Re: [Freesurfer] mri_convert : ERROR: cannot unpack mosiacs without ASCII header

Current versions of the Mac freesurfer binaries are not compatible with the v5.3 release. Too much has changed since then. If you wanted to use the newest version on the code you will need to download the latest dev version of freesurfer from this page (see "Development Version"): https://surfe

Re: [Freesurfer] mri_convert : ERROR: cannot unpack mosiacs without ASCII header

There was an obscure error having to do with the ascii header when unpacking skyra data on the mac, that might be it. Zeke, can you get Ismail a version of mri_convert appropriate for his OS? doug On 7/20/16 10:34 AM, Koubiyr, Ismail wrote: Hi Doug, I tried it on the cluster and it worked,

[Freesurfer] Error with mri_glmfit_sim (dev version f)

Hi List, I am getting a couple of strange error when running a 3-group F-test. WARNING: unrecognized mri_glmfit cmd option mri_glmfit.bin WARNING: 251446 NaNs found in volume analysis/Ftest/cache.th20.pos.sig.cluster.mgh... And as a result, I consistently get huge clusters: # ClusterNo Max

Re: [Freesurfer] Flattening the surface

Hi Bruce, I tried "mri_tessellate Brain_FS.mgz 255 lh_test.orig.nofix” command to generate a surface, but received an error message as below: changing type of input volume to 8 bits/voxel... $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28

Re: [Freesurfer] Flattening the surface

If you have a segmented volume, you can use mri_tessellate to create the surface, then introduce the cut(s) and run mris_flatten -1 on the resulting patch. You can check out our wiki http://surfer.nmr.mgh.harvard.edu/fswiki which has info on this process, although the flattening isn't terribly

Re: [Freesurfer] Flattening the surface

Hi Bruce, Great! I’m not an expert in FreeSurfer, so can you give me some advice how to generate a surface of our volumetric data and flatten it? Thanks, Younghoon Kim -- Younghoon Kim, Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab

Re: [Freesurfer] Flattening the surface

HI Younghoon I guess that could work. You will need to introduce at least one cut if not more if you surface has substantial Gaussian curvature cheers Bruce On Wed, 20 Jul 2016, Younghoon Kim wrote: Hi Bruce, We are only interested in the surface image of the volumetric data. For flatt

Re: [Freesurfer] Flattening the surface

Hi Bruce, We are only interested in the surface image of the volumetric data. For flattening, we do not care about the interior of the volume, so we would like to remove the volume data inside. So what we want is to peel off the surface from the segmented brain area and flatten that surface. Th

Re: [Freesurfer] tkmedit issue - image too bright in tkmedit after running gcut

Hi Fred that just means that you need to change the window levels. Note that we have deprecated the use of tksurfer and tkmedit and don't really support them any longer cheers Bruce On Wed, 20 Jul 2016, Uquillas, Federico D'Oleire wrote: > Hi fellow FreeSurfer users, > > I just did a gcut pro

Re: [Freesurfer] Flattening the surface

Hi Younghoon what structure are you talking about? In general it doesn't make sense to flatten volumetric structures. We flatten the cortex, which is a folded 2D sheet. What would you do with the interior of the volume? cheers Bruce On Wed, 20 Jul 2016, Younghoon Kim wrote: Hello, We hav

[Freesurfer] Flattening the surface

Hello, We have a volumetric data (mgz file) of a segmented brain region. We want to detect the surface of this segmented brain volume (i.e. deep brain region) and flatten it into a 2D image with its original surface texture. We’ve noticed that Freesurfer supports an algorithm to flatten volumetri

Re: [Freesurfer] Beta-Zero Correction - No Phase File

Hi Doug, Thanks for getting back to me. I've tried mri_convert $Input_file --split $Output_file to split up the fieldmaps but I'm getting 6 to 12 different outputs (depending on the fieldmap) rather than just the mag and phase files which is what I was expecting. Have you encountered this be

[Freesurfer] TRACULA dmri_paths, single time point in longitudinal stream

Hi Anastasia, I was wondering what the resolution to this thread was: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg42734.html It sounds like a new version of dmri_paths was deemed necessary to appropriately process single time points in the longitudinal T

Re: [Freesurfer] error during longitudinal -long stream

Hi Martin, We run all cross, base and long with 5.3. I guess the problem maybe we run cross on a computer and then copy the results to another computer to run the cross and long. the "*fsaverage" is not copied. Does this matter？* Best， Jinsong On Wed, Jul 20, 2016 at 12:21 AM, Martin Reuter w

Re: [Freesurfer] Fwd: question about voxel size

Hi Dorsa I don't see any holes in the thalamus in your aseg, nor separated pieces. What voxel coords do you mean? Remember to look at the data in other orientations. Things that look like islands in one view may be peninsulas in anothers cheers Bruce On Wed, 20 Jul 2016, Dorsa Haji Ghaffar

[Freesurfer] Fwd: Connectome Research Coordinator (Senior), University of Pennsylvania

Dear colleagues, The Penn Frontotemporal Degeneration Center at the University of Pennsylvania (http://ftd.med.upenn.edu/) is seeking a research coordinator for the multi-site FTD Connectome study. Please see the details below; applications should be directed to http://jobs.hr.upenn.edu/postings/1

Re: [Freesurfer] Fwd: question about voxel size

I mean the holes in the thalamus and also some parts that are labeled as thalamus but not attached to the rest of thalamus volume. On Wed, Jul 20, 2016 at 10:49 AM, Bruce Fischl wrote: > what missing parts do you mean? The segmentation seemed pretty reasonable, > but the contrast wasn't good eno

Re: [Freesurfer] Fwd: question about voxel size

what missing parts do you mean? The segmentation seemed pretty reasonable, but the contrast wasn't good enough to say how accurate it was in some places On Wed, 20 Jul 2016, Dorsa Haji Ghaffari wrote: Yes it is taken at 3T. I have asked our team to provide these information about the MRIs and

Re: [Freesurfer] Fwd: question about voxel size

Yes it is taken at 3T. I have asked our team to provide these information about the MRIs and will let you know when I hear back. I also wanted to ask if you know a good way to refine the thalamus and fill out the missing parts within the volume? Thank you Dorsa On Tue, Jul 19, 2016 at 5:10 PM, Br

[Freesurfer] R: problems by running longitudinal mass univariate analysis

Dear Martin to follow-up mu previous question, I was finally able to run the lme_mass_fit_vw script till the end. Unfortunately, it came out that converge of the algorithm was failed in 99% of the locations. I have only one study group (with a variable number of follow-up , and I used as design

Re: [Freesurfer] mri_convert : ERROR: cannot unpack mosiacs without ASCII header

Hi Doug, I tried it on the cluster and it worked, which is weird because it was not working before … Any idea what might be the problem on my system ? Thanks again. Ismail On Jul 19, 2016, at 10:32 PM, Douglas Greve mailto:gr...@nmr.mgh.harvard.edu>> wrote: I used the same version, but I use

Re: [Freesurfer] ExploreDTI Workshop!

FYI - we're holding the next ExploreDTI Workshop! When: 28-30 November, 2016 Where: Utrecht Details: http://www.exploredti.com/workshop Cheers, Szabolcs On Sat, Feb 27, 2016 at 8:00 PM, Szabolcs David wrote: > Thrilled to announce that we are going to hold an ExploreDTI workshop in > Utrecht (J

Re: [Freesurfer] reading lh.BA1_exvivo.label recon-all error

Hello Renata, Their was a brief period of time in the Dev version of freesurfer when certain labels didnt exist in the fsaverage subject. You just happen to download and install that version. I believe if you download the latest version from this page (see "Development Version") that error will

[Freesurfer] Factors affect cortical thickness in normal population

Dear FS experts, We have few dataset of normal patients. They will be arranges as controls. I am wondering the factors affecting normal patients cortical thickness: Age, Sex Native Language Hand prefer IQ Any others? thanks Lawrence ___ Freesurfer maili

Re: [Freesurfer] PVE correction tool on Freesurfer 6

Hi Doug, Thanks for your help! For your response to question #1 from my previous email(copied below), then if all PET images were smoothed so that they all have a uniform resolution of 8mm FWHM, would I put 8 for the psf flag? > 1)*mri_gtmpvc --i pet.nii.gz --reg template.reg.lta--psf FWHM--

Re: [Freesurfer] Hippocampal subfields --> Can't find a *ctf file?

ok thanks a lot for the quick answer. let me know when it works. our mri voxel size is 1 mm isotropic. (if it changes anything, I am working on ubuntu 14.04). Cheers, Pierre On Wed, Jul 20, 2016 at 11:15 AM, Iglesias, Eugenio wrote: > Thanks a lot, Pierre. > I’ll get this sorted out as soon as

Re: [Freesurfer] Hippocampal subfields --> Can't find a *ctf file?

Thanks a lot, Pierre. I’ll get this sorted out as soon as possible. I’m in the process of modifying the module so it supports data with resolution >1mm, and also incorporating the longitudinal segmentation method described in https://doi.org/10.1016/j.neuroimage.2016.07.020 Cheers, Eugenio Jua

Re: [Freesurfer] Hippocampal subfields --> Can't find a *ctf file?

Hi, I downloaded the new freesurfer development version and I still have the same problem when running the hippocampal-subfields "Invalid MEX-file '/tmp/MCR_4195017647/.mcrCache8.0/segmen0/autofs/cluster/koen/koen/GEMS-Release/bin/kvlGEMSMatlab.mexa64': libkvlGEMSCommon.so: cannot open shared obj

Re: [Freesurfer] error during longitudinal -long stream

Hi Jinsong, I have never seen this. Stable 5.3 is very stable and I doubt it is a bug. How did you process base and cross sectionals? Also with 5.3 ? I would recommend to process cross and base with 5.3, then re-run the long and see if you can replicate this problem. Let me know what happens.