Hi Bruce,

On Wednesday 21 February 2007 20:25, Bruce Fischl wrote:

Hi Martin,

what is IOD? We use multiframe images (multiecho) all the time using:

IOD stands for Information Object Definition, but is it not that important. What is important is that my 3D volume is not stored in a directory with one slice per file, but all the slices in ONE single file. The DICOM header is in this case composed of SharedAtributes+ConcatenatedPerFrameAttributes+PixelData

mri_convert -nth $echono <input dicom series> output_echo${echono}.mgz

what error do you get?

It's actually warning, but the geometry of the image is not determined correctly and therefore tkmedit refuses to display the image:

$mri_conver IM-0001-0001.dcm IM-0001-0001.mgz mri_convert IM-0001-0001.dcm IM-0001-0001.mgz reading from IM-0001-0001.dcm... 1 DICOM 3.0 files in list Found 1 DICOM Files WARNING: NumberOfFrames 0 != Found Count of slices 1. reading DICOM image... ------------------------------------------------- DICOM meta-header

file name /Users/kavec/tmp8/IM-0001-0001.dcm Date and time study date 20070206 study time 105754 series time 121550.04000 acquisition time 121550.04000 Identification patient name TEST JONES manufacturer Philips Medical Systems Dimensions number of rows 288 number of columns 288 number of frames 1 pixel width not found pixel height not found slice thickness 1 field of view 0 image number 1 (might be not reliable) transfer syntax UID 1.2.840.10008.1.2.1 Acquisition parameters echo time not found repetition time not found inversion time not found echo number not found flip angle not found bits allocated 16 Spatial information first image position notfound last image position notfound image orientation notfound -------------------------------------------------

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1.10422e-42, 1.10422e-42, 7.02051e-43) j_ras = (-1.99546, 4.25209e-40, 2.32459e-40) k_ras = (0, -1.4013e-42, 2.20284e-42) writing to IM-0001-0001.mgz...

$ tkmedit -f ./IM-0001-0001.mgz MRIresample(): source matrix has zero determinant; matrix is: 0.000 -0.000 0.000 0.000; 0.000 0.000 -0.000 0.000; 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 1.000;

Error: Loading volume ./IM-0001-0001.mgz

Couldn't read the anatomical volume.

Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size.

Thanks in advance

Bruce

On Wed, 21 Feb 2007, Martin Kavec wrote:

...

Hi,

our MR scanner produces DICOMs with enhance MR IOD, i.e. multiframe image file. When I try to use this format with FreeSurfer mri_convert fails. I assume it is not designed for this type of images, isn't it? Anybody knows a workaround?

Thanks in advance for help (and great software),

Martin _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Hi, I was interested in comparing surface area between two groups on a node-by-node basis (something like average area of the triangles touching each node) and noticed there were automatically-generated files named lh.area and lh.area.pial

I was wondering if these files contained the appropriate data for doing something like that, and if so whether there's any documentation you can recommend on how they are generated in Freesurfer.

Thanks,

-Aaron-

Hi Aaron,

they are generated from the ?h.white and the ?h.pial surfaces, and should be what you want.

cheers, Bruce

On Thu, 22 Feb 2007, Goldman, Aaron (NIH/NIMH) [C] wrote:

Hi, I was interested in comparing surface area between two groups on a node-by-node basis (something like average area of the triangles touching each node) and noticed there were automatically-generated files named lh.area and lh.area.pial

I was wondering if these files contained the appropriate data for doing something like that, and if so whether there's any documentation you can recommend on how they are generated in Freesurfer.

Thanks,

-Aaron-

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

I agree. You could look at the jacobians across subjects, which will sort of get at what you want, or surface area by parcellation unit is a good idea. On Fri, 23 Feb 2007, Don Hagler wrote:

Just a comment: Surface area on a vertex-wise basis doesn't seem very informative. Before topology fixing, the surface area should be about the same for all vertices (differences should be more or less random). Topology fixing will add or remove vertices, so the surface area in a "fixed" region will go up or down depending on the type of defect. So if you do a vertex-wise group average of surface area, you will possibly get a map of where you are most likely to get topological defects. On the other hand, doing a group-level analysis of total surface areas within cortical parcellations is more likely to be meaningful.

...

From: "Goldman, Aaron (NIH/NIMH) [C]" aarong@mail.nih.gov To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] surface area Date: Thu, 22 Feb 2007 14:46:16 -0500

Hi, I was interested in comparing surface area between two groups on a node-by-node basis (something like average area of the triangles touching each node) and noticed there were automatically-generated files named lh.area and lh.area.pial

I was wondering if these files contained the appropriate data for doing something like that, and if so whether there's any documentation you can recommend on how they are generated in Freesurfer.

Thanks,

-Aaron-

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

The average US Credit Score is 675. The cost to see yours: $0 by Experian. http://www.freecreditreport.com/pm/default.aspx?sc=660600&bcd=EMAILFOOTE...

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer