Freesurfer January 2016

freesurfer@nmr.mgh.harvard.edu

130 participants
204 discussions

Centroid of a binary volume question
by pfotiad＠nmr.mgh.harvard.edu 25 Jan '16

25 Jan '16

Dear FS Community, I was wondering whether there is a way to create a binary volumetric file of just the centroid of a binary volume (represented maybe as a dot of 1x1x1 mm^3 voxel size). I know how to find the coordinates of the centroid (through either the fslstats command or MATLAB), but I didn't know whether there was a way to create a new binary volume of just the centroid through the terminal. (I would do it manually, but I have ~500 binary volumes that I would like to apply the same method to). Thank you in advance for your help! Best, Panos

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separate non-contiguous labels
by dgw 25 Jan '16

25 Jan '16

Hi, I want to separate each label in the Yeo parcellations into each of their separate contiguous labels. Is there a command, which can do this in Freesurfer? Example lh.yeo7.annot the network 7 label has 5 non-contiguous components Is there a command to separate these into 5 separate labels? Thank You, Dan

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Brainstem segmentations (6.0)
by Cat Chong 25 Jan '16

25 Jan '16

Hello Experts, We used the brainstem segmentation that is built into FS 6.0, to interrogate midbrain volumes. My question was: the way FS segments the midbrain, does it include the cerebral peduncles? cheers,Cat

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R: Re: R: Re: FDR map: hide very little cluster
by stdp82＠virgilio.it 25 Jan '16

25 Jan '16

Please give an example of the command line. I have performed fdr correction by tksurfer. Should I save that map? Thanks Stefano >----Messaggio originale---- >Da: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> >Data: 25-gen-2016 17.30 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] R: Re: FDR map: hide very little cluster > >just use the FDR thresholded input and set --thmin to 0.5 > >On 01/25/2016 11:21 AM, stdp82(a)virgilio.it wrote: >> Thanks. But I do not know how I can obtain a corrected sig.nii.gz. >> In this way I have obtained only summary.txt. >> If I add --vwsig vwsig cds file is request. >> >> Stefano >> >> ----Messaggio originale---- >> Da: Douglas Greve <greve(a)nmr.mgh.harvard.edu> >> Data: 25-gen-2016 17.10 >> A: <freesurfer(a)nmr.mgh.harvard.edu> >> Ogg: Re: [Freesurfer] FDR map: hide very little cluster >> >> Use the --minarea option to mri_surfcluster (not the CSD). >> >> On 1/25/16 10:39 AM, stdp82(a)virgilio.it wrote: >>> Hi list, >>> please, could you help me because from several days I'm trying to have a solution. >>> I have performed a seed-based fcMRI analysis by FAST. >>> After mri_glmfit, I have obtained a sig.nii.gz which contains uncorrected results.I have corrected by FDR using the graphical interface provided in tksurfur. The FDR corrected contains some very small areas (<5-10 voxels) which I would like to hide in order to present a more clear map. How is possible to do it?I have tried with mri_surfcluster. To have vwsig.nii.gz I should have a CSD file. But this file >>> could be also produced when FDR correction is applied? I'm very confused. >>> Thank you very much for your work. >>> Kind regards. >>> Stefano >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> >> _______________________________________________ >> 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. > >

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R: R: Re: FDR map: hide very little cluster
by stdp82＠virgilio.it 25 Jan '16

25 Jan '16

mri_surfcluster --in intercept/sig.nii.gz --hemi rh --sign abs --no-adjust --fdr 0.05 --minarea 5 --sum summaryfile --subject fsaverage --annot aparc produces only summary.txt mri_surfcluster --in intercept/sig.nii.gz --hemi rh --sign abs --no-adjust --fdr 0.05 --minarea 5 --sum summaryfile --subject fsaverage --annot aparc --vwsig vwsig.nii.gzERROR: need csd with --vwsig How can I obtain/visualize the correspective map to summary.txt? Thanks, Stefano ----Messaggio originale---- Da: stdp82(a)virgilio.it Data: 25-gen-2016 17.25 A: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: [Freesurfer] R: Re: FDR map: hide very little cluster Please could you suggest me an example of command line.I'm trying from several day without results.Thank you very much. Stefano ----Messaggio originale---- Da: Douglas Greve <greve(a)nmr.mgh.harvard.edu> Data: 25-gen-2016 17.10 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] FDR map: hide very little cluster Use the --minarea option to mri_surfcluster (not the CSD). On 1/25/16 10:39 AM, stdp82(a)virgilio.it wrote: Hi list, please, could you help me because from several days I'm trying to have a solution.I have performed a seed-based fcMRI analysis by FAST. After mri_glmfit, I have obtained a sig.nii.gz which contains uncorrected results.I have corrected by FDR using the graphical interface provided in tksurfur. The FDR corrected contains some very small areas (<5-10 voxels) which I would like to hide in order to present a more clear map. How is possible to do it?I have tried with mri_surfcluster. To have vwsig.nii.gz I should have a CSD file. But this file could be also produced when FDR correction is applied? I'm very confused. Thank you very much for your work. Kind regards. Stefano _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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R: Re: FDR map: hide very little cluster
by stdp82＠virgilio.it 25 Jan '16

25 Jan '16

Thanks. But I do not know how I can obtain a corrected sig.nii.gz.In this way I have obtained only summary.txt.If I add --vwsig vwsig cds file is request. Stefano ----Messaggio originale---- Da: Douglas Greve <greve(a)nmr.mgh.harvard.edu> Data: 25-gen-2016 17.10 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] FDR map: hide very little cluster Use the --minarea option to mri_surfcluster (not the CSD). On 1/25/16 10:39 AM, stdp82(a)virgilio.it wrote: Hi list, please, could you help me because from several days I'm trying to have a solution.I have performed a seed-based fcMRI analysis by FAST. After mri_glmfit, I have obtained a sig.nii.gz which contains uncorrected results.I have corrected by FDR using the graphical interface provided in tksurfur. The FDR corrected contains some very small areas (<5-10 voxels) which I would like to hide in order to present a more clear map. How is possible to do it?I have tried with mri_surfcluster. To have vwsig.nii.gz I should have a CSD file. But this file could be also produced when FDR correction is applied? I'm very confused. Thank you very much for your work. Kind regards. Stefano _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 1

R: Re: FDR map: hide very little cluster
by stdp82＠virgilio.it 25 Jan '16

25 Jan '16

Please could you suggest me an example of command line.I'm trying from several day without results.Thank you very much. Stefano ----Messaggio originale---- Da: Douglas Greve <greve(a)nmr.mgh.harvard.edu> Data: 25-gen-2016 17.10 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] FDR map: hide very little cluster Use the --minarea option to mri_surfcluster (not the CSD). On 1/25/16 10:39 AM, stdp82(a)virgilio.it wrote: Hi list, please, could you help me because from several days I'm trying to have a solution.I have performed a seed-based fcMRI analysis by FAST. After mri_glmfit, I have obtained a sig.nii.gz which contains uncorrected results.I have corrected by FDR using the graphical interface provided in tksurfur. The FDR corrected contains some very small areas (<5-10 voxels) which I would like to hide in order to present a more clear map. How is possible to do it?I have tried with mri_surfcluster. To have vwsig.nii.gz I should have a CSD file. But this file could be also produced when FDR correction is applied? I'm very confused. Thank you very much for your work. Kind regards. Stefano _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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FDR map: hide very little cluster
by stdp82＠virgilio.it 25 Jan '16

25 Jan '16

Hi list,please, could you help me because from several days I'm trying to have a solution.I have performed a seed-based fcMRI analysis by FAST.After mri_glmfit, I have obtained a sig.nii.gz which contains uncorrected results.I have corrected by FDR using the graphical interface provided in tksurfur. The FDR corrected contains some very small areas (<5-10 voxels) which I would like to hide in order to present a more clear map. How is possible to do it?I have tried with mri_surfcluster. To have vwsig.nii.gz I should have a CSD file. But this file could be also produced when FDR correction is applied? I'm very confused.Thank you very much for your work.Kind regards. Stefano

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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 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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Freesurfer January 2016