Re: [Freesurfer] change the algorithm

Dear Bruce, thank you for your fast and helpful response. I have read in some papers (e.g. paper1

[Freesurfer] mri_defacing: a faulty stripping of cortex

Hello, I'm having a problem to use MRI_defacing (default radius 7), which stripped off some frontal areas as well. Does anyone have any similar problems/solutions? I've increased the radius up to 14, which seems reducing the stripping areas, but still remained this stripping problem within

Re: [Freesurfer] Freesurfer Digest, Vol 148, Issue 28

Hi Arkadiy Doug is on vacation and his response time is likely to be slow. Can you tell us exactly what script you mean? cheers Bruce On Sun, 19 Jun 2016, Arkadiy Maksimovskiy wrote: Hi Doug, Still no luck getting the script- the site does not load for some reason. Any chance you might b

Re: [Freesurfer] registering to fsaverage

try it with the noconform as the first argument. I think it will ignore it at the end Hi Dr. Fischl I ran the following mri_average and consistently get this message. It seems to be trying to read my output as one of the input volumes. If I don't specify an output it re-writes my last file i

Re: [Freesurfer] registering to fsaverage

yes, your last file on the command line should be the output file (the average) cheers Bruce On Mon, 20 Jun 2016, Trisanna Sprung-Much wrote: As a follow-up, here is the mri_info for one of my overlays in the folder and the output file that mri_average seems to create (if I don't specify an o

Re: [Freesurfer] mri_defacing: a faulty stripping of cortex

YOu could try increasing the density of the search (which will slow it down considerably). Maybe -s 7? It's hard to diagnose without looking at your data, so feel free to upload it if this fails and also send us the exact command line you ran On Mon, 20 Jun 2016, HONG Sujin wrote: Hello,

Re: [Freesurfer] Hippocampal subfields error

I am also experiencing same problem. I tried to change ct., but when I change the extension to ctf,It also give errors as below. Error:CTF file '/usr/local/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.ctf' failed to open for 'Read' access. Error message: 'Open a zip file for read/modify

Re: [Freesurfer] registering to fsaverage

thanks, Bruce. Yes in the end through trial and error I tried "mri_average -noconform input output" and it worked. I was surprised that I had to put the -noconform first as normally one can put the argument anywhere in the command. Best Trisanna -- Ph.D. Candidate McGill University Integrated Pr

Re: [Freesurfer] registering to fsaverage

Hi Trisanna the binaries that take mandatory command-line arguments (i.e. without a -- or - in front of them) require all options to be given before the mandatory arguments cheers Bruce On Mon, 20 Jun 2016, Trisanna Sprung-Much wrote: thanks, Bruce. Yes in the end through trial and error

Re: [Freesurfer] Error loading a constructed annotation file

Hi Nora sorry for the long response time. Doug is on vacation and that slows everything down! Can you send the full command line and full terminal output? I think the "1 -1 NOT_FOUND ..." error refers to not being able to find an annotation/parcellation NOT to the orig surface. cheers Bruce

Re: [Freesurfer] matlab crashes on selxavg

A follow up, in case anyone else encounters thread-related bugs: It *appears* that this error was resolved by adding the line maxNumCompThreads(4); to *startup.m* stephen *stephen v. shepherd phd* The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7699 On

[Freesurfer] FS V6.0 GTM PVC ROI definition

Hello Freesrufer Team, I am trying to use the Partial volume correction procedure implemented in the freesurfer 6 beta version and have a few questions. In your recent Neuroimaging paper, the left and right hemispheres were combined by taking the average of the two as they did not show any age-by

[Freesurfer] XQuartz 2.7.9 update results in errors

Hi All, My lab is having difficulty loading the freeview gui after updating to the latest version of XQuartz (2.7.9). We were wondering if others have experienced this issue? We have reverted by to XQuartz 2.7.8 on our machines for now. In case relevant, this errors seems to span Mac OS versions.

Re: [Freesurfer] FS V6.0 GTM PVC ROI definition

Hi Pradeep Doug is on vacation and is the best one to answer your question. If you don't get a response in a week or 10 days can you repost? thanks Bruce On Tue, 21 Jun 2016, Pradeep wrote: Hello Freesrufer Team,  I am trying to use the Partial volume correction procedure implemented in t

Re: [Freesurfer] FSFAST- Cerebellum

Hi Sabin, The structures 601-628 FreeSurferCololLUT.txt correspond to anatomical substructures of the cerebellum (e.g., Crus I, etc). Is that what you want? Or are you looking to use the functional parcels defined in Buckner 2011? In addition, I do not know how mri_segstats works, so I cannot ver

[Freesurfer] cortical surface pattern matching

Hi, has anyone created functionality to compare the spatial correlation/similarity of two patterns in the form of cortical surface overlays. What I am looking at is a have scalar at every point on the cortical surface. obviously this is just a list of vertices with a scalar value associated

Re: [Freesurfer] FS V6.0 GTM PVC ROI definition

Thank you! I will. On Mon, Jun 20, 2016, 7:00 PM Bruce Fischl wrote: > Hi Pradeep > > Doug is on vacation and is the best one to answer your question. If you > don't get a response in a week or 10 days can you repost? > > thanks > Bruce > On Tue, 21 Jun > 2016, Pradeep wrote: > > > Hello Freesru