Freesurfer October 2011

freesurfer@nmr.mgh.harvard.edu

95 participants
160 discussions

Re: [Freesurfer] normalised functional volumetric data to fsaverage
by Douglas N Greve 11 Oct '11

11 Oct '11

you need to map your T1 template to fsaverage (probably using bbregister). Then call tkmedit or tksurfer with a --reg file (see the multimodal integration tutorial). BTW, you should not confuse this with doing a surface-based analysis. doug Ritobrato Datta wrote: > Hi Doug, > > This email over the weekend fell through the cracks. Can you please let me know how to do this ? > > Thank you very much > > Rito > > ----- Original Message ----- > From: "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> > To: "Ritobrato Datta" <ridatta(a)mail.med.upenn.edu>, "Doug Greve" <greve(a)nmr.mgh.harvard.edu> > Sent: Friday, October 7, 2011 11:02:53 PM > Subject: Re: [Freesurfer] normalised functional volumetric data to fsaverage > > > Doug? > > > On Oct 7, 2011, at 10:58 PM, Ritobrato Datta <ridatta(a)mail.med.upenn.edu> wrote: > > Hello, > > I have normalised the volumetric data to the T1 template using spm8 and did 2nd level grp analysis. Now I want to map the results onto fsaverage surface. I have a results.nii file (t-map in normalised space) > How do I do that ? > > Please let me know. > > Thanks > > Rito > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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selfreqavg
by Michelle Umali 11 Oct '11

11 Oct '11

Hi Jon, Thanks! I have a question about when selfreqavg. When do I use selfreqavg? Is it called when I run fieldsign-sess or do I have to run it in addition to the below? I've been doing the following: mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 -retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -force mkanalysis-sess -a rtopy.self.rh -surface self rh -TR 2 -retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -force preproc-sess -surface self lhrh -fwhm 5 -per-run -s sj09 -force selxavg3-sess -a rtopy.self.lh -s sj09 selxavg3-sess -a rtopy.self.rh -s sj09 fieldsign-sess -a rtopy.self.lh -occip -s sj09 fieldsign-sess -a rtopy.self.rh -occip -s sj09 Thanks for your help. Michelle On Mon, Oct 10, 2011 at 5:30 PM, Jonathan Polimeni <jonp(a)nmr.mgh.harvard.edu > wrote: > hi michelle, > > the Sereno et al. 1995 Science paper has details about the phase encoded > retinotopic data analysis, especially in the endnotes of the article. also > for more details you can look at the MATLAB code embedded in the command > 'selfreqavg', which is used for the basic retinotopy analysis and is quite > readable. > > hope this helps, > > > -jon > > > > On Wed, 21 Sep 2011, Michelle Umali wrote: > > > Hi Freesurfers. > > Is there text describing the retinotopy analysis in Freesurfer > > mathematically? > > > > Thanks. > > Michelle > > > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >

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nonlabeled vertices in bert
by Ben Hamida Cammoun Leila Faiza 10 Oct '11

10 Oct '11

Hello, 1) I reiterate my question, because i cannot continue processing. Some vertices are not labeled in the rh.aparc.annot in bert as 35643,36746,37788..... 2) The parcels of my subject are not connex. Below is the detail on my first email. Thank you very much for answering me De : Ben Hamida Cammoun Leila Faiza Envoyé : jeudi 6 octobre 2011 14:53 À : Objet : nonconnexity and holes in parcels Hello, I am using freesurfer v5.1.0 (on ubuntu). when processing reconall on my data I notice on the parcellation aparc.annot two strange points: some isolated small regions not annotated, as well as the non connexity of some parcels. I checked the bert aparc.annot on inflated surface and I found the same problem of non connexity, for instance some medialorbitofrontal labeled vertices (vertex index 108562) in rostralanteriorcingulate, or vertex num 103429 labeled as insula in lateralorbitofrontal parcel. In lingual there is also a small hole without annotation like vertices: 35643,36746,37788..... is this normal? if yes, how can we correct that? thanks in advance

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WM hypointensities and corpus callosum mislabeling
by Warren Winter 10 Oct '11

10 Oct '11

Hello, In a number of our subjects I've been finding white matter hypointensities around the anterior edge of the caudate, as well as mislabelings of the corpus callosum as cerebral white matter (at and/or around slice 128, sagittal). Has anyone else encountered these problems, and are there fixes that don't involve manually doctoring the mislabelings (such as setting a particular flag for recon)? I am quite new to FS so please forgive any rudimentary misunderstandings. Thank you! Warren -- Warren Winter Lab Coordinator Children's Hospital Boston Division of Developmental Medicine 1 Autumn Street, AU 650 Boston, MA 02215 857-218-5224

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Cerebellum pail surface
by Ansam El Shaikh 10 Oct '11

10 Oct '11

Hi, I'm trying to get red and green lines for cerebellum.. How can I do?. There are green and red lines for the cortex. Should I re-convert the data? Thank you.

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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

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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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Freesurfer October 2011