Dear FS developers,

Firstly, let me thank you for FreeSurfer: I use FS almost daily, and it is fantastic.

Now, onto the bug report:

When reading an analyze header with a modified hdr.hist.originator field, load_analyze_hdr.m sometimes “runs out” of bytes and leaves the last field (hdr.hist.smin) empty. When I pass the hdr struct to write_analyze_hdr.m, an invalid, 344 byte header is written (due to this empty hdr.hist.smin field). I will explain how to replicate the issue after first explaining what I think is happening and how I think it can be fixed.

I notice that on line 119 of load_analyze_hdr.m, the comment reads “Is this correct? Should be unsigned char”; so, perhaps someone had this issue previously, or hand an inkling that the code was problematic. Because of varying character encodings, fscanf(fp,’%c’,10) may read more than 10 bytes, which means all later fields will not be set properly.

The fix is simple, and there are a few options:

1) When opening the hdr file, force ‘US-ASCII’ encoding so each character is precisely 1 byte:

(lines 59 and 63) fp = fopen(hdrfile,’r’,’b’,’US-ASCII’);

(line 75) fp = fopen(hdrfile,’r’,’l’,’US-ASCII’);

*This is the preferred solution as it preserves the “readability” of the field. It also would apply to all the other instances of fscanf.*

2) use fread with uchar

(line 119) hdr.hist.originator = fread(fp,10,’uchar’);

3) use fread with char*1

(line 119) hdr.hist.originator = fread(fp,10,’char*1’);

I noticed this bug in the following context. I received a nifti file with an incorrect resolution in the header. When I corrected the resolution using matlab (load_nifti.m -> correct nii.pixdim -> save_nifti.m), converted the nifti image to analyze (mri_convert -ot analyze in.nii out.img), loaded the resulting analyze header in matlab with hdr = load_analyze_hdr(‘out.hdr’), and tried to run write_analyze_hdr(hdr,’new.hdr’), the new.hdr file was an invalid, 344 byte header file. I would be happy to send along sample images if needed.

I am hoping that you will add this fix to later versions of FreeSurfer, and perhaps consider updating 5.3.0, as well.

Thanks and best wishes,

Kate

Kathryn I. Alpert

Software Developer, Neuroimaging and Applied Computational Anatomy Lab

Northwestern University Feinberg School of Medicine
312.725.2832
k-alpert@northwestern.edu

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