Re: [Freesurfer] mri_robust_template- Segmentation Fault

The link works for me. You can also try ftp instead of http. Best, Martin On Thu, 2012-06-28 at 14:41 -0400, Usman Khan wrote: > Hi there Freesurfer, > I am running into a seg fault while running mri_robust_template on > freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 on a Centos6.2 > build.

[Freesurfer] mri_robust_template- Segmentation Fault

Hi there Freesurfer, I am running into a seg fault while running mri_robust_template on freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 on a Centos6.2 build. Thinking that this may perhaps be an OS-related issue, I tried to download FS binaries from http://www.freesurfer.net/pub/dist/freesurfer/

Re: [Freesurfer] Pial and WM boundary edits

Hi Skyler after adding control points one usually runs: recon-all -subjid -autorecon2-cp -autorecon3 cheers Bruce On Thu, 28 Jun 2012, Skyler Gabriel Shollenbarger wrote: > To whom it may concern, > > After running autorecon2 (recon-all -subjid -autorecon2) there were > areas that

Re: [Freesurfer] lh.pial question

you could create a patch by cutting them out in tksurfer On Thu, 28 Jun 2012, Borzello, Mia wrote: > Hi all, > > Is there a way to edit the pial files (e.g. lh.pial)? I want to delete a few > vertices we think are causing errors for a 3D printing we are trying to do. > > Thanks, > m > >

[Freesurfer] Pial and WM boundary edits

To whom it may concern, After running autorecon2 (recon-all -subjid -autorecon2) there were areas that required correcting for both the pial and WM boundaries. I added control points to correct the WM boundaries and saved them using File > Save Control Points. I also used the select vo

Re: [Freesurfer] TRACULA question: pathstats.overall.txt

Thank you very much. We would like to do the weighted measure, as we believe it would be more sensitive and robust to WM abnormalities in our patient population. Minjie On Thu, Jun 28, 2012 at 11:52 AM, Anastasia Yendiki wrote: > > Yes, if you wanted to do a weighted average of your measure. O

[Freesurfer] Building ROI from SPM5 MNI results

Hi Everyone, I would like to "import" an ROI into a FS analysis and extract thickness measures form within this region. Is this at all possible? Thanks Anson K, ** Electronic Mail is not secure, may not be read every day, and should not be

Re: [Freesurfer] TRACULA question: pathstats.overall.txt

Yes, if you wanted to do a weighted average of your measure. Or you could just theshold and binarize path.pd and use it a simple ROI to do an unweighted average. On Thu, 28 Jun 2012, Minjie Wu wrote: > Dear Dr. Yendiki, > > Thank you very much for your quick response. To calculate the weighted

[Freesurfer] lh.pial question

Hi all, Is there a way to edit the pial files (e.g. lh.pial)? I want to delete a few vertices we think are causing errors for a 3D printing we are trying to do. Thanks, m ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.

Re: [Freesurfer] TRACULA question: pathstats.overall.txt

Dear Dr. Yendiki, Thank you very much for your quick response. To calculate the weighted DTI measure, per your previous emails, we would need to normalize path.pd.nii.gz, right? If this is the case, we could use the following equation correct for weighted measurement: dti_para (DTI parameter imag

Re: [Freesurfer] TRACULA question: pathstats.overall.txt

Hi Minjie - These commonly used measures are provided for your convenience. You can always use the reconstructed path distribution volume path.pd.nii.gz, thresholded or not, as a mask to average your measurement of choice. a.y On Thu, 28 Jun 2012, Minjie Wu wrote: > Dear TRACULA Developer &

[Freesurfer] Recent paper on FreeSurfer reliability

Dear Bruce, Doug, Nick, and other co-workers, As authors of the recent paper “The effects of FreeSurfer version, workstation type, and Macintosh operating system version on anatomical volume and cortical thickness measurements” we would like to take the opportunity to respond to the numerous

[Freesurfer] Corrections in Skull Stripping lead to changes in aseg.stats - underlying reasons

Hello, After making some corrections to the skull stripping (by hand) and running recon-all I was really puzzled to notice that there had been changes in the aseg.stats. Here are the statistics: # Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter volume, 222913.677586, mm^3 # M

[Freesurfer] Hippocampal segmentation doubts

Dear Freesurfer expertsI'm starting to deal with the FS v5.1 hippocampal subfields segmentation, and I have a couple doubts...If I have my subjects segmented from an older FS version, Would be any problem when running the -hippo-subfields?I'm guessing not, but I wanna be sure. Because, as I've look

[Freesurfer] TRACULA question: pathstats.overall.txt

Dear TRACULA Developer & User, I am wondering if it is possible to add other DTI measurements to the pathstats.overall.txt along with those DTI parameters already included (FA, MD, AD, RD)? Thank you very much. Minjie ___ Freesurfer mailing list Freesur