Freesurfer

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30084 discussions

Brain stem segmentation in Freesurfer 6 {Disarmed}
by Alshikho, Mohamad J. 26 Jan '16

26 Jan '16

Dear Freesurfers, After segmenting the brain stem using FS6 tools. I used Free view to visualize the final images. In Free view I opened "orig.mgz", "wmparc.mgz" and "brainstemSsLabels.v10.mgz" Then I tried to check the segmented structures by flipping the images. I noticed an overlap between Ventral DC ( left and right) and mid brain ( as an output of brain stem segmentation). I "wmparc.mgz" atlas: Ventral DC and brain stem are totally different segments. Now After segmenting the brain stem. I see that the Ventral DC belongs to the mid brain. Is this natural? Thanks in advance for any suggestion! Mohamad

3 4

Incomplete output
by maryam koochaki 26 Jan '16

26 Jan '16

Dear experts,I am kind of new at working with freesurfer.recon-all process has completed without error, but when I look at brainmask volume on freeview, one of the issues is that lateral ventricle is completely excluded. I have tried to edit it with editing the white matter volume, but no success so far. I do not know how to correct it. Have anybody here had the same issue? Thanks,Maryam

2 1

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

2 1

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

2 1

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

1 0

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

2 1

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