[Freesurfer] group analysis all measures same results

Dear guys, I was doing group analysis (command-line) on two groups (patients and control, no age or other information). The data has been "qcached", and after following the three steps as "mris_preproc, mri_glmfit and mri_glmfit-sim" shown in the tutorial on the Freesurfer website, I obtained the

Re: [Freesurfer] mkbrainmask-sess and inorm-sess

Run preproc-sess instead. inorm-sess is no longer used On 03/04/2016 05:18 PM, Ji Won Bang wrote: > Thanks for your help! > > I'd like to run mkbrainmask-sess & inorm-sess under version 5.3.0 > > What I used to run are: > mkbrainmask-sess -s $SUBJECT -funcstem fmc -df sessdirfile -fsd >

Re: [Freesurfer] Deflate surface

sure, glad to hear it worked Bruce On Fri, 4 Mar 2016, marmaduke woodman wrote: > On 03/04/2016 10:50 PM, marmaduke woodman wrote: >> On 03/04/2016 10:19 PM, Bruce Fischl wrote: >>> I think you can map it to fsaverage5 then use mri_surf2surf with >>> -sval-xyz to map the fsaverage5 surface back

Re: [Freesurfer] mkbrainmask-sess and inorm-sess

Thanks for your help! I'd like to run mkbrainmask-sess & inorm-sess under version 5.3.0 What I used to run are: mkbrainmask-sess -s $SUBJECT -funcstem fmc -df sessdirfile -fsd bold_retino inorm-sess -s $SUBJECT -motioncor -funcstem fmc -df sessdirfile -fsd bold_retino However, since version

Re: [Freesurfer] mkbrainmask-sess and inorm-sess

You specify it when you run mkanalysis-sess On 03/04/2016 04:36 PM, Ji Won Bang wrote: > In a simple word, my question is: > > under version 5.3.0, how can I specify funcstem (stem of functional > volume)? I don't see any argument for that.. > > Thanks a lot. > > Best, > Ji Won > > 2016-03-04

Re: [Freesurfer] mkbrainmask-sess and inorm-sess

The functional stream changed a lot from version 4 to version 5. The commands and workflow are very different now On 03/04/2016 04:31 PM, Ji Won Bang wrote: > Dear. Freesurfer experts. > > Hi. How are you? > > It might be very naive question. > > When using version 4.5.0 I used the command: >

Re: [Freesurfer] Deflate surface

On 03/04/2016 10:50 PM, marmaduke woodman wrote: > On 03/04/2016 10:19 PM, Bruce Fischl wrote: >> I think you can map it to fsaverage5 then use mri_surf2surf with >> -sval-xyz to map the fsaverage5 surface back to each subject Sorry for the noise, fwiw, this seems to do the trick: mri_surf2surf

Re: [Freesurfer] Deflate surface

On 03/04/2016 10:19 PM, Bruce Fischl wrote: > I think you can map it to fsaverage5 then use mri_surf2surf with > -sval-xyz to map the fsaverage5 surface back to each subject This seems to generate a surface with the number of vertices in the subject, (160k) not fsaverage5 (10k), though perhaps

Re: [Freesurfer] mkbrainmask-sess and inorm-sess

In a simple word, my question is: under version 5.3.0, how can I specify funcstem (stem of functional volume)? I don't see any argument for that.. Thanks a lot. Best, Ji Won 2016-03-04 16:31 GMT-05:00 Ji Won Bang : > Dear. Freesurfer experts. > > Hi. How are you? > > It

[Freesurfer] Cortical thickness last step

Hello again, To calculate cortical thickness, I am running step-4 & 5 following the instructions from https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness So running step 4: *mri_surf2surf --s S01_LP --trgsubject fsaverage --hemi lh --sval lh.thickness --tval

[Freesurfer] mkbrainmask-sess and inorm-sess

Dear. Freesurfer experts. Hi. How are you? It might be very naive question. When using version 4.5.0 I used the command: mkbrainmask-sess -s $SUBJECT -funcstem fmc -df sessdirfile -fsd bold_retino However under the version 5.3.0, mkbrainmask-sess does not have -funcstem. May I use -maskstem

Re: [Freesurfer] Deflate surface

I think you can map it to fsaverage5 then use mri_surf2surf with -sval-xyz to map the fsaverage5 surface back to each subject On Fri, 4 Mar 2016, marmaduke woodman wrote: > On 03/04/2016 10:06 PM, Bruce Fischl wrote: >> what are you trying to achieve? > > A per-subject ~10k vertex pial surface

Re: [Freesurfer] Deflate surface

On 03/04/2016 10:06 PM, Bruce Fischl wrote: > what are you trying to achieve? A per-subject ~10k vertex pial surface with a corresponding annot. We use it as a spatial domain for simulating neural activity; 150k vertices is too many for this purpose. > It might be easiest to use something

Re: [Freesurfer] Deflate surface

what are you trying to achieve? It might be easiest to use something like fsaverage5 as the downsampled surface. Then you would just map your subjects to fsaverage5 using the existing sphere.reg files cheers Bruce On Fri, 4 Mar 2016, marmaduke woodman wrote: > On 03/04/2016 09:10 PM,

Re: [Freesurfer] Deflate surface

On 03/04/2016 09:10 PM, marmaduke woodman wrote: > However, I'd like to recover the cortical parcellation for the > downsampled surface. I tried to decimate the pial & white surfaces, generate a corresponding thickness file and then mris_sample_parc -ct /opt/freesurfer/FreeSurferColorLUT.txt

Re: [Freesurfer] Deflate surface

Hi On 03/04/2016 07:06 PM, Bruce Fischl wrote: > I think there are some tools around for downsampling the surfaces like > mris_decimate. Have you tried any of them? Yes, indeed mris_decimate works well for the downsampling. However, I'd like to recover the cortical parcellation for the

[Freesurfer] Cortical thickness using freesurfer

Dear all, I am working on calculation of cortical thickness from a set of subjects. I am following the instructions from https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness and I am able to run up-to step-2 successfully i.e. I can display the ROIs on fsaverage subject volume. But

Re: [Freesurfer] Deflate surface

Hi Marmaduke I think there are some tools around for downsampling the surfaces like mris_decimate. Have you tried any of them? cheers Bruce On Wed, 2 Mar 2016, marmaduke woodman wrote: > Hi > > I would like to resample the cortical surface on the sphere at a lower > resolution, and then

Re: [Freesurfer] Doubts with Longitudinal Analysis Repeated Measures ANOVA

Hi, I can't help you with ANOVA (never done that), but you can - either subtract the two time points and then do a regular group analysis https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis - or run a Linear mixed effects model

Re: [Freesurfer] minimum files to process longitudinal freesurfer

Hi Ahearn, the base needs a few files from all cross time points for processing. An individual -long run needs files from the base and from *all* cross time points. What is needed and how the stream works is described on the wiki although that may not be complete, especially in situations

Re: [Freesurfer] hello freesurfer developer~

for asymmetryc, see https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi On 03/04/2016 09:28 AM, A-reum Min wrote: > hello experts > > i have some question to you > > Question 1. > i want to compare two groups(patients group VS control groups) for > cortical thickness asymmetry. > so.. am i using a

Re: [Freesurfer] hello freesurfer developer~

usually if the thickness is 0 that means that the vertex is not part of cortex, typically because it is on the "medial wall" (adjacent to ventricle) or in the hippocampus or some other non-neocortical structure On Fri, 4 Mar 2016, A-reum Min wrote: hello experts i have some question to you

Re: [Freesurfer] hello freesurfer developer~

hello experts i have some question to you Question 1. i want to compare two groups(patients group VS control groups) for cortical thickness asymmetry. so.. am i using a lh.thickness.fsaverage.mgh and rh.thickness.fsaverage.mgh for each group subjects right..? Question 2. Left hemisphere whole

Re: [Freesurfer] Problem with mriconvert

what if you change the destination directory? Does it work? On Fri, 4 Mar 2016, Óscar Soto Angona wrote: Hi, Yes, we have permission, and the disk have plenty of space :/ On Thu, Mar 3, 2016 at 6:30 PM, Douglas N Greve wrote: Do you have write permission to

[Freesurfer] mean thickness

Dear Freesurfer team, Forgive me if this is a foolish question... I wanted to overlook cortical thickness, area and volume measures in Gnumeric file after recon-all (checking edits made). However, for several subjects I noticed that the values of mean thickness (final column) were calculated

Re: [Freesurfer] Problem with mriconvert

Hi, Yes, we have permission, and the disk have plenty of space :/ On Thu, Mar 3, 2016 at 6:30 PM, Douglas N Greve wrote: > Do you have write permission to that folder? Is the disk full? > > On 03/02/2016 11:12 AM, Óscar Soto Angona wrote: > > Hello, > > > > We are

[Freesurfer] minimum files to process longitudinal freesurfer

Hello, I need to process a good few thousand T1 images on a machine that I can't store all the data on. I'd like to transfer as few files as possible to the processing machine so that I can perform longitudinal processing. I have successfully longitudinally processed some patients with a sub

Re: [Freesurfer] How to find the difference between to different fMRI datasets?

Thanks Douglas! 1 - I have two functional files per subject (.mgh). Is it possible to insert two files per subject in mris_preproc? In my former functional analysis I haven't concatenated my data using a FSGD-file when running mris_preproc. 2 - Can you calculate the difference between two

[Freesurfer] TRACULA Adding a new tract to the finished analysis

Dear Anastasia and Tracula users, I ran the longitudinal pipeline of Tracula with my subjects and I finished without error. However, I just realized now that I only added cingulum gyrus ending but not the angular bundle. I am interested in tracts that passes through hippocampus so angular bundle