I’m glad to hear it worked out. We have all done this….

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Andrew
Sent: Monday, August 2, 2021 12:07 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] niiRead: error opening file, through mri_convert

        External Email - Use Caution        

Bruce, thank you for this response. In fact I had the T1 path wrong despite having read it over and over 20 times.. listing directory contents indeed revealed my error…

-andrew

On Jul 30, 2021, at 13:38, Fischl, Bruce <BFISCHL@mgh.harvard.edu> wrote:

Can you load /Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii in freeview? Maybe run ls -l on it?

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@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 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I’m trying to reconstruct an old pipeline that I don’t completely understand (so sorry if this is very elementary or out of date), and one step is to convert the freesurfer T1 segmentation ribbon.mgz to .nii format using mri_convert.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 freesurfer interface I see the T1 and the segmentation are fine; but mri_convert seems to fail on looking for the T1:

The command (from inside Matlab) is:

mri_convert  --reslice_like /Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii -rt nearest /Applications/freesurfer/7.1.1/subjects/ah2/mri/ribbon.mgz /Users/amhaun01/Documents/HERIdata/anatomy/ah2/t1_class_test2.nii

Output looks like:

mri_convert --reslice_like /Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii -rt nearest /Applications/freesurfer/7.1.1/subjects/ah2/mri/ribbon.mgz /Users/amhaun01/Documents/HERIdata/anatomy/ah2/t1_class_test2.nii 

reading from /Applications/freesurfer/7.1.1/subjects/ah2/mri/ribbon.mgz...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 0, -1)

k_ras = (0, 1, 0)

reading template info from volume /Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii...

error: niiRead(): error opening file /Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii*****

It is failing to read the T1 and then it does not save the output file. 

But the input files (T1.nii and ribbon.mgz) are all where they should be. 

What could I be doing wrong?

thanks,

-Andrew

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