[Freesurfer] registering functional labels to another anatomical data

A. Is there a way to convert the functional labels from Brain A to Brain B? Or do I need to re-do the whole functional analysis using the Brain B? Best, Yuko Yotsumoto ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] DTI directions and slice angulation

of not using the correction. I'd appreciate any comments/suggestions. Thank you, Yuko Yotsumoto ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only

Re: [Freesurfer] SNR on DTI data

in the white matter aseg mask? Thank you in advance! Yuko Yotsumoto Mar 18, 2014 1:26 PM、Anastasia Yendiki ayend...@nmr.mgh.harvard.edu のメール： Signal-to-noise ratio = mean / standard deviation On Tue, 18 Mar 2014, Yuko Yotsumoto wrote: Anastasia, Thank you so much for your reply

[Freesurfer] ADC, Radial diffusivity, Axial diffusivity and thresholds

, just average the values within a ROI. [2] Use some arbitrary thresholds to each of ADC, RD, AD. [3] create a mask that contains voxels of the above-threshold-FAvalues, then, calculate mean within the mask. Any suggestions? Best, Yuko Yotsumoto

[Freesurfer] SNR on DTI data

values, I just need SNR for the whole DTI data for each group. Any suggestions will be appreciated! Yuko Yotsumoto --- - Yuko Yotsumoto, Ph. D. Associate Professor The University of Tokyo, Department of Life Sciences Bldg #2, 3-8-1

Re: [Freesurfer] How to avoid overlaps between volume labels?

Thank you all for your suggestions. I binarized my labels, used mri_concat --max, then re-binarize the volumes. It worked great. Thanks again, Yuko Yotsumoto On Jun 7, 2012, at 6:58 AM, Douglas Greve wrote: It depends on how graceful you want to be with resolving the overlap. One simple way

Re: [Freesurfer] dt_recon error

someone who knows about your sequences as to what the actual values you should use. doug On 12/9/11 10:09 PM, Yuko Yotsumoto wrote: Hi Doug, Thank you for your reply. If so, then it cannot extract the bvecs and bvals. If you supply them in a file on the command line I don't quite

Re: [Freesurfer] dt_recon error

. The expected format is given in the help. You'll have to ask someone who knows about your sequences as to what the actual values you should use. doug On 12/9/11 10:09 PM, Yuko Yotsumoto wrote: Hi Doug, Thank you for your reply. If so, then it cannot extract the bvecs and bvals. If you supply

Re: [Freesurfer] dt_recon error

Doug, Never mind. I think I just figured it out!0 Yuko On Dec 12, 2011, at 6:18 PM, Yuko Yotsumoto wrote: Thanks Doug, In the dt_recon help, The bvalues are in a simple text file, one for each direction (including b=0). The bvectors (gradient directions) are also in a simple text

Re: [Freesurfer] dt_recon error

, your dicom file might be from a different versioned scanner than dt_recon is used to seeing. If so, then it cannot extract the bvecs and bvals. If you supply them in a file on the command line, it should run properly. doug Yuko Yotsumoto wrote: Hello, I'm having a problem with dt_recon

[Freesurfer] dt_recon error

-ec.ecclog dwi-ec.nii dwi-infodump.dat dwi.nii mri_glmfit.log In dwi-infodump.dat, I see bunch of lines, but I don't see sWiPMemBlock.alFree. Please help! Thanks, Yuko Yotsumoto #@#--- Fitting Tensors Wed Dec 7 10:15:52 JST 2011 cd /Users/yuko/Documents/FreeSurfer

Re: [Freesurfer] mri_glmfit-sim error with v5.0

calls mri_glmfit, and gives warnings? When I paste mri_glmfit --y ces.008.nii --wls cesvar.008.nii --osgm --surface fsaverage lh --glmdir MPglm.wls --nii.gz in the command line, it works without any error. Thanks in advance! Yuko Yotsumoto % full error message regarding the second

[Freesurfer] Rejoindre mon réseau sur LinkedIn

LinkedIn Yuko Yotsumoto souhaite se connecter à vous sur LinkedIn : -- Je vous invite à faire partie de mon réseau professionnel en ligne sur le site LinkedIn. Accepter l'invitation de Yuko Yotsumoto http://www.linkedin.com/e

[Freesurfer] parametric modulator with FS-FAST

like to do this with FS-FAST. I found this post in the archive, but I need some more info. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg14181.html Thanks! Yuko Yotsumoto --- Yuko Yotsumoto, Ph. D. Associate Professor The Global Centers

[Freesurfer] freesurfer 4.5 download

Hi, I'm trying to download freesurfer 4.5 for leopard-ppc, but connection keeps failing. Could someone check the link? http://www.freesurfer.net/pub/dist/freesurfer/4.5.0/ Thank you, Yuko Yotsumoto ___ Freesurfer mailing list Freesurfer

[Freesurfer] mkanalysis-sess and -TER

Hi all, ( freesurfer-Darwin-leopard-i686-stable-pub-v4.5.0 ) I created sequences for event-related design, using optseq2. optseq2 --ntp 150 --tr 2 --psdwin 0 20 1 --ev TG1 2 22 --ev IG1 2 22 --ev CNT 2 22 --ev TGIG 2 22 --ev TGCN 2 22 --nsearch 2000 --focb nCB10pt --nkeep 15 --o

Re: [Freesurfer] funcroi-table-sess: average baseline activity?

it to report a mean of a contrast. So, you can just specify any contrast in your analysis, or you can download a new version: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/funcroi-table-sess I've updated the docs for this one as well. thanks doug Yuko Yotsumoto wrote

[Freesurfer] funcroi-table-sess: average baseline activity?

Hi all, I'm using: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 I've posted two questions (Q1 Q2 below) in my previous email regarding ROI analysis, and I'd like to add one more (Q3). Q1) If I don't want to use any thresholding for ROI analysis, can I use -sign abs -thresh 0 with

Re: [Freesurfer] funcroi-table-sess: average baseline activity?

Thanks Doug, On Dec 7, 2010, at 12:02 AM, Douglas N Greve wrote: I'm using: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 Q1) If I don't want to use any thresholding for ROI analysis, can I use -sign abs -thresh 0 with funcroi-config? Even easier: just don't specify a contrast.

Re: [Freesurfer] funcroi-table-sess

(using the -frame option), then construct the waveforms from these files. It's a bit of a hassle, but scriptable. doug Yuko Yotsumoto wrote: Hi All, I'm using : freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 I'd like to plot HDR for each condition for each subject. With FreeSurfer

[Freesurfer] funcroi-table-sess

Hi All, I'm using : freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 I'd like to plot HDR for each condition for each subject. With FreeSurfer v4.5.0, I did so with func2roi-sess and roisummary-sess. With v5.0, those commands do not seem to work. I could get a table with: funcroi-config

Re: [Freesurfer] func2roi-sess question : label2mask_linear: there were 0 label hits

folder... Yuko Yotsumoto # log [Yukos-iMac:sessions/VM/VMan] yuko% funcroi-sess -roi lh.DLPFC.roicfg -df sessdirfile -s VM20 --- /Users/yuko/Documents/FreeSurfer/sessions/VM/VM20 Wed Dec 1 10:00:40 JST 2010 mri_label2label --hemi lh --srclabel

[Freesurfer] func2roi-sess question : label2mask_linear: there were 0 label hits

need to add/change to make func2roi-sess work. Thank you! Yuko Yotsumoto ### fucn2roi-sess log file $Id: func2roi-sess,v 1.16 2010/03/25 16:22:53 greve Exp $ /Users/yuko/Documents/FreeSurfer/sessions/VM/VMan /Applications/freesurfer/fsfast/bin/func2roi