[Freesurfer] Problems converting MNC to NII

Hi! I am having some troubles converting MNC files to NII while preserving the exact values in the MNC file. I have tried to use mri_convert and mnc2nii, but in both cases, the values in the file output get changed. The help of mri_convert mentions that the output for MNC files may not work. Is the

[Freesurfer] bvecs and bvals don't have the same number of entries

Hi everybody, I'm trying to run trac all -prep on my data but I'm getting this error "bvecs and bvals don't have the same number of entries". I've checked my bvals and bvecs, which are in attach, but they seems to be formatted in the right way. The other 2 bvals and bvecs in DTI folder are the one

Re: [Freesurfer] Problems converting MNC to NII

Hi Caspar hmm, I don't know why that would be the case. Can you send the full command line and screen output? cheers Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: > Hi! > I am having some troubles converting MNC files to NII while preserving the > exact values in the MNC file. I have

[Freesurfer] dmri_motion Error bvals

Hi, Within the new Tracula update and with outputs resulted from *trac-all -prep -noqa* I ran *: * *dmri_motion --out './test.txt' --dwi './dwi_orig.nii.gz' --bval './bvals' --mat './dwi.ecclog'* And an error message appears: *machine x86_64Output motion measure file: /home/lapsi/

Re: [Freesurfer] Fwd: trac-all -path error

Hi Anastasia, I din't see anything missing from the brainmask or aparc+seg. I sent you the brainmask and aparc+seg files did you find anything wrong. if not, what else could cause the segmentatino fault? Thanks - Original Message - From: "Anastasia Yendiki" To: "Jon Wieser" Cc: "fr

Re: [Freesurfer] Problems converting MNC to NII

Hi Bruce, I have tried the two following commands, and various flags on mri_convert: mnc2nii -nii -int paxinos-MNI.mnc paxinos-MNI.nii mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii Yhe output of the latter would be: mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii $Id: mri_convert.c,v 1.179.2

Re: [Freesurfer] Fwd: trac-all -prep error

Hi Anastasia, I didn't see anything blatently wrong with the apar+aseg or the DWI's. Can you be more specific as to what I should be looking for Thanks! Jon - Original Message - From: "Anastasia Yendiki" To: "Jon Wieser" Cc: "freesurfer" Sent: Friday, January 10, 2014 6:16:56 PM Sub

Re: [Freesurfer] Problems converting MNC to NII

how do you know that the values were there before? Try running mri_diff on the .nii and the .mnc and see if it finds any differences Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: > Hi Bruce, > I have tried the two following commands, and various flags on mri_convert: > mnc2nii -nii -

Re: [Freesurfer] Problems converting MNC to NII

Hi Bruce, mri_diff does not return any differences. However, when I load the MNC file into Matlab using loadminc ( http://www.mathworks.com/matlabcentral/fileexchange/32644-loadminc), I do retain all the values between 0 and 255. Also, I have something like an annotation file for the MNC file that

[Freesurfer] FreeSurfer installation

Hi dear all, I want to use freesurfer for tractography by FSL. I downloaded freesurfer-linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz and I want to install it but I don't know how. Please help me. Thanks in advance, Neda ___ Freesurfer mailing list Frees

Re: [Freesurfer] Problems converting MNC to NII

Hi Bruce, I am confused, too. If the conversion is proper, why does mri_binarize not find values below ~53? when I call mri_binarize with -match on the MNC file or on any of the converted NIFTI files? Caspar 2014/1/22 Bruce Fischl > Hi Caspar > > now, I'm confused. So it sounds like mri_conve

Re: [Freesurfer] Problems converting MNC to NII

Hi Caspar now, I'm confused. So it sounds like mri_convert is doing the conversion properly then? Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, mri_diff does not return any differences. However, when I load the MNC file into Matlab using loadminc (http://www.mathworks.com/

Re: [Freesurfer] Problems converting MNC to NII

can you send us the full command line and screen output of the mri_binarize command? On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, I am confused, too. If the conversion is proper, why does mri_binarize not find values below ~53? when I call mri_binarize with -match on the MNC file

Re: [Freesurfer] Problems converting MNC to NII

mri_binarize --i paxinos-MNI.nii --match 1 --o labels/1.nii $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /rdata3/space3/data/cschwiedrz/cooked/anatomicals/mni_macaque cmdline mri_binarize --i paxinos-MNI.nii --match 1 --o labels/1.nii sysname Linux hostname wiener machine x

Re: [Freesurfer] FreeSurfer installation

Hi Neda, Have you read over the linux install directions in the link below? You will need to register and get a license file. After that you should look over the setup and config instructions. https://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall https://surfer.nmr.mgh.harvard.edu/fswiki/Setu

Re: [Freesurfer] Problems converting MNC to NII

same thing 2014/1/22 Bruce Fischl > and what if you run it on the mnc? > > On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: > > mri_binarize --i paxinos-MNI.nii --match 1 --o labels/1.nii >> >> $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ >> cwd /rdata3/space3/data/cschwiedr

[Freesurfer] Multiple Frames

Hello folks, I am attempting to run FreeSurfer (v5.1) on a downloaded NifTI structural T1 MRI from the Human Connectome Project, in particular 100307_3T_AFI.nii. Unless I am mistaken, their preprocessed data doesn't include aseg data, at least identified in a manner I am familiar with. Neverthele

Re: [Freesurfer] Multiple Frames

p.s. thanks Matt Bruce On Wed, 22 Jan 2014, Glasser, Matthew wrote: > AFI is a bias transmit scan, not an MPRAGE. Look for T1w. > > On 1/22/14 11:44 AM, "Bruce Fischl" wrote: > >> Hi Al, >> >> can you run mri_info on 100307_3T_AFI.nii? Is that an AFI scan? I'm not >> familiar with their naming

Re: [Freesurfer] Multiple Frames

that's what I wondered. AFI = "Actual Flip angle Imaging" usually On Wed, 22 Jan 2014, Glasser, Matthew wrote: > AFI is a bias transmit scan, not an MPRAGE. Look for T1w. > > On 1/22/14 11:44 AM, "Bruce Fischl" wrote: > >> Hi Al, >> >> can you run mri_info on 100307_3T_AFI.nii? Is that an AFI

Re: [Freesurfer] Problems converting MNC to NII

then is seems like the problem is with your mnc, not with anything we are doing, right? On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: same thing 2014/1/22 Bruce Fischl and what if you run it on the mnc? On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: mri_binari

Re: [Freesurfer] Problems converting MNC to NII

or, since the correct values display if I load the same MNC file with Matlab, it could be a problem with mri_binarize? 2014/1/22 Bruce Fischl > then is seems like the problem is with your mnc, not with anything we are > doing, right? > > On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: > > sa

Re: [Freesurfer] Problems converting MNC to NII

and what if you run it on the mnc? On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: mri_binarize --i paxinos-MNI.nii --match 1 --o labels/1.nii $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /rdata3/space3/data/cschwiedrz/cooked/anatomicals/mni_macaque cmdline mri_binariz

Re: [Freesurfer] Multiple Frames

Hi Al, can you run mri_info on 100307_3T_AFI.nii? Is that an AFI scan? I'm not familiar with their naming convention. I'll cc Matt Glasser who can probably help. cheers Bruce On Wed, 22 Jan 2014, Alfred Ochs wrote: Hello folks, I am attempting to run FreeSurfer (v5.1) on a downloaded Nif

Re: [Freesurfer] Problems converting MNC to NII

Can you describe the potential problem with mri_binarize more fully? On 01/22/2014 12:50 PM, Caspar M. Schwiedrzik wrote: > or, since the correct values display if I load the same MNC file with > Matlab, it could be a problem with mri_binarize? > > > 2014/1/22 Bruce Fischl

Re: [Freesurfer] Problems converting MNC to NII

Hi Doug, when I try to use mri_binarize with -match, certain values, especially ones smaller than about 50, are not found. This happens with the original MNC file as well as with NIFTI files that I converted from the MNC file. When I load the MNC file in Matlab, all the values that mri_binarize did

Re: [Freesurfer] FreeSurfer installation

Hi dear Louis, yes I read this link https://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall but when I write this command setenv FREESURFER_HOME /usr/local/freesurfer I see this message: bash: setenv: command not found best, Neda On Wed, Jan 22, 2014 at 9:06 PM, Louis Nicholas Vinke < vi...@nmr

Re: [Freesurfer] Cortical Flat Mapping Crash

Hi Bruce, Our system is Centos 6. We can try it on another system today, although we don't have another system that is as fast/efficient as our Centos 6 machine. Sherryse -- Sherryse Corrow, Ph.D. / Postdoctoral Fellow Human Vision and Eye Movement Lab Department of Ophthalmology & Visual Sci

Re: [Freesurfer] Cortical Flat Mapping Crash

h, I'm not sure then. Maybe some version of open GL? Perhaps Nick or Zeke can comment? On Wed, 22 Jan 2014, Sherryse Corrow wrote: > Hi Bruce, > > Our system is Centos 6. We can try it on another system today, although > we don't have another system that is as fast/efficient as our Centos 6

Re: [Freesurfer] Multiple Frames

BTW: If you download the structural preprocessed data, the HCP data already includes aparc+aseg.nii.gz in both "native" space and transformed to MNI152 space. If you want the data values contained in the native space aseg.stats file of FreeSurfer, you can quickly get that as part of the spreadshe

[Freesurfer] surface repositioning tool documentation

Hi, Is there documentation for the use of freeview's surface repositioning tool? Including the recon-all steps that should be rerun to ensure that the surface edits are reflected in the surface stats? Are edits made with this tool applied to future runs through the recon-all process (like pial and

Re: [Freesurfer] FreeSurfer installation

Hi Neda, Your terminal is probably setup to use the bash environment by default. If you type tcsh, then you'll be using C shell and that command should then work. I see that this is not on the install page, but on the setup/config page there is a note about it. There are also alternate comma

Re: [Freesurfer] Problems converting MNC to NII

I've looked at the volume you sent. One problem may be that the minc file might have a scale factor which we are not properly reading. When I use mnc2nii it produces a nifti file that has a slope of 1.00392. Not much, but it is there. The values that come out are not integer and there is nothi

Re: [Freesurfer] glm specification in longitudinal analyses for one group

Hi Sandra, so you reduce the 2 thickness measures within subject to a rate of change (mm/time), then you have a single map for each subject and now your question is about your glm modeling. So the question is basically about cross sectional modeling in you GLM. Your equ 7 and 8 test if the