Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

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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TIV
by Lee HL 16 May '06

16 May '06

Hi, Pardon my ignorance. How does the program determine the volume for TIV? Thanks! Kind regards, HweeLing

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freesurfer installation problems
by Chacko Cherian 16 May '06

16 May '06

Hello all, I am having some trouble in using the freesurfer version I had downloaded.The FREESURFER_HOME file is missing and so I cannot source or setenv anytime I want to use it.Do I need to tar and unzip again or is there any other way? Thanks in advance Chacko. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Re: Freesurfer Digest, Vol 27, Issue 13
by tao＠ucsd.edu 16 May '06

16 May '06

Hi: I have one question regarding the parcellate_subject and morph_subject After recon-all is complete, I setenv of CSURF_DIR to $FREESURFER_HOME, and then run parcellate_subject, got following error: reading atlas from /usr/pubsw/packages/freesurfer/average/lh.atlas2002_simple.gcs... GCSAread: couldn't allocate labels to -21852 Cannot allocate memory Does anyone can give me any hints? Thanks! Tao

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error on parcellate_subject
by tao＠ucsd.edu 16 May '06

16 May '06

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nifti q-form
by Strien, N van 16 May '06

16 May '06

Hi Is the information concerning the q-form header field in Nifti-1 still accurate (in relation to freesurfer): please see: http://nifti.nimh.nih.gov/nifti-1/support/FreeSurferandNIfTI1/view?searchte… I am planning to update my data conversion code and include the q-form header field in a meaningful way. It would be nice if I could get it to work properly with both fsl and freesurfer. Kind regards, Niels van Strien

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aseg.stats question
by Sasha Wolosin 15 May '06

15 May '06

Dear all, I would like to know what some of the abbreviations of areas in the aseg.stats file stand for, in particular: Left-F3orb Left-lOg Left-aOg Left-mOg Left-pOg Left-Stellate Left-Porg Left-Aorg and "Right-Thalamus" vs "Right-Thalamus-Proper" Where may I find documentation on these names? 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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apar+aseg.mgz values
by Stefano Pellegrini 15 May '06

15 May '06

Hi all, I would like to use the aparc+aseg.mgz as a mask image. I am mainly interested in the cortex segmentation and if I am not wrong the [2000-2034] values corresponde to the 35 (34 + 1 unknown) values correspond to the 34 areas of the Desikan atlas for the right emisphere. Are these the values that are listed in the rh.aparc.stats file? Can I say that the value 2000 in the aparc+aseg.mgz correspond to the unclussified voxel of the cortex in the right emisphere? Thanks, -stefano

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mri_vol2surf projfac-avg
by Don Hagler 15 May '06

15 May '06

In the stable3 version of mri_vol2surf, there is an option listed "projfac-avg". I can't tell if it is working or not. In the output messages, it says that ProjFrac = 0.5 (or whatever value is given with -projfrac) but there is no mention of the projfrac-avg min and max. Is the program doing what it is supposed to and not giving any relevant messages, or is the lack of messages an indicator that it is just doing the basic projfrac without averaging along the normal?

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two short questions, (flat maps, paint-sess)
by Sebastian Moeller 12 May '06

12 May '06

Dear fellow FreeSurfers, I got two small questions, I would be delighted to recieve some guidance on. The first one is for the monkey experts, I want to flatten the full hemispheres of my processed monkey brains, and I got around to cut away the medial wall to exclude those non-cortex areas from the map; where I am stuck now is making "tension relieve" cuts. Mainly my question is, what are the "canonical" cuts people make on monkey brains to flatten them fully (ideally I would like to see them on an inflated monkey hemisphre, but good landmarks would be also very welcome). Second question is about paint-sess/surf-sess. While trying to display my paint-sess created overlays on the inflated surfaces using surf-sess one out of three monkeys (total so far) gives real bad surface maps (they do not match the expected areas of activation from a tkmedit comparison run) and "spams" the surf-sess log with "MRISreadValues: vertex index out of range". If I set -projfrac from 0.5 to 1 I get acceptable maps for this monkey as well and no more errors. So to get to the point, what is the story behind -projfrac and what is it for? I would be really happy to learn more about this variable. Ahoi & Thanks in Advance Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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