Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

amygdala nuclear subregions
by Jacobs H (NP) 08 Jan '16

08 Jan '16

Dear FreeSurfer developers, In the FreeSurferColorLut file I see labels for the subregions of the amygdala. Is it possible to extract the volumes for these regions? And how can I do this? I don't see them in the aseg or aparc stat files. Many thanks! Heidi

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R: R: Re: FDR correction
by stdp82＠virgilio.it 08 Jan '16

08 Jan '16

Hi list, I have resolved my issue on the previous point 2 by downloading matlab file on: https://sites.google.com/site/kittipat/mvpa-for-brain- fmri/convert_matlab_nifti after the command that you suggest: fdrthresh = fast_fdrthresh(p,0.05); the script produce p=0.053 Therefore, coming back to my answer I guess that no setting of the FDR threshold to 0.05/3 is requested in order to correct for multiple comparison (right and left hemispheres + subcortical). Is it correct? On the previous point 4 my answer remains open. I have used this command line: >mri_surfcluster --in sig.nii.gz --hemi rh --sign abs --no-adjust --fdr 0.05 -- >minarea 5 --sum summaryfile --subject fsaverage --annot aparc but I have difficulty to undestand which is the option to visualize the map corrected by mri_surfcluster. Additionally, from --help I do not understand the use of --ocn and --cst options. Best regards, Stefano >----Messaggio originale---- >Da: stdp82(a)virgilio.it >Data: 7-gen-2016 15.40 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: [Freesurfer] R: Re: FDR correction > >Thanks. > >- on question 2: >I have run >rh = MRIread('sig.mgh'); >but this error occur >Undefined function 'MRIread' for input arguments of type 'char'. >no help is permitted on MRIread > >-on question 3: >I'm using this command line to visualize the map describing the functional >connectivity form seed to cortex > >tksurfer fsaverage rh inflated -aparc -overlay R_seed/my-glm.wls/group. >diff/sig.nii.gz -fminmax 1.3 3 >tksurfer fsaverage lh inflated -aparc -overlay L_seed/my-glm.wls/group. >diff/sig.nii.gz -fminmax 1.3 3 > >in this way I visualize correctly for right and left hemisphere the >connectivity from ipsilateral seed. >If I would visualize the the connectivity from contralateral seed, how can I >do? > >If I use >tksurfer fsaverage lh inflated -aparc -overlay R_seed/my-glm.wls/group. >diff/sig.nii.gz -fminmax 1.3 3 >tksurfer fsaverage rh inflated -aparc -overlay L_seed/my-glm.wls/group. >diff/sig.nii.gz -fminmax 1.3 3t > >-on question 4: >I have resolved with this command line: >mri_surfcluster --in sig.nii.gz --hemi rh --sign abs --no-adjust --fdr 0.05 -- >minarea 5 --sum summaryfile --subject fsaverage --annot aparc > >but I have difficulty to undestand which is the option to visualize the map >corrected by mri_surfcluster. >Additionally, from --help I do not understand the use of --ocn and --cst >options. > >Best regards, > > >Stefano > > > > > >>----Messaggio originale---- >>Da: greve(a)nmr.mgh.harvard.edu >>Data: 7-gen-2016 0.34 >>A: <freesurfer(a)nmr.mgh.harvard.edu> >>Ogg: Re: [Freesurfer] FDR correction >> >> >> >>On 01/06/2016 11:00 AM, stdp82(a)virgilio.it wrote: >>> Hi list, >>> >>> I would like to ask you a number of questions regarding the FDR which >>> is performed following seed-based fcMRI using FS-FAST. >>> 1-In the previous mail you have suggested me to use mir_fdr command >>> line (version 6.0). Because I have some problem with new version >>> license (as reported in previous mail) and, overall I have run my data >>> using version 5.3, I would ask you whether FDR integrated in tksurfer >>> (version 5.3) is however reliable as the FDR included in 6.0? >>Yes, they call the same code. >>> >>> 2-Becouse the FDR analysis was performed separately for the right and >>> left hemispheres and the subcortical structures, should I set the FDR >>> threshold to 0.05/3 in order to correct for multiple comparison? (I >>> have one group) >>I'm not sure. You can try to run both hemispheres in matlab, somethiing like >>lh = MRIread('sig.lh.mgh'); >>lhp = 10^-abs(lh.vol); >>rh = MRIread('sig.rh.mgh'); >>rlhp = 10^-abs(rh.vol); >> >>p = [lhp rhp]; >>fdrthresh = fast_fdrthresh(p,fdr); >> >>> >>> 3- Is easy for me to follow the guidelines and visualize the cortical >>> areas which are functionally connected with the omolateral seed. How >>> can I do to visualize also the the cortical areas which are >>> functionally connected with the controlateral seed? If change only the >>> rh/lh in command line the visualization of the results is wrong. >>I don't understand. >>> >>> 4- I'd like to perform mri_surfcluster on a group to eliminate cluster >>> < 5 >>> voxels from sig.nii.gz after FDR correction. I'm running >>> mri_surfcluster --in >>> sig.nii.gz --hemi rh --sign abs --fdr 0.05 --minarea 5 --sum >>> summaryfile --ocn >>> ocnid >>> but --subject ... must be included. >>> How should do I do? I would like to run my analysis on group results, >>> not on a single subject. >>If this is from a group analysis, the subject is probablly fsaverage >>> >>> Thanks for your work. >>> Regards, >>> >>> >>> Stefano >>> >>> >>> >>> _______________________________________________ >>> 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. >> >> >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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Control points on noisy scans
by zalewk＠u.washington.edu 07 Jan '16

07 Jan '16

Good afternoon Freesurfer team, I have a small data set with some exceptionally noisy scans resulting in a mix of hyper and hypo-intense striations in the sagittal plane. Ideally I'd like to conserve as much data as possible considering the small number of subjects despite the quality of the scans. The control points added seem to be able to correct only hyper or hypo-intense artefacts alone, but not both in the same scan. Are there any parameters I could alter to correct such large mis-segmentations over a specific area? (Examples are attached in this email) Best, Kody Zalewski

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MPRAGE Data
by Scott E 07 Jan '16

07 Jan '16

Hi folks, Hopefully I'm not asking this question in the wrong place -- please let me know if I am! I have a T1 MPRAGE data file which I'm trying to process into images. I can't, however, figure out how this data is organized within the file. The manufacturer can't provide me details of how to decode the data without a research agreement, and as I don't own the MRI machine itself, I cannot enter into such an agreement. Does anyone have experience decoding raw MPRAGE data? Thanks! Scott

3 4

Recon-all get stucked without error during processing
by Matthieu Vanhoutte 07 Jan '16

07 Jan '16

Dear FS epxerts, I have launched a recon-all process on a subject. Unfortunately, I tried two times but the process get stucked at the same step without error. Please found the recon-all.log associated attached to this mail. Thanks in advance for helping ! Best regards, Matthieu

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R: Re: FDR correction
by stdp82＠virgilio.it 07 Jan '16

07 Jan '16

Thanks. - on question 2: I have run rh = MRIread('sig.mgh'); but this error occur Undefined function 'MRIread' for input arguments of type 'char'. no help is permitted on MRIread -on question 3: I'm using this command line to visualize the map describing the functional connectivity form seed to cortex tksurfer fsaverage rh inflated -aparc -overlay R_seed/my-glm.wls/group. diff/sig.nii.gz -fminmax 1.3 3 tksurfer fsaverage lh inflated -aparc -overlay L_seed/my-glm.wls/group. diff/sig.nii.gz -fminmax 1.3 3 in this way I visualize correctly for right and left hemisphere the connectivity from ipsilateral seed. If I would visualize the the connectivity from contralateral seed, how can I do? If I use tksurfer fsaverage lh inflated -aparc -overlay R_seed/my-glm.wls/group. diff/sig.nii.gz -fminmax 1.3 3 tksurfer fsaverage rh inflated -aparc -overlay L_seed/my-glm.wls/group. diff/sig.nii.gz -fminmax 1.3 3t -on question 4: I have resolved with this command line: mri_surfcluster --in sig.nii.gz --hemi rh --sign abs --no-adjust --fdr 0.05 -- minarea 5 --sum summaryfile --subject fsaverage --annot aparc but I have difficulty to undestand which is the option to visualize the map corrected by mri_surfcluster. Additionally, from --help I do not understand the use of --ocn and --cst options. Best regards, Stefano >----Messaggio originale---- >Da: greve(a)nmr.mgh.harvard.edu >Data: 7-gen-2016 0.34 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] FDR correction > > > >On 01/06/2016 11:00 AM, stdp82(a)virgilio.it wrote: >> Hi list, >> >> I would like to ask you a number of questions regarding the FDR which >> is performed following seed-based fcMRI using FS-FAST. >> 1-In the previous mail you have suggested me to use mir_fdr command >> line (version 6.0). Because I have some problem with new version >> license (as reported in previous mail) and, overall I have run my data >> using version 5.3, I would ask you whether FDR integrated in tksurfer >> (version 5.3) is however reliable as the FDR included in 6.0? >Yes, they call the same code. >> >> 2-Becouse the FDR analysis was performed separately for the right and >> left hemispheres and the subcortical structures, should I set the FDR >> threshold to 0.05/3 in order to correct for multiple comparison? (I >> have one group) >I'm not sure. You can try to run both hemispheres in matlab, somethiing like >lh = MRIread('sig.lh.mgh'); >lhp = 10^-abs(lh.vol); >rh = MRIread('sig.rh.mgh'); >rlhp = 10^-abs(rh.vol); > >p = [lhp rhp]; >fdrthresh = fast_fdrthresh(p,fdr); > >> >> 3- Is easy for me to follow the guidelines and visualize the cortical >> areas which are functionally connected with the omolateral seed. How >> can I do to visualize also the the cortical areas which are >> functionally connected with the controlateral seed? If change only the >> rh/lh in command line the visualization of the results is wrong. >I don't understand. >> >> 4- I'd like to perform mri_surfcluster on a group to eliminate cluster >> < 5 >> voxels from sig.nii.gz after FDR correction. I'm running >> mri_surfcluster --in >> sig.nii.gz --hemi rh --sign abs --fdr 0.05 --minarea 5 --sum >> summaryfile --ocn >> ocnid >> but --subject ... must be included. >> How should do I do? I would like to run my analysis on group results, >> not on a single subject. >If this is from a group analysis, the subject is probablly fsaverage >> >> Thanks for your work. >> Regards, >> >> >> Stefano >> >> >> >> _______________________________________________ >> 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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How to convert a surface to a smooth contour?
by Gronenschild Ed (NP) 07 Jan '16

07 Jan '16

Hi, With tkmedit a surface (e.g. lh.pial) can be converted into a smooth contour superimposed onto T1. I would like to use such contour in my own application. To do this I've tried mri_surf2vol using the --mkmask option resulting in a binary file showing only a very rough and patchy (fragmented) "contour". How can I derive a smooth contour like in tkmedit? Cheers, Ed

2 1

Unknown cortical parcellation in S_calcarine (lh.aparc.a2009s.annot)
by Matthieu Vanhoutte 07 Jan '16

07 Jan '16

Dear FS's experts, Projecting volumic data onto native surface (brain mask: "Unknown_S_calcarine_ROI_mask.jpg"), I observed that a thin region in the S_calcarine was set to 0. I loaded then the inflated left surface and the l.aparc.a2009s.annot ("Unknown_S_calcarine_ROI_annot.jpg") and took into account that this region inside the S_calcarine was set as "unknown" in the parcellation file . What does it mean and is this possible to correct for this ? Best regards, Matthieu

2 1

claustrum segmentation
by Alessandro Calamuneri 07 Jan '16

07 Jan '16

Hi freesurfer experts, I have a few questions on claustra segmentations. I tried to look into archives but did not find an answer to all my points so far.. I have a group of subjects in which I would like to segment claustrum. Looking at lookup table a color is assignied for both left and right claustra; however, after running segmentation, I opened aparc+aseg results and did not find claustra. My questions are: 1) Results of aparc+aseg.mgz are different from aparc.a2009s+aseg ones; which one does correspond to *Desikan-Killiany *and which one to *Destrieux*? I mean, looking at tutorials, aparc.a2009+aseg should correspond to Destrieux, but I could not find aparc.DKTlas40+aseg, thus I am not sure about naming conventions... 2) Do both atlases in principle permit to segment claustrum? In this case, would missing of claustra be due to poor quality of my data? how could I work on processing pipeline to improve my parcellation and thus obtaining claustra? 3) If claustrum is not automatically segmented, would you please provide some hints on how to add a new structure based on manual segmentations and include them in segmentation pipeline? Any suggestion will be appreciated. Best Regards, Alessandro

2 1

P files
by Bruce Fischl 06 Jan '16

06 Jan '16

Begin forwarded message: > From: "Marinelli, Luca (GE Global Research)" <marinell(a)research.ge.com> > Date: January 6, 2016 at 10:26:38 PM EST > To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>, Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Cc: "Marinelli, Luca (GE Global Research)" <marinell(a)research.ge.com> > Subject: Re: [Freesurfer] P files > > Hi John, > > Can you please reach out to me directly at marinell(a)research.ge.com so I > can better understand your needs and see if there is anything I can do to > help? > > Best, > > Luca > > > > > > > > >> On 1/6/16, 9:35 PM, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: >> >> Hi John >> >> Luca Marinelli (ccd) might be able to help you. >> >> cheers >> Bruce >> >>> On Thu, 7 Jan 2016, John Anderson wrote: >>> >>> Dear Freesurfer experts, >>> I want to inquire if there is any tool in Freesurfer that can help to >>> convert the p files ( raw data generated by GE scanner ) to DICOMs >>> >>> >>> Thanks for any advice! >>> >>> Bests, >>> John >> >> >> 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 >> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compl >> ianceline&d=CwIGaQ&c=IV_clAzoPDE253xZdHuilRgztyh_RiV3wUrLrDQYWSI&r=eSTAoNl >> ku4a3XnNWAquvb-o6CJqTPTXMUCt91ZS0mc8&m=wgtGJqDdB3Yobmvr8MXewimixBYbYOpxEkH >> l8_Pac3I&s=RjenNXRWYQ_Xu93C2YeHP-fmxk1hQRnhVGVMd2Q9E3I&e= . 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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