Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Tracula Memory Requirements
by Moiyadi, Ammar 11 Oct '11

11 Oct '11

Hi Freesurfers, I've been getting a memory allocation error (below) when running trac prep and trac paths on my computer with 6 gb ram. Since I was able to run these steps on a computer with 16 gb, I want to know, what is the minimum memory requirement for running tracula? Is the memory allocation error resulting from a lack of memory or is there something else going on that I am not aware of? Error: Loading BEDPOST parameter samples from /usr/local/freesurfer5.1/subjects/1052/dmri.bedpostX MRIalloc(256, 256, 50): could not allocate 262144 bytes for 431th slice Thanks always, Ammar Moiyadi, BS Professional Research Assistant Department of Psychiatry University of Colorado Anschutz Medical Campus 303-724-5490

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cannot save edited main volume
by Wei-Ta Chen 11 Oct '11

11 Oct '11

Hi: When I finish white matter editing and try to save the edited main volume by "Save Main Volume" of the "File" menu on TKMedit Tools window, there is a dialogue asking me:"Are ou sure you wish to save the changes to the main volume". When I clicked yes, error message appeared as follows:" Error. Couldnt save volume. This session was started in read-only mode. you cannot save changes." I changed my file permission to 777 (but I forgot to check my original permission settings) and saved again but in vain. Why was this error message? What should I do for now to avoid losing the edited WM results? Thanks for your help. Best, Wei-Ta Chen

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WM hypointensities
by carolina.mr 11 Oct '11

11 Oct '11

2 1

QDEC analysis
by krista kelly 11 Oct '11

11 Oct '11

I'm using QDEC to analyze cortical thickness differences between groups and I have a few questions: 1) There are a few variables that I need to control for. First variable is scanner - I used two different scanners of different field strengths (1.5T GE and 3T Siemens) so I wanted to control for scanner. I also wanted to control for age and gender. Here's my ideal design setup: discrete variables - groups, scanner, gender nuisance variable - age contrast would be 1 -1 0 0 0 0 I realize that scanner, gender, and group are all discrete variables, and that age would be a continuous one. However, in the design tab, I am not able to select all 3 discrete variables (groups, scanner, and gender). Should I designate scanner or gender as a nuisance variable instead? Would it matter which one I use as the nuisance variable? Possible setup: discrete vars - groups, scanner nuisance vars - age, gender contrast - 1 -1 0 0 (Correct?) 2) If I use DODS, should I demean the ages if age is a nuisance variable? 3) If I use a smoothing kernel during the analysis, then create an ROI and map that ROI to each individual subject, will the resulting .stats file in each subjects stats folder reflect the smoothed data or does mapping onto each ROI just extract the raw unsmoothed data from each vertex? Thanks! Krista

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question about contrast file during group analysis with command line
by ZhiLiangLong 11 Oct '11

11 Oct '11

Hi all : I'm performing general linear model (GLM) analysis in the surface,the attachments above are FSGD file and contrast files(the last three attachments).i wonder if my contrast files are correct. the attachment named diff-C-H-thickness.txt is about difference between C and H and the last two are about difference between C and p and difference between P and H,Here,C H and P represent three groups Any suggestions appreciated

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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. > >

2 1

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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