Freesurfer August 2011

freesurfer@nmr.mgh.harvard.edu

124 participants
212 discussions

full flat patch issue
by francesca strappini 11 Aug '11

11 Aug '11

Hi, I'm trying to create a full flat map. The process of flattening seems has finished without any errors, but I got this error message when I tried to show up the full flat patch: lh.full.flat.patch.3d: face[0] = 0, but face 0 not in vertex 0 face list Thanks a lot Francesca

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tksurfer & rtview
by Michelle Umali 11 Aug '11

11 Aug '11

Dear Freesurfers, In an effort to figure out why my field sign data is a bunch of blue/red speckles, I looked at the polar and eccentricity maps separately on the surface. In both maps, I found that the values range from 0 to approximately 65. Does that seem to be OK, and if so, what do these numbers represent in terms of polar angle or eccentricity? Also, it seems that the color ranges in the overlay cannot show any values above 4; is there a way to visualize larger ranges (such as 0 to 65)? Thank you very much. Michelle

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Volumetric analysis of thalamus in freesurfer
by Knut J Bjuland 11 Aug '11

11 Aug '11

I am working to do a volumetric analysis in Freesurfer using Thalamus. I do not know if this is the correct way to go. Should I first register thalamus to a surface using tkregister? There was also another post on this list, which suggested using tkregister2? I am also search to find a tutorial on how to create a volmask and the use it to calculate statistic in Freesurfer for Thalamus. Knut J

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Fwd: Segmentation of hippocampal subfilelds
by mohan boddu 11 Aug '11

11 Aug '11

---------- Forwarded message ---------- From: mohan boddu <bmohan.boddu(a)gmail.com> Date: Tue, Aug 9, 2011 at 6:17 AM Subject: Re: [Freesurfer] Segmentation of hippocampal subfilelds To: Koen Van Leemput <koen(a)nmr.mgh.harvard.edu> Hello, I would like to thank you for the information, but the problem is, I am a CS student working on this and I dont have much idea about it. Basically my task is to convert those images into ROI mask. For this I have to follow the instructions in the website stated below: http://brainybehavior.com/neuroimaging/2010/06/saving-individual-labels-fro… But the process stated in the above website works for label maps, and if the images generated in the "*segmentation of hippocampal subfields*" ( http://www.freesurfer.net/fswiki/HippocampalSubfieldSegmentation) (8 images are generated for each side) stage are probability maps then what should be given as upper threshold(-uthr) and lower threshold(-thr) values. And as the last step says to divide it by its label number to normalize it. Is it necessary for the probability maps, if it is, then what would be the number that we have to divide? Sorry, if I am not clear and thank you very much for helping me out. On Tue, Aug 9, 2011 at 10:41 AM, Koen Van Leemput <koen(a)nmr.mgh.harvard.edu>wrote: > Hi Mohan, > > The segmentation results are given as probability maps: a (unsigned > 8-bit) value of 0 means probability 0 , 255 means probability 1, and > everything in between scales linearly. > > The proper way to obtain "crisp" label maps from these images is to > assign each voxel to the label map that has the highest probability, > so you'd need to read in all probabilty maps, visit each voxel and > compare the probabilities in the voxel for all structures. > > Generating such "scrisp", winner-takes-all label maps is not > recommended to calculate e.g., volumes etc, though... > > Hope this helps, > > Koen > > > On Mon, Aug 8, 2011 at 2:26 PM, mohan boddu <bmohan.boddu(a)gmail.com> > wrote: > > I have completed the segmentation of hippocampal subfileds, but now I > would > > like to know the generated images are in probability map or label map? If > > they are in label map what would be the best upper and lower thresholds > to > > generate the ROI mask images. Could you please also tell me the way to do > > so. > > > > -- > > --Mohan Boddu-- > > Research Assistant > > Department of Radiology and Imaging > > Research II Building > > Indiana University School Of Medicine > > Indiana University-Purdue University Indianapolis > > Indianapolis, IN 46202 > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > 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. > > > > > -- --Mohan Boddu-- Research Assistant Department of Radiology and Imaging Research II Building Indiana University School Of Medicine Indiana University-Purdue University Indianapolis Indianapolis, IN 46202 -- --Mohan Boddu-- Research Assistant Department of Radiology and Imaging Research II Building Indiana University School Of Medicine Indiana University-Purdue University Indianapolis Indianapolis, IN 46202

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repeated measures ANOVA
by swoodman＠nmr.mgh.harvard.edu 11 Aug '11

11 Aug '11

Hello all, We would like to analyise our repeated measures DTI data using an ANOVA. We are wondering if someone might have experience running AVOVA's on 3D data? Is there a particular tool used or did you use MATLAB for this type of analysis? Thank you, Sandra Sandra Woodman Mood and Motor Control Laboratory Athinoula Martinos Center for Biomedical Imaging Massachusetts General Hospital

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mri_glmfit & .nii files
by Chindhuri Selvadurai 11 Aug '11

11 Aug '11

Hi freesurfers, I am trying to run an analysis right now, however, after using isxconcat, I am only finding ces.nii.gz files in the output directory and no .nii files. output dir: /cluster/manoach/milton/subjects/group_analysis/volume/m1 subjects_dir: /cluster/manoach/milton/subjects command: mri_glmfit --y /group_analysis/volume/m1/mstmct_v_base/type_v_rest/ces.nii.gz --glmdir group_analysis/volume/m1/ --osgm Not sure why this is the case.. any help would be appreciated! Thanks!

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: Memory and CPU Allocation?
by tapsya＠nmr.mgh.harvard.edu 11 Aug '11

11 Aug '11

Dear FSFAST, I am using the program selxavg3-sess on 3D data for a single session (i.e. selxavg3-sess -s avml07 -analysis $ana_vol -force) and it errors out with the following message: OLS Residual Pass run 1 t= 0.0 ??? Error using ==> unknown Out of memory. Type HELP MEMORY for your options. Error in ==> fast_selxavg3 at 469 rho1run = sum(rrun(1:end-1,:).*rrun(2:end,:))./rsserun; I am using FSFAST v 5.1. My analysis uses FIR design, 6 runs in each session with 18 contrasts. I executed the program on clusters 'launchpad' (@ Martino's center) and allocated 49GB to it. My question is how much CPU and memory you recommend I should allocate? I have also attached the log file in this email. Any help is greatly appreciated! Thanks. Wishes, Tapsya

2 1

VRML support
by andrei sherstyuk 11 Aug '11

11 Aug '11

Greetings, I have problems exporting the surface data in VRML format. When I load the resulting .wrl file into Blender (a 3D modeling tool), the resulting surface is full of holes (bad/missing polygons) and connectivity of vertices is all wrong -- I see edges where they are not supposed to be. Is is a common problem with VRML export? I used "write_vrml 1" command, tksurfer version 5. Any help will be greatly appreciated. Cheers, Andrei

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Label2label on fsaverage
by Rouhollah Abdollahi 10 Aug '11

10 Aug '11

Dear freesurfer experts I've tried to export my label file from individual space to fsaverage space by using this command: mri_label2label --srclabel rh.V1.label --srcsubject SUB1 --trgsubject SUB1 --trglabel rh.V1_reg.label --regmethod surface --srcsurfreg sphere --trgsurfreg sphere.reg --hemi rh and when I tried to load the output label file on fsaverage surface like inflated one it shows a lot of point looks like it is not deformed properly. Is it related to registration to fsaverage or something esle? The question is how I can register the subjects surfaces to fsaverage surfaces? -- With Best Regards Rouhi

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FSGDF matrix
by Antonella Kis 10 Aug '11

10 Aug '11

Dear Bruce, I am ready to start my GLM group analysis. I am trying to construct the FSGDF by constructing an my_age_fsgd.txt file. I was reading the tutorial and I am not sure if I need to put together my patients and controls in my FSGDF since my group study will be for patients versus controls. Please advise me. Thank you. Antonella

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Freesurfer August 2011