[Freesurfer] Postdoctoral fellowship - NORMENT Oslo

A 3 year postdoctoral fellowship in Multimodal Imaging at NORMENT is currently available. NORMENT is a Norwegian Centre of Excellence, and coordinates a translational multicenter study involving all University hospitals in Oslo and several groups at the Universities of Oslo and Bergen. The main

Re: [Freesurfer] finding local extrema in surface data

Hi Sabine, Perhaps you can transform ?h.sphere and corresponding surface data into a polar image in which you can try to find the local extrema. Cheers, Ed ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mail

[Freesurfer] extract individual thickness values from uncorrected clusters from qdec

Dear freesurfer expert, I run an analysis in qdec as a "features selection" step for a following analysis. Basically, I am interested in all the clusters "loosely" related to my variable of interest. In the light of this, I am looking at uncorrected (for multiple comparisons) clusters in my vol

[Freesurfer] From manual coregistration of 4D.nii to spm space

I am currently performing an analysis of some fMRI data I've collected. I've had a lot of trouble coregistering the functional images to my high-res structural. SPMs automatic functions can't do it; I've tried almost every possible option. I assume the problem is due to my rather small functionals

Re: [Freesurfer] Tracula output variability & reinit

We generally have 2 scans per subject, pre- and post-intervention. But the subject I sent you data for and the list of fa values earlier in this thread has 6 scans. The runs at 7500, 20k, and 50k samples used all 6 scans. To save time, I just ran 2 scans through the trac-all -path for the 100k run(

Re: [Freesurfer] Longitudinal Qdec Statistics

HI Kari, whenever you change a statistical model, you get different results, as you are 'asking' different questions. For example testing for factor A, when regressing out Factor B is very different from testing A when regressing out C. Let's say A is weight and B is IQ, so you look for an wei

Re: [Freesurfer] lme_realizedPower

Hi Fabio I think (I'mnot a dedicated statistician) you cannotconclude to any extent that the cortical thickness in the two groupsis the same. You can only say that there wasn't enough evidence ofdifferences between the two groups in terms of your measurements. I don't understandwhat you mean wi

[Freesurfer] cortical parcelling with freesurfer

Dear freesurfer experts, I am having few questions about using freesurfer to finely (1000) parcel cortical structures consistently through subjects. Since I cannot do GCs atlas on my own, the main idea is running recon_all for all of them and then register via mri_cvs_register all subjects to one

Re: [Freesurfer] cortical parcelling with freesurfer

Hi Antonio if you want the parcels to be in register you should use the sphere.reg instead of the sphere file in mris_make_face_parcellation. I'll leave the other questions for Doug:) Bruce On Tue, 23 Jun 2015, Napolitano Antonio wrote: Dear freesurfer experts, I am having few questions ab

Re: [Freesurfer] Tracula output variability & reinit

Hi Peggy - Thanks for clarifying. I'd like to see if things work differently when you have 6 time points vs. 2 time points. In theory, it should not. Could you please upload for me the full set of directories from all time points and base template (all the tracula generated directories from e

Re: [Freesurfer] mri_label2label problem revisited

Hi Michael what version are you using? I thought this was fixed long ago cheers Bruce On Tue, 16 Jun 2015, Michael Kranz wrote: Hi guys, I have created a custom surface label in the fsaverage template. I then used mri_label2label to map onto an individual subject. Despite the fsaverage label

Re: [Freesurfer] cortical parcelling with freesurfer

Hi Antonio, why not draw your labels on fsaverage, and then map them to each subject (look at mri_surf2surf or mri_label2label, mri_segstats ). In my opinion you don't need the do all the registration of volumes, you only work on surfaces. Probably someone here can give you the exact commands

Re: [Freesurfer] Fwd: Questions on labeling ROIs with values on inflated cortical surfaces

Hi Xixi, Do you want to create a customized annotation file to load on a surface? or do you want to load multiple labels with different colors? Best, Ruopeng On 06/16/2015 03:33 PM, Xixi Wang wrote: Hi FreeSurfer users, I’m trying to label different ROIs with corresponding decoding accurac

Re: [Freesurfer] Segmentation fault in mris_fix_topology when compiling with gcc 4.8 + AVX2

I would be very interested on the data set (and exact command) you used that exhibited a 25% speed up. Because our tests showed little to no improvement in run time when using the -march=core-avx2 during compiling. -Zeke > Oh PS, AVX gives about 25% speed up compared to SSE. Would it be useful >

Re: [Freesurfer] mri_label2label problem revisited

Hi Bruce, Not the same Michael but I see this all the time with 5.3. Interestingly, transforming annotations using mri_surf2surf does not run into the issue — perhaps that is what you're thinking of? Best, Michael On Tue, Jun 23, 2015 at 8:20 AM, Bruce Fischl wrote: > Hi Michael > > what vers

Re: [Freesurfer] mri_label2label problem revisited

ok, thanks Michael, we will investigate On Tue, 23 Jun 2015, Michael Waskom wrote: Hi Bruce, Not the same Michael but I see this all the time with 5.3. Interestingly, transforming annotations using mri_surf2surf does not run into the issue — perhaps that is what you're thinking of? Best, Mic

Re: [Freesurfer] Convert RAS coordinates to LPS

Doug, thanks for your help with this. I gave this a try using the inverse of the vox2RAS affine from the LPS image: inv_M2*(M1*v1) = v2 The results look as if the voxel CRS coords are a bit translated towards the inferior. This is most likely due to your second note. I don't think it converted

[Freesurfer] tkregister2 erros between bold and mni152 through registeration of T1 to mni152

Hello Freesurfer expert I got two errors when I registered bold image to patient's own T1 image and registered T1 to mni152 and got transform data (reg.mni152. data) between bold and mni152. 1) I typed tkregister2 --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --mov template.nii.gz --reg

[Freesurfer] FS-FAST using a ROI as seed

Hi list,I'd like to performed FS-FAST using a ROI as seed.Should I use fcseed-config? Thus, what should I put instead of -segid?Thanks and regards. Stefano ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mail

[Freesurfer] Constraint to FS-FAST analysis

Hi list,is it possible to put a constraint to FS-FAST analysis. More specifically use as seed a subcortical region (e.g. thalamus) and a target (e.g. frontal pole)?If yes which is the option in the command line? Stefano ___ Freesurfer mailing list Fre

[Freesurfer] [FreeSurfer] Freeview Crash PETSC ERROR

Hello, We are having issues installing Freeview on Macbook pro (2015) 2.2 GHz, 16GB DDR3, OSX 10.9.4, Integrated 1.5 GB intel iris pro graphic processing. Installing lastest Freesurfer and Freeview downloads of Darwin lion v5.3.0. After installing Freesurfer , license and environment setup, th

Re: [Freesurfer] Preproc-sess failed

I did that, and run the command 3dvolreg.afni on Terminal to check. The Error still remain: *3dvolreg.afni: error while loading shared libraries: libXp.so.6: wrong ELF class: ELFCLASS32* 2015-06-23 10:39 GMT+07:00 Z K : > From reading the email thread history, it appears you may have downloaded >