Freesurfer December 2005

freesurfer@nmr.mgh.harvard.edu

35 participants
51 discussions

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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retinotopy and FsFast
by Jane Aspell 17 May '06

17 May '06

Hi Thanks for all your previous help with freesurfer. I am trying to use FsFast to do retinotopy analysis and have been following the instructions at: https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis I come undone at the stage of running the actual analysis, where the command should be: >sfa-sess -s avdk -a rtopy what does 'avdk' refer to? when i run it i get: ERROR: could not find session avdk when i try it with the arguments: >sfa-sess -analysis rtopy -sf sessid which is similar to the arguments needed for 'selxavg-sess' i get a similar error of not been able to find my (particular subject's) session. i believe i have set up the all the directory structures etc correctly for the sessions format as previous steps worked fine. any ideas what's going wrong? thanks Jane Aspell

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Short Course in fMRI
by Doug Greve 10 Apr '06

10 Apr '06

Mark Vangel and I are offering a short course in the statistical signal processing of fMRI. October 31 (Mon) & November 1 (Tue), 2005 7th Floor Auditorium Building 149 Charlestown Navy Yard Free, but limited to 40 attendees. Register at: http://www.nmr.mgh.harvard.edu/martinos/training/shortCoursefMRIStats.php doug

1 1

threshold
by Sasha Wolosin 04 Jan '06

04 Jan '06

Dear all, In group analysis, how are the various thresholds (min, mid, max) related to p-values? 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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cma colors
by Sasha Wolosin 28 Dec '05

28 Dec '05

Dear all, I am interested in using the CMA parcellation. Is the atlas lh.curvature.buckner40.filled.desikan_killany.gcs equivalent to the CMA parcellation? 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.

2 1

CMA parcellation
by Sasha Wolosin 27 Dec '05

27 Dec '05

Dear all, I am interested in using the CMA parcellation to create ROI's. Is it possible to create ?h.aparc.annot files using the CMA parcellation scheme instead of the surface-based parcellation scheme? 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.

1 0

overlay thickness maps
by Kirk, Gregory 24 Dec '05

24 Dec '05

I would like to overlay lh.thickness, rh.thickness on inflated for single subject, not the glm results, how to do that is well documented from the tutorial/tutorial group study tried tksurfer subject lh inflated - got the gray surface next file->load overlay -> $SUBJECTS_DIR/subject/surf choose lh.thickness * calculate identity map it redraws the surface but there is no colormap of the thickness can I do what I am trying ? Happy Holidays Greg.

4 3

Paracingulate Gyri Parcellating
by Faden, Eric (NIH/NIMH) [F] 23 Dec '05

23 Dec '05

After reading the paper I am still a little confused about how the Subcortical Parcellation labels the parasingulate gyri when some people have one and others have two? Can anyone shed a little light on this issue? -Eric

4 11

wmfill problem
by Sven Panis 22 Dec '05

22 Dec '05

Hi surfers, I experience a problem during the first step of the create surface routine : fill white matter. Specifically, the ponscall.dat file in mri/tmp is empty and at the start of step two (tessellate RH white matter) I'm asked to confirm that "the images in .../mri/filled/COR-0 cannot be found .... wmfill first." I have already tried to enter the coordinates of the corpus callosum and the pons manually (paying attention to the fact that xTal = coronal, yTal = horizontal, zTal = saggital + to make sure the cc is disconnected), without result... (I use the values in the Volume Index, no Talairachs). Do I have to pay attention to other things when entering coordinates manually? Or does anyone of you have an idea about what's going wrong? Any help appreciated! Thanks and enjoy the holidays, Sven Panis University of Leuven Department of Psychology Tiensestraat 102 3000 Leuven BELGIUM tel: +32-16-32.60.94 Mailto: sven.panis(a)psy.kuleuven.be Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm

3 3

RE: [Freesurfer] Sulcal depth
by Bagnato, Francesca (NIH/NINDS) [F] 22 Dec '05

22 Dec '05

Yes, this is what I mean. Thanks, -francesca Francesca Bagnato, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 USA ph #: 001-301-402.6391 fax #: 001-301-402.0373 -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thursday, December 22, 2005 5:37 PM To: Bagnato, Francesca (NIH/NINDS) [F] Cc: Fornito, Alexander; freesurfer(a)nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Sulcal depth you mean in a parcellation unit? It's whatever the parcellation unit is defined to be. On Thu, 22 Dec 2005, Bagnato, Francesca (NIH/NINDS) [F] wrote: > As far as the cortical thickness of sulci is concerned, the program > refers to the cortex in between two giry, right? > Thanks, > -francesca > > Francesca Bagnato, MD > NIB-NINDS-NIH > 10 Center Drive > Building 10, Room 5B16 > Bethesda, MD, 20892 > USA > ph #: 001-301-402.6391 > fax #: 001-301-402.0373 > > > -----Original Message----- > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Sent: Thursday, December 22, 2005 5:30 PM > To: Fornito, Alexander > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Sulcal depth > > not all that easily, although I guess we could write out something from > mris_inflate that has the units of mm. > > On Fri, 23 Dec 2005, Fornito, Alexander wrote: > >> Hi all, >>> From my understanding, ?h.sulc can be used to measure sulcal depth. >> I'm wandering if it is possible to use this to get the depth of a > sulcus within an ROI, and if so, how you would extract the relevant > measures, i.e.., would it be obtainable through mris_anatomical_stats? >> Thanks, >> Alex >> >> Alex Fornito >> M.Psych/PhD (clin. neuro.) candidate >> Melbourne Neuropsychiatry Centre and Department of Psychology >> The University of Melbourne >> alexander.fornito(a)wh.org.au >> >> ________________________________ >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

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Freesurfer December 2005