Freesurfer

freesurfer@nmr.mgh.harvard.edu

2 participants
30134 discussions

per-run and Native space
by SHAHIN NASR 17 Mar '14

17 Mar '14

I am trying to preproc-sess my data (fwhm 1.5, per-run, native space) with this command preproc-sess -fwhm 1.5 -fsd bold -per-run I expect it to generate fmcpr.sm1.5.nii.gz for each run of my dataset. Although preproc-sess finishes without any error, it only generates fmcpr.nii.gz and when I run selxavg3-sess, it returns an error that > cannot determine format of > test/bold/013/fmcpr.sm1.5 and exits. Would you tell me why those files are not generated? Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

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Pial surface errors due to bad GM/WM contrast: What to do?
by Elijah Mak 17 Mar '14

17 Mar '14

Hello Freesurfer Community, I have a basic question about pial edits. I have a couple of subjects with very thin cortical measurements.Looking at the images, I think it could be an issue of weak intensity contrast between the GM and WM resulting in the erroneous pial surfaces? I have attached 2 screenshots in this email. In such a scenario, what can be done to correct the pial surfaces? Thank you very much for looking into this. Best Regards, Elijah

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(no subject)
by Getaneh Bayu 15 Mar '14

15 Mar '14

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dmri_motion
by Ruth Carper 15 Mar '14

15 Mar '14

Hi, I've been using dmri_motion to quantify motion in our DTI data. Can you give any guidance on selecting values for the -D and -T flags? I didn't see anything in the wiki or in your related papers and it can have a substantial effect on the outputs. Thanks.

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

14 Mar '14

Great - thanks for your help - got it all working now!

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Consistent Dura issues
by Jonathan Holt 14 Mar '14

14 Mar '14

Hi all, I’m working with a particularly stubborn data set whose defining characteristic is dura along the posterior of the brain. It’s become so consistent that I’m hoping to find a way to perhaps tweak recon-all so as to take care of the issue in a more automated manner and save many many man hours of manual work. Is this possible? jon attached is an example of the general problem

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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

2 1

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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