Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer

External Email - Use Caution Thank you! So the answer to the first question is that yes I can convert it back to a curvature file and that curvature file can be loaded as an overlay. So this must mean that the problem is with reading the .asc file rather than the file being co

[Freesurfer] Postdoctoral positions available

Multiple Postdoctoral Positions in Computational Neuroscience Available at Boston University, and beyond. Three, NIH-supported postdoctoral positions in computational neuroscience are available immediately at Boston University in the labs of Uri Eden and Mark Kramer. The positions center on

[Freesurfer] Postdoctoral positions available

Three, NIH-supported postdoctoral positions in computational neuroscience are available immediately at Boston University in the labs of Uri Eden and Mark Kramer. The positions center on two projects: Project: Measure, model, and modulate cross-frequency coupling. Team: An interdisciplinary team

Re: [Freesurfer] qdec analysis with more than 2 covariates

External Email - Use Caution Hi Doug, Thank you for your response. I tried the link which you sent yesterday. But got stuck while creating qdec.fsgd file. Below i have pasted the terminal output after loading the data. 1 Left-Lateral-Ventricle continuous 0 2 Left-Inf-Lat-Vent

Re: [Freesurfer] Longitudinal stream : LME and limits of model

External Email - Use Caution Hi Martin, It's been a long time since this discussion but I return on this from now... The problem is that I followed longitudinal images of two groups where I had mainly missing time points at the end. Than you suggested: *If you have mainly missing

Re: [Freesurfer] FreeSurfer Errors (2)

can you send the command-line output as text? On 10/16/2018 11:12 AM, Sparsh Jain wrote: > > External Email - Use Caution > > Hey! > I sent two responses on Friday. The second response was bigger than 1 > MB so it awaited moderator approval. I don't know if you received it > eventually.

Re: [Freesurfer] Correction Needed for the Midline

Hi Maxime, I'm having trouble finding your data - can you please use the filedrop instead? https://gate.nmr.mgh.harvard.edu/filedrop2/ Thanks, Bram From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Maxime Perron Sent: Friday, October 12, 2018 11:17:0

Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer

Hi Amanda can you try it in freeview? tksurfer has been deprecated for a while now cheers Bruce On Tue, 16 Oct 2018, Worker, Amanda wrote: External Email - Use Caution Thank you! So the answer to the first question is that yes I can convert it back to a curvature file and

[Freesurfer] Adding longitudinal time points to clean dataset {Disarmed}

External Email - Use Caution Hello Freesurfer experts, We have a large longitudinal dataset (n=~200) of up to 4 time points per participant. All images were processed using Freesurfer v6.0 and have already undergone QA, and editing the cross, Base or long where needed. We are

[Freesurfer] updateing freesurfer.

External Email - Use Caution I tried updating freesurfer 6.0 using the command fs_update. I get the following output. > Build is freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c > >Running this will update some of your freesurfer binaries. > > Shall I proceed? [y/

Re: [Freesurfer] Correction Needed for the Midline

External Email - Use Caution Hi Bram, No worries. Here is the link : http://gate.nmr.mgh.harvard.edu/filedrop2/?a=al9nxdabh5h Thanks, Maxime  On Oct 16, 2018, at 1:11 PM, Diamond, Bram Ryder wrote: Hi Maxime, I'

Re: [Freesurfer] Correction Needed for the Midline

External Email - Use Caution Sorry. Here are the good links :  http://gate.nmr.mgh.harvard.edu/filedrop2/?p=1maf5ah0hw0 http://gate.nmr.mgh.harvard.edu/filedrop2/?p=abmzg2jvk9t Maxime  On Oct 16, 2018, at 2:22 PM, Maxime Perron wrote:

Re: [Freesurfer] Correction Needed for the Midline

Hi Maxime, What did you edit in the aseg? It looks like the CC_* have been mislabeled. Bram From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Maxime Perron Sent: Tuesday, October 16, 2018 2:23:22 PM To: Freesurfer support list Subject: Re: [Freesurf

Re: [Freesurfer] Nonsensical Vertex Coordinates, please help with interpretation

When you look at the vertex in matlab, are you correctly accounting for the fact that FreeView uses 0-based indexing and matlab uses 1-based? Eg, vertex 234741 in Freeview would be 234742 in matlab. You seem to be using 234740 in matlab below On 10/15/2018 05:11 PM, Bruss, Joel E wrote: > >    

Re: [Freesurfer] Correction Needed for the Midline

External Email - Use Caution Hi Bram, I modified the label of the lateral ventricules because they were mislabeled too (Freesurfer_S043_test). I didn't change the label of the CC_*. Do you think that can fix the middle line? ​  Thanks, Maxime De : freesurfer-bo

Re: [Freesurfer] create label from cluster obtained with mri_glm-fit-sim

Hmm, not sure what to tell you. The label is derived directly from the annot. If you click on a vertex in the branch, does it appear to be in the label based on what displays in the control panel? If you load it on the inflated surface, do you still see the branch? On 10/15/2018 08:42 PM, Ting

Re: [Freesurfer] qdec analysis with more than 2 covariates

That looks like the terminal output for qdec. You cannot use qdec with your design. If you have questions about the FSGD, I'll be happy to answer them. On 10/16/2018 11:00 AM, vittal korann wrote: > > External Email - Use Caution > > Hi Doug, > > Thank you for your response. > I tried th

Re: [Freesurfer] Correction Needed for the Midline

Possibly - I would definitely start there. The surfaces are following the corpus callosum into the right hemisphere because the aseg labeling is off. Best, Bram From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Maxime Perron Sent: Tuesday, October 1

[Freesurfer] fsfast preproc-sess: viewing preproc surface outputs

External Email - Use Caution Hi FS Team, We are running our first fsfast pipeline, and starting with a single subject to test everything. We successfully ran preproc-sess with the following command: preproc-sess -s 11987_20180731 -surface fsaverage lhrh -mni305 -fwhm 5 -per-run -

Re: [Freesurfer] Correction Needed for the Midline

External Email - Use Caution There surely seems to be a link indeed; I'll look at where to correct the labeling and will give you feedback on the result. In the meantime, should you have any advice on such an optimal way, I'll be glad to hear it. I'll keep you posted soon

Re: [Freesurfer] [External] Re: Nonsensical Vertex Coordinates, please help with interpretation

External Email - Use Caution I couldn't remember if it's 1+ or 1-. Either way, either direction give similar coordinates that don't match up to what I can see in FreeView. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Greve, Douglas

Re: [Freesurfer] [External] Re: Nonsensical Vertex Coordinates, please help with interpretation

which coords are you looking at? They should be the "surface RAS" coords. On 10/16/2018 04:05 PM, Bruss, Joel E wrote: > > External Email - Use Caution > > I couldn't remember if it's 1+ or 1-.  Either way, either direction > give similar coordinates that don't match up to what I can see

Re: [Freesurfer] fsfast preproc-sess: viewing preproc surface outputs

You can load them in freeview through tksurferfv, something like tksurferfv fsaverage lh inflated -aparc -ov fmcpr.odd.sm5.fsaverage.lh.nii.gz There's not much to see:) On 10/16/2018 03:00 PM, Jacob Matthews wrote: > > External Email - Use Caution > > Hi FS Team, > > We are running our

Re: [Freesurfer] FreeSurfer Errors (2)

External Email - Use Caution I attached that to the previous email, but it got rejected by the moderator for some reason! Sparsh On Tue, Oct 16, 2018 at 1:03 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > can you send the command-line output as text? > > On 10/16/

Re: [Freesurfer] create label from cluster obtained with mri_glm-fit-sim

External Email - Use Caution If I loaded the label to the inflated surface, it also gives me the cluster with branches. As you can see in the below. If I loaded the annot file to the inflated surface, it works well. Thanks for your help. Ting > On Oct 16, 2018, at 1:51 PM

[Freesurfer] Raw Data for Clusters

External Email - Use Caution Dear FreeSurfer Experts, I am running Qdec 1.4 and I want to extract raw data (in this case, volume) from the significant clusters after Monte-Carlo simulation. In this particular case, the summary file shows 5 significant clusters after correction: #