Re: [Freesurfer] Thalamic Nuclei segmentation results

External Email - Use Caution Hi Vasudev, What lookup table are you using to visualize the results? Are you using FreeView from the development version, and visualizing the segmentation with the default lookup table? Cheers, /Eugenio Juan Eugenio Iglesias Centre for Medical

[Freesurfer] Thalamic Nuclei segmentation results

External Email - Use Caution Dear all, I have used Freesurfer pipeline for Thalamic Nuclei segmentation, the results of segmentation appear to be very poor, i am annexing the results , please kindly review if there is any thing wrong with the segmentation results. Thanks

Re: [Freesurfer] recon-all terminated in middle : continuing an analysis of an existing subject

Hi Vasudev, if you're using freesurfer 6.0 or the development version, you can update the recon-all makefile by running the following (this might require sudo): cd $FREESURFER_HOME/bin mv recon-all.makefile recon-all.makefile.backup curl

Re: [Freesurfer] masking cortical thickness

Use the --outmask option On 10/07/2018 08:59 AM, N Saf wrote: > > External Email - Use Caution > > Dear Douglos, > > I did not understand how to use mri_label2label with the mask > option(there is srcmask options not mask alone !). I extract my labels > and as you explained I wanted to

Re: [Freesurfer] nu_correct disk i/o issues

BTW, this should not be a problem in the next version On 10/07/2018 08:29 AM, Jasper van den Bosch wrote: > > > Michael, I can't thank you enough. > > Knowing that it writes to /tmp made all the difference. > In my case I mounted an external directory on /tmp instead of the > sessiondir

Re: [Freesurfer] Extract individual vertex thickness values from cortical parcellations

You can use matlab. read_curv.m will read in a thickness. read_annotation.m will read in the annotation. Look at the help in both for more info On 10/06/2018 11:36 AM, lindsay hanford wrote: > > External Email - Use Caution > > Hello Freesurfer Community, > > I am looking for a way to

Re: [Freesurfer] very bad result using "mris_ca_train" and "mris_ca_label"

Hi Maedeh the surface file should be the one that defines the common coordinate system (usually sphere.reg) and the annotation should refer to a file in the subject's label dir. Every subject in your list must have both files. cheers Bruce On Tue, 9 Oct 2018, Maedeh Khalilian wrote:  

Re: [Freesurfer] Talairach failed in monkey brain

The file passed to --reg should be a registration file. This is a text file with the transformation matrix and a few other things, not a volume file. On 10/8/18 5:28 PM, Frehiwot Woldeyes wrote: External Email - Use Caution Hello Freesurfers, I was attempting to reconstruct a monkey

Re: [Freesurfer] Recon-all with/without T2 give the same stats

But are the lh.thickness files the same or different? On 10/9/18 1:46 AM, Jianzhong Chen wrote: External Email - Use Caution Hi Dr. Greve, I checked the lh.aparc.stats and rh.aparc.stats, the thicknesses (and the other measures like volume and area) are all the same. Thanks,

[Freesurfer] very bad result using "mris_ca_train" and "mris_ca_label"

External Email - Use Caution Dear Dr.Bruce Fischl Thank you very much for your great sense of responsibility. Sure, i have sent you a zip file named "Maedeh_results"(it was a rather big sized one so i had to send it through Wetranser). Hope you have received it. However, a

[Freesurfer] m.khalil...@sutech.ac.ir sent you files via WeTransfer

External Email - Use Caution m.khalil...@sutech.ac.ir sent you some files 1 file, 378 MB in total ・ Will be deleted on 16 October, 2018 Download link: