Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Arcuate fascicle and SLFIII
by stdp82＠virgilio.it 14 Mar '14

14 Mar '14

Hi list, in Wakana et al., 2007, the SLF was divided in parietal and temporal components. As I understand it, the same subdivision has been made in Yendiki et al, 2011. In details, SLFp should correspond to SLF III and SLFt to arcuate fascicle.Tractography studies showed that the anatomy of the arcuate fasciculus is very complex (Catani et al., 2008). Additionally to direct segment connecting Wernicke’s area with Broca’s area, there is an indirect pathway consisting of two segments, an anterior segment frontal cortex to the inferior parietal lobule (also defined as SLFIII, Urbanski et al., 2011) and a posterior segment linking the inferior parietal lobule with temporal cortex. Becouse the physiological role of these tracts is different, I wonder to know which of these tracts correspond to SLFt? Thank you very much! Stefano

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Re: [Freesurfer] Fwd: converting to fsaverage space
by Barbara Weiland 14 Mar '14

14 Mar '14

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freeview bug
by Jeff Stevenson 14 Mar '14

14 Mar '14

hi freesurfer folks, just had a nasty bug crash my whole mac workstation. yikes! i loaded lh and rh pial surfaces into freeview and went to assign annotation files to each and when i did i inadvertantly (aka randomly) selected the wrong file in labels dir- a .csv file i believe - instead of throwing an error dialogue with an appropriately snarky message it brought my whole system down, protected memory and all. never seen that before. after automatic reboot all was fine but this one is nasty. all current work was lost. hw was std mac pro osx 10.7.5, 96 GB mem. jeff

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integrating Freesurfer with Surfstat
by 조규호 14 Mar '14

14 Mar '14

Could anyone help me deal with error in integrating Freesurfer with Surfstat ? Because "MNI object" data was not available not like as written in the web documentation (http://www.math.mcgill.ca/keith/surfstat/) I used my own patient's MRI data with Freesurfer software. (CIVET software is also inaccessible to me.) After Recon-all , I employed the files "lh.thickness and lh.pial " from "surf" folder as input. (As written in "VIEWING DATA" Section in the online document) I ran the command : SurfStatReadSurf('/Users/zhau/Dropbox/subj7442103/surf/lh.thickness') And the error : Unable to read /Users/zhau/Dropbox/subj7442103/surf/lh.thickness, magic = 16777215 Error in SurfStatReadSurf1 (line 20) if nargin<2 Output argument "surf" (and maybe others) not assigned during call to "/Applications/MATLAB_R2013a.app/toolbox/surfstat/SurfStatReadSurf1.m>SurfStatReadSurf1". Error in SurfStatReadSurf (line 69) [s,ab]=SurfStatReadSurf1(filenames{1,j},ab,numfields1); It seems I do not understand the structure of input file. How could I solve this? Thanks in advance. Kyoo Ho Cho

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Re: [Freesurfer] Fwd: converting to fsaverage space
by Barbara Weiland 14 Mar '14

14 Mar '14

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Re: [Freesurfer] Fwd: converting to fsaverage space
by Barbara Weiland 14 Mar '14

14 Mar '14

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view time course in freeview
by charujing123 14 Mar '14

14 Mar '14

Hi FS experts, For the sig.mgh, can I see the time course vertex by vertex in freeview? Thanks. All the best. Rujing Zha

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freesurfer coordinates question
by David Phillips 13 Mar '14

13 Mar '14

Hello, Is there any way to extract a three dimensional coordinate representation of the different brain regions (i.e., their centroids) that freesurfer is estimating the cortical thickness of? Any help is appreciated and apologies if this question has been answered before. regards, David

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bvals and bvecs for dt_recon
by Gennan Chen 13 Mar '14

13 Mar '14

Hi! All, Is there an utility to extract bvals and bvecs from GE’s DTI dicom files into the format dt_recon can use? I try to run dt_recon as it is but it did not pick up those values. Those files are from ADNI. Gen ________________________________ This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator

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Re: [Freesurfer] Fwd: converting to fsaverage space
by Douglas N Greve 13 Mar '14

13 Mar '14

Hi Barbara, please post to the list. Thanks! the vol2surf command output should be .mgh or .mgz, not .mg (or maybe that is just a typo in the email). If it is, then you should load the mgh file as an overlay, not as a surface, eg tksurfer [subj] lh inflated -overlay file.mgh -fminmax .5 1000 setting the min threshold to .5 assures that you can see the ROI doug On 03/13/2014 05:10 PM, Barbara Weiland wrote: > Hi - > > Sorry to not have been clearer. > > I have /functional ROIs defined by the Greicius > lab// (http://findlab.stanford.edu/functional_ROIs.html) just as in > this post to the Freesurfer list from //Mon Dec 2 15:22:08 EST 2013:/ > / > / >> Doug, Thank you for your very helpful suggestion. Indeed, doing so >> made it so I could quickly take any parts (or all) of each Greicius >> network and put them in individual subject space. In case this may >> help anyone else, the final series of commands were (in this case, >> for the whole anterior salience network): *mni152reg --s [subj]* >> mri_label2vol *--seg anterior_Salience.nii.gz \* --reg >> $SUBJECTS_DIR/[subj]/mri/transforms/reg.mni152.2mm.dat \ --invertmtx >> --o anterior_Salience_[subj].nii.gz \ --temp >> $SUBJECTS_DIR/[subj]/mri/orig.mgz Cheers, Paul > > These ROIs were originally in MNI space and I used the commands listed > above from Paul to move them to subject space first creating the > reg.mni152.2mm.dat for each subject. LECN….nii is one of these > network ROIs. I can see this ROI using free view and it looks > correct. What I want is to extract volume and thickness for this ROI. > As outlined below,I thought I needed to first convert this to a > surface and tried: > >>> mri_vol2surf --src $SUBJECTS_DIR/[subj]/label/LECN_subjXXX.nii --out >>> $SUBJECTS_DIR/[subj]/label/LECN_subjXXX_lh_surf.mg --srcreg >>> $SUBJECTS_DIR/[subj]/mri/transforms/reg.mni152.2.dat --hemi lh >> > > I tried to look at the output (LECN_subjXXX_lh_surf.mg) by using > tksurfer [subj] lh inflated and then load the it from the GUI onto the > inflated surface -- this says that the > file (LECN_subjXXX_lh_surf.mg) "has 0 vertices! > Probably trying to use a scalar data file as a surface!" > > Do I need to move the LECN….nii to be a surface or should I just be > able to make a label from it? I assumed I need the ROI information to > be a label to use mris_anatomical_stats? > Thank you, > Barbara > > > Barbara Weiland, Ph.D. > Research Asst. Professor > CU Change Lab > Dept. of Psychology & Neuroscience > University of Colorado Boulder > barbara.weiland(a)colorado.edu <mailto:barbara.weiland@colorado.edu> > > > > On Mar 13, 2014, at 1:14 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > >> >> Can you give more details? What is LECN_...nii? Where did it come from? >> What space is it in? MNI152 I assume? What does it mean you can't load >> it? Load it with what? What is your command line? >> doug >> >> >> >> >> >> On 03/13/2014 01:36 PM, Barbara Weiland wrote: >>> Hi - >>> >>> I am trying to extract volumes & thickness stats of networks and >>> followed the commands from the post in the subject line to create >>> network .nii files in each subject's space. Based on some other >>> postings, I thought I needed to first move the volumes to surf for >>> each hemisphere, i.e.: >>> >>> mri_vol2surf --src $SUBJECTS_DIR/[subj]/label/LECN_subjXXX.nii >> >>> --out $SUBJECTS_DIR/[subj]/label/LECN_subjXXX_lh_surf.mgh >> >>> --srcreg $SUBJECTS_DIR/[subj]/mri/transforms/reg.mni152.2.dat --hemi lh >> >> >>> But this does not seem to create the surf correctly - I am unable to >>> load it. >>> I have also tried to use mri_cor2labels to create labels directly >>> front the .nii files but found that the first column in the label >>> files were all -1 (which I found in a previous posting meant the >>> volumes needed to be moved to surface first as I tried above)?? >>> I ultimately want to use mris_aatomical_stats with these labels to >>> output stats. Any help would be appreciated, >>> thanks, >>> Barbara >>> >>> Barbara Weiland, Ph.D. >>> Research Asst. Professor >>> CU Change Lab >>> Dept. of Psychology & Neuroscience >>> University of Colorado Boulder >>> barbara.weiland(a)colorado.edu <mailto:barbara.weiland@colorado.edu> >>> <mailto:barbara.weiland@colorado.edu> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> 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. >> > -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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