Freesurfer July 2006

freesurfer@nmr.mgh.harvard.edu

53 participants
88 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

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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

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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

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Intel Mac
by Ray Fix 19 Aug '06

19 Aug '06

Hello, Any plans for a Mac OS X Tiger Intel release? Ray

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Freesurfer install error OS Tiger, GSL error
by Charles-Henri Malbert 07 Aug '06

07 Aug '06

Dear collegue, I was using Freesurfer 0.9 and I try to install freesurfer 3. The install went smoothly and I update the cshrc file. The launch of Xterm went fine and the postinstall generate no errors (i.e. the GSL lib was found at GSL_DIR). When trying to test the install using tkmedit bert orig.mgz an error was generated saying that the GSL lib was not found at pubsw (dyld: Library not loaded: /usr/pubsw/packages/ gsl/1.6/lib/libgsl.0.dylib). Indeed no pubsw folder was found at usr. I was using fink and gsl was already installed in sw folder as part of Amide installation (a gnu front end of Xmedcon). May be the problem was arround there? What's the problem Thanks in advance Charles-Henri Malbert DMV, Dr es Sci, HDR Directeur de Recherches UMR SENAH 35590 Saint-Gilles Tel: 02 23 48 50 71 Fax: 02 23 48 50 80

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mri_volcluster and neuroanatomical labels
by Paymon Hosseini 31 Jul '06

31 Jul '06

Hello, I was wondering if there is a Freesurfer command for getting neuroanatomical labels for the output clusters of mri_volcluster. thank you very much for your help, paymon

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slice time correction?
by cameo＠nmr.mgh.harvard.edu 31 Jul '06

31 Jul '06

Hi all, I was wondering if fs-fast implements slice time correction at any point during processing? if so does it default to correction for either interleaved or linear acquisition and can this be modified? Thanks, Cameron

2 1

Help getting outer bits of brain
by Jake Freimer 31 Jul '06

31 Jul '06

I ran through autorecon1 and 2 for two subjects using the dicom images. One came out ok, but one is still missing some brain (as seen in the attached screen shots). I was wondering if there was a way to change the settings autorecon uses, because our scanner makes the inside so much brighter, or a way to batch convert rather than edit control points on all our subjects. Thanks -- -Jake

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skullstrip
by dasoscia＠buffalo.edu 31 Jul '06

31 Jul '06

I keep getting this error when trying to skullstrip a scan... *************************WATERSHED************************** preflooding height equal to 25 percent Sorting... T1-weighted MRI image modification of the preflooding height to 15 percent Count how many 110 voxels are present : 53463 Find the largest 110-component... heap usage = 133076 Kbytes. removing small segments (less than 1 percent of maxarea).done And identify it as the main brain basin...done Main component: 46289 voxels first estimation of the COG coord: x=124 y=107 z=123 r=86 first estimation of the main basin volume: 2722274 voxels ******************************************* *********************************************** *********************************************** White matter intensity 4 is lower than CSF intensity 24. Please examine input images. Will terminate ... *********************************************** *********************************************** *********************************************** ********************************************************** MRIstripSkull failed. ************************************************************ Linux localhost.localdomain 2.6.9-5.ELsmp #1 SMP Wed Jan 5 19:29:47 EST 2005 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Mon Jul 31 11:25:35 EDT 2006 Attached are some slices from my T1 images, numbered according to coronal slice number. I noted that they do look a little odd/different than previous scans. Suggestions? Thanks Dave

2 1

caudate/putamen values for mri_segstats
by Nguyen, Thang Q 28 Jul '06

28 Jul '06

Hello all, I used mri_segstats to get subcortical volumes my subjects. However, for some of the regions like the putamen and caudate, I get values of zero. I have been told that these values are either no longer in use or have not been in use yet. Is there a way of manually getting values for these regions? Thank you for all the help, -Thang

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Freesurfer July 2006