Freesurfer

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retinotopy description
by Michelle Umali 10 Oct '11

10 Oct '11

Hi Freesurfers. Is there text describing the retinotopy analysis in Freesurfer mathematically? Thanks. Michelle

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Rejoindre mon réseau sur LinkedIn
by Huiguang He via LinkedIn 10 Oct '11

10 Oct '11

LinkedIn ------------ Huiguang He souhaite se connecter à vous sur LinkedIn : ------------------------------------------ Freesurfer, Je vous invite à faire partie de mon réseau professionnel en ligne sur le site LinkedIn. Accepter l'invitation de Huiguang He http://www.linkedin.com/e/-qq80um-gtldw1um-5w/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… Voir le profil de Huiguang He http://www.linkedin.com/e/-qq80um-gtldw1um-5w/rsn/72703165/ArO9/?hs=false&t… ------------------------------------------

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warped flat occip patches and fieldsign maps
by Michelle Umali 08 Oct '11

08 Oct '11

Dear freesurfers, I've been analyzing my retinotopy , have finally been able to run fieldsign-sess without running into dimension mismatch errors. Everything seemed ok until I tried looking at the fieldsign maps on flat patches. Some patches are warped with odd out of plane swirls. In others, all i get are odd shaped shards and triangles. What might be the cause? thanks, Michelle

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normalised functional volumetric data to fsaverage
by Ritobrato Datta 07 Oct '11

07 Oct '11

Hi All, I have some functional beta maps normalised to the T1 template using spm8 and I am wondering how to map them onto the fsaverage surface ? In native subject space, I pipe a functional scout image into bbregister to get a registration matrix which is then used to map volumetric beta maps to native freesurfer surface and fsaverage surface. How do I do this with the normalised functional data ? Thanks Ri

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What kind of data could be processed by FreeSurfer
by Jie Shi 07 Oct '11

07 Oct '11

I am using recon-all command to process some analyze images. But it seems that this command does not work for all .img images. For example, I have an image with the following information: 256x256x124 0.7mm x 0.7mm x 1.5mm data type: uint8 description: position:0 0 0 file orientation: 1 0 0 0 1 0 0 0 1 working orientation: 1 0 0 0 1 0 0 0 1 Will the dimension, resolution, and data type all matter in the process?

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Table for aparc+aseg
by Shigetoshi Takaya 07 Oct '11

07 Oct '11

Dear FreeSurfers, In aparc+aseg file, each segmented or parceled region seems to be labeled by its own intensity (e.g. the intensity is 53 in the right hippocampus, 10 in the left thalamus...) when I see it on FSL viewer. Where can I find the table that shows the relationship between the intensity and the name of brain region? I want to extract the specific brain regions (e.g. parahippocampal gyrus, fusiform gyrus...) from the result of aparc+aseg, and use them for the seed mask or the termination mask in structural connectivity analysis (tractography). I appreciate your help. Thank you, Shige

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retinotopy analysis description
by Michelle Umali 07 Oct '11

07 Oct '11

Dear Freesurfers, I am trying to describe how freesurfer conducts it's retinotopy analysis to make the polar, eccen and fieldsign maps. Is there a detailed description of this somewhere? I can't seem to find an indepth description on the wiki. Thanks. Michelle

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Cut plane feature in tksurfer
by Jodie Davies-Thompson 07 Oct '11

07 Oct '11

Dear FreeSurfers, I am following the cut plane steps on the freesurfer wiki (http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOccipitalFlattenedPatch) I marked a closed areas, press the 'cut closed line' button, left-click in the area, and then press the 'fill uncut area' button. Upon clicking this last button, tksurfer crashes and the below error appears. tksurfer.bin: tnl/t_vertex.c:407: update_input_ptrs: Assertion `a[j].inputstride == vptr->stride' failed. Abort I've seen two other posts with the same problem (links below), but no solution. Can anyone advise on this? Regards, Jodie http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg14612.html http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg16303.html -- Jodie Davies-Thompson, Postdoctoral Fellow Department of Ophthalmology& Visual Sciences UBC/VGH Eye Care Centre 2550 Willow Street Vancouver, BC Canada V5Z 3N9 Tel: 604-875-411 ext 69003

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cwp and QDEC color scale
by Antonella Kis 07 Oct '11

07 Oct '11

Hello Surfers, I would appreciate if you can help me with the following question: what should be the range values on the QDEC and/or GLM color scale if the cwp values for the cached clusters at thresh 2 and cwpvalthresh .99 are between 0.4465 and 0.9710? Many thanks. AK

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Process monkey data
by Pedro Paulo de Magalhães Oliveira Junior 07 Oct '11

07 Oct '11

I have data from 100 monkeys and I need to compare cortical thickness among two groups. In the wiki page there is an entry MonkeyData that has a set of scripts which break-down the steps needed, unfortunately I'm having trouble with this scripts and FS 5.1 Are there an updated version of those procedures? Thanks PPJ -- iOS 5.0

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