[Freesurfer] control points from cross transferred to long

Hi, On this page https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits it mentions "it is recommended to check if all CPs are accurately placed in the long." I was wondering what is the best way to do this? I know I can type in the RAS coordinates from the control.dat file and check

Re: [Freesurfer] FW: Permutation output

Hi Doug, I am attaching the permutation log file. Thanks! Pablo Date: Mon, 17 Aug 2015 11:15:14 -0400 From: gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: Permutation output Can you send me the log file from the glmdir folder? The l

[Freesurfer] check Talairach registration using Freeview

Hi there, I have two questions regarding Talairach registration. _*Question 1:*_ I would like to check Talairach registration according to this page: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview I see this line for the tutorial: freeview -v tal_before/mri/T1.mgz tal

Re: [Freesurfer] visualizing paths stats by voxel

Hey Anastasia, thanks for looking into this. > Am 17.08.2015 um 20:33 schrieb Anastasia Yendiki > : > > > Hi Janosch - Looking at the stats files of your subjects, just by a quick > count of the number of lines, I see that there are some subjects that have > only 1 time point and some that h

Re: [Freesurfer] visualizing paths stats by voxel

Hi Janosch - Looking at the stats files of your subjects, just by a quick count of the number of lines, I see that there are some subjects that have only 1 time point and some that have multiple time points, and that the pathstats.byvoxel.txt files have different lengths between those two type

Re: [Freesurfer] Brain on a Single Sphere

No I don't think so, Sorry Bruce > On Aug 17, 2015, at 12:45 PM, Saeed Mahdizadeh Bakhshmand > wrote: > > Hello Experts, > > Is there any command that can map both hemispheres of the brain into one > single sphere? It will be equal to combining two inflated hemispheres into > one spherical

Re: [Freesurfer] selxavg3-sess, -svres

Hi Doug, thanks for the response. The residual from unwhittening data is the same as those produced by the full model. One more question. I transferred the functional data from functional space to the anatomical space using mri_vol2vol without resample: mri_vol2vol --reg register.dof6.dat --m

Re: [Freesurfer] Trakula

Hi Bahram - Can you please send us your entire trac-all.log file? Thanks! a.y On Fri, 14 Aug 2015, B M wrote: Dear experts, I have the last version of tTrakula. i did the first step with   trac-all -prep -c bmdaten/Auswertung/ALS-Review/Trakula/dmrirc This worked properly to the end as shown

[Freesurfer] Brain on a Single Sphere

Hello Experts, Is there any command that can map both hemispheres of the brain into one single sphere? It will be equal to combining two inflated hemispheres into one spherical brain surface that has its own scalar overlays. Best, Saeed ___ Freesurfer m

Re: [Freesurfer] Extracting MNI Coordinates from the Destrieux Atlas: Checking steps

sorry, can you include them in a single email. I already deleted your previous one :) On 8/17/15 11:30 AM, Elijah Mak wrote: Hi Douglas, Sorry about that! I hope this works. I have pasted the earlier correspondence here with your response below: Re: [Freesurfer] Extracting MNI Coordinates

Re: [Freesurfer] Extracting MNI Coordinates from the Destrieux Atlas: Checking steps

Hi Douglas, Sorry about that! I hope this works. I have pasted the earlier correspondence here with your response below: Re: [Freesurfer] Extracting MNI Coordinates from the Destrieux Atlas: Checking steps

Re: [Freesurfer] registering 2 scans

I would probably use bbregister to register the volumes, then use mri_surf2surf with the --reg option to map the surfaces from one space to another. On 8/14/15 1:59 PM, Hibert, Matthew Louis wrote: > Hi Bruce, > My goal is to compare the surfaces and segmentations from the reconstructions > of

Re: [Freesurfer] Is the fsaverage in the MNI space?

On 8/14/15 10:15 AM, chenhf_uestc wrote: Dear freesurfer experts, The freesurfer online manual stated that before group analysis, we should*resample data* onto the*common space (fsaverage)*. I have three questions here. First, Is the fsaverage file in the MNI space? There is no such thing as

Re: [Freesurfer] Extracting MNI Coordinates from the Destrieux Atlas: Checking steps

sorry, what is this in reference too? Please remember to include the text from previous exchanges so we have context for questions. We answer a lot of email on freesurfer@... and it is hard to keep track of things. On 8/14/15 7:00 AM, Elijah Mak wrote: Hi Douglas, Thanks for the help! Howev

Re: [Freesurfer] mris_preproc -iv option

It samples halfway between the white and pial On 8/13/15 6:52 AM, Silas wrote: Dear Freesurfer team, How does mris_preproc map volume data onto the surface when using the -ivoption? Is an average between the white and pial boundaries taken, orare only the voxels taken into account that inte

Re: [Freesurfer] Question about the outputs of recon-all

it is hard to say that they are in the same space. To be in the same space, they have to have the same origin, direction cosines, and voxel size. Likely your functional results are in MNI152 whereas fsaverage is in MNI305. There is no such thing as "MNI space" per se. If this is the case, I wo

Re: [Freesurfer] FW: Permutation output

Can you send me the log file from the glmdir folder? The log file that has "perm" in the name? On 8/12/15 11:33 AM, pablo najt wrote: Will do that from now on. the output is as follow: This is the output I am getting which I believe is not what I need for check the permutation output C.datF.

Re: [Freesurfer] selxavg3-sess, -svres

They are not the "same". As you point out they have a correlation of .98, not 1.0. What you are discovering is the inconvenient truth that task signal accounts for a very small proportion of variation. Welcome to fMRI:). I think the reason why the residual does not equal y - X*beta is that they

[Freesurfer] help with mris_make_face_parcellation

Hi, I’m interested in using mris_make_face_parcellation, but I can’t find any documentation on the input arguments and outputs. Could you give me more information on this command or direct me to the proper website? Thanks, Sophie -- Sophie Wohltjen Post-baccalaureate Fellow Laboratory of Brain

Re: [Freesurfer] Hyppocampal subfields v 6.0 on segmentations with prior versions

Ciao Nicola, With 5.3, you won't have any problems. I haven't tried with 5.1 but it should be fine as well. This all said: ideally you would run everything with the same version for the sake of reproducibility. Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.co