Re: [Freesurfer] niiRead: error opening file, through mri_convert

I’m glad to hear it worked out. We have all done this…. Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Andrew Sent: Monday, August 2, 2021 12:07 PM To: Freesurfer support list Subject: Re: [Freesurfer] niiRead: error opening file, through mri_convert External Email

Re: [Freesurfer] niiRead: error opening file, through mri_convert

gt;> On Behalf Of Andrew > Sent: Friday, July 30, 2021 1:44 PM > To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > Subject: [Freesurfer] niiRead: error opening file, through mri_convert > > External Email - Use Caution >

Re: [Freesurfer] niiRead: error opening file, through mri_convert

Can you load /Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii in freeview? Maybe run ls -l on it? From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Andrew Sent: Friday, July 30, 2021 1:44 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] niiRead: error

[Freesurfer] niiRead: error opening file, through mri_convert

External Email - Use Caution Hello, I’m trying to reconstruct an old pipeline that I don’t completely understand (so sorry if this is very elementary or out of date), and one step is to convert the freesurfer T1 segmentation ribbon.mgz to .nii format using mri_convert. Through

Re: [Freesurfer] niiRead error

It does work with 6.0, thank you! 2017-07-31 20:59 GMT+03:00 Douglas Greve : > I think this may be fixed in 6.0 > > On 7/31/17 12:43 PM, Francesca Strappini wrote: > > Thanks for the reply. > > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0. > > I opened it with fslview and it looks like a nor

Re: [Freesurfer] niiRead error

I think this may be fixed in 6.0 On 7/31/17 12:43 PM, Francesca Strappini wrote: Thanks for the reply. freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0. I opened it with fslview and it looks like a normal 3-dimentional file. Thanks Francesca 2017-07-31 16:38 GMT+02:00 Douglas Greve

Re: [Freesurfer] niiRead error

Thanks for the reply. freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0. I opened it with fslview and it looks like a normal 3-dimentional file. Thanks Francesca 2017-07-31 16:38 GMT+02:00 Douglas Greve : > what version of FS are you running? > > > On 7/30/17 12:37 PM, Bruce Fischl wrote: > >

Re: [Freesurfer] niiRead error

what version of FS are you running? On 7/30/17 12:37 PM, Bruce Fischl wrote: > Hi Francesca > > why is the nifti 5-dimensional? The code is complaining that it doesn't > know how to intepret the input volume > > cheers > Bruce > On Sun, 30 Jul 2017, Francesca > Strappini wrote: > >> Hi, I'm tryin

Re: [Freesurfer] niiRead error

Hi Francesca why is the nifti 5-dimensional? The code is complaining that it doesn't know how to intepret the input volume cheers Bruce On Sun, 30 Jul 2017, Francesca Strappini wrote: > Hi, I'm trying to register to the surface a t-test map created with afni > (3dttest++) but I got this error

[Freesurfer] niiRead error

Hi, I'm trying to register to the surface a *t*-test map created with afni (3dttest++) but I got this error message: mri_vol2surf --mov movierestTest.nii.gz --regheader fsaverage --surf-fwhm 3 --hemi lh --o movierestTest_lh.nii.gz srcvol = movierestTest.nii.gz srcreg unspecified srcregold = 0 src

Re: [Freesurfer] niiRead(): error opening file SUBJECTS_DIR/Enzo_recon1/dti.nii

It's trying to find a file called SUBJECTS_DIR/Enzo_recon1/dti.nii. This is a relative path, i.e., it's trying to find it under the directory where you are currently cd'd. This seems like a problem with defining paths properly for unix, rather than a tracula problem per se. On Wed, 30 Sep

Re: [Freesurfer] niiRead(): error opening file SUBJECTS_DIR/Enzo_recon1/dti.nii

Ok! Thank you! I will try again! 2015-09-30 19:16 GMT-03:00 andrea cristina Lima : > Em 30/09/2015 11:30, "andrea cristina Lima" > escreveu: > >> I got the error below. Could you help me? I've already check the dti file >> and it seems Ok. Tks >> >> macprolim446:Antonio_recon1 LIM44$ trac-all -p

[Freesurfer] niiRead(): error opening file SUBJECTS_DIR/Enzo_recon1/dti.nii

I got the error below. Could you help me? I've already check the dti file and it seems Ok. Tks macprolim446:Antonio_recon1 LIM44$ trac-all -prep -c /Users/LIM44/Desktop/Freesurfer/subjects_freesurfer/Enzo_recon1/conf_tracula1_fls.txt INFO: SUBJECTS_DIR is /Users/LIM44/Desktop/Freesurfer/subjects_

Re: [Freesurfer] niiRead(): error opening file SUBJECTS_DIR/Enzo_recon1/dti.nii

Em 30/09/2015 11:30, "andrea cristina Lima" escreveu: > I got the error below. Could you help me? I've already check the dti file > and it seems Ok. Tks > > macprolim446:Antonio_recon1 LIM44$ trac-all -prep -c > /Users/LIM44/Desktop/Freesurfer/subjects_freesurfer/Enzo_recon1/conf_tracula1_fls.txt

Re: [Freesurfer] niiRead error

Hi Katarina it looks like that file might be corrupted. Where did you get it from? Can you view it in freeview? Maybe that partition was full when you copied it there or something similar? cheers Bruce On Mon, 31 Aug 2015, Katarina Trojacanec wrote: Dear experts, After running recon-all

[Freesurfer] niiRead error

Dear experts, After running recon-all I got this output: --- Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-cent