Re: [Freesurfer] vertex-wise contra-lateral mapping on an ico surface

I figured it out. The trick was to invoke recon-all -curvHK on the "average" ico7 surface. This produced the necessary precursors to run mris_left_right_register who's outputs can be used for inter-hemispheric vertex mapping with mri_label2label. -Burke Rosen On Thu, Jul 13, 2017 at 5:38 PM, Bu

Re: [Freesurfer] Switch FreeSurfer Desikan-Killiany atlas to Civet

Dear Trisanna, thank you for the reference. However, I did not find any specific information in this paper what specific methods are used in CIVET and what is the difference in implementation between CIVET and FreeSurfer. Antonin I believe the cortical thickness measures are taken slightly d

[Freesurfer] dmri_motion -T threshold

Hi All, I've been using dmri_motion to quantify motion in our DTI data. We are uncertain how to determine what the -T threshold should be. We have read through the wiki and the related papers and are confused what this number represents, how it effects the output, and the rational for selecting

Re: [Freesurfer] mri_concat to perform average cortical thickness & pial surface

You cannot simply concatenate the thickness files. Use mris_preproc, which will sample them to fsaverage space and then concatenate them On 07/14/2017 12:49 PM, Dev vasu wrote: > Dear all, > > I have 115 subjects , and I would like to perform average cortical > thickness ,pial surface . > > I h

[Freesurfer] SPC in surface area

Hi everyone, I have a questions concerning the SPC values for an individual brain region. I am looking at group differences (3 groups) in SPC in surface and found one region that was significant after correcting for multiple comparisons. I want to follow up with pairwise comparisons. Is there a

Re: [Freesurfer] FS Version 6 Long Processing

Hi FreeSurfer Team, My lab has recently begun editing longitudinal data in version 6 and have found that we cannot use the same flags for -autorecon2 as we did when running longs in version 5.1. Typically, after making any necessary edits to a long, we run -autorecon2-pial -autorecon3. This fla

[Freesurfer] mri_concat to perform average cortical thickness & pial surface

Dear all, I have 115 subjects , and I would like to perform average cortical thickness ,pial surface . I have used mri_concat for this and i am getting dimension mismatch *" mri_concat k***/surf/lh.thickness --mean --o /media/vasudev/vkirsch4/Data_Driven/Thickness_Pial/lh_thickness/lh.thic

Re: [Freesurfer] Help for dmri_pathstats error

Dear DTI Experts: I wonder if there is anyone that might know a direction to look into this error? I just need to know what program generates this "path.map.txt" for the tracula script dmri_pathstats to run through. dmri_pathstats --intrc START_610/dpath/lh.cst_AS_avg33_mni_bbr --dtbase START_61

Re: [Freesurfer] ERROR: dimension mismatch between input volume and seg - VolumeROICorticalThickness

Did you get exactly the same error? On 07/14/2017 02:05 AM, M Janani wrote: > > Hi Douglas Greve > , > > Thanks for your support. > > I tried with the --reshape-factor 6. But it didn’t

Re: [Freesurfer] spmregister

what is your freeview command? On 07/14/2017 08:46 AM, John Anderson wrote: > >> Dear Freesurfer experts, >> I want to derive registration matrix between pcasl image and the >> structural space in Freesurfer (i.e. orig.mgz) >> If I open orig.mgz and the pcasl image in Freesurefr I see overlap >

Re: [Freesurfer] Switch FreeSurfer Desikan-Killiany atlas to Civet

On 07/14/2017 05:13 AM, 沙志强 wrote: > Hello FreeSurfer Developers, > > I am attempting to switch the Desikan-Killiany atlas of FreeSurfer to > Civet. But I have no idea to solve the problem. Would you like to give > me some suggestions or some detailed steps to help me accomplish the > tasks ?

Re: [Freesurfer] problems with recon-all in 6.0

Not sure. First, let's make sure that the dicom can be converted with mri_convert 01001/0/2/1.dcm deleteme.mgh try that and let us know if it succeeds On 07/14/2017 04:13 AM, Lars M. Rimol wrote: > Hi, > > I'm trying to run recon-all in FreeSurfer 6.0 but I keep getting > error messages and s

Re: [Freesurfer] Mid point on Freeview

Thanks Bruce - yes sorry I meant the curvature measure. Thank you! -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Thu, Jul 13, 2017 at 10:01 PM, Bruce Fischl wrote: > Hi > > do you mean in the curvature display? If so, it is the "0" point at which > red t

Re: [Freesurfer] Switch FreeSurfer Desikan-Killiany atlas to Civet

I believe the cortical thickness measures are taken slightly differently. This paper might offer some insights. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4408913/ Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Jul 14, 2017 at 8:29 AM, Ant

Re: [Freesurfer] Switch FreeSurfer Desikan-Killiany atlas to Civet

Dear Zhiquiang, as a regular user of FreeSurfer I am wondering, what is the advantage of using Civet instead of FreeSurfer? Are there some functionalities in Civet which are not available in FreeSurfer? Or does Civet offer better performance/accuracy/precision in estimation of surface models f

Re: [Freesurfer] what program generates "path.map.txt" for dmri_pathstats to run?

esurfer/2013-January/027405.html> <https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-January/027405.html> Any help would be really helpful. Regards, Janani ::DISCLAIMER:: ---

[Freesurfer] HELP! FDR vs clusterwise correction for multiple comparisons

Dear Doug and Bruce I have a couple of questions regarding multiple comparison correction. Any help with this would be really appreciated! I am conducting a cortical thickness analysis between 2 groups (patients vs controls). My understanding is that first I should check for an age-cortical thi

[Freesurfer] Switch FreeSurfer Desikan-Killiany atlas to Civet

Hello FreeSurfer Developers, I am attempting to switch the Desikan-Killiany atlas of FreeSurfer to Civet. But I have no idea to solve the problem. Would you like to give me some suggestions or some detailed steps to help me accomplish the tasks ? Best wishes, Zhiqiang Sha_

[Freesurfer] problems with recon-all in 6.0

Hi, I'm trying to run recon-all in FreeSurfer 6.0 but I keep getting error messages and some strange behavior: ls 01001/0/2/ 100.dcm 106.dcm 111.dcm 117.dcm 122.dcm 128.dcm 133.dcm 139.dcm 144.dcm 14.dcm 155.dcm 160.dcm 166.dcm 171.dcm 17.dcm 22.dcm 28.dcm 33.dcm 39.dcm 44.dcm

[Freesurfer] R: Re: R: Re: 3G1V.fsgd

Hi list, by applying the model reported above I obtained opposite maps for slope and intercept. E.g. In HC-MCI folder, the sig.nii.gz for slope and intercept show the same maps which inverse color (pos/neg). I guess that there is an error in my model for 3GV1. Please could you check in. Thanks S