Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30065 discussions

newbie, white matter volumes
by Romke Rouw 05 Sep '06

05 Sep '06

Hi all, I would like to compare two groups of human subjects on volumetric measures of cerebral white matter. Does anyone know how to get more detailed information on white matter volumes ? (per brain region, or per white matter structure). Thanks! Romke

2 1

transform back to origin coordination ?
by tulu 05 Sep '06

05 Sep '06

Dear Freesurfer experts, I use freesurfer and when I finish recon-all autorecon1, I would like to transform Brainmask.mgz image back to origin coordination. How to do it ? Thank replay Kl chen

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Mri convert
by Lee HL 04 Sep '06

04 Sep '06

Hi Bruce and all, I wish to convert the MGZ format image into ANALYZE format image. I used the command line to convert the MGZ format image: "mri_convert -i brainmask.mgz -o brainmask.img --out_type spm". When I display the image using SPM, the coordinate (0, 0, 0) appears at the posterior commissure. However, when I display the mgz format image using tkmedit, the coordinate (0, 0, 0) appears at the anterior commissure. Was I using the correct command line to convert the image? Thanks! Cheers, HweeLing

2 3

func2tal-sess question
by Cameron Ellis 01 Sep '06

01 Sep '06

Hi, Quick simple question I hope: does running func2tal-sess with two groups at once with a sessid that includes them both and running func2tal with each group separately result in any difference? And if you do need to resample your groups separately do you need to do this under 2 different analyses? Thanks, Cameron

2 1

Hardware/Distro Gottchas?
by Grant McAuley 31 Aug '06

31 Aug '06

Hello, We are about to install Free Surfer on a machine with Intel Core 2 Duo E6400, 2Gb DDR2 and Nvidia Geforce 7300GT video using an Ubuntu or Fedora Core distribution. Are there any 'gottchas' I should know about with this hardware or Linux distros (I will be using the latest drivers and distros)? -- Grant McAuley Research Affairs IS Support Loma Linda University 909-558-1000 Ext 87750 gmcauley(a)llu.edu

1 0

license file
by Frederick Klauschen 31 Aug '06

31 Aug '06

Hi, I have difficulties registering and obtaining a license file. On the page: https://surfer.nmr.mgh.harvard.edu/fswiki/Registration clicking on the link: "Follow this link to obtain a license key" http://surfer.nmr.mgh.harvard.edu:631/printersregistration.html gives me an access denied message. Frederick __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

2 1

mritotal.log
by Chacko Cherian 30 Aug '06

30 Aug '06

Hello all, I wanted to know where the mritotal.log file is created.I checked the /scripts directory but couldnt find it there. I'd like to have a look at the Final objective function value for the subjects I'm running. Thanks in advance Chacko Cherian.

3 2

thickness standard deviation
by Sasha Wolosin 30 Aug '06

30 Aug '06

Dear all, I am interested in measuring mean thickness within ROI in MPRAGEs of children. My mean thickness values tend to be around 3.3 mm, with a standard deviation of about 1mm. I am concerned that these standard deviations are somewhat high. What typical values should I be expecting for standard deviation? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

5 8

FSL to FsFast: registration problem
by Paymon Hosseini 30 Aug '06

30 Aug '06

Hi I used both FSL and FsFast to process a set of fMRI data. after using FSL, I used "reg-feat2anat --feat xxxx.feat --subject xxxx" to check the fMRI to T1 registration in FSL. for some reason, I cannot get the FSL registration to come close to the one done by FsFast (please look at figure at http://web.mit.edu/paymon/www/regis.pdf) the left most figure, shows the fMRI to t1epi to T1 registration done entirely in FsFast using "autoreg-sess". the two right most figures, show registrations done in FSL followed by "reg-feat2anat --feat xxxx.feat --subject xxxx". Visually, the registration done with FsFast looks much better than the ones done with FSL and then transformed to FsFast. here is my question: should I be suspicious of the my registration process in FSL, or am I not applying reg-feat2anat correctly, and hence causing a poor fMRI to T1 registration. I am using FSL 3.3.7, and FsFast under nmrenv. thanks a lot for your help, paymon

1 0

Regarding missing DICOM fields
by Niels Bergsland 29 Aug '06

29 Aug '06

Hi, We have some old scans that were originally in ACR-NEMA format which we have converted to DICOM. The problem is that they are missing both the ImagePositionPatient and ImageOrientationPatient fields. Is there anyway to use freesurfer without having these two fields? Based on the post by Doug which I found at http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg03409.html , I am afraid not... Thank you for any help. Regards, Niels Bergsland

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