What if you use mri_convert to convert them to a mgz or nii volume? Do you get the same error?
Ruopeng
On Sep 1, 2021, at 10:52 AM, Peled, Noam <NPELED@mgh.harvard.edumailto:NPELED@mgh.harvard.edu> wrote:
Hello! I’m trying to use freeview to visualize FSPGR dicoms files. I’m using ubuntu 18.04 with tcsh shell. I’m getting the following error: sh: 1: Syntax error: Bad fd number
Here is the full error message:
Starting DICOMRead2() dcmfile =~/Desktop/04254335/05641194 dcmdir = ~/Desktop/04254335 Ref Series No = 3 Found 200 files, checking for dicoms Found 200 files, checking for dicoms 5 /05641194 Found 198 dicom files in series. Found 198 dicom files in series. oms 5 /05641194 First Sorting Computing Slice Direction Vs: 0 0 1 Vs: 0 0 1 Second Sorting IsDWI = 0, IsPhilipsDWI = 0 Counting frames nframes = 1 nslices = 198 ndcmfiles = 198 INFO: rescale not needed PE Dir = ROW (dicom read) Loading pixel data JPEG compressed, decompressing cd ~/Desktop fsdcmdecompress --i ~/Desktop/04254335/05641194 --o /tmp/basuia.tmp.decompressed.dcm.yK9HZZ --jpeg >& /tmp/basuia.tmp.decompressed.dcm.yK9HZZ.dcmdjpeg.out sh: 1: Syntax error: Bad fd number ERROR: 512, see /tmp/basuia.tmp.decompressed.dcm.yK9HZZ.dcmdjpeg.out for more details QObject::~QObject: Timers cannot be stopped from another thread
Thanks, Noam _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer