Re: [Freesurfer] White/pial surface failure

Hi Trevor would you consider moving to V6? The high res stream is *much* better in it than 5.3. If you can't, upload the subject and we will take a look cheers Bruce On Thu, 14 Dec 2017, Trevor K Day wrote: Hello,   We are trying to run the high-resolution pipeline and it has failed sp

Re: [Freesurfer] ?h.DKTatlas100.gcs to annot

Do you want to do it from your own data? If so, then use annot2std run it with --help to get more details On 12/13/2017 11:16 AM, tony han wrote: > > Hi, > > > Is it possible to get an annot file for ?h.DKTatlas100.gcs, not for > individuals, but for fsaverage atlas? I want to plot the 'standar

Re: [Freesurfer] JRE error in fsfast/matlab

Can you try something for me? Run your command with -monly sxa.m This will create the sxa.m file. Then start matlab and run that file On 12/13/2017 03:19 PM, Yagmur Ozdemir 19 wrote: > Yes it terminates prematurely. > > Best > Idil > > From: freesurfer-bo

Re: [Freesurfer] mri_surf2surf on edited subjects

Can you send the terminal output? Also, can you check the  number of vertices in the xhemi folder and make sure that the lh in the xhemi matches the rh in the main folder? On 12/13/2017 05:13 PM, Defenderfer, Matthew K wrote: > > Hi all, > > > I am trying to transfer a surface file from fsavera

Re: [Freesurfer] Qdec Table Loading Error

there are lots of strange characters in that file (as revealed with the od octal dump program). Maybe run dos2unix on the file or create it from scratch. On 12/14/2017 12:00 PM, Arsenije Subotic wrote: > > Hi Douglas, > > > I tried doing that but it seems that the issue is that when I open >

Re: [Freesurfer] A note about the Freesurfer license file

Hi Mike, Is it possible that freesurfer is reading the wrong license file? What are you naming the new license as? FS could be reading a hidden “.license” file in FREESURFER_HOME instead. best, Andrew > On Dec 7, 2017, at 4:35 PM, Angstadt, Mike wrote: > > I am getting this same glibc messa

Re: [Freesurfer] free surfer v5 & 6

Hi Lilla we have a large dataset already processed with FSv5.1; before processing it with FSv6, we thought to assess -on a smaller subset - how significant are the differences between the measurements output by the two versions. On the other point, my question was about differences between the

Re: [Freesurfer] White/pial surface failure

Hi Bruce, My apologies, I had forgotten that we had set FREESURFER_HOME up in our pipelines separately, and had I just got the version off of my shell. We are using freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Should I upload the subject somewhere? Thanks, Trevor From: Bruce Fisch

Re: [Freesurfer] A note about the Freesurfer license file

Andrew, Thank you for suggesting that. Turns out that's exactly what seems to have been the problem. Renamed the .license file and now things seem to be working. Not sure why there was even a .license file there, as I've been using license.txt as directed in the installation instructions and em

Re: [Freesurfer] White/pial surface failure

sure, our ftp site Bruce On Thu, 14 Dec 2017, Trevor K Day wrote: Hi Bruce,   My apologies, I had forgotten that we had set FREESURFER_HOME up in our pipelines separately, and had I just got the version off of my shell.   We are using freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb9

[Freesurfer] Correlation between CTh and Clinical Data

Dear Experts: I am very new to freesurfer glmfit and this post may seem dumb. I wanted to find the correlation between Cth and Education for each of HC and RRMS group regressing out the effect of gender and (demeaned) age. My fsgd file is something like below. GroupDescriptorFile 1 Title

[Freesurfer] Issue with Freesurfer installation

I just recently followed the steps to install Freesurfer on my Mac. The installation initially seems to have gone fine, but when I try to test the installation by using the listed "Example 1: Convert the sample-001.mgz to nifti format," I get the following error: freesurfer-Darwin-OSX-sta

[Freesurfer] mri_nlfilter

Dear Dr Bruce, Kindly, I have question regarding the command "mri_nlfilter". I am sorry if my questions is simple, but I highly appreciate any explanation to improve my understanding. I see in the man list of the command "mri_nlfilter" that it can apply Gaussian filtering and blurring kernell.

Re: [Freesurfer] mri_nlfilter

Hi John mri_nlfilter implements what I think is the first example of nonlocal filtering/nonlocal means from this paper: http://ieeexplore.ieee.org/document/745732/ it tries to avoid displacing edges as happens in straight Gaussian filtering cheers Bruce On Thu, 14 Dec 2017, John Anderson w

[Freesurfer] mri_cnr with mask

Is it possible to get CNR info on a masked region? I have tried these commands but see only unexpected tiny values or NaN for results: mri_binarize --i $SUBJECTS_DIR/$subj/mri/aseg.mgz --match $mndx --o $tmpmask mri_mask $SUBJECTS_DIR/$subj/mri/norm.mgz $tmpmask $norm_tmpmask mri_cnr $SUBJECTS_D

Re: [Freesurfer] White/pial surface failure

Thanks, uploaded as 170661-T1_256.nii.gz Trevor From: Bruce Fischl Sent: Thursday, December 14, 2017 11:29 AM To: Freesurfer support list Subject: Re: [Freesurfer] White/pial surface failure sure, our ftp site Bruce On Thu

Re: [Freesurfer] White/pial surface failure

Hi Trevor we need the whole subject dir tarred and gzipped. cheers Bruce On Thu, 14 Dec 2017, Trevor K Day wrote: Thanks, uploaded as 170661-T1_256.nii.gz   Trevor   From: Bruce Fischl Sent: Thursday, December 14, 2017 11:29 AM To: Freesurfer support list Subject: Re: [Freesurfer] White

Re: [Freesurfer] White/pial surface failure

Gotcha, uploaded From: Bruce Fischl Sent: Thursday, December 14, 2017 3:39 PM To: Freesurfer support list Subject: Re: [Freesurfer] White/pial surface failure Hi Trevor we need the whole subject dir tarred and gzipped. ch

[Freesurfer] Job Posting: Research Methods Specialist for Psychiatry Neuroimaing Lab, Toronto

The Kimel Family Translational Imaging-Genetics Laboratory is a large multidisciplinary research laboratory dedicated to discovering the causes of severe mental illness and advancing treatments for severe mental illness. The focus of the laboratory is on combining brain imaging and genetics, brain

Re: [Freesurfer] Issue with Freesurfer installation

Hi Scott, It looks like "/Users/scottpruett/sample-001.mgz" doesn’t exist because your cp command never ran (you have to specify a destination). Try: cp $FREESURFER_HOME/subjects/sample-001.mgz . best, Andrew On Dec 14, 2017, at 4:00 PM, Pruett, Scott mailto:brandon_pru...@brown.edu>> wrote: