Hi Jim,
It seems that AFNI dataset cannot be converted correctly in "csurf" interface. I tried
to resolve this problem as follows:
Suppose the AFNI dataset is: anat+orig.BRIK and anat+orig.HEAD, they are in
~/mri/orig/anat.
1. cd ~/mri/orig
2. mri_convert ./anat/anat+orig.BRIK ./
3. tkmedit local
(You can see the images now, but maybe some of them are in the wrong planes. Use flip
function of tkmedit to flip them to the correct planes)
4. In the window that you just run "tkmedit local": FlipCorView or flip_corview_xyz
(You can see help information of the function. I used "flip_corview_xyz x -z -y" for
my data. It is a good idea to check the images by comparing them with those of
anat+orig opened with AFNI)
5. Please remember to save the volume
6. Use "csurf" to see the "orig" images of the converted volume
BTW: Because the anatomical volume is flipped, the functional volume needs to be
flipped, too. This process is so complicated that I think it is better to wait for the
new version of FreeSurfer. Hope that the new one can convert AFNI BRIK correctly.
Good luck,
Xiangchuan Chen
****** The following is the original message ******
From: James Eliassen ([EMAIL PROTECTED])
To: freesurfer ([EMAIL PROTECTED])
Date: 2001-08-22 Time: 17:16:00
Subject: Re: Freesurfer´s problem
>Hi Bruce and Rafael,
>
>I have more details now. We are having a problem with the
>Convert/Average step in Freesurfer. We have two high-res anatomicals
>(originally saggital slices), 1x1 mm in plane, 1mm thick. They were
>256x256 FOV and 160 slices. We convert the raw Siemens .ima files
>(Vision system at 1.5T) to AFNI BRIKS. Then we co-register the two
>AFNI BRIKS with AFNI's 3d Registration plugin tool. They appear to be
>co-registered to within a mm or so of each other. These 2 BRIKS are
>made up of shorts (as opposed to bytes, but the problem is the same
>if we convert them to byte files first). We place these two separate
>BRIKS and associated HEAD files into
>~freesurfer/Subjects/SubName/mri/orig/001 and 002/ and then perform
>"Setup Structural Scans." After identifying the proper directories
>and files and reading the header (using the freesurfer button, which
>correctly reads this information) we push the Convert/Average button.
>The images that come out can be viewed on our web server
>
>http://fmri.neuro.brown.edu/freesurfer.html
>
>The saggital image shows what looks to be an ear in white amongst the
>noise (i.e., the correct orientation of the slab), but the other two
>planes indicate that the same image is present throughout the slab.
>
>Any further question and suggestions will be graciously accepted!
>
>-jim
>
>>Hi Rafael and Jim,
>>
>>could you give us more details about your problems? 2 anatomicals should be
>>fine for reconstruction (one will work as well if it is high enough
>>quality, but the surfaces won't be as accurate). Saggital acquisitions
>>should be fine. Have you successfully reconstructed surface models? Is the
>>problem you're having with functional overlay?
>>
>>cheers,
>>Bruce
>>
>>--------------------------------------------------------
>>Bruce Fischl email: [EMAIL PROTECTED]
>>Mass. General Hosp. NMR Center. tel:(617)-726-4897
>>Rm. 2328, Building 149, 13th Street fax:(617)-726-7422
>>Charlestown, MA 02129 USA
>>
>>
>>
>>
>>On Mon, 20 Aug 2001, James Eliassen wrote:
>>
>>> Hi Rafael,
>>>
>>> We did not solve the problem. The trouble is that only one slice is
>>> represented in the dataset (after the convert/average step), so it
>>> may look like an image viewed from the appropriate plane, but because
>>> the (single) image is the same throughout, views in the other planes
>>> just appear as black and white lines.
>>>
>>> There were three possibilities, we think.
>>>
>>> 1. We were only using two high-res anatomical image sets, instead of
>>> the recommended 3.
>>>
>>> 2. the brik2bfloat version we were using was out of date, although
>>> the versions I was able to locate at the time (February/March or so)
>>> were the same as the one we had.
>>>
>>> 3. Our hi-res anatomicals (siemens MPRAGE's) were acquired in the
>>> saggital plane and converted to afni briks. Maybe Freesurfer did not
>>> like the saggital images. I think there is a way to convert the
>>> images to the coronal plane but we didn't solve that problem.
>>>
>>> Good luck, let me know if you have success.
>>>
>>> -jim
>>>
>>>
>>> >Dear James:
>>> > IÌm trying to use Freesurfer, but I have the problem of the white
>>> >and gray lines on black background. Did you solve the problem? What
>>> >is the solution?
>>> > IÌll appreciate very much your help. Thank you in advance,
>>> > Rafael.
>>> >
>>> >Send reply to: [EMAIL PROTECTED]
>>> >
>>> >
>> > >
>> > >Get 250 color business cards for FREE!
>> > >http://businesscards.lycos.com/vp/fastpath/
>> >
>> >
>
>--
>
>
>-----------------------------------
>Jim Eliassen, Ph.D.
>Box 1953
>Dept. of Neuroscience
>Brown University
>Providence, RI 02912
>USA
>
>For courier service--
>ADD : 190 Thayer Street, Metcalf Research Laboratory, Room 337
>DELETE : Box 1953
>
>office 401-863-9984
>lab 401-863-1874
>fax 401-863-1074
>
>http://fmri.neuro.brown.edu/Eliassen.html
>-----------------------------------
****** End of the original message ******
