Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

Re: [Freesurfer] mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05)
by Erik Lindberg 25 Jan '16

25 Jan '16

Dear Douglas and Freesufers, You suggested: mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05) I tried this and was expecting that I would get a three-dimensional mask in which the statistical significant part would be white and the rest black. This seems not to be the case. While the program is telling me that it is creating a mask in which x-number of voxels are included I cannot see anything when I open the thresholded.mgh (in Freeview) Further when I look at the dimensions of the generated image it seems to have 27307 “slices” in one direction but only one and 6 slices in the other directions. Is this the wrong approach for creating a 3-dimensional mask for the region with the significant clusters? Best Eric

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[All] position available immediately
by Bruce Fischl 25 Jan '16

25 Jan '16

Research Coordinator Position in Psychiatric Neuroimaging at the MGH-Martinos Center: We are looking to hire a college graduate with at least one year of research experience and strong organizational and interpersonal skills as a full time research coordinator. The position involves working on or several projects investigating the neural basis and nature of cognitive deficits in schizophrenia and autism spectrum disorder. The techniques employed include polysomnography (sleep electroencephaolography), functional magnetic resonance imaging (fMRI), magneto- and electroencephalography (MEG/EEG), and diffusion tensor imaging (DTI). Responsibilities are varied and will include conducting overnight sleep studies at the MGH Clinical Research Center. The coordinator will work closely with the Principal Investigator, lab mates, and collaborators on all aspects of the research projects. Training in data acquisition and analysis will be provided. Responsibilities include managing patient studies, recruitment, screening and characterization of participants, maintaining accurate records, and assisting with grant applications, human subject applications, and publications. Knowledge of Mac and/or Linux/UNIX operating systems as well as some programming experience are an asset, as is a high level of comfort with novel computer applications and environments. We use Matlab and/or unix scripting in many of our analyses. A background in psychology, statistics, and neuroscience is an asset. A mentored research project is encouraged. The candidate must be mature and responsible with excellent organizational, interpersonal as well as oral and written communication skills. S/He must be able to work independently in a fast-paced environment, juggle and prioritize multiple tasks, feel comfortable working with clinical and non-clinical study populations, working as part of a team and seek assistance when appropriate. This is an excellent research opportunity for someone bound for graduate school in psychology, cognitive neuroscience, or medicine. Position is available immediately. A two-year commitment is required. Please submit a resume, writing sample, college transcript (unofficial is fine) and contact information for three references to Dara Manoach <dara(a)nmr.mgh.harvard.edu> Dara S. Manoach, Ph.D. Psychiatric Neuroimaging and Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Charlestown Navy Yard 149 13th Street, Room 1.111 Charlestown, MA 02129 email: dara(a)nmr.mgh.harvard.edu phone: 617-724-6148 fax: 617-726-4078 http://nmr.mgh.harvard.edu/manoachlab ••• I am dictating emails. Please excuse typos, word substitutions and the lack of appropriate capitalization and punctuation. ••• _______________________________________________ All mailing list All(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/all

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Re: [Freesurfer] mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05)
by Erik Lindberg 25 Jan '16

25 Jan '16

Dear Bruce and Freesurfers, I probably then go about this in the wrong way. My aim is to create a binary mask for regions that I found differences in - in a group-comparison. I then want to export the mask so I can use it as seed area in an fMRI analysis. Can this be done Thanks Eric Hi Erik what is the dimensionality of sig.cluster.mgh? You can tell this with mri_info. It is problaby a surface overlay (so nvertices in one dimension), and can't be viewed in the volume but only on the surface. cheers Bruce

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hippocampal subfields - multispectral segmentation with FLAIR
by Luigi Antelmi 25 Jan '16

25 Jan '16

Dear members, in our center we are evaluating whether to introduce a T2 into a protocol that, among others, already includes a T1 and a FLAIR sequences. Our main concern is to to maximize the information-to-duration ratio of the entire protocol. In order to improve the subfields' segmentation we read that it is better to add a T2 or "other" sequences. Will the FLAIR alone (+T1) can work well as the T2? If instead the T2 is preferable, what is the coarsest-but-still-informative resolution you suggest? Thank you for sharing your experience! Have a nice day, Luigi.

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Processing .mnc files
by Ankita Chatterjee 24 Jan '16

24 Jan '16

I ran the command recon-all -all -s t2 -i t1xxxxx.mnc as Bruce suggested and the process took off but has been running for more than 6 hours and seems to be not doing anything after the step which reads MRISunfold() max_passes = 1 ----------- it has a few steps after that, but doesn't say that it completed. The last line reads - randomSeed 1234. Is it hung? Should I exit the program? Thank you for your help! Ankita

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mritotal failed - help with manual registration
by will brown 24 Jan '16

24 Jan '16

Hi all, After attempting recon-all I received the error "mritotal failed, see transforms/talairach.log" etc which I understand may have something to do with bad output from registration. I've checked orig.mgz which does look out of line - the orientation is off so that it appears the subject has their head tilted off to one side (see Image1.jpg). I have tried to fix this manually with the help of this tutorial: http://freesurfer.net/fswiki/FsTutorial/Talairach_freeview Hovever, the "movable" blurry image that I'm trying to line up with my subjects image does not match the coronal, sagittal or horizontal views, e.g. when I click "coronal" my subject is displayed correctly but the movable image is displayed horizontally (see Image2.jpg and Image3.jpg). Am I missing something obvious? (and am I even on the right track given this error?) Thanks in advance for any help. Cheers, Will

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freeview on ubuntu
by Neda Mohammadi 24 Jan '16

24 Jan '16

Dear experts, I installed FreeSurfer on Ubuntu with these commands: sudo apt-get install tcsh cd /usr/local/ sudo tar -xzvf ~/freesurfer-*.tar.gz echo "FREESURFER_HOME=/usr/local/freesurfer" >> ~/.bashrc echo 'source $FREESURFER_HOME/SetUpFreeSurfer.sh' >> ~/.bashrc sudo gedit /usr/local/freesurfer/.license sudo ln -s /usr/lib/libtiff.so.{4,3} Every thing is Ok except freeview. When I load freeview this error is appeared. freeview.bin: error while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or directory Any guidance on this would most appreciated. Thanks in advance, -- *Best Regards,* *Neda*

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Processing .mnc files {Disarmed}
by Arindam Chatterjee 23 Jan '16

23 Jan '16

Hello Freesurfer experts, I am still learning various aspects of Freesurfer, so pardon my questions. I am trying to run recon-all on a mnc file. It is in a folder such as /Sample1/subjects/t1/t1xxxx.mnc. I am pointing my SUBJECTS_DIR to /Sample1/subjects. But when I run recon-all -s t1, I get and error - ERROR: nothing to do. Should I be storing the .mnc file in a different location? So it looks like it is not finding the .mnc file or can Freesurfer not process a .mnc file and I have to convert it to another format like .dcm? Also, if I am able to run recon-all, what output should I analyze to determine the gyrification index? Thanks in advance for any pointers. Ankita -- Arindam Chatterjee (515) 419-7384 www.linkedin.com/in/chatterjeea

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Re: [Freesurfer] QDEC. Error in Analyze: command failed: mri_glmfit
by BAUTISTA-PERPINYA Maximilià 23 Jan '16

23 Jan '16

Thank you for the reply Douglas, Factor 1 (diagnosis) has 3 levels (BPD, CCP, NPC). I created using the vi editor, one line for each level. Same as factor 2. Max On dijous 14 gener 2016 22:20 CET, Douglas N Greve <greve(a)nmr.mgh.harvard.edu> wrote: > how many levels does factor 1 have? How did you make the factor file?> > On 01/14/2016 05:30 AM, BAUTISTA-PERPINYA Maximilià wrote: > > Hi there experts, > > > > I'm runing qdec to analyze my subject data. I am able to import the qdec.table.dat, but the problem comes in the Design step. I select 'Volume-based' measure, 'Diagnosis' as my discrete independent variable and 'LeftAmygdala' as the continuous variable. I don't select any nuisance factor. I then set my Design Name: 'LAmyDiagnosis' and click Analyze, but gives me the following error: > > > > --------------------------------------------------------------------------------------------------------------- > > > > ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels > > ninputs = 137 > > Checking inputs > > nframestot = 137 > > Allocing output > > Done allocing > > nframes = 137 > > Writing to /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/y.mgh > > gdfReadHeader: reading /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/qdec.fsgd > > INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. > > Continuous Variable Means (all subjects) > > 0 LeftAmygdala 1502.65 189.974 > > Class Means of each Continuous Variable > > 1 diagnosisBPD 1497.7548 > > 2 diagnosisCCP 1540.8923 > > 3 diagnosisNPC 1488.5490 > > INFO: gd2mtx_method is dods > > Reading source surface /home/freesurfer/Desktop/test005/subjects/fsaverage/surf/lh.white > > ERROR: no contrasts specified. > > Error in Analyze: command failed: mri_glmfit --y /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/y.mgh --fsgd /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/qdec.fsgd dods --glmdir /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis --surf fsaverage lh > > > > --------------------------------------------------------------------------------------------------------------- > > > > Any recommendations? Any help is much appreciated :) > > > > > > Best, > > > > Max > > > > _______________________________________________> > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________> 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. -- Maximilià Bautista-Perpinyà, BSc Master student at Joint Master in Neuroscience (JMN) Université de Strasbourg (in partnership with Universität Freiburg and Universität Basel) & Master Intern at Biological and Personality Psychology Laboratory Department of Psychology, Universität Freiburg (+49) 015759302368 maximila.bautista-perpinya(a)etu.unistra.fr maxbauper(a)gmail.com -- Maximilià Bautista-Perpinyà, BSc Master student at Joint Master in Neuroscience (JMN) Université de Strasbourg (in partnership with Universität Freiburg and Universität Basel) & Master Intern at Biological and Personality Psychology Laboratory Department of Psychology, Universität Freiburg (+49) 015759302368 maximila.bautista-perpinya(a)etu.unistra.fr maxbauper(a)gmail.com

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recon-all finishing without error but happens too quickly and output not present
by AMY LIN 22 Jan '16

22 Jan '16

Hi all, I'm trying to re-run subjects through recon-all for version 5.3.0 on a Mac 10.10.5 using Centos 6 but am not getting the normal output. There seems to be several strange things happening. The process ends almost instantaneously and says that it finished without error, so I don't get any errors or warnings. The correct subject directory folders are created (mri, bem, scripts, etc), but most of them are empty. The only folder that has anything in them are the scripts folder and the mri folder, which has the orig and transforms folders and are pretty much empty. It seems that the program is only running the mri_convert command on the 001.mgz file, writing the output to the folder that I've specified and then finishes without error. I've tried to run the commands on both local and remote servers to rule out an issue with the server and from different user accounts to rule out permission issues as I am a new lab member. I've also tried several different subjects to rule out problems with the scans. Also, these subjects have been run previously on an older version of FS, so the problem is likely not with the scans themselves. Any help at all would be much appreciated!

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