[Freesurfer] mni152reg

Hello Freesurfer Experts, I am trying to create a registration matrix from subject space to MNI152: mni152reg --s bert However, this error appeared: fslregister --mov /usr/local/fsl/data/standard/MNI152_T1_2mm_brain.nii.gz --s bert --reg /usr/local/freesurfer/subjects/bert/mri/transforms/reg.mni1

[Freesurfer] Fwd: CNR in the hippocampus

Dear Freesurfer expert, I'm reposting this mail. any suggestions? Thank you efrat -- Forwarded message -- From: Efrat Kliper Date: Tue, Jun 9, 2015 at 8:11 AM Subject: CNR in the hippocampus To: freesurfer@nmr.mgh.harvard.edu Dear Freesurfer expert, I received a comment f

Re: [Freesurfer] Fwd: CNR in the hippocampus

Hi Efrat sorry, we are all just getting back from HBM. Our atlas includes example of older adults with and without AD, so this should not be an issue. cheers Bruce On Mon, 22 Jun 2015, Efrat Kliper wrote: Dear Freesurfer expert, I'm reposting this mail. any suggestions? Thank you efrat  

[Freesurfer] lme_realizedPower

Dear Freesurfers, I have used an LME model to describe the evolution of cortical thickness in a patient group during therapy and to compare it, at the end of the therapy, with an HC group. An F-test, using the lme_F function gives no significant difference. Now I would like to understand to whi

Re: [Freesurfer] (no subject)

Hi you can use mris_expand to do this, although of course we just divide up the space evenly since we don't know where the actual laminar boundaries are. cheers Bruce p.s. e.g.: mris_expand -t -n 6 lh.white lh.expanded will write out 6 intermediate surfaces On Mon, 15 Jun 2015, Yun Wang

Re: [Freesurfer] Need vertex in 2D template space

Hi Bruce, Thanks to your advise, the combination of *mri_surf2surf **my_subject* -> *fsaverage*(paint features to average brain) + *mris_convert -c *.ascii*(output features to ascii) works well, all my subjects can have the same number of vertice. And it looks like the original xyz coordinate

Re: [Freesurfer] Need vertex in 2D template space

sure, the average subject has a sphere and you can do it there. Or you can flatten and use euclidean coordinates On Mon, 22 Jun 2015, xtong wrote: Hi Bruce, Thanks to your advise, the combination of mri_surf2surf my_subject -> fsaverage(paint features to average brain) + mris_convert -c *.asc

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

Thank you for this information. -Zeke On 06/22/2015 02:22 AM, Chris Adamson wrote: > Everyone, > > I know this is a fairly specific issue but nonetheless. > > If you compile Freesurfer 5.3.0 with the option –march=core-avx2 with > gcc 4.8 it can cause mris_fix_topology to segfault at > utils/mris

Re: [Freesurfer] (no subject)

Thanks! Yun Wang > On Jun 22, 2015, at 7:40 AM, Bruce Fischl wrote: > > Hi > > you can use mris_expand to do this, although of course we just divide up the > space evenly since we don't know where the actual laminar boundaries are. > > cheers > Bruce > > p.s. e.g.: > > mris_expand -t -n 6

Re: [Freesurfer] finding local extrema in surface data

you can try mri_surfcluster. It will give you the vertex of the maximum in each cluster. Run it with --help for more info. doug On 6/21/15 10:09 AM, Bruce Fischl wrote: Hi Sabine not that I know of. Maybe someone else does? sorry Bruce On Sun, 21 Jun 2015, Sabine Oligschläger wrote: Dear

Re: [Freesurfer] Preproc-sess failed

I'm not sure what to tell you. Zeke, do you have any ideas? Alternatively, you can just install afni on your machine. Once you verify that the installation works, copy 3dvolreg from the installation. On 6/21/15 3:55 PM, Thục Trinh wrote: Hello Douglas, I already had *3dvolreg.afni* in */freesu

Re: [Freesurfer] Tracula output variability & reinit

Thanks for looking at the data. 1- Since the data has already been acquired, I can't change that. For our new study we are setting up, we'll definitely use isotropic resolution, and we'll probably acquire a fieldmap to correct for epi distortions. FSL has some recommendations at FDT/FAQ

Re: [Freesurfer] Preproc-sess failed

Trinh, Attempt to determine where libXp.so.6 was installed on your system after you installed it using yum. For example, on my system libXp.so.6 exists in directory "/usr/lib64". Once you determine the location where the library resides, add that directory to your LD_LIBRARY_PATH after you sou

[Freesurfer] reg-feat2anat update

Hi FS experts, I had a quick query I was hoping you could help with; I am trying to load functional data analyzed in FSL in Freesurfer using reg-feat2anat (http://freesurfer.net/fswiki/FsTutorial/RegisterFeatOntoAnatomical) and seem to be having the same problem as the person in this thread:

Re: [Freesurfer] Tracula output variability & reinit

Ok, I didn't realize you were using the longitudinal stream. So the data sets that you sent were from one of the time points? How many time points are there for a subject? The longitudinal stream uses all the time points at once, which makes the convergence a bit slower than the cross-sectio

Re: [Freesurfer] Freeview Update

On 06/19/2015 09:33 PM, joseph veliz wrote: > Thanks Zeke, > > > Could you please help me understand if there would be any > inconsistencies or variation between data sets edited by Freeview on a > newer macbook pro vs data sets edited by Freeview on a older iMac? This should not be an issue. Ed

[Freesurfer] Convert RAS coordinates to LPS

Hi, I'm converting some structural images from RAS ( orig.mgz conformed space) to LPS using: mri_convert orig.mgz orig_LPS.nii --in_orientation 'RAS' --out_oreintation 'LPS' My question is, if I have some RAS coordinates defined from the original orig.mgz image, how do I also convert those coord

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

Oh PS, AVX gives about 25% speed up compared to SSE. Would it be useful for me to send the data that it segfaults on? -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Z K Sent: Tuesday, 23 June 2015 1:50 AM To: F

Re: [Freesurfer] Convert RAS coordinates to LPS

The coordinates won't change because the underlying coordinate system is the same regardless of how it is sliced. The voxel col, row, slice mapped to a coordinate will change. If that is what you mean, then you'll need to get the voxel-to-ras matrix with mri_info --vox2ras file.nii for each ori

[Freesurfer] Longitudinal Qdec Statistics

Hello Freesurfers, I am using Qdec for longitudinal statistics with symmetrized percent change (spc) on 3 different discrete/fixed factors across 2 time-points. Given that Qdec limits the discrete factors to 2, I ran the effects with different combinations of the discrete factors and I get very di

Re: [Freesurfer] Preproc-sess failed

Hello Douglas and ZK, I set the path for shared library in my .basrch file, but it still does not work and comes up with this Error: *3dvolreg.afni: error while loading shared libraries: libXp.so.6: wrong ELF class: ELFCLASS32* *ERROR: 3dvolreg.afni* *Invalid null command.* Trinh 2015-06-23 3:03

Re: [Freesurfer] Preproc-sess failed

hello, I am using CentOS release 6.4 ( final) 64bit and Freesurfer v.5.3.0. I think that makes the confliction. 2015-06-23 8:26 GMT+07:00 Thục Trinh : > Hello Douglas and ZK, > I set the path for shared library in my .basrch file, but it still does > not work and comes up with this Error: > *3dvo

Re: [Freesurfer] Preproc-sess failed

From reading the email thread history, it appears you may have downloaded the apple OS X version of 3rvolreg.afni and overwrote the original, which is the cause of the error. Please extract the original version of that binary from the original tarball. If you no longer have it you can download i