Re: [Freesurfer] "Can't locate shellwords.pl" error

When there is an alignment failure using the talairach method freesurfer reverts to mni tools. The mni tools will error out with mritotal on more modern linux platforms because mritotal references shellwords.pl which no longer ships with perl (starting around 5.14). So in order to solve this erro

[Freesurfer] 6.0 release date?

Dear FS experts, My colleagues and I are planning some projects and we were wondering if there are any news on the release date of the FreeSurfer 6.0 stable version. We noticed that there was a new developmental version released today, is that good news? An approximation of whether it will be a m

Re: [Freesurfer] 6.0 release date?

We actually have a tentative date of Dec 21 (next Wednesday!). In the middle of testing now On 12/15/2016 11:09 AM, Bruce Fischl wrote: > Hi Renata > > > we are hoping it goes out in either late Dec or early-to-mid Jan, but of > course it depends on it passing lots of tests, so we can't say for

Re: [Freesurfer] 6.0 release date?

Hi Renata we are hoping it goes out in either late Dec or early-to-mid Jan, but of course it depends on it passing lots of tests, so we can't say for sure cheers Bruce On Thu, 15 Dec 2016, Vaz pandolfo, Renata wrote: > Dear FS experts, > > My colleagues and I are planning some projects and

Re: [Freesurfer] 6.0 release date?

Awesome, thanks! Cheers, Renata On Thu, Dec 15, 2016 at 5:15 PM, Douglas N Greve wrote: > We actually have a tentative date of Dec 21 (next Wednesday!). In the > middle of testing now > > > On 12/15/2016 11:09 AM, Bruce Fischl wrote: > > Hi Renata > > > > > > we are hoping it goes out in eithe

Re: [Freesurfer] 6.0 release date?

Okay, thank you! Cheers, Renata On Thu, Dec 15, 2016 at 5:09 PM, Bruce Fischl wrote: > Hi Renata > > > we are hoping it goes out in either late Dec or early-to-mid Jan, but of > course it depends on it passing lots of tests, so we can't say for sure > > cheers > Bruce > > > On Thu, 15 > Dec 20

Re: [Freesurfer] problem of using freesurfer

I download mri_coreg from this website to put it on my virtual machine ubuntu \local\user\freesurfer\bin directory. But I run it and it say https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_coreg \local\user\freesurfer\bin\mri_coreg can not execute binary file? Do you know why? Thanks Fran

Re: [Freesurfer] how to make label from volumetric mask?

You need to include a --surf arg to mri_cor2label. Look at the --help On 12/15/2016 09:41 AM, Niia Nikolova wrote: > Dear Freesurfers, > > I have some binary ROI masks of MT/V5 that I’ve drawn from activation > maps in fslview, which I would like to transform into labels so that I > can project

[Freesurfer] mri_coreg question

Hello FS experts I followed the instruction to download the mri_coreg file from website https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_coreg put it on my virtual machine ubuntu \local\user\freesurfer\bin directory. But I run it and it say

Re: [Freesurfer] incorrect pial surfaces after watershed adjustment

not without more information. If you upload the tar and gzipped subject directory and give us a set of voxel coords that you want us to look at we will take a look cheers Bruce On Wed, 14 Dec 2016, Rizvi, Batool wrote: > Hi Bruce, > > Running -autorecon2 -autorecon3 did not seem to fix the surf

[Freesurfer] Infant brain atlas

I asked this last week with no response: Does the infant brain atlas mentioned in this paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4332305/ exist yet or will it be included in version 6? Thanks Eric Axelson Research Specialist Department of Psychiatry University of Iowa eric-axel...@uio

Re: [Freesurfer] problem of using freesurfer

I usesudo chmod u+x mri_coreg, so it should can be run. Frank Yu On Thu, Dec 15, 2016 at 10:51 AM, Frank Robert wrote: > > I download mri_coreg from this website to put it on my virtual machine > ubuntu \local\user\freesurfer\bin directory. But I run it and it say > > https://gate.nmr.mgh.

Re: [Freesurfer] Infant brain atlas

The manually segmented brains exist. They will not be part of FS 6.0, but we are planning an independent release for them early next year. Lilla On Thu, 15 Dec 2016, Axelson, Eric D wrote: I asked this last week with no response:   Does the infant brain atlas mentioned in this paper http

Re: [Freesurfer] mri_coreg question

My guess is that your Ubuntu virtual machine is 32bit? If so it will not be able to run our 64bit binaries. We no longer build 32bit binaries. On 12/15/2016 12:07 PM, Frank Robert wrote: > Hello FS experts > > I followed the instruction to download the mri_coreg file from website > > > https://ga

Re: [Freesurfer] mri_coreg question

Hello ZK Yes, Ubuntu is 32-bit. I installed it half-year ago, only had such version. Does FreeSurfer provide 64-bit ubuntu version on Windows? Best Regards Frank Yu On Thu, Dec 15, 2016 at 3:18 PM, Z K wrote: > My guess is that your Ubuntu virtual machine is 32bit? If so it will not > be ab

[Freesurfer] (no subject)

Hi I am using freesurfer for calculation cortical thickness in my subjects. Firstly, I have converted all the T1 weighted images from dcm into nii.gz format. After that, I have run the recon-all in one subject using this script 'recon-all -i CON_101.nii -s CON_101 -all' , but it shows error The

Re: [Freesurfer] (no subject)

Is CON_101.nii in the/home/kumarlab/Downloads/Freesurfer_VBM folder? If not, you must specify the full path to the the file On 12/15/2016 06:26 PM, Sadhana Singh wrote: > Hi > > I am using freesurfer for calculation cortical thickness in my subjects. > > Firstly, I have converted all the T1 weig

Re: [Freesurfer] (no subject)

Hi Sadhana is the file CON_101.nii or CON_101.nii.gz? If the latter, you should give that to recon-all. There is also no need to convert to nifti - you can give recon-all a *single* file in the correct dicom series and it will happily to its thing cheers Bruce On Thu, 15 Dec 2016, Sadhana S

[Freesurfer] questions about registration tool in Freesurfer

Dear FS experts I want to use Freesurfer registration tools. I check https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferCommandsRegistration?highlight=%28modality%29 1). Here it is the term " modality" I want to get clarification. It is easy to know Modality is different between CT, MRI and

Re: [Freesurfer] Revisiting GM ROI list

Hi- Just gently re-bumping this question/thread. Noting that the previous thread with recommendations about non-GM ROIs, which I used in the coming up with the GM list above, is here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50005.html Thanks, pt On Mon, Dec 12, 2016 at