Freesurfer September 2013

freesurfer@nmr.mgh.harvard.edu

124 participants
243 discussions

Re: [Freesurfer] Significant clusters before and after Monte Carlo
by Anita van Loenhoud 17 Sep '13

17 Sep '13

Hi Doug, I mean that before doing any correction, I can press 'Find Clusters and Goto Max', which will show me clusters based on my visualisation threshold. As far as I understood, it will go to the most significant vertex within each cluster and display that value. So before Monte Carlo, I found a cluster in the RMF, and the most significant vertex in there was -4.42. After Monte Carlo, I again see a cluster in the RMF. Now, when I again press 'Find Clusters and Goto Max' it gives me a new value of -2.19. I guess I have a difficulty with interpreting these 'new values' after Monte Carlo. Do I understand correctly from your previous comment that after this correction, they don't correspond to single vertices anymore? If my question is too elaborate for this mailinglist, could you recomment me some literature that might help me? Thanks so much! Anita

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Re: [Freesurfer] MNI coordinates
by Douglas Greve 17 Sep '13

17 Sep '13

It was not in version 5.1, try 5.3 or let me know what platform you are using and I can send it to you. doug ps. Please remember to post to the list and not to us personally. thanks! On 9/17/13 2:09 AM, Simon Baker wrote: > Hi Doug, > > There are several posts in which you mention the mri_surfcluster > --centroid option as a method for obtaining MNI coordinates of the > centroid of each parcellation label. When I type the below command, I > get and error saying "ERROR: Option --centroid unknown". What am I > doing wrong? > > mri_surfcluster --in lh.thickness --clabel lh.G_and_S_cingul-Ant.label > --sum sum.lh.G_and_S_cingul-Ant --centroid --thmin 0 --hemi lh > --subject ### > > I am using Freesurfer version 5.1 and the Destrieux parcellation. > > Thank you, > > Simon > > > > On 24 July 2013 13:59, Douglas Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > We don't have those number available, but you can generate them > with something like: > > #1 Convert the annotation to a set of labels. This is for the > Desikan atlas, but you can spec the destrieux instead > mri_annotation2label --subject fsaverage --hemi lh --outdir > ~/tmp/aparc > > # For each label, run mri_surfcluster to get the centroid > mri_surfcluster --in ~/subjects/fsaverage/surf/lh.thickness > --clabel lh.pericalcarine.label --sum sum.lh.pericalcarine > --centroid --thmin 0 --hemi lh --subject fsaverage > > This will actually be weighted by the thickness, but that should > not matter much > > The centroid coordinates will be in MNI305 space > > doug > > > > > On 7/23/13 11:57 AM, LAOUCHEDI MAKHLOUF wrote: >> Hi >> i am using corticals parcels (destrieux) as nodes in a >> connectivity study using the NBS (Network Based Statistics) tool; >> i want to assign MNI coordinates for these nodes. is there any >> MNI coordinates in freesurfer for each component of this >> parcellation (not for every vertex in those components) or any >> other strategy to assign coordinates for these components ? >> >> otherwise, i intend to non-linearily register the freesurfer's >> labels for a healthy subject in MNI and for each label i will use >> coordinates of one of its points to represent that label >> >> thanks for help >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@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. > > > > > -- > > Simon Baker > PhD Candidate > Faculty of Medicine, Nursing and Health Sciences > Monash University

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Intracranial volume measures
by Rashmi Singh 16 Sep '13

16 Sep '13

Hello FreeSurfer experts I was looking into the aseg.stat files following reconall runs and found that intracranial volume measurements were really small for some subjects, while other measures were comparable ( example below) May you suggest the reason for that. Cortex vol lhcorticalWM rhcorticalWM subcortWM Total GM Supratentovol ICV 604672.2727 293117.0313 295386.1719 588503.2031 137454 742126.2727 1305366.506 2295517.424 508022.5115 277588.2969 273433.7188 551022.0156 141394 649416.5115 1172142.031 807193.8392 538498.8818 212168.7188 211857.9063 424026.625 141688 680186.8818 1057642.049 1100334.147 573133.8927 270262.7813 271187.8125 541450.5938 128431 701564.8927 1217341.888 354564.6828 Thanks, Rashmi

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Total gray matter volume for aparc.2009?
by Yizhou Ma 16 Sep '13

16 Sep '13

Dear Freesurfer experts, I'm doing ROI analysis on surface area and gray matter volume using the aparc.2009 parcellation. Now that I wanted to use corresponding whole brain measures as covariates, I could not find whole brain gray matter volume measures in the aparc.a2009s.stats file. However, I find one in the aseg.stats file. Since I believe these two file use different approaches to estimate gray matter volume, I'm stuck with what I choose for the whole brain measure. Do I use the value in aseg.stats or do I add up the volumes of regions in aparc.a2009s.stats? And advice is appreciated. Thanks, Cherry

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Research Fellow/Postdoc in Pain Neuroimaging, University of Michigan, Ann Arbor, MI
by Alexandre Dasilva 16 Sep '13

16 Sep '13

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Repost family wise error rate correction
by Venkatesh Rajagopalan 16 Sep '13

16 Sep '13

Hi All, I am sorry to repost this message as I did not hear from you. I am wondering whether someone could tell me how I can do family wise error rate correction. I ran mri_glmfit with sim option and how I can perform the FWER correction using mri_surfcluster. Thanks Venkatesh Kessler Foundation is proud to be recognized as one of the Best Places to Work in New Jersey. The information in this transmission is intended for official use of the Kessler Foundation. It is intended for the exclusive use of the persons or entities to which it is addressed. If you are not an intended recipient or the employee or agent responsible for delivering this transmission to an intended recipient, be aware that any disclosure, dissemination, distribution or copying of this communication, or the use of its contents, is strictly prohibited. If you received this transmission in error, please notify the sender by return e-mail and delete the material from any computer.

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RE : RE : mri_glmfit_script.csh
by Stéphane Poulin 16 Sep '13

16 Sep '13

Ok, ________________________________________ De : Douglas Greve [greve(a)nmr.mgh.harvard.edu] Date d'envoi : 16 septembre 2013 11:42 À : Stéphane Poulin Objet : Re: RE : [Freesurfer] mri_glmfit_script.csh Hi Stephane, please post to the list and not to me separately. thanks! doug On 9/16/13 5:25 PM, Stéphane Poulin wrote: > Sorry Doug, > I have been using this script since my fellowship training at the Martinos and thought it was commonly used. > I have not used the mri_glmfit as explained in FS tutorials (ex https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis) > In any case you can solve my issue just looking at the script (attached) it would be appreciated. If not, I'll get into the tutorials. > Thanks, > Stephane > > ________________________________________ > De : freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] de la part de Douglas Greve [greve(a)nmr.mgh.harvard.edu] > Date d'envoi : 16 septembre 2013 10:25 > À : freesurfer(a)nmr.mgh.harvard.edu > Objet : Re: [Freesurfer] mri_glmfit_script.csh > > what is mri_glmfit_script.csh? Please send the actual mri_glmfit command line and terminal output. > doug > > On 9/16/13 3:58 PM, Stéphane Poulin wrote: >> Dear Freesurfer experts, >> >> If I want to correlate a variable with cortical thickness using mri_glmfit_script.csh, >> >> fsgd file >> >> GroupDescriptorFile 1 >> Title <name of the analysis> >> Class Main >> Variables <variable of interest> >> Input subject1 Main <results of subject 1 on variable of interest> >> … >> >> and contrast.mat >> >> 0 1 >> >> Question: red/yellow on the statistical surface map = positive correlation between cortical thickness and variable of interest (and blue negative correlation)? >> >> Thanks, >> >> Stephane >> >> _______________________________________________ >> 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 > > > 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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Re: [Freesurfer] Significant clusters before and after Monte Carlo
by Anita van Loenhoud 16 Sep '13

16 Sep '13

Hi Doug, Thanks for your reply. I was using 1.3 for visualization and 2 for simulation. So that's probably where it went wrong? When I set both thresholds to 2, significant clusters after Monte Carlo were also there before the simulation. Just to double-check: can the values associated with these significant clusters be different before and after Monte Carlo? For example, before Monte Carlo the value of the rostralmiddlefrontal was -4.42, after Monte Carlo it's -2.19. That's normal, right? Thanks again, Anita

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mri_glmfit_script.csh
by Stéphane Poulin 16 Sep '13

16 Sep '13

Dear Freesurfer experts, If I want to correlate a variable with cortical thickness using mri_glmfit_script.csh, fsgd file GroupDescriptorFile 1 Title <name of the analysis> Class Main Variables <variable of interest> Input subject1 Main <results of subject 1 on variable of interest> … and contrast.mat 0 1 Question: red/yellow on the statistical surface map = positive correlation between cortical thickness and variable of interest (and blue negative correlation)? Thanks, Stephane

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Re: [Freesurfer] recon all question
by Rashmi Singh 16 Sep '13

16 Sep '13

I am doing volumetric studies where instead of using ICV, I use total brain volume as a co-variate. This is why I need total brain volume measurements. Do you suggest that its not a good idea to use mri-binarize of brain.mgz for calculating it? Earlier freesurfer experts had suggeted me to use this option. Rashmi _______________________ ________________________________________ From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] Sent: Friday, September 13, 2013 9:09 AM To: Rashmi Singh Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: RE: [Freesurfer] recon all question what do you want to do with the brain volume? Are you really after ICV/TIV? We use the det. of the jacobian of the tal xform as per Randy Buckner, and for it we have compared to actual ICV volumes derived from T2 volumes and manual stripping For the FLAIR, we usually get a T2-space based FLAIR that is also 1mm isotropic. Once you are done with recon-all, you run it again with the switch -FLAIRpial <path to flair volume> and it will do a post-hoc surface deformation to avoid dura. cheers Bruce On Fri, 13 Sep 2013, Rashmi Singh wrote: > Thank you Bruce ! > mri_binarize was suggested to me by the freesurfer group, so now I am a little concerned when you say that this has not been assessed for accuracy. May you suggest how otherwise do you get the total brain volume ( which you suggest is more accurate), as this measurement is not present in the freesurfer output stat files. > > May you please elaborate a little more the steps of using T2-FlAIR for recon all or suggest me where I can find the detail information ( may be on the website). While scanning we do collect T2-FLAIR that is linked with T1 for each subject. Is that what you mean by get a T2-FLAIR? Also, what is a -T2Flair swicht? > Sorry, with a background of molecular biology and being a novice in image analysis, it really takes me time and lots of effort to understand imaging and its analysis. Your guidance is appreciated. > Thanks, > > Rashmi > ________________________________________ > From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] > Sent: Friday, September 13, 2013 8:46 AM > To: Rashmi Singh > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] recon all question > > 1. I don't think I know anyone who has done this, and we haven't assessed > it for accuracy. > > 2. The best thing to do is get a T2-FLAIR and run it with the -T2Flair > switch after recon-all is done. This does a great job avoiding dura > > cheers > Bruce > > > On Fri, 13 Sep 2013, Rashmi Singh wrote: > >> Hey Bruce, >> I have two more questions. >> 1) I was suggested to use mri_binarize with brain.mgz to get the total brain volume. Is there any reference that I can cite regarding use of mri_binarize to calculate total brain volume. >> >> 2)I learnt that using T2 weighted image along with T1 weighted image from the same scanning session generates a good contrast and gives better segmentation/parcellation outputs using FreeSurfer. >> May the FreeSurfer experts guide me through this. >> >> Thanks, >> Rashmi >> ________________________________________ >> From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] >> Sent: Thursday, September 12, 2013 5:27 PM >> To: Rashmi Singh >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] recon all question >> >> Hi Rashmi >> >> putting them in the orig folder with those numbers will get recon-all to >> do motion correction and averaging. >> >> cheers >> Bruce >> On Thu, 12 Sep 2013, Rashmi Singh wrote: >> >>> >>> Hello Freesurfer experts, >>> I am doing volumetrics study. During the scan we get 2-3 mprage per >>> scan for a subject. >>> While running the FreeSurfer, if I want to use the three mprages for >>> that subject as an input file, may I just keep the three mgz files >>> (001.mgz, 002 .mgz and 003.mgz) in the orig folder and run the simple >> recon >>> all command :=Recon-all -s (subject file name) -all or do I need to have >>> some additional l flags so that recon all command will use the three T1 >>> images to get one output file? >>> Thanks, >>> Rashmi >>> >>> >> >> >> 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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Freesurfer September 2013