[Freesurfer] 答复: Longitudinal proceesing for Pediatric data

Hi Martin Thanks a lot for your reply! Is there any reference that the longitudinal processing would fail if the difference in head size exceeded any certain value? Best, Dong 发件人: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] 代表 Martin

[Freesurfer] recon-all error

Hello, New to freesurfer using Linux (successfully reconstructed several images on a mac) - can you help me determine how to correct the error in this attached attempt at a recon? Many thanks, Linette Tue Feb 14 22:56:38 EST 2017 /home/cnslab/Desktop/freesurfer/subjects/5098Post

Re: [Freesurfer] Cortical Parcellations in individual space using Yeo et al 2011

Hi Emma, I recommend that you follow the mri_surf2surf and mri_label2vol route. As recommended in the other emails, you should probably load the resulting parcellations and make sure they look ok. As far as I know, "mris_ca_train" and "mris_ca_label" are not quite so applicable here because they

Re: [Freesurfer] Fwd: LGI using Yeo Atlas

Hi Martin, Sorry for the slow reply. Antonin is right about the mri_segstats. To map the surface parcellation from fsaverage to your individual subject's anatomical space, you can do the following: # Transform from fsaverage to subject's surface >> mri_surf2surf --srcsubject fsaverage

Re: [Freesurfer] Longitudinal analysis of rates or percent changes

Hi Katarina, if your run it regularly, and then run it including the —generic-time, and get the same result twice, we can conclude that the —generic-time has not effect. You should be fine. Best, Martin > On 14 Feb 2017, at 19:38, Katarina Trojacanec >

[Freesurfer] Converting Surface Masks to Labels

Hi, I'm sorry for what seems like a trivial question. I couldn't find this answer in the tutorials or old archive. I have statistical data in the surface that I have thresholded and binarized to form a mask. I can load the mask as an overlay in tksurfer. My understanding is that you need to

Re: [Freesurfer] tractstats2table error

Hi Adarsh – What operating system are you running this on? It runs fine for me with this input file when I test it on both a mac and a linux computer. a.y From: > on behalf of Adarsh Nellore

[Freesurfer] Cortical Parcellations in individual space using Yeo et al 2011

Hello, I'm preparing to do resting state analyses and I'd like to use the Yeo 2011 network atlas for the cortical parcellations. Looking through the archive, I know that mri_surf2surf with the -sval-annot flag can be used to convert the fsaverage from the Yeo et al 2011 study to an individual

Re: [Freesurfer] -trac-all -prep FS 5.3 Memory Allocation Issue

Hi Abby – It looks like the first subject was run before installing the 2014 TRACULA update, and the second subject was run after installing that update. Can you try running the first subject from scratch (in a new output directory) now that the update has been installed? This will tell us if

Re: [Freesurfer] fast_selxavg3() failed\n

It is looking for a folder called motion.sm3.lh in the current directory. This would have been created when you ran mkanalysis-sess. Does that exist? and does the analysis.info file exist inside it? On 02/11/2017 02:41 PM, Fatemeh.Molaei-Vaneghi wrote: > Dear FreeSurfers, > > I'm trying to

[Freesurfer] Volume maps unit in FreeView

Hi, I have a very simple question. I have cortical volume maps (averaged over 30 subjects). I can view those in FreeView using lh.pial overlaid with lh.mean.volume.mgh file. In overlay > configure option, I had to set the min as 0 and max as 4 to display the average volume. Now the color bar is

Re: [Freesurfer] tractstats2table error

Hi Anastasia, The file I have seems very similar to the file in that link. I've pasted my file below: # Title Pathway Statistics # # generating_program /usr/local/freesurfer/bin/dmri_pathstats # cvs_version # cmdline /usr/local/freesurfer/bin/dmri_pathstats --intrc

Re: [Freesurfer] tractstats2table error

Hi Adarsh – The command works fine with our data. When you open your input file, does it look like the example in the tutorial below? http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics#Anisotropyanddiffusivityaveragedoveranentirepathway Thanks, a.y From:

Re: [Freesurfer] tractstats2table error

Hi Anastasia, This was the full command: tractstats2table --inputs /usr/local/freesurfer/subjects/control_data/diffusion_tracs/Control200/dpath/lh.slft_PP_avg33_mni_flt/pathstats.overall.txt --overall --tablefile

[Freesurfer] Intensity Re-scaling Relative to Full Brain Atlas

Hi Experts! Quick question: is it possible to re-scale intensities relative to the full brain atlas? Details: Per step 3 of the following tutorial: https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer I wanted to re-scale the the intensities relative to the full brain atlas. The command:

[Freesurfer] Fw: Re: bbregister

Thank you very much! Kindly, I have one follow up question:   I have VOI 20X20X20 mm have been created during an MR spectroscopy session. This VOI was placed in specific loacation on the T1 image. I have created this VOI using the command "mri_volsynth"  and I want to move it from native space

Re: [Freesurfer] Longitudinal proceesing for Pediatric data

Hi Dong, it can work, if time points are close to each other (so not much head growth). Feel free to try, but make sure you are carefully looking at the surfaces, that no gray matter is clipped in later time points. The alternative is to only do cross sectional processing. Best, Martin >

Re: [Freesurfer] Longitudinal analysis of rates or percent changes

Hi Martin, Thanks for your reply. I removed the time column from the qdec table (below is some sample content of the new qdec table): fsid fsid-base age weight diagnosis gender Glob_CDR NPI-Q_TotScr MMSE_TotScr FAQ_TotScr visit1_2_3_4 ADNI_sub1_sc ADNI_base1 81.3 y AD M x x x x sc

[Freesurfer] Error from tractstats2table

Hi there, I generated tractographies using the TRACULA pipeline and I'm not trying to generate the necessary statistics for them using tractstats2table. This is the command I'm using: tractstats2table --inputs /usr/local/freesurfer/subjects/control_data/

Re: [Freesurfer] Parallelization not working as implemented

I will have to inspect our Mac test results for parallel processing, but generally speaking we do not see much performance increase in terms of run times after using 4 threads. On 02/13/2017 06:13 PM, Francis Tyson Thomas wrote: > I did provide the execution times in my first email. I have

[Freesurfer] cluster as ROI

Dear FreeSurfer Experts, I compared 2 groups in QDEC in spc (from pre to post) and found a cluster that survives Monte Carlo correction. Now I would like to extract the data for each participant and each time point from that cluster so that I can plot the change. How could I do this? I tried

[Freesurfer] Question on saving interim files when generating an fsavearge

Hello. We are looking to save the interim subject files generated when creating an fsaverage. These seem to be automatically deleted at the end of the process so we were wondering if there is a flag or script that would save these for us? Thanks for your help. John D. West, M.S. Principal

Re: [Freesurfer] Control Points editing

Hi Andrea 1. the control points don't need to go into locations that are misclassified, just ones that the intensity is signifantly different from (and usually less than) 110. They can be correctly segmented as WM. 2. Each control point changes things in a region so they can have a global

[Freesurfer] Control Points editing

Hi FreeSurfer experts, I have some questions (maybe trivial) about Control Points editing. 1) Following the guide in your website and exploring your tutorial subject "cp_before" I understood that a Control Point has to be placed in a region that is definitely white matter but the standard