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,

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

[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

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

[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

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

[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

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

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] 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

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

Dear DTI experts: I am wondering if anybody could provide any information to help me out with this constant error that I am desperate to resolve? I just need to know what program generates this "path.map.txt" for the tracula script dmri_pathstats to run through? dmri_pathstats --intrc

[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

[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

[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

[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

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

Hi Douglas Greve, Thanks for your support. I tried with the --reshape-factor 6. But it didn't work for me. The segmentation was created using the below mentioned data 1.