[Freesurfer] mri_convert, primary slice direction and resampling
Hi, Can mri_convert work with slice orientation other than axial? My input is sagittal (slices collected from right to left), but when I create files from mri_convert the header reads axial. This is particularly problematic when converting to analyze format from dicoms or another file type because the dimensions of the sagittal slices are applied the transverse plane. Using in_orientation and out_orientation options, the images will display correctly, but the header still reads axial. Can mri_convert subsample an image by retaining every other voxel without interpolating between voxels? Thank you, ~julia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_convert, primary slice direction and resampling
To more fully explain the road block, this is the output of 'mri_info analyzefile --slicedirection' MatlabRead: readHeader returned NULL WARNING: analyzeRead(): matfile analyzefile.mat exists but could not read ... may not be matlab4 mat file ... proceeding without it. - INFO: could not find analyzefile.mat file for direction cosine info. INFO: use Analyze 7.5 hdr-hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in analyzefile.mat file I am running on a Mac. Does this have anything to do with it? I don't have matlab on the mac, but on a windows virtual machine. thanks ~julia On 4/16/07, Julia Hamstra [EMAIL PROTECTED] wrote: Hi, Can mri_convert work with slice orientation other than axial? My input is sagittal (slices collected from right to left), but when I create files from mri_convert the header reads axial. This is particularly problematic when converting to analyze format from dicoms or another file type because the dimensions of the sagittal slices are applied the transverse plane. Using in_orientation and out_orientation options, the images will display correctly, but the header still reads axial. Can mri_convert subsample an image by retaining every other voxel without interpolating between voxels? Thank you, ~julia -- UC Davis Neuroscience Graduate Group The M.I.N.D. Institute - Amaral Lab (916) 703-0376 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_convert does not recognize dicom files
Hello, I am unable to use mri_convert to import dicom files. Below are examples of the errors. For a GE scan: mri_convert -it ge -ot mgz -i 01.v2 -o orig.mgz reading from 01.v2... genesisRead(): can't determine file name format for ./01.v2 For a Siemens scan: mri_convert -it siemens_dicom -ot mgz -i 0001.dcm -o orig.mgz reading from 0001.dcm... ERROR (ScanSiemensSeries): ./0001.dcm is not a Siemens DICOM file ERROR: could not find any files (SeriesList==NULL) Similar errors are given when the generic dicom is used. Other programs, such as Osirix and Analyze are able to process the DICOM files. Is there an obvious error in the command? What else should I consider? Thank you ~julia -- UC Davis Neuroscience Graduate Group The M.I.N.D. Institute - Amaral Lab (916) 703-0376 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_convert in 4D
I am viewing it with tkmedit. For the timeseries, it only displayed some of it. I also tried viewing it with fslview. There it was a single dashed line in the coronal view. Here is the output:mri_convert -it dicom -ot nii i6757552.MRDC.1 run.nii.gz reading from i6757552.MRDC.1...1260 DICOM 3.0 files in listFound 1260 DICOM FilesWARNING: NumberOfFrames 0 != Found Count of slices 1260.reading DICOM image...- DICOM meta-headerfile name /data/Cued_Recall/CR_ds7/s6757551/i6757552.MRDC.1Date and time study date 20050601 study time 183408 series time 190627 acquisition time 190627Identification patient name ds060105 manufacturer GE MEDICAL SYSTEMSDimensions number of rows 64 number of columns 64 number of frames 1260 pixel width 3.43752 pixel height 3.4375 slice thickness 7 field of view 220.001 image number 1 (might be not reliable) transfer syntax UID 1.2.840.10008.1.2.1Acquisition parameters echo time 30 repetition time 720 inversion time 0 echo number 1 flip angle 1.5708 bits allocated 16Spatial information first image position -108.281 -113.295 54.3301 last image position -108.281 -60.2276 88.2841 image orientation 1 -0 0 -0 0.538953 -0.842336 -TR=720.00, TE=30.00, TI=0.00, flip angle=90.00i_ras = (-1, 0, 0)j_ras = (0, -0.538953 , - 0.842336)k_ras = (0, -0.842337, 0.538951)writing to run.nii.gz...thanks~julia On 4/8/06, Bruce Fischl [EMAIL PROTECTED] wrote:how are you displaying it? And can you send the entire output? On Fri, 7 Apr2006, Julia Hamstra wrote: Hi, I am getting two errors when creating NIFTI files from dicoms using mri_convert. The first is that the 4D images are being spatially contactonated. It does not seem to be treating it as a timeseries. This is the command: mri_convert -it dicom -ot nii s6761334/i6761335.MRDC.1 run.nii.gz Additionally it is an oblique acquizition so the coronal view is not displaying the plane of acquizition (as intended), but an orthogonal cut through multiple slices. Am I missing an option or additional information? I searched the options and couldn't figure out anything that helped. The problem applies to the co-planar oblique structural scan too. I'm guessing there is something simple that I am overlooking. What may that be? thanks ~julia -- Human Memory Lab8950 Villa La Jolla DriveSuite C212La Jolla, CA 92093phone: (858)534-1227fax: (858)534-1240[EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
