Freesurfer January 2010

freesurfer@nmr.mgh.harvard.edu

78 participants
123 discussions

Re: [Freesurfer] images with poor resolution
by Nick Schmansky 25 Jan '10

25 Jan '10

Dana, First I would run: recon-all -s subid -clean to remove any prior control points and edits. Then I would open nu.mgz: tkmedit subjid nu.mgz and *sparingly* put control points well into white matter areas on a few different slices. you only need a half dozen or so. to add control points, see: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints except you will add them to nu.mgz, to make sure that T1.mgz gets created properly. Then create a file name xopts.txt containing these lines: mri_normalize -gentle Then run: recon-all -s subjid -autorecon1 -expert <path_to>/xopts.txt and when done, open brainmask.mgz tkmedit subjid brainmask.mgz and check again to get a sense of the low value for white matter and high value for gray matter, then run: recon-all -s subjid -autorecon2 -seg-wlo wlo -seg-ghi ghi replacing wlo and ghi with those values. if the surfaces still look bad, you can add a line to the xopts.txt file : mris_make_surfaces -max_gray val -min_gray_at_white_border val replacing the two 'val's with something you find appropriate, then run: recon-all -s subjid -autorecon2-pial -autorecon3 \ -expert <path_to>/xopts.txt good luck! Nick On Mon, 2009-10-05 at 16:56 -0400, Dana W. Moore wrote: > Hi Nick, > > Below is Bruce's response to a problem I'm having with the gray/white > segmentation. (Pasted below, you can see the brainmask.mgz volume and > surfaces--the entire brain is labeled as white matter). I could use > some guidance in carrying out his advice. He says to adjust the > intensity normalization using control points and then use expert opts > for mri_segment and mris_make_surfaces. > > When I look at the brain.mgz volume, the white matter tends to have an > intensity of 110, as it should, but the gray matter at times goes as > high as 115. I was thinking, I could set ghi to 115 and wlo to 110. > Then, I am not sure how to actually run the corrections and what > language to use to implement the control points and mri_segment > adjustments. I will save control points and then run: recon-all > -autorecon2-cp -autorecon3 -subjed <subject>. Can I somehow include > the mri_segment adjustments into this command, or do I have to run > that separately? > > I am also not sure how options for mris_make_surfaces might help. > > I appreciate your help with this! > > Thanks, > dana > > > > > [] > > At 04:40 PM 10/2/2009, Bruce Fischl wrote: > > Hi Dana, > > > > it looks like the gray/white density estimation failed. Try setting > > them with the expert opts for mri_segment and mris_make_surfaces > > (Nick can point you in the right direction if you can't figure it > > out). Things like max gm at white border and such. > > > > cheers, > > Bruce > > > p.s. it also looks like the intensity normalization went too far due > to the low contrast. You'll probably need to add some control points > and run it with the -gentle option > > > > > On Fri, 2 Oct 2009, Dana W. Moore wrote: > > > > > Hi everyone, > > > > > > I am trying to salvage some images that were done with poor > > > gray/white boundary contrasts. First, FreeSurfer includes an area > > > of dura in the skull strip. I tried adjusting the watershed but > > > it made no differences. FreeSurfer is subsequently unable to > > > detect the gray/white boundary and labels the dura as cortex: > > > > > > [] > > > > > > > > > > > > Looking at the raw images, the gray/white boundaries are faint but > > > visible. Is there anything I can adjust to try to make this work > > > with FreeSurfer? > > > > > > Thanks, > > > Dana > > > > > > > > > Dana W. Moore, Ph.D. > > > Neuropsychology Fellow > > > Cornell Neuropsychology Service > > > Weill Medical College of Cornell University > > > New York Presbyterian Hospital > > > Department of Neurology & Neuroscience > > > 428 East 72nd Street, Suite 500 > > > New York, NY 10021 > > > Phone: 212-746-2823 > > > Fax: 212-746-5584 > > > Email: dwm2003(a)med.cornell.edu > > Dana W. Moore, Ph.D. > Neuropsychology Fellow > Cornell Neuropsychology Service > Weill Medical College of Cornell University > New York Presbyterian Hospital > Department of Neurology & Neuroscience > 428 East 72nd Street, Suite 500 > New York, NY 10021 > Phone: 212-746-2823 > Fax: 212-746-5584 > Email: dwm2003(a)med.cornell.edu > >

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selxavg3-sess questions
by Sebastian Moeller 25 Jan '10

25 Jan '10

Hi List, hi Doug, I just started to use freesurfer 4.5.0 for functional data (before I only used 3.0.5). Now I see that the whole analysis workflow has changed from mkanalysis-sess.new -> selxavg-sess -> mkcontrast-sess -> stxgrinder-sess to mkanalyss-sess -> mkcontrast-sess -> selxavg3-sess, now what happens when I want to add/change contrasts after running selxavg3-sess? Do I still run stxgrinder-sess or rerun selxavg3-sess (can I avoid recalculating the full GLM)? And more interesting, I seem to use mkanalysis-sess.new incorrectly as I get much worse results from the selxavh3 analysis than from the old one. Is there anything special to take into consideration of non human primate analysis (I already fix up the gamma function and autocorrelation timewindows to reflect the use of mion in monkeys). If anyone has a good idea what to try I am all ears... best Sebastian

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Re: [Freesurfer] Flip surface model
by Jürgen Hänggi 25 Jan '10

25 Jan '10

Hi Bruce, Doug, and Mert Thanks a lot Regards Jürgen On [DATE], "Bruce Fischl" <[ADDRESS]> wrote: > I'll take that to mean "no,I don't have anything I am comfortable > distributing yet" :) > > On Thu, 21 Jan 2010, Douglas N Greve wrote: > >> I've been working on this piece-meal. I think it's a bad idea to just throw >> stuff out there without testing it. It will instantly become the standard and >> then it will be a mess to try to undo. >> >> Bruce Fischl wrote: >>> I see, so you don't want to flip it, you want to register left and right. >>> Mert and Doug: do either of you have stuff you would be comfortable >>> distributing yet? >>> On Thu, 21 Jan 2010, Jürgen Hänggi wrote: >>> >>>> Hi Bruce >>>> >>>> We investigated patients with unilateral pain. For some patients, the pain >>>> was on the left side, for others it was on the right side. We would like >>>> to >>>> do a group analysis on cortical thickness maps vertex-wisely but we do not >>>> know whether it is possible to flip a surface model (e.g. the left >>>> cortical >>>> thickness map) so that we can pool patients with pain on the left with the >>>> patients who have pain on the right. >>>> >>>> Regards >>>> Jürgen >>>> >>>> >>>> >>>> On [DATE], "Bruce Fischl" <[ADDRESS]> wrote: >>>> >>>>> Hi Jürgen, >>>>> >>>>> why would you flip the MR? What problem are you trying to solve? >>>>> >>>>> Bruce >>>>> On Thu, 21 >>>>> Jan 2010, Jürgen Hänggi wrote: >>>>> >>>>>> Dear FS experts >>>>>> >>>>>> As far as I know from Doug, there are preliminary tools for flipping a >>>>>> surface model (reversing left and right hemisphere) >>>>>> >>>>>> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11896.html >>>>>> >>>>>> Because these tools are not yet available I would like to know whether >>>>>> you >>>>>> would recommend to flip the raw MR image and the running recon-all on >>>>>> this >>>>>> flipped MR image. >>>>>> >>>>>> Thanks in advance >>>>>> Best regards >>>>>> Jürgen >>>>>> >>>>>> >>>>>> ------------------------------------------------------------------------- >>>>>> --- >>>>>> 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. >>>>>> >>>>>> ------------------------------------------------------------------------- >>>>>> --- >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>>> >>>> >>>> >>>> >>>> --------------------------------------------------------------------------- >>>> - >>>> 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. >>>> >>>> --------------------------------------------------------------------------- >>>> - >>>> >>>> >>>> >>>> >>>> >>>> >> >> ---------------------------------------------------------------------------- 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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a question about control points
by Guang Zeng 25 Jan '10

25 Jan '10

Hi, there, I have some scans which have poor white matter and gray matter contrast, and the results of the intensity normalization step are pretty bad. So I add some controls, the results looks much better now. But I met a question now, I sent these results-improved subjects to FS longitudinal stream without those controls points, the longitudinal results are as bad as before. My command line is: recon-all -base subj_based_id -tp subj1 -tp subj2 -all recon-all -long subj1 subj_base -all recon-all -long subj2 subj_base -all I think the problem is the FS surfer longitudinal stream will copy the orig.mgz of each time point, map them to the base template, and then go through FS stream again. How can I map my added control points to the base template, and use them in the longitudinal stream, or I should map it to somewhere at the recon-all -base subj_based_id -tp subj1 -tp subj2 -all step. Thanks! Guang _________________________________________________________________ Hotmail: Free, trusted and rich email service. http://clk.atdmt.com/GBL/go/196390708/direct/01/

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some questions about group analysis
by liyari5018 25 Jan '10

25 Jan '10

Hi all, When I completed the recommended recon-all step, I want to get the volume(or size) of amygdala for ecah individual subject and to do correlation analysis with psychological scale, how can I do this ??? For a group level analysis , should i do some head size correction befor ??? Thanks for your reply!!! L J

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inflation error
by Davide Rivolta 25 Jan '10

25 Jan '10

Dear all, I am quite a new Freesurfer user and I am having a problem with the brain inflation. This is the error message: ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0034, pval=0.000 < threshold=0.0050) recon-all exited with ERRORS at Mon Dec... I am not sure why because I have used the same procedure without problems for many other participants. Thanks for your help, Regards Davide

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White matter edits and talairach.xfm
by Jesse Bledsoe 24 Jan '10

24 Jan '10

Hello FreeSurfer experts, I have been reconstructing many brains and noticed that the surfaces are quite bumpy. Here are a few things I have done to fix or understand more about the consistently bumpy surfaces I seem to generate after reconstruction: 1) Checked the talairach.xfm files with tkmedit and tkregister2 (it looked fine in all planes) 2) I have run mri_convert on original, talairach, and ac-pc aligned dicoms (Bruce, you were right, there did not appear to be any improvement from the original. Actually, the originals produced fewer surface errors). I have attached four .jpg images of white matter errors (bumps) in both tksurfer and tkmedit views with the same white matter points. Can you tell me if you see any errors in tkmedit that I am missing? I dont' seem to see any considerable pial/white matter inconsistencies yet continue to produce very bumpy surfaces. Also, why do some brains produce more bumps than others? I realize that a bad talairach may cause errors but my talairachs seem to be fine. Thanks in advance for all of your time, Jesse

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?h.aparc.annot data for N27 brain?
by John Sheppard 24 Jan '10

24 Jan '10

Hi all, I am curious if there is any way to get a copy of the ?h.aparc.annot (label) data for the Colin N27 brain? I wish to use these annotation data for my analysis, but need the original ..annot files as I need to translate the annotation data into my standard mesh space that I am doing my group analysis with. The folks at AFNI put out a zipped archive with surface data for N27, but this archive didn't include original ?h.aparc.annot files that I could work with (only some type of processed data in niml format that I wasn't able to convert to a standard 1D file for mapping purposes). I am following up with AFNI as well but haven't heard back yet. Thanks very much, John Sheppard -- John P. Sheppard Undergraduate Student Departments of Biomedical Engineering & Statistics Research Assistant Department of Communication Sciences & Disorders Northwestern University E-mail: john-sheppard(a)northwestern.edu Phone: +1 630 957 8321 Address: 1927 Sherman Ave, Unit G Evanston, IL 60201, USA

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painting polar angle retinotopy with abblocked design
by Natalia Zaretskaya 22 Jan '10

22 Jan '10

Hi all, hi Doug, I am analysing polar angle retinotopy with abblocked design, but can not figure out how to paint the output of sfa-sess correctly, so that I see something reasonable. I know that my analysis generally worked fine, because when I can view the phase.nii overlay, and it looks quite polar. It's just that it is not thresholded. I would really appreciate a hint! Best regards, Natalia

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bad ADNI data results
by Guang Zeng 22 Jan '10

22 Jan '10

Hi, there, I sent about 50 ADNI data to FreeSurfer pipeline last week, I found half of them have bad segmentation and parcellation results. I think most of them have the same type of errors and may because of the skull-stripping results are wrong. Could you please help me check the attached pics, see if I am correct. And please give me some suggestions to fix this problem. I really appreciate your help! Thanks a lot! Guang _________________________________________________________________ Hotmail: Trusted email with Microsoft’s powerful SPAM protection. http://clk.atdmt.com/GBL/go/196390706/direct/01/

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Freesurfer January 2010