Search found 45 matches

by PeterK
Wed Aug 18, 2004 1:37 am
Forum: BrainVISA
Topic: Can someone explain me how to use DTI interpolated tracking?
Replies: 4
Views: 4727

Have you made sure you saved the starting point regions ? (you just have to select "save" in the "session" menu of the ROI box in Anatomist, or hit ctrl-S). I don't use the tracking module every day (Yann is on holiday and will be back in about 3 weeks) but as far as I see when ...
by PeterK
Thu Aug 12, 2004 9:41 pm
Forum: BrainVISA
Topic: Fractional Anisotropy & Apparent Diffusion Coefficient S
Replies: 7
Views: 7684

Zahir Momin wrote:
Zahir
ImageJ isn't a good volume/ROI analysis tool. I use Medx and Afni. I think the FA data are 16 bit unsigned int.
by PeterK
Wed Aug 11, 2004 8:25 pm
Forum: BrainVISA
Topic: Fractional Anisotropy & Apparent Diffusion Coefficient S
Replies: 7
Views: 7684

Re: Fractional Anisotropy & Apparent Diffusion Coefficie

You can open ima files with basically any other software that has a "raw" import option. For ROI analysis you can try MNI Display, which is an ROI painting and analysis tool.
by PeterK
Wed Aug 11, 2004 8:23 pm
Forum: BrainVISA
Topic: Can someone explain me how to use DTI interpolated tracking?
Replies: 4
Views: 4727

Can someone explain me how to use DTI interpolated tracking?

Can someone please explain me how to use the FACT method? My anisotropy maps look fairly good. I select a tracking section. I select a few "starting point" somewhere in corpus collosum - but the bundles generated are empty. What am I doing wrong. Am I supposed to "paint" the trac...
by PeterK
Tue Jul 13, 2004 3:25 pm
Forum: BrainVISA
Topic: Working with inflation for morphometry
Replies: 13
Views: 11760

A related question. Say I want to depict certain information (cortical thickness) on the inflated map. I do have the thickness value for each node in the "un-inflated" state - how would I go about depicting them on "inflated" state. Do you save the deformation information anywhe...
by PeterK
Mon Jul 12, 2004 4:35 pm
Forum: BrainVISA
Topic: Working with inflation for morphometry
Replies: 13
Views: 11760

A related question. Say I want to depict certain information (cortical thickness) on the inflated map. I do have the thickness value for each node in the "un-inflated" state - how would I go about depicting them on "inflated" state. Do you save the deformation information anywher...
by PeterK
Fri Jul 09, 2004 8:13 pm
Forum: Anatomist
Topic: How can I make an RGM texture for anatomist?
Replies: 1
Views: 3635

How can I make an RGM texture for anatomist?

For now it seems like that the tex files only allow you store an indexed texture value.
Is there a way where RGB fractions per nodes are stored and displayed directly?
by PeterK
Thu Jul 08, 2004 10:03 pm
Forum: BrainVISA
Topic: error about DTI Interpolated Tracking !
Replies: 2
Views: 3627

Re: error about DTI Interpolated Tracking !

When I did DTI Interpolated Tracking on my PC( win 2000), BV reports me some error as fellows: DcmDataDictionary: cannot open file: D open D:\newDataBase\DTI\DTI01\diffusion\Track01\DTI01_Track01_bundles.bundlesdata Warning: wrong filename_base in graph, trying to fix it In my Track01 subdirectory,...
by PeterK
Thu Jul 08, 2004 10:02 pm
Forum: BrainVISA
Topic: Working with inflation for morphometry
Replies: 13
Views: 11760

A quick note about gyral parcelation tool. I've tried it a number of times, but it only created an empty graph. It was looking for label 105 and said that it is not found. Seems like it is missing a label translation file or something
by PeterK
Thu Jul 08, 2004 10:02 pm
Forum: BrainVISA
Topic: Working with inflation for morphometry
Replies: 13
Views: 11760

A quick note about gyral parcelation tool. I've tried it a number of times, but it only created an empty graph. It was looking for label 105 and said that it is not found. Seems like it is missing a label translation file or something
by PeterK
Sat May 22, 2004 6:59 pm
Forum: BrainVISA
Topic: Histo analysis
Replies: 2
Views: 4062

This is a generic message I get when the data quality is subpar. Can be translated as "garbage in - garbage out" :lol:

You can try to run a 3D median filter to boost SNR, but it usually doesn't help
by PeterK
Sat May 22, 2004 6:55 pm
Forum: BrainVISA
Topic: MRI segmentation
Replies: 7
Views: 9967

Re: MRI segmentation

SPGR "inversion-recuperation" - Do you mean that you've used an MPRAGE kind of sequence - e.g. a low flip angle GRE sequence with an inversion recovery pulse in front? If so, your inversion pulse probably zeros out signal from CSF - thus making your 3D volume two compartmental - GM and WM,...
by PeterK
Thu Mar 18, 2004 4:00 pm
Forum: BrainVISA
Topic: Modify AnatomistShowFoldGraph.py
Replies: 11
Views: 15642

Hmm, I'm not sure if you can edit python code to do it - but if you just to make an active selection you can use "select label" option and to type the name of the label. That of course will just highlight the selected label - it won't get rid of the rest of the objects. One way you can dis...
by PeterK
Wed Mar 10, 2004 7:37 pm
Forum: BrainVISA
Topic: Siemense DTI data processing
Replies: 2
Views: 9103

You should not worry too much Peter, with 10 averaging, you should get a pretty nice SNR... for these 6 directions. This should allow you to work. However, in the future I advice you to reduce the number of repetitions and increase the number of directions. This should reduce the risk of bias relat...
by PeterK
Wed Mar 10, 2004 5:42 pm
Forum: BrainVISA
Topic: Siemense DTI data processing
Replies: 2
Views: 9103

Siemense DTI data processing

Hey guys, I've collected some DTI data on a siemens TRIO and wondering if BV will be able to process them These are 6-directions data 2x2x3 mm and only 10 averages, so I'm concerned that SNR might not be sufficient. Has a siemense DTI import module been implemented already? I'd really like to give i...