[Freesurfer] FreeSurfer TrackVis Transforms

Dear expert.Hi. I'm a newbie using Freesurfer software, and I want to transform the data of .trk file which is from Trackvis tool. (https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferTrackVisTransforms)As there is an information for transforming trk file into the space of Freesurfer surface, I rea

Re: [Freesurfer] How to run part of TRACULA

Hi Nasia - They both have preprocessing steps because recon-all runs on the T1 and trac-all runs on the DWIs, so they preprocess different images. You cannot skip any of the steps in recon-all and still get a segmentation. The point of the autorecon schemes is mostly to repeat only one part

Re: [Freesurfer] FreeSurfer TrackVis Transforms

Hi - Check out the dmri_trk2trk command. In your case, you'd need to pass it a transformation file from the registration between your diffusion and structural data, which you can compute with bbregister. Best, a.y On Mon, 15 Aug 2016, "김재명" wrote: Dear expert. Hi. I'm a newbie using Fr

[Freesurfer] FSFAST ROI atlas

HI all- I am using FSFAST to extract ROI time series values for further connectivity analysis. I've used Desikan, Destriuex and DKT atlas. However, I was wondering if anyone has used Power et.al 2011 rois and/or HCP's newly defined 180/per hemi rois to extract time series data. If so could you pl

Re: [Freesurfer] mri_preproc error

Hi Younghoon, You can adjust those settings from the GUI after you load the surface and overlays. Just click “Configure Overlay” button on the left panel after you load the overlay. Best, Ruopeng > On Aug 14, 2016, at 9:41 PM, YoungHoon Kwon wrote: > > Hello Freesurfer Developers, > > I'm

Re: [Freesurfer] FSFAST ROI atlas

I have not used them myself. On 8/15/16 10:23 AM, Sabin Khadka wrote: HI all- I am using FSFAST to extract ROI time series values for further connectivity analysis. I've used Desikan, Destriuex and DKT atlas. However, I was wondering if anyone has used Power et.al 2011 rois

[Freesurfer] TRACULA extracting diffusion measures using ASEG or WM parc

Hi Anastasia, Is it possible to extract diffusion measures FA, ADC etc. within the subcortical (ASEG) or WM parc ROI regions using the Freesurfer tools? If possible, can you show how it can be done? Thank you in advance. Best, Yoon ___ Freesurfer m

Re: [Freesurfer] TRACULA extracting diffusion measures using ASEG or WM parc

Hi Yoon - Please see "FA ROI analysis" in the diffusion tutorial on the freesurfer wiki: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Diffusion_DtiIntegration#FAROIAnalysis Best, a.y On Mon, 15 Aug 2016, Chung, Yoonho wrote: Hi Anastasia, Is it possible to extract diffusion mea

Re: [Freesurfer] How to run part of TRACULA

Dear Anastasia, Now I understand and it makes perfect sense! Thank you very much for your answers. Best, Nasia Metoki *Athanasia Metoki* Psychology Doctoral Student - Brain and Cognitive Sciences Program Cognitive Neuroscience Laboratory Temple University Department of Psychology 1701 N 13th St.

[Freesurfer] dividing Freesufer subfields into one anterior, middle and posterior region

Dear FS experts. I want to divid the FS subfield segementation into a anterior part, one middle part and posterior segment - or potentially divide the rang into 10% of the whole rang - and then move backword until I extracted 10 subparts. Is there some way I can do that? Thanks Erik _

Re: [Freesurfer] dividing Freesufer subfields into one anterior, middle and posterior region

Hi Erik, there’s no FreeSurfer program to do this in a straightforward manner. But you can: 1. read in the hippocampal subfield segmentation into matlab with the MRIread function in the $FREESURFER_HOME/matlab directory. 2. extract the major axis with the hippocampus using PCA. 3. Subdivide th

[Freesurfer] Job postings: Post-doc & Data manager/programmer

The Olin Neuropsychiatry Research Center, located in Hartford CT, USA is looking to fill 2 open positions. The Olin Neuropsychiatry Research Center has an opening for a post-doc specializing in neuroinformatics, big-data analysis, and machine learning. The Olin Center is the psychiatric research c

[Freesurfer] Zero cortical thickness

Hi, I have read in the mailing list about zero cortical thickness, but I still have some doubts. I am calculating the average cortical thickness of some areas, and there are a few that almost all the subjects' thickness is zero, others only some subjects score zero. For the ones that almost all s

Re: [Freesurfer] Zero cortical thickness

what do you mean by "area"? do you mean one of the cortical ROIs or do you mean a general location? On 8/15/16 4:13 PM, A Nunes wrote: > Hi, > > I have read in the mailing list about zero cortical thickness, but I > still have some doubts. > > I am calculating the average cortical thickness of s

[Freesurfer] Subject: Re: Zero cortical thickness

Hi Douglas, I meant a surface area extracted from a surface based atlas. Thanks Adonay ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended o

[Freesurfer] which CUDA version driver to use

Dear Freesurfers, I'd like to experiment with faster proceesing, in fact I'd like to try CUDA. However there are several possible drivers for my quadro K2000. I'm not sure which one to choose. Should I install the latest 7.5. version, or use the older version 6, or even older? I'm not sure if the

[Freesurfer] 'Invalid' license file

Hi, Our IT department have recently upgraded our cluster OS and now Freesurfer complains that its license is invalid. I have tried rebuilding, and acquiring a new license, but these do not fix the problem. The license file I am using works in my Ubuntu 12.04 computer - it has been copied across

[Freesurfer] recon-all -base -all, "Word too long" error.

Dear FreeSurfer experts, I am FreeSurfer longitudinal processing the thirty time points data. When I tried the step 2 process to make a template, the process stopped with an error. The error message as the below. === ... mri_diff --notallow-pix /home/Desktop/MyProject/CO30/mri/rawavg.