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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. > > >

1 0

P files
by John Anderson 06 Jan '16

06 Jan '16

3 2

FDR correction
by stdp82＠virgilio.it 06 Jan '16

06 Jan '16

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? 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) 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. 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. Thanks for your work.Regards, Stefano

2 1

.w file for freeview
by peng 06 Jan '16

06 Jan '16

Hi Freesurfers, I tried to overlay .w file onto a surface, and failed. I dug the previous posts and know this file format is obsolete now. However I wish to know in which version of freeview can I still use this file format, if possible. It will be great if you can provide the link for it. If this is not possible, is there a matlab tool similar to 'write_file.m' so I can output my data in matlab to the newer format (substitution of w-file)? Thanks in advance. best Peng

3 5

Recon-all Run Time
by Marissa Pifer 06 Jan '16

06 Jan '16

Hi Freesurfers, I've recently downloaded free surfer onto a new computer. It's working correctly, but the running time for the recon-all -all command is 30-50 hours. This is in contrast to when I've used free surfer on previous computers where the run time was 6-12 hours. I'm wondering why this would be the case and if anyone else has run into this problem. Marissa

2 2

Need help finding minimum number of vertices for monte carlo correction
by Tara Miskovich 06 Jan '16

06 Jan '16

Hello Freesurfer experts, I need help me finding how to get the minimum number of vertices required to pass the cluster-corrected threshold with monte carlo simulations used in qdec for a surface based analysis? This is per a reviewer request, but I cannot find anything on the wiki or in the mail archives on how to get this value. Can someone please help me with this issue? -- Thank you, Tara

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