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30099 discussions

mri_glmfit-sim
by Jürgen Hänggi 26 Nov '14

26 Nov '14

Dear FS experts We would like to force FS's mri_glmfit-sim function of FS 5.3.0 to report all results and not only the significant results. This was the behavior of this function until FS version 4.5.0. Please can you guide as to the relevant lines in the mri_glmfit-sim function and indicate what have to be changed. Thanks in advance Best regards Jürgen Hänggi ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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parcellation of group stats maps?
by Scott Hayes 26 Nov '14

26 Nov '14

Hi, Is there a way to generate an intersection between a cortical thickness stats map (e.g., sig.mgh) in fsaverage space and native space neuroanatomy using FS parcellations (e.g., lh.apac.anot.)? We would like to plot cortical thickness of the significant clusters for each subject, but separate the significant clusters by the parcellations, e.g., if the significant cluster spans parahippocampal and fusiform cortex, I would like those plotted separately (preferably w/o drawing ROIs--and again, not using the entire PHC or fusiform parcellation--only the portion that is significant in the group analysis). It seems like this might be possible to accomplish w/ a single command, but we have not been able to pinpoint the exact command w/ the necessary flags. Any guidance would be appreciated. Thanks, Scott

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Re: [Freesurfer] Fwd: Eccentric lesions (fwd)
by Lilla Zollei 26 Nov '14

26 Nov '14

Hi Octavian, If you have an OK aseg volume, you could try to fit a surface over it using mris_make_surfaces with the -cover_seg flag. Lilla On Tue, 25 Nov 2014, Bruce Fischl wrote: > > > ---------- Forwarded message ---------- > Date: Tue, 25 Nov 2014 08:05:55 -0600 > From: Octavian Lie <octavian.lie(a)gmail.com> > Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Fwd: Eccentric lesions > > It looks like there is only gray matter (int 42), similar to cortical ribbon > gray, no white matter in that gyrus in aseg, both in the original recon, and > after painting gyral centers in brainmask. > Octavian > > On Tue, Nov 25, 2014 at 7:51 AM, Octavian Lie <octavian.lie(a)gmail.com> > wrote: > Dear Bruce, > > I am not sure how an ok aseg.mgz would look like for a lesion like > that, but it looks like it includes one larger gyrus excluded by the > pia, see attached, I would be happy to retrieve that one as it is the > bulkiest of all the ones left out. > Thank you, > > Octavian > > On Tue, Nov 25, 2014 at 7:38 AM, Bruce Fischl > <fischl(a)nmr.mgh.harvard.edu> wrote: > Hi Octavian > > I wouldn't use control points since it really isn't > healthy wm. The only > thing you can do is edit the wm.mgz and possibly also the > brainmask, but > it's so abnormal looking you may not be able to get > accurate surfaces. > How does the aseg look? If it is ok there may be one other > option. > > cheers > Bruce > > > On Tue, 25 Nov 2014, Octavian Lie wrote: > > > Dear All, > > any suggestion about this type of problem? I tried > control points through > > the middle/axis of the atrophic gyri (intensity 30-90 in > T1 or brainmask), > > wm.mgz edits through the same (adding from brainmask by > cloning those > > voxels; painting 110; or 255 brush), and modifying > brainmask directly by > > painting 110 internsity voxels through the same (gyri > interiors, where wm is > > supposed to be). Did not work, the atrophic gyri > continue to remain outside > > the pia. Again, this is an example of an eccentric > lesion with gyral > > atrophy, without interruption in the gray matter ribbon > but very faint wm > > signal through the base of the affected gyri. > > Thanks, > > Octavian > > > > > > > > ---------- Forwarded message ---------- > > From: Octavian Lie <octavian.lie(a)gmail.com> > > Date: Tue, Nov 18, 2014 at 10:50 AM > > Subject: Eccentric lesions > > To: "freesurfer(a)nmr.mgh.harvard.edu" > <freesurfer(a)nmr.mgh.harvard.edu> > > > > > > Dear All, > > > > I am interested at getting as good pial/cortical > reconstructions as possible > > on a series of epilepsy pt scans, some showing eccentric > (cortical) lesions > > (focal encephalomalacias, infarcts, or after focal > resections). One > > particularly difficult lesion type to get an accurate > cortical surface is > > where there are prongs of grey matter bulging out (like > a bag of worms), > > (mostly) without visible wm, see attached picture. These > prongs are > > maintained in the brainmask.mgz and > brain.finalsurfs.mgz, but not included > > in the pia with the default recon. Lesion voxel > intensities vary from 30-90. > > I tried cp, wm edits (using brainmask or T1 as > referece), both, did not > > matter, it did not work. > > > > Since I am not intested in wm/subcortical segmentation > but just in a good > > pia, I was wondering if I 'create' thin wm tracts > through the center of > > these gm prongs to help pial segmentation. If this is a > valid option, should > > I create those in brainmask, brain.finalsurfs or wm.mgz, > and should I use > > 110 or 255 for the brush? > > Any other suggestions are appreciated. Nevertheless, I > know there is a lot > > of tweaking of each lesion, and I try for more of a > global approach to these > > kinds of lesions. > > > > Thank you, > > > > Octavian. > > > > > > > _______________________________________________ > 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. > > > >

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Poor subcortical segmentation
by Mihaela Stefan 26 Nov '14

26 Nov '14

Hello Freesurfers, We noticed that our subcortical segmentations have a poor quality (see attachment). Is there a way to improve the segmentation in an automated fashion (avoiding long hours of manual editing)? We use FS 5.3 on Ubuntu 12.04. Thanks! Mihaela

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kvlQuantifyHippocampalSubfieldSegmentations.sh resultsDirectory 1, 10 gives error line 22: cd: left: No such file or directory
by Knut J Bjuland 25 Nov '14

25 Nov '14

Dear Freesurfer experts, I have processed my subject with recon-all and subfields hippocampal segmentation. . I have tried to use kvlQuantifyHippocampalSubfieldSegmentations.sh on a subset of my subjects. I have these subjects A B C D E fsaverage in a folder. When I try to exclude fsaverage by using this command kvlQuantifyHippocampalSubfieldSegmentations.sh ~/subjects/hippo 1 5. I get this error message. cd A/ Quantifying subject A/ left Doing left side cd left /usr/local/freesurfer/bin/kvlQuantifyHippocampalSubfieldSegmentations.sh: line 22: cd: left: No such file or directory failed to do cd left I have issued this command both in tsch and in bash. However, when I run the command without any options in the same folder, it works but bails out as expected when it reaches fsaverage- Best regards, Knut J. Bjuland PhD candidate NTNU

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Re: [Freesurfer] tksurfer curvature and overlay displays
by Graham Wideman 25 Nov '14

25 Nov '14

At 11/24/2014 08:23 AM, Bruce Fischl wrote: >Hi Graham > >have you tried freeview? We stopped development on the tktools some time >ago. > >cheers >Bruce Hi Bruce, thanks for replying. Yes, I did proceed to try the same task in Freeview (which in general has a nicer UI, to be sure). Some notes: Test case: For subject bert, display principal curvature k1 (of smoothwm) on smoothwm and on inflated. Using Freeview latest version, in Linux Mint 15. Freeview Problems/Bugs ----------------------- 1. The Threshold frequency histogram widget with color adjustment handles is a great idea, but has several problems. a. Horizontal range of the freq hist defaults to entire range of the variable, which, for k1, is one to two orders of magnitude larger than the range of the bulk of the data. Consequence: the bulk of the data appears compressed to a tiny range near zero, in a tiny number of bins, and it's impossible to set the adjustment handles. This mechanism needs to accept manual upper and lower limits (and options to clip outliers to that value, or exclude them). b. The "Use percentile" checkbox doesn't seem to do anything that I could discover. c. The mouse hit detection for selecting and dragging the color adjustment handles often doesn't work. This is some combination of: -- The target area of the handles is too small. -- Clicking the handle but missing instead moves some other handle to the clicked location -- Sometimes the hit detection seems to think you're pressing/clicking on the mirror-image side of the graph. Press at +10, and it's like you pressed at -10. 2. It would be great to be able to clone (or save/load) display settings associated with one surface onto another. This way, time spent configuring the display of a particular variable on, say, smoothwm, would not have to be redone (inevitably imperfectly) to display the same variable on another surface like inflated, which is a frequent need. mris_convert ------------- 3. crv->text, text->crv. I didn't find a tool that would convert between crv and text format and back, to make it easy to use some other tool to clip k1 to tractable limits. Maybe mris_convert does this, but if so, the help for that program could use some revision: --------------- Usage: mris_convert [options] <input file> <output file> ... -c <scalar file> input is scalar curv overlay file (must still specify surface) --------------- a. 'curv' perhaps also includes 'crv'? b. Why is 'surface' needed? The curv/crv files contain everything they need for conversion. Requiring surface makes it seem like the conversion is going to do something more elaborate than just convert binary <--> text. c. And does 'surface' mean just an argument like 'orig' or 'pial', or the name of a surface file? Perhaps it just means that mris_convert still looks for an <input file> argument, but doesn't use it? Anyhow, I didn't trust that this was going to do what I intended. ------- I DID end up getting the display I wanted: I inspected a k1.crv file in a hex editor, discovered it was the same as old "new" .curv format, and wrote some python code to read/write/filter such a file. With this I could produce a clipped version of k1, which did work tractably in Freeview and produced a nice display. -- Graham

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Digest mode for mailing list and responding to mails
by Janosch Linkersdörfer 25 Nov '14

25 Nov '14

Hi list, I recently switched to the digest mode for the mailing list. Since then, I don't receive answers to my mails as mails anymore, making it harder to respond to them (or any other mail on the list). Does anybody experience the same issues? How did you solve them? Thanks, Janosch

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Freeview in a VM (Debian)
by Elena Molina 25 Nov '14

25 Nov '14

Hi all, I am running FS in a VM (Debian, wheezy) and I would like to create a 3D reconstruction of the hippocampus in .png. For that, I executed the following code lines: >> mri_extract_label aseg.mgz 17 lh.nii >> mri_extract_label aseg.mgz 53 rh.nii >> freeview -slice 500 500 500 -v lh.nii:isosurface=on rh.nii:isosurface=on -viewport 3d -cam azimuth -90 elevation 25 dolly 5 -ras 0 0 10 -ss 3dhipo.png But I have an error with the freeview command: freeview.bin: cannot connect to X server How can I solve it? Is there another way to generate the .png? Best Regards, Elena

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Freesurfer Version
by Cristian Patrick Zeni 25 Nov '14

25 Nov '14

Gentleman Which Version of Freesurfer should I download for use with the OS X Yosemite 10.10.1? Thanks Cristian

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TRACULA- DKI?
by Cat Chong 25 Nov '14

25 Nov '14

Dear Tracula Team, Quick question: Is Tracula able to to process diffusion kurtosis data, and yield, let's say, 'mean kurtosis' parameters for specific fiber tracts?cheers,Cat

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