structural, fMRI, DWI), as part of a clinical research program on Alzheimer's disease. Principal Responsibilities: The primary responsibility of this position includes post-processing and analyzing brain MRI data within the Foundation's Alzheimer's disease clinical research and its flagship project, the Alzheimer and Families (ALFA). The ALFA study is a large longitudinal cohort of sons and daughters of Alzheimer's disease (AD) patients, to explore the preclinical stage of this condition with the aim of identifying novel risk factors and biomarkers. This study will enhance our knowledge of the processes involved before the onset of AD to develop interventions aimed to prevent or delay the disease. Within this study we are collecting a comprehensive amount of data, including blood samples, mental health, quality of life and risk factors, as well as, neuroimaging procedures to assess brain function. The Barcelonabeta Brain Research Center (Barcelonabeta) is a new research infrastructure, constituted by the Pasqual Maragall Foundation and with the participation of the Pompeu Fabra University, dedicated to research on Alzheimer's disease. The new building will be completed by summer 2014, and will contain excellent technical facilities including a research-dedicated 3T MR scanner, dedicated to clinical research on neurodegenerative diseases. Barcelonabeta is a research institute affiliated to Pompeu Fabra University and is also part of the Barcelona Biomedical Research Park (PRBB), a large research facility that hosts seven different research institutions related to biomedical research, including the Hospital del Mar Research Institute (IMIM), the Experimental and Health Sciences Department (CEXS) of the UPF, the Regenerative Medicine Centre of Barcelona (CMRB), and the Centre for Research in Environmental Epidemiology (CREAL), among others, in a multidisciplinary, collaborative and stimulating international environment in close contact with a clinical setting, thus conducive to translational research. Required Qualifications: · PhD in Biomedical Engineering, Medical Physics, Neuroscience or related disciplines. · Strong background in MRI analysis and related statistical methods for research (SPM, Freesurfer, FSL or similar). · Experience with image processing and data analysis. · Ability to think independently and work collaboratively. Benefits · Starting date: April 2014. · The postdoctoral position is scheduled initially for three years (open to renewal). · Salary will depend on experience. Additional Information: To apply, please submit a single PDF file containing the following: 1) Cover letter describing research interests and relevant background; 2) CV with list of publications; 3) The names of three individuals who could provide reference letters. All files or inquiries should be submitted electronically to: rh(a)fpmaragall.org Juan D. Gispert Head Neuroimaging Research Pasqual Maragall Foundation T. +34 93 316 09 90 Dr. Aiguader, 88 (Edifici PRBB) - 08003 Barcelona. Spain. http://www.fpmaragall.org/en_index.html ________________________________ Aquest missatge i els seus annexos poden contenir informació confidencial i exclusiva per al destinatari. El seu contingut no constitueix un compromís per part de l'emissor. Si rep aquest missatge per error, si us plau elimini'l sense revisar-lo ni reenviar-lo i notifiqui-ho al remitent. Gràcies per la seva col·laboració. Este mensaje y sus anexos pueden contener información confidencial y exclusiva para el destinatario. Su contenido no constituye un compromiso por parte del emisor. Si recibe este mensaje por error, por favor elimínelo sin revisarlo ni reenviarlo y notifíquelo al remitente. Gracias por su colaboración. This message and attachments may contain confidential and exclusive information intended only for the individual named. The content of this message does not imply any commitment by the sender. If you have received this e-mail by mistake, please delete it before reading or distributing and notify the sender. Thank you for your cooperation. [cid:image006.jpg@01CD0B4C.79CA6620] Gràcies per estalviar paper. Gracias por ahorrar papel.Thanks for saving paper.

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-hippo-subfields error
by Garikoitz Lerma-Usabiaga 17 Oct '13

17 Oct '13

Hi, I had a subject already run through recon-all. After making recon-all -s ID -hippo-subfields or recon-all -s ID -hippo-subfields -make all it is failing. It is the first subject ever failing with the hippo-subfields. The rest of the subjects are ok. This subject is properly segmented (tkmedit ID brainmask.mgz -surfs -aseg is ok). Any recommendations on what to do next? thanks! Gari PS1 please find attached the last recon-all invocation log. PS2 I have the screen output as well, there was more detail in that, in case it would help recognizing the problem.

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