Freesurfer August 2006

freesurfer@nmr.mgh.harvard.edu

48 participants
74 discussions

aseg, aparc regions reference table (aka "data dictionary")?
by Graham Wideman 22 Dec '06

22 Dec '06

Folks: It would be *really* great if there was a page somewhere (or just a file) giving some info on the various measures that are captured in the aseg and aparc files. For each measure (in the table or the "comments" above the table): -- Description of what it includes -- some are obvious from the name, others not. -- Whether it's deprecated. -- Whether FS V-whatever actually produces this value, or just zero. (Very useful, and probably not too much work? Plus I'd like to adapt this info so as to pull only the non-inert rows from the data file). (Or is there some other way to determine this?) -- Some suggestions on what numbers need to be added to get popular subtotals. I've just read through the last six months of freesurfer list traffic, and I see numerous questions along these lines... and replies with some clues here and there. Also references to papers, but these don't detail the nitty gritty of what FS V-something actually does. Probably numerous users would get a lot of use out of having this info in one place. Thanks, Graham

2 1

editing pre-existing annotations
by Eric Feczko 09 Nov '06

09 Nov '06

Hey, Is there a way to add structures/labels to a pre-existing annotation file? I sampled an annotated atlas onto a subjects surface. But when I load the annotation and try to create a new label, I can't export the edited annotation without eliminating the new label. I tried to create a new color lookup table with the new structure included, and I can load the table in tksurfer just fine. However, when I also try to import the pre-existing annotation(in order to edit it), the color table existing in the annotation overrides the color lookup table I load. If it try to load the table after importing the annotation, the new structure/label does not show up in the label window. If anyone can help me with this issue, that would be great, thanks! -Eric

3 2

Question
by Wan Park 26 Sep '06

26 Sep '06

Hello, my name is Wan Park and I am working at Columbia University. After converting General Electric DIACOM files into COR, I go to the Setup Structural Scans. There I set the Structural Scan Dir and then Convert/Average. After that, Start the Process Volume, but it seems that there is a problem when it tries to strip the skull. i receive this message: Images (brain): /Users/../Volumes/ste/freesurfer/subjects/scott/mri/brain/COR-001.. not found ... strip skull first So I go to see the logs and I find this: /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_normalize /Users/../Volumes/stem/freesurfer/subjects/scott/mri/orig /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 reading from /Users/../Volumes/stem/freesurfer/subjects/scott/mri/orig... normalizing image... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 3D bias adjustment took 3 minutes and 23 seconds. Command Finished /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_watershed /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 /Users/../Volumes/stem/freesurfer/subjects/scott/mri/brain ************************************************************ The input file is /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 The output file is /Users/../Volumes/stem/freesurfer/subjects/scott/mri/brain If this is incorrect, please exit quickly the program (Ctl-C) *************************WATERSHED************************** preflooding height equal to 25 percent Sorting... first estimation of the COG coord: x=125 y=148 z=132 r=54 first estimation of the main basin volume: 693155 voxels ******************************************************** ******************************************************** ******************************************************** White matter intensity 0 is lower than CSF intensity 26. Please examine input images. Will terminate ... ******************************************************** ******************************************************** ******************************************************** ************************************************************** MRIstipSkull failed. ************************************************************** Command Finished Could you tell me what's wrong? Thanks, Wan Park

4 3

anonymizing dicom files
by Najmeh Khalili M. 25 Sep '06

25 Sep '06

sorry about nonstop posting! I'm trying to remove the patient names from dicom files. I was advised to use dcm_modify_elements but it fails on DCM_Openfile. Is there a straight forward way of doing this? Thanks Naj P.S. Doug, I am still looking for the graddir tags :)

8 10

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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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.

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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

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Freesurfer August 2006