Re: [Freesurfer] tracula FS 5.2

Hi Daria We had the same problem on Macs, although they had enough memory. A work around would be to reduce the number of training subjects in the trctrain folder. When we used 26 instead of 33 training subjects, the error disappeared. Cheers Jürgen On [DATE], "Antonenko, Daria" <[ADDRESS]> wr

Re: [Freesurfer] tracula FS 5.2

Hi Anastasia, my first idea was also that something else might disturb the process, but i replicated the error several times and observed the memory load in the system monitor without running anything else, seemed not memory-intensive at all.. I use a 10 b0 + 64dir DTI sequence, 2.3×2.3×2.3 mm3

Re: [Freesurfer] tip and tricks with patient with one big ventricle...

Hi Bruce: And, where is version 5.3 ?... in the "nightly dev builds" ?... Sincerely, Gonzalo Rojas Costa On Thu, May 2, 2013 at 9:29 PM, Bruce Fischl wrote: > Hi Gonzalo > Try it with 5.3, or upload and I can r. It for you > Bruce > > > > On May 2, 2013, at 2:16 PM, Gonzalo Rojas Costa >

Re: [Freesurfer] Flattening a specific surface parcellation or a group of spatially adjacent parcellations

He will need to change the aparc to labels, or I can try to if d time to add it Bruce On May 2, 2013, at 11:04 PM, Douglas Greve wrote: > > Bruce, did you ever write something that automatically makes cuts based > upon the aparc? I think Bilal is also looking for something like that. > doug

Re: [Freesurfer] Flattening a specific surface parcellation or a group of spatially adjacent parcellations

Bruce, did you ever write something that automatically makes cuts based upon the aparc? I think Bilal is also looking for something like that. doug On 5/2/13 9:31 PM, Bruce Fischl wrote: > Hi Bilal > I think I wrote something called label2patch or label2flat for this propose. > Let me know if

Re: [Freesurfer] Flattening a specific surface parcellation or a group of spatially adjacent parcellations

Hi Bilal I think I wrote something called label2patch or label2flat for this propose. Let me know if you can't find it. You will still need to run mris_flatten on each patch Bruce On May 2, 2013, at 1:54 PM, Bilal Ahmed wrote: > Hi, > > I was wondering if there is a simple way to flatten s

Re: [Freesurfer] tip and tricks with patient with one big ventricle...

Hi Gonzalo Try it with 5.3, or upload and I can r. It for you Bruce On May 2, 2013, at 2:16 PM, Gonzalo Rojas Costa wrote: > Hi Bruce: > > I tested 4.5 and 5.1 versions... with the first I processed > complete, and with 5.1 only autorecon1 section... > > Sincerely, > > > Gonzalo Rojas C

[Freesurfer] version 5.3 coming out soon

Hi All, We have recently uncovered problems with version 5.2. Based on these problems, we are recommending that people stop using 5.2, mainly in regards to usage of the surface data. A new version, 5.3, will be released within two weeks, and a beta version for each platform will be available with

Re: [Freesurfer] mri_convert Segmentation fault (core dumped) lubuntu 13.04

Jorge and Marco, The beta of v5.3 I mentioned is now available for centos6_x86_64 here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-BETA/ Please let me know if it works for you on Fedora 18 and Ubuntu 13. As I understand the problem, it is not with glibc directly, but rather glib

Re: [Freesurfer] mri_convert Segmentation fault (core dumped) lubuntu 13.04

That is the same error I got when using Fedora 18 and should be due to the newest version of glibc. Em Qui, 2013-05-02 às 11:46 -0400, Nick Schmansky escreveu: > Joerg, > > Later this evening or tomorrow we'll post a beta that has the fixes for > this problem for you to try on Ubuntu. When its r

[Freesurfer] Inputting specific talairach coordinates?

Dear FreeSurfers, I have a very basic question (which I'm hoping also has a basic answer!): I know that the Talairach coordinates provided in tksurfer are based on a conversion using MNI space, but I'm wondering: is there a way to input specific Talairach coordinates into Freesurfer to identify a

Re: [Freesurfer] ROI analyses

Thanks Doug! If I may follow up: > 3) (I can't see whether there's a tutorial for this, as the main FS > > site seems to be down at the moment) How can a group comparison of CT > > be done inside a given ROI, and in what ways can the ROI be specified? > > I guess the command line version of QDEC

Re: [Freesurfer] Using the muscle ROI in the FreeSurferColorLUT

Thanks Bruce, Sorry for the naiive questions - I'm still pretty green. If I define a label for, say, the head of the left sternocleidomastoid, using tkmedit, could I then generalize that label to the rest of my patient cohort using mri_label2label? Thanks, Jeff > Hi Jeff > > our standa

Re: [Freesurfer] tip and tricks with patient with one big ventricle...

Hi Anna what command line did you run? Bruce On Thu, 2 May 2013, Anna Deferia wrote: Hello FreeSurfer, I have tried adding control points and running recon for the control points multiple times but no changes to the volume are made. Does anyone know what I could be doing wrong? Thank you, Ann

Re: [Freesurfer] tip and tricks with patient with one big ventricle...

Hi Bruce: I tested 4.5 and 5.1 versions... with the first I processed complete, and with 5.1 only autorecon1 section... Sincerely, Gonzalo Rojas Costa On Thu, May 2, 2013 at 1:31 PM, Bruce Fischl wrote: > what version are you running? The newer ones are *much* better at this > Bruce > >

[Freesurfer] Flattening a specific surface parcellation or a group of spatially adjacent parcellations

Hi, I was wondering if there is a simple way to flatten specific surface parcellations without manually specifying cuts. For example if I want a flattened patch pertaining to the left temporal pole for fsaverage, I would have to manually specify the cut points and then extract and flatten it. As w

Re: [Freesurfer] tip and tricks with patient with one big ventricle...

what version are you running? The newer ones are *much* better at this Bruce On Thu, 2 May 2013, Gonzalo Rojas Costa wrote: Hi: I has the MPRAGE of a patient with one big ventricle, and the other has normal shape and size... Any tip and tricks to process it ?... Because freesurfer fails from

[Freesurfer] tip and tricks with patient with one big ventricle...

Hi: I has the MPRAGE of a patient with one big ventricle, and the other has normal shape and size... Any tip and tricks to process it ?... Because freesurfer fails from the beggining of the process (VERY BAD talairach registration)... I test -bigventricle option of recon-all, but I got the same

Re: [Freesurfer] FLASH params for mri_em_register

Great, thanks! BTW, Doug, your primer on the hell of transformation matrices is very nice. On 2 May 2013, at 18:19, Douglas N Greve wrote: > > Funny you should mention that. Martin just wrote a program to convert lta's > from one type to another. Martin, can you share with Fred? > doug > >

Re: [Freesurfer] FLASH params for mri_em_register

Funny you should mention that. Martin just wrote a program to convert lta's from one type to another. Martin, can you share with Fred? doug On 05/02/2013 01:13 PM, Fred Dick wrote: > Yes - maybe it is an idiotic one, but is there a straightforward way to write > out a tkregister-tweaked talaiar

Re: [Freesurfer] FLASH params for mri_em_register

Yes - maybe it is an idiotic one, but is there a straightforward way to write out a tkregister-tweaked talaiarch.lta with the correct geometry so that mri_ca_normalize/register will read it right? On 2 May 2013, at 18:04, Douglas N Greve wrote: > Hi Fred, so do you still have an outstanding

Re: [Freesurfer] FLASH params for mri_em_register

Hi Fred, so do you still have an outstanding question? doug On 05/02/2013 12:55 PM, Fred Dick wrote: > Hi Doug > > totally no worries (this hardly counts as a delay!). > > I'm running it as > > tkregister2 --ltaout tal-out.lta --gca [sub] --check-reg > > As you had suggested, the source and dst a

Re: [Freesurfer] FLASH params for mri_em_register

Hi Doug totally no worries (this hardly counts as a delay!). I'm running it as tkregister2 --ltaout tal-out.lta --gca [sub] --check-reg As you had suggested, the source and dst are switched (in talaiarch.lta, the .gca is the dst, whereas in new output file, it's the src). Also, the RB...gca

Re: [Freesurfer] Exiting with errors but not sure why

In your recon-all command, you specify the input as a folder: "-i /autofs/space/huygens_001/users/mia/subjects/MGH008_MRI/". You have to pass it a specific file (dicomor some other format). doug On 05/02/2013 12:17 PM, Borzello, Mia wrote: > Great! I've attached it. > > Thanks, > m > > _

Re: [Freesurfer] Exiting with errors but not sure why

Great! I've attached it. Thanks, m From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, May 02, 2013 11:45 AM To: freesurfer@nmr.mgh.harvard.edu Su

Re: [Freesurfer] FLASH params for mri_em_register

Hi Fred, sorry for the delay. How are you running tkregister2 to produce a new lta? Is the only difference between the lta files the matrix? Or did the src and dst geometry and/or type change? doug On 05/02/2013 05:52 AM, Fred Dick wrote: > Hi Doug > > sorry to nudge - any thoughts on lta twea

Re: [Freesurfer] mri_convert Segmentation fault (core dumped) lubuntu 13.04

Joerg, Later this evening or tomorrow we'll post a beta that has the fixes for this problem for you to try on Ubuntu. When its ready, the centos6_x86_64 build will appear in this directory: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-BETA/ Nick > Dear freesurfer administrators,

Re: [Freesurfer] mri_glmfit-sim - error of fwhm

Hi Sophie, the problem may be that you have used "0,001" instead of "0.001". doug On 05/02/2013 10:40 AM, Sophie Maingault wrote: > Dear experts, > > I have a error message when I use the command : mdi_glmfit-sim —glmdir > X —cwpvalthresh 0,001 —cache 3 abs > > ERROR : cannot find > /usr/local

Re: [Freesurfer] Exiting with errors but not sure why

Hi Mia, I'm glad your enjoyed the course. Can you send the recon-all.log file from the subject/scripts folder? doug On 05/02/2013 11:36 AM, Borzello, Mia wrote: > Hi freesurfers! > > Great tutorial this week! > > I've recently run a recon, and it's exited with errors, but I'm not > completely su

[Freesurfer] Exiting with errors but not sure why

Hi freesurfers! Great tutorial this week! I've recently run a recon, and it's exited with errors, but I'm not completely sure why. I've attached the error.log, but le tme know if I should attach another file. Thanks so much, Mia error.log Description: error.log __

[Freesurfer] mri_glmfit-sim - error of fwhm

Dear experts, I have a error message when I use the command : mdi_glmfit-sim ‹glmdir X ‹cwpvalthresh 0,001 ‹cache 3 abs ERROR : cannot find /usr/local/freesurfer/average/mult-comp-cor/fsaverage_sym/lh/cortex/fwhm00/a bs/th20/mc-z.csd I don't understand why because to create this glmdir I use a

[Freesurfer] display selected gyrus in specific color

Dear freesurfer experts, I try to combine some selected gyrus and display them all in red color, other brain structures will keep in gray color in freeview. I search for color lookup table page but don't know if I need to change the .annot file or not. How to correctly do that ? sincerely JL___

Re: [Freesurfer] FLASH params for mri_em_register

Hi Doug sorry to nudge - any thoughts on lta tweaking? cheers, Fred On 30 Apr 2013, at 16:44, Bruce Fischl wrote: > Hi Fred, > > I'll have to defer to Doug on this > Bruce > On Tue, 30 Apr 2013, Fred Dick wrote: > >> Hi Bruce >> >> >> On 30 Apr 2013, at 13:36, Bruce Fischl wrote: >> >