Re: [Freesurfer] trac-all using nifti

External Email - Use Caution Hi Anastasia, Sure, I will try that. Thanks for the advice! Regards, Heidi On Fri, Sep 21, 2018 at 4:49 PM Yendiki, Anastasia wrote: > You need to specify one more option, like -prep, etc. Please follow the > instructions on the tutorial and, if th

Re: [Freesurfer] trac-all using nifti

You need to specify one more option, like -prep, etc. Please follow the instructions on the tutorial and, if the problem persists, send the exact command line that you ran and the full text of the output that you got. On Sep 21, 2018 2:42 AM, Heidi Emmanuel Foo wrote: External Email -

Re: [Freesurfer] trac-all using nifti

External Email - Use Caution Hi Anastasia, I think I ran trac-all -c config.txt. Regards, Heidi On Thu, Sep 20, 2018 at 10:18 PM Yendiki, Anastasia < ayend...@mgh.harvard.edu> wrote: > What is the trac-all command line that you run? > -- > *From:* fr

Re: [Freesurfer] Ynt: linux data and macbook

sorry, we need way more detail On 9/20/18 11:59 PM, emre wrote: External Email - Use Caution thalamus and hippocampus Gönderen Outlook Gönderen: Greve, Douglas N.,Ph.D. adına freesurfer-boun...@

[Freesurfer] Ynt: linux data and macbook

External Email - Use Caution thalamus and hippocampus Gönderen Outlook Gönderen: Greve, Douglas N.,Ph.D. adına freesurfer-boun...@nmr.mgh.harvard.edu Gönderildi: 21 Eylül 2018 Cuma 00:15 Kime: freesurfer@nmr.mgh.harvard

[Freesurfer] Dead Links to 3rd Party Libraries

External Email - Use Caution Hi, I’m trying to build Freesurfer according to the instructions athttp://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page However, the FTP link to prebuilt 3rd party libraries seems to be down. The directory “ftp://surfer.nmr.mgh.

Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault

Hi Matt - I am asking about the raw diffusion images. You sent a screenshot of an FA map that looked truncated, with slices missing from the bottom of the brain (which explains why the error happened for the ILF, which would go through that missing part of the brain). Does dmri/dwi.nii.gz look l

[Freesurfer] segmentThalamicNuclei.sh do not produce .stats

External Email - Use Caution Hi list, the segmentThalamicNuclei.sh do not produce thalamic-nuclei.lh.v10.T1.stats. All the other files are produced (ThalamicNuclei.v10.T1.volumes.txt/mgz). The segmentation viewed by freeview is fine. Thanks. Stefano___

Re: [Freesurfer] linux data and macbook

what segmentation? On 09/20/2018 12:53 PM, emre wrote: > > External Email - Use Caution > > > hi freesurfer team, > > I analyzed the data at linux, this data i can use in macbook for > segmantation? > (linux only reconall -all, other analyze in macbook) > > Is it possible without problems

[Freesurfer] ERROR: no voxels found in segmentation- Outputs of segmentThalamicNuclei.sh in FS-FAST

External Email - Use Caution Hi I'm using as seed in FS-FAST the outputs of segmentThalamicNuclei.sh. However when I run fcseed-config -segid 8103 -fcname L_AV.dat -fsd rest -mean -cfg mean.L_AV.config fcseed-sess -sf sessid -cfg mean.L_AV.config this error occurs: Voxel Vol

Re: [Freesurfer] asegstats2table - env: python2: No such file or directory

External Email - Use Caution > On September 20, 2018 at 9:12 PM std...@virgilio.it wrote: > > > External Email - Use Caution > > I'm using last version dev with MacOS High Sierra 10.13.6. > > I have run, for each subject: > > segmentThalamicNuclei.sh > I don't

[Freesurfer] asegstats2table - env: python2: No such file or directory

External Email - Use Caution I'm using last version dev with MacOS High Sierra 10.13.6. I have run, for each subject: segmentThalamicNuclei.sh but when I run the command line "asegstats2table", I obtain: env: python2: No such file or directory Thanks Stefano___

Re: [Freesurfer] Reporting Cohen's D for a significant cluster

Hi Bruce, Thank you so much for the tip and the quick response. For some reason, the position and Cohen’s D value do not change when I input the vertex and I think this might be due to an outdated Freeview version (2.0) that I am using. I attempted to load the new one from this link: https://sur

Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault

External Email - Use Caution If you are referring to the T1 raw images, no they appear normal and the standard Freesurfer pipeline generates correct volumes. If you are referring to the DTI raw images off the scanner, they also don't appear to have brain parts missing, although so

[Freesurfer] linux data and macbook

External Email - Use Caution hi freesurfer team, I analyzed the data at linux, this data i can use in macbook for segmantation? (linux only reconall -all, other analyze in macbook) Is it possible without problems? thanks, good luck Gönderen Outlook __

[Freesurfer] Clarification about .annot file format

External Email - Use Caution Howdy, There is a discussion regarding the .annot file format over at the nibabel github repository, regarding the interpretation of the flag/alpha value: https://github.com/nipy/nibabel/issues/649 If one wishes to create an .annot file with colours

Re: [Freesurfer] Reporting Cohen's D for a significant cluster

Hi Arkadiy if you have the surface loaded you can always type a vertex number into the info field (that shows the current selected vertex) at the bottom of the freeview window. It will then jump to that vertex, and adjust the views accordingly cheers Bruce On Thu, 20 Sep 2018, Maksimovskiy,

Re: [Freesurfer] Reporting Cohen's D for a significant cluster

Update: It occurred to me that reporting it for the max verted might be the best idea. In this case, might anyone know what is the best way to navigate the Freeview to a specific vertex number (is there a place where I can input that number). Thanks again. From: "Maksimovskiy, Arkadiy" Date: T

[Freesurfer] Reporting Cohen's D for a significant cluster

Dear Experts, I was requested to report the Cohen’s D value for a significant cluster, which resulted from a cortical thickness analysis. I was able to calculate it and open the resulting Cohen’s D mgh file in Freeview, together with the file, indicating a significant cluster. As expected, when

Re: [Freesurfer] Troubles to determine the type of recon editing needed

Hi Matthieu only recon2 will use it, but you can specify it for all of them cheers Bruce On Wed, 19 Sep 2018, Matthieu Vanhoutte wrote: External Email - Use Caution Dear Bram, According recon-all help "If a subject has enlarged ventricles due to atrophy, include the -bigven

[Freesurfer] Error running recon-all

External Email - Use Caution Hi. I am getting the following error trying to run recon-all (with Version 6.0), it is failing while running the routine mri_nu_correct.mni: Can't locate MNI/Startup.pm in @INC (@INC contains: /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64

Re: [Freesurfer] error with trac-all -prep

External Email - Use Caution Thanks Anastasia, I'll give this approach a try. On Thu, Sep 20, 2018 at 8:31 AM Yendiki, Anastasia wrote: > That's correct! You can source the setup script of whichever version you > need to use. > -- > *From:* freesurfer

Re: [Freesurfer] error with trac-all -prep

That's correct! You can source the setup script of whichever version you need to use. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Vinny K Sent: Thursday, September 20, 2018 8:25:31 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] e

Re: [Freesurfer] error with trac-all -prep

External Email - Use Caution Hi Anastasia, Thanks for your reply. I needed the dev version in order to utilize the new thalamic segmentation nuclei tool: http://freesurfer.net/fswiki/ThalamicNuclei I'll download the stable one as well and use that one for Tracula. I'm assuming

Re: [Freesurfer] error with trac-all -prep

Hi Vinny - Unless there was a specific reason why you were using a dev version (a feature that you needed and wasn't working in the stable one), please use the stable one in general. Best, a.y From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Vinny K

Re: [Freesurfer] trac-all using nifti

What is the trac-all command line that you run? From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Heidi Emmanuel Foo Sent: Wednesday, September 19, 2018 11:06:09 PM To: Freesurfer support list Subject: Re: [Freesurfer] trac-all using nifti Ext

Re: [Freesurfer] error with trac-all -prep

External Email - Use Caution Hi Anastasia, A similar post had encountered a similar problem a while back: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-July/046979.html Should I install the latest stable release of FreeSurfer and run only the trac-all -prep step us

[Freesurfer] freeview automated screenshots using color wheel scale & qt library issues

External Email - Use Caution Hi, I am attempting to generate automated screenshots with freeview version 3.July 2018 and I noticed that when applying the color wheel option for a surface overlay the coloring would be wrongly applied and I would need to enter the configuration wind

[Freesurfer] mris_fill ERROR: dyld: lazy symbol binding failed:

External Email - Use Caution Hello freesurfer experts, when trying to run ‘ft_prepare_mesh’ command from fieldtrip with MATLAB R2018a, I run into an error. dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/.