Re: [Freesurfer] V1 Atlas ( brodman maps)

Thank you Dr Bruce, I want to calculate PET signal in each Brodman map! I will give an example: If I want to caclulate PET singal for every parcellate and segment in the atlas "wmparc.mgz". I do the following:   bbregister  --t1 --mov T1.nii.gz --init-fsl --reg t1.reg.dat --s SUBJID    mri_vo

Re: [Freesurfer] X graphics issues via SSH

On 11 May 2016 at 16:03, Rockers, Elijah D. wrote: > Running a Mac Pro, OS X El Capitan 10.11.4 > With ATI Radeon Graphics card, and XQuartz v 2.7.9 > > I am able to run Qdec and freeview perfectly fine on my machine. The problem > comes when I attempt to SSH into another machine and use these pr

Re: [Freesurfer] V1 Atlas ( brodman maps)

Hi John recon-all should create lh.BA.annot and rh.BA.annot parcellations that contain all the Brodmann areas we know how to label cheers Bruce On Thu, 12 May 2016, John Anderson wrote: Dear experts,  I want to use the atlas V1 to calculate PET signal for Brodman areas. How can I create th

[Freesurfer] V1 Atlas ( brodman maps)

Dear experts,  I want to use the atlas V1 to calculate PET signal for Brodman areas. How can I create this atlas in the form of “aseg.mgz” or ”wmparc.mgz” ( i.e all the BAs in one file) to feed it in the command “mri-segstat”? Bests, John  ___ Freesur

[Freesurfer] External Regressor of Interest in FS-FAST

The references to external regressors in mkanalysis-sess are a little sparse on how I would go about analyzing a continuous regressor: I have a mixed design experiment: TaskBlock1 Rest TaskBlock2 Rest … TaskBlockN Rest x6 Runs Within each block are jittered events (5 of condition A, 5 of conditi

[Freesurfer] Announcing the the HCP Course 2016 in Boston Aug 28-Sept 1

The Human Connectome Project (HCP) is pleased to announce the 2016 HCP Course: “Exploring the Human Connectome” , to be held August 28-September 1 (Sunday-Thursday) at the Joseph B. Martin Conference Center

Re: [Freesurfer] Direction of bbregister transformation

Your understanding is correct. This was the convention when I started working with FS 18 years ago. It's hard to change :) On 05/11/2016 03:09 PM, Michael Waskom wrote: > Hi Freesurfers, > > I have a question about the direction of the transformation written > out to the register.dat file by bbr

[Freesurfer] X graphics issues via SSH

Hello freesurfers, Running a Mac Pro, OS X El Capitan 10.11.4 With ATI Radeon Graphics card, and XQuartz v 2.7.9 I am able to run Qdec and freeview perfectly fine on my machine. The problem comes when I attempt to SSH into another machine and use these programs (it used to work fine, but I am w

Re: [Freesurfer] Normalization for functional connectivity

I already used this argument during preprocessing. According to the explanation here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough in step-3, time-series data are sampled onto fsaverage then I am not sure why 2nd-level analysis is showing me significant self conn

Re: [Freesurfer] Normalization for functional connectivity

I would suggest you to check if preproc is done using the argument -mni-305-2mm. On Wed, May 11, 2016 at 12:48 PM, Sahil Bajaj wrote: > Hi Dr. Greve, > > This works for me if I define seeds into subject-wise anatomical space. > > Now, location of seed regions across subjects might differ because

[Freesurfer] Direction of bbregister transformation

Hi Freesurfers, I have a question about the direction of the transformation written out to the register.dat file by bbregister. I have looked at the fscoordinates powerpoint presentation, which I think is telling me that this matrix actually maps from the orig.mgz RAS coordinates to the functiona

Re: [Freesurfer] Correct/best way to find the midthickness surface

Hi Michael I think the 3rd is the best. It's guaranteed to not self-intersect and be smooth, which the other two methods are not cheers Bruce On Wed, 11 May 2016, Michael Waskom wrote: > Hi Freesurfers, > I have seen at least three ways for identifying an intermediate surface > between the whi

Re: [Freesurfer] Normalization for functional connectivity

Hi Dr. Greve, This works for me if I define seeds into subject-wise anatomical space. Now, location of seed regions across subjects might differ because these are defined in subject-wise anatomical space. Hence subject-wise connectivity maps are generated from subject-wise seeds but these can be

Re: [Freesurfer] recon-all error on ubuntu 16.04

Hi Zeke, Thank you for clarifying this, it did help. You are right the perl version is 5.22 I will give the development version a try. best, mads On 05/11/2016 04:51 PM, Z K wrote: > Hello Mads, > > This is a recently discovered issue with the mni tools that ship with > freesurfer v5.3 and t

[Freesurfer] Correct/best way to find the midthickness surface

Hi Freesurfers, I have seen at least three ways for identifying an intermediate surface between the white and pial surfaces: - Multiply the surface normal vector for each white surface vertex by half of the cortical thickness and add it to each vertex coordinate - Average the white and pial coord

Re: [Freesurfer] QDEC - cannot allocate memory

That fixed the error. Thank you so much for your help! Marissa Pifer On Wed, May 11, 2016 at 11:32 AM, Douglas N Greve wrote: > Try re-running recon-all -qcache for that subject and see if the error > goes away > > On 05/11/2016 10:56 AM, Marissa Pifer wrote: > > The error was generated on tha

Re: [Freesurfer] QDEC - cannot allocate memory

Try re-running recon-all -qcache for that subject and see if the error goes away On 05/11/2016 10:56 AM, Marissa Pifer wrote: > The error was generated on that first subject 03-1, but it was > successful on all of the other subjects. Is there something wrong with > that file that we have to exc

Re: [Freesurfer] QDEC - cannot allocate memory

The error was generated on that first subject 03-1, but it was successful on all of the other subjects. Is there something wrong with that file that we have to exclude that subject from the analysis? Marissa On Wed, May 11, 2016 at 10:38 AM, Douglas Greve wrote: > OK, it is failing on the mri_

Re: [Freesurfer] recon-all error on ubuntu 16.04

Hello Mads, This is a recently discovered issue with the mni tools that ship with freesurfer v5.3 and the latest version of perl (which probably comes with Ubuntu 16). I know the issue exists with perl version 5.22 but I dont know with what version the issue started. This has been fixed in th

Re: [Freesurfer] QDEC - cannot allocate memory

OK, it is failing on the mri_concat command. It may be that one of those inputs is causing the problem. Can you run the command with each input separately, eg, mri_concat /Users/marchaut/Documents/myprojects/SOARmaster/SOAR03-1.long.SOAR03/surf/lh.thickness.fwhm10.fsaverage.mgh --o deleteme.mg

Re: [Freesurfer] group roi to individual native functional

Register your average subject to each individual with mri_coreg (see below) using --s subject --dof 12, then use mri_label2vol with --seg ROI.nii.gz to map the ROI into the individual space. If the ROI is surface-based, then you could recon-all your average, map the ROI to the surface with mri

Re: [Freesurfer] recon-all error on ubuntu 16.04

Hi Martin, Thanks for your reply. rawavg.mgz and orig.mgz does exist. When I run the command I get the following error: mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz /home/XYZ/Projects/tmp/fs_test/test/mri /home/XYZ/Toolboxes/freesurfer/bin

Re: [Freesurfer] group roi to individual native functional

The average subject is the average of my own subjects (18). I registered each individual subject's functional data to the average subject with spm_register. On Tue, May 10, 2016 at 5:43 PM, Douglas N Greve wrote: > What is the average subject? How did you compute the registration > between the

Re: [Freesurfer] recon-all error on ubuntu 16.04

Hi Mads, is the file being copied (does /home/XYZ/Projects/tmp/fs_test/test/mri/rawavg.mgz and orig.mgz exist)? If not, maybe some disk space / IO problem. Also what happens when you run mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz dir

Re: [Freesurfer] cerebellar surface

yes, recon-all does not generate surfaces for anything other than cortex. On Wed, 11 May 2016, Alexopoulos, Dimitrios wrote: OK, but even a hull-like surface would be suffice for visualization purposes. I am more interested to confirm that the surface needs to generated independently from th

Re: [Freesurfer] cerebellar surface

OK, but even a hull-like surface would be suffice for visualization purposes. I am more interested to confirm that the surface needs to generated independently from the default cerebral cortex surface. From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu]

Re: [Freesurfer] QDEC - cannot allocate memory

Here is everything in the terminal after I hit analyze: Data table loading completed successfully. SUBJECTS_DIR is '/Users/marchaut/Documents/myprojects/SOARmaster' lh-Avg-Intercept-thickness --- Does the average thickness differ from zero? 1.000 1.000; lh-Diff-1-2-Int

[Freesurfer] recon-all error on ubuntu 16.04

Dear FreeSurfer group, I get an error trying to run basic recon-all on a ubuntu 16.04 system. It finish with errors after a few minutes and I cannot find any help in the recon-all.log (pasted below). I have made the symbolic links from the installation notes. Any ideas or thoughts on what the

Re: [Freesurfer] Manual segmentation issues

PS: For instance you can notice that the added voxels in the axial slice, coordinates * -39.69, 10.78, 11.54*were not included in the surface. By the way, the subject is 13 months old. On Tue, May 10, 2016 at 5:06 PM, Saturne Fox wrote: > Bruce, > > I just uploaded the directory through the