[Freesurfer] Not able to find file in gtmseg

Dear FreeSurfer experts, Hello, I am trying to use Freesurfer's (developmental version) PVE correction tool and I haveone question. The data to be PVE-corrected are some preprocessed PET data downloaded from the Alzheimer's DIsease Neuroimaging Initiative (ADNI) database. Basiclly, the dynamic

Re: [Freesurfer] Get a given point's ROI

you can load it into matlab with load_mgh.m or MRIread.m cheers Bruce On Wed, 29 Jun 2016, Yuan Lin wrote: Hi Bruce, Thank you for your response. I can show the aparc+aseg.mgz with the FreeSurferColorLUT.txt on freeview now. But how can I get the index matrix using MATLAB? Is there any co

Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 1e+08

Thank you for catching this. Really appreciate your help. - Arkadiiy ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person t

Re: [Freesurfer] Freesurfer Digest, Vol 148, Issue 28

Thank you!! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was se

Re: [Freesurfer] Get a given point's ROI

Hi Bruce, Thank you for your response. I can show the aparc+aseg.mgz with the FreeSurferColorLUT.txt on freeview now. But how can I get the index matrix using MATLAB? Is there any command to read .mgz file in MATLAB? Or can I convert the .mgz file to .vtk file? Thank you so much. Best, Lin >

[Freesurfer] longitudinal tracula

Hi, When running TRACULA with longitudinal data, is it necessary for all scan waves of a given subject to be included in a single dmrirc file?  My initial thought was “no”, that it would be fine to run one scan wave per subject per dmrirc file (as long as the “baselist” variable is set

Re: [Freesurfer] Get a given point's ROI

Hi Lin you could look that point up in the subject's aparc+aseg.mgz. This will give you an index into the file $FREESURFER_HOME/FreeSurferColorLUT.txt cheers Bruce On Wed, 29 Jun 2016, Yuan Lin wrote: > Dear FreeSurfer experts, > > I am a beginner to learn to use FreeSurfer. Now I have a quest

[Freesurfer] Get a given point's ROI

Dear FreeSurfer experts, I am a beginner to learn to use FreeSurfer. Now I have a question to be solved. I have gotten the reconstruction results of a subject after using the command recon-all. How can I know a given point belongs to which region of interest? For example, how can I know whether

[Freesurfer] Announcement: fsurf, a command line tool for running freesurfer on the Open Science Grid

Dear FreeSurfer community, The Open Science Grid (http://www.opensciencegrid.org) is a federation of university and laboratory HPC facilities which share computing capacity to support science. We have developed a command line tool "fsurf" you can use from your laptop or desktop computer to subm

Re: [Freesurfer] No intensity command

Hi Bruce, Thank you for your reply. I am looking at differences in WM intensity, but am concerned that the intensity normalization will reduce tissue differences in addition to addressing inhomogeneity from the MRI. The WM is normalized to an average of 110, but is there any way to keep the va

Re: [Freesurfer] No intensity command

Hi Sabrina what are you trying to accomplish? This is unlikely to work well (if at all), as we depend on the normalization cheers Bruce On Wed, 29 Jun 2016, Sabrina Yu wrote: Hello,  I have a question about taking out the intensity normalization commands in recon-all. I want to eliminate

[Freesurfer] No intensity command

Hello, I have a question about taking out the intensity normalization commands in recon-all. I want to eliminate all normalization steps so that the WM will not be set at an average of 110. Using the ReconAllDevTable (https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable

Re: [Freesurfer] registering to fsaverage

Hi Bruce I simply use mri_vol2surf --mov spam.mnc --output overlayspam.mgz --regheader subject --hemi lh --surf pial Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Wed, Jun 29, 2016 at 1:23 PM, Bruce Fischl wrote: > how do you create the overl

[Freesurfer] Motion values during structural run

Hi Freesurfer Experts, Is there a way to calculate average displacement during a T1_MEMPRAGE scan (similar to using fmcpr.nii to calculate avg displacement during functional runs)? Thank you, Anais Rodriguez-Thompson Clinical Research Coordinator Brain Genomics Laboratory Martinos Cen

Re: [Freesurfer] Hippocampal Subfields Segmentation

I could finally look into this. It is indeed weird. The CTF is indeed embedded in the executable… Zeke/Nick, can you shed some light on this? Cheers, Eugenio Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 27

Re: [Freesurfer] registering to fsaverage

how do you create the overlay? On Wed, 29 Jun 2016, Trisanna Sprung-Much wrote: Hi Bruce To create the spam I used minctools:  mincaverage  input.mnc output.mnc  I blurred the spam using mincblur input.mnc output.mnc -fwhm 3  When I open the spams using minc software, the % shown is from

Re: [Freesurfer] registering to fsaverage

Hi Bruce To create the spam I used minctools: mincaverage input.mnc output.mnc I blurred the spam using mincblur input.mnc output.mnc -fwhm 3 When I open the spams using minc software, the % shown is from about 10-40% (i.e. the max overlap). For some reason when I create an overlay from this

[Freesurfer] Tracula : ERROR: cannot unpack mosiacs without ASCII header

Hi everyone, I’m reposting my problem if someone could help me I would really appreciate it. I have some problems trying to run TRACULA on some DWI data. It is a mosaic Siemens DWI. I first converted the DICOM files with dcm2nii to get the bvec and bval files. Then I run the trac-all -prep -c c

Re: [Freesurfer] registering to fsaverage

Hi Trisanna what commands did you use to generate the volumetric probability map? Bruce On Wed, 29 Jun 2016, Trisanna Sprung-Much wrote: Hi Bruce So, when I take a probability map formed using linear volumetric registration with minc tools and saved as .mnc and convert it to an overlay.mg

Re: [Freesurfer] Order of overlays

Hi Reza, Right now in freeview aparc annotation is always drawn on top of overlays, just like in tkSurfer. I'll add an option draw it underneath the overlays. Best, Ruopeng On 06/29/2016 10:09 AM, Bruce Fischl wrote: Hi Reza can you use freeview? We don't do any development on tksurfer and

Re: [Freesurfer] tutorial_data

I can see the sub directories and the distributions via ftp. Best - Don > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer- > boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent: Wednesday, June 29, 2016 10:57 AM > To: Freesurfer support list

Re: [Freesurfer] tutorial_data

try again - hopefully the stale mounts of been fixed now cheers Bruce On Wed, 29 Jun 2016, Bennet Fauber wrote: > Looks like all downloads are broken, as the same message appears when > trying to download the binary distribution, > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/fre

Re: [Freesurfer] tutorial_data

It looks like things aren't quite linked up. I can reach the server with ftp and I can see directory pub. But there's no directory pub/dist . Best - Don > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer- > boun...@nmr.mgh.harvard.edu] On Behalf Of Bru

Re: [Freesurfer] tutorial_data

it should all be working now, no? On Wed, 29 Jun 2016, Bennet Fauber wrote: > Looks like all downloads are broken, as the same message appears when > trying to download the binary distribution, > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Linux-centos6_x86_64-stable-pu

Re: [Freesurfer] Order of overlays

Hi Reza can you use freeview? We don't do any development on tksurfer and hardly use it anymore. Not sure if this is possible in freeview, I'll leave that for Ruopeng cheers Bruce On Wed, 29 Jun 2016, Reza Rajimehr wrote: Hi, In Tksurfer, we want to show functional activity map and borders o

Re: [Freesurfer] checking freesurfer output

Hi Gabor the only way is to look at the parcellation over the white surface I guess. There are some not-very-well documented interventions, but maybe your best bet would be just to exclude subjects (since it almost never fails) cheers Bruce On Wed, 29 Jun 2016, Gabor Perlaki wrote: > Dear

Re: [Freesurfer] tutorial_data

Looks like all downloads are broken, as the same message appears when trying to download the binary distribution, ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz There are no files on the server advertised to the public: Name (s

[Freesurfer] Qdec-correction for multiple comparison

Dear FS experts, I will re post this thread again looking for your help and support:   I ran cortical thickness analysis between two groups using Qdec and I want to correct the results for multiple comparison. In Qdec there are two choices to correct the data for multiple comparison (FDR and

[Freesurfer] Order of overlays

Hi, In Tksurfer, we want to show functional activity map and borders of aparc on a surface. The borders of aparc are always drawn on top of the activity map, which sometimes hide small activation blobs. Is it possible to draw the activity map on top of the aparc borders? Reza

Re: [Freesurfer] checking freesurfer output

Dear Bruce, Thank you for your answer. We will check the pial and white surfaces, but how to check the accuracy of the cortical parcellation beyond that? We don't find any suggestion on Freesurfer's troubleshooting page how to realize or correct such an error, where the pial and white surfaces are

Re: [Freesurfer] Failed to download Freesurfer from ftp, server seems empty

Hi! I found a non official github repository here: https://github.com/neurodebian/freesurfer you can try to compile that source code in the meantime. On Wednesday, 29 June 2016, Bruce Fischl wrote: > Hi Minos > > we are having major hardware issues that we hope to have resolved > tonight. Try a

[Freesurfer] Diffusion MRI Workshop, 12-16 September, 2016

Dear Freesurfer users, Registration is officially open for the 4th ISMRM Diffusion MRI Workshop "Breaking Barriers in Diffusion MRI" to be held September 12-16 in Lisbon, Portugal! Dates: September 12-16, 2016 Venue: Sheraton Lisboa, Lisbon, Portugal Deadline for abstracts: July 21, 2016 Fac