[Freesurfer] FS-FAST subcortical mni305

Hi, I'm performing FS-FAST for functional connectivity analysis.I have performed all step for cortical labels.Now, I'd like to perform the analysis for subcortical structure.Which are the correct lines? Using preproc-sess -s Sess01 -fwhm 5 -surface fsaverage lhrh -mni305 -fsd rest -per-run for e

Re: [Freesurfer] mris_pmake update

Hi, Is it also possible to get an updated version for the mris_pmake binary? This is freesurfer-i386-apple-darwin11.4.2-stable5-20130514 version. Thanks! Sarah ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/

Re: [Freesurfer] Data interest of the CorticalParcellation_Yeo2011

Hi Annie, Can you tell us the exact mri_surf2surf command you use? Cheers, Thomas On Fri, May 15, 2015 at 5:24 PM, 陳昱潔 wrote: > Hi Dr. Yeo, > > Thank you very much for your help! It is the exactly we need! > Only a little question that when we ran mris_surf2surf > Something seems wrong , but I

[Freesurfer] Segmentation of hippocampal subfields version 6.0

hi list, where can I download the new version 6.0 of hippocampal subfields segmentation? And in general the new FS version 6.0? Thanks Stefano ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listi

Re: [Freesurfer] Segmentation of hippocampal subfields version 6.0

Hi Stefano FS version 6 is not ready yet - it's still in testing. Hopefully we will have a beta for people to tryout soon Bruce On Fri, 15 May 2015, std...@virgilio.it wrote:  hi list, where can I download the new version 6.0 of hippocampal subfields segmentation? And in general the new FS

[Freesurfer] R: Re: Segmentation of hippocampal subfields version 6.0

Thanks. The new version will involve also changes in the measure of perirhinal and parahippocampus? Stefano Messaggio originale Da: fis...@nmr.mgh.harvard.edu Data: 15-mag-2015 15.31 A: , "Freesurfer support list" Ogg: Re: [Freesurfer] Segmentation of hippocampal subfields version 6.0

Re: [Freesurfer] R: Re: Segmentation of hippocampal subfields version 6.0

yes, it will involve changes in pretty much everything (to one degree or another) cheers Bruce On Fri, 15 May 2015, std...@virgilio.it wrote: Thanks. The new version will involve also changes in the measure of perirhinal and parahippocampus? Stefano Messaggio originale Da: fis...@nmr

[Freesurfer] error in atlas creation

Hello, I have been stumped by this error I keep getting using the rebuild_gca_atlas.csh script. I am trying to build a cerebellar atlas, so I am wondering if the problem is with the brains we parcellated, or with my installation etc. The brains consist of manually segmented cerebellums from th

[Freesurfer] 전달: fsfast fmcpr was not created.

Hello I did recon-all of dementia patient images. Recon-all -s 0101RG-ana finished without error on the terminal. After I ran fsfast preproce-sess, 7 files didn't exist in the output folder. ;1.register.dof6.dat, 2.fmcpr.nii, 3.fmcor.mc.dat, 4.mcprextreg, 5.fmcpr.sm5.fsaverage.lh.nii, 6.fmcpr.sm5.

[Freesurfer] Qdec not receiving keyboard input

Hi Freesurfer Experts, Recently, Qdec 1.5 has not been receiving any keyboard input on the Subjects page, yet it does receive keyboard input on the Design page, when I change the Design name for example, and then does not accept keyboard entries on the the Display page, like when I try to change t

Re: [Freesurfer] xhemi final iteration

You will need a new version of make_average_surface, which you can get from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface make a back up of your current version, ie, cp $FREESURFER_HOME/bin/make_average_surface $FREESURFER_HOME/bin/make_average_surface

[Freesurfer] White Matter Corrections

Dear FreeSurfer Team, I am quite new to FreeSurfer/Freeview (and neuroimaging in general) and was wondering about "fixing" white matter holes that are identified using the ?h.smoothwm.nofix surface. This is based on the error spotting techniques suggested in the online troubleshooting tutorial, t

[Freesurfer] Qdec not receiving keyboard input

Hi Freesurfer Experts, Recently, Qdec 1.5 has not been receiving any keyboard input on the Subjects page, yet it does receive keyboard input on the Design page, when I change the Design name for example, and then does not accept keyboard entries on the the Display page, like when I try to change t

[Freesurfer] freeview data checking for longitudinal

Hi, I am trying to create a command line for data checking the same participant over multiple longitudinal timepoints in freeview. However at the moment I am running into issues. Can someone provide me an example of a freeview command to be used if I wanted to overlay the scans? Any help is g

Re: [Freesurfer] freeview data checking for longitudinal

Hi Bryan, what issues are you running into? Just open the images from all time points on top of each other. Make sure to load the ones from the .long.base dirs. The same can be done for surfaces. freeview tp1.long.base/mri/norm.mgz tp2.long.base/mri/norm.mgz ... Martin On 05/15/2015 03:03

[Freesurfer] Manual labels in terms of anatomical regions

Dear Experts,   in my analysis i have created a set of surface labels based on significant clusters using tksurfer. For a given label I would like to know which atlas-based anatomical region (e.g., as defined by the Freesurfer annotations) it occupies. I know I can load annotations in tksurfer

[Freesurfer] Export value for each vertex in mgh file

Hi dear freesurfer expert,Is there any command which can be used to export the value of each vertex of a mgh file (e.g., lh.thickness.fsaverage.mgh) and list all the values by generating a file (may be a .txt file)? Because I want to plot the values for further steps.Thank you!!kaiThe Chinese