Freesurfer

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30090 discussions

OptSeq2 eff and first order and contrast
by A a 13 Jun '13

13 Jun '13

Hello all, A question regarding the usage of Optseq2 I have this command line optseq2 --ntp 200 --tr 2.5 --psdwin 0 15 2.5 --ev ev20 2.5 20 --ev ev40 2.5 20 --ev ev60 2.5 20 --tnullmin 5 --tnullmax 7.5 --nkeep 1 --o OptSeq_TRIALS/3_null9_6 --nsearch 10000 Now the efficiency tha I get is around 0.5. How I can tell this is a good or bad efficiency ? Is there a comparable level? Also if I would like to test for the first order effect of using a parametric modulation, can I test this using OptSeq2? Lastly, if I would like to test the efficiency of a contrast, say ev60 > ev20, how I do this ? Thanks Adnan

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Re: [Freesurfer] License problem
by Nick Jones 13 Jun '13

13 Jun '13

Regarding any license issue under Opensuse 12.3 and the libcrypt incompatibility. So grab a libcrypt from an older opensuse (one where freesurfer was working, for me, I used libcrypt.so from 11.3, but 12.1 may be a better candidate if it works). Place it somewhere ($FREESURFER_HOME/lib is a good candidate), then add the location to the LD_LIBRARY_PATH environment variable so that freesurfer finds the old libcrypt. There is another workaround but you must contact Nick Schmansky, I don't remember the details. Thanks Nick

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segmentation
by 小麦 13 Jun '13

13 Jun '13

Hi expert, How can I segment the white matter,gray matter and the cerebral hemisphere ,and rebuild the surface? Thanks in advance, Best wishes, lucy

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"ERROR:: Too many arguments." from recon-all / make_outer_surface
by Tudor Popescu 13 Jun '13

13 Jun '13

Hi all, The command: recon-all -s M19 -localGI resulted in: make_outer_surface('/media/math/all38subj/M19/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/media/math/all38subj/M19/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit ================= ERROR:: Too many arguments. I found a previous thread<http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23414.html>in which someone was getting this error due to a space in the path, but my path doesn't have any spaces or any other dodgy characters. What could the problem be? Thanks. Tudor

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Editing masks
by Joshua deSouza 12 Jun '13

12 Jun '13

Hello all, I am having a problem with generating values of the vertices at the hippocampal area. I believe it is a masking issue as reviewing the mask after the glmfit analysis I see that the mask does not cover the entire medial region excluding the corpus callosum. Can I do anything to change the mask as to add deeper brain regions at the hippocampal area? Thank you Joshua

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fMRI ROI masks from Brain Voyager QX to FS
by stdp82＠virgilio.it 12 Jun '13

12 Jun '13

Hi list, I performed fMRI analysis by Brain Voyager QX. The masks that describe the fMRI regions of interest are in .vpm and .srf. 1-There is a solution to export these masks obtained by BrainVoyager QX in FS and visualize them on FS surface?2-I'd like to extract from each ROI individuate by fMRI in BX, the cortical thickness values. Is it possible? Thank you very much, Stefano

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download error
by Hua, Le - SJHMC 12 Jun '13

12 Jun '13

Hi, I am currently trying to download the new 5.3 release for macbook lion osx. It downloads fine until about 1.9 GB, then it keeps stalling without giving me any error messages. I have let it continue to run over 20 hours and still no progress beyond 1.9 GB. This occurs with both safari and firefox. The page for 5.2 version is unavailable. Any thoughts or suggestions? Thanks, Le

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Re: [Freesurfer] tkmedit on ssh remote machine error
by Z K 12 Jun '13

12 Jun '13

Jon, Here are my findings. -If I ssh from Mac to Linux everything works as expecting, meaning I am running tkmedit on the remote machine but displaying it on the Mac client, and it appears as I would expect. -If I ssh from Mac to Mac I am able to call the tkmedit command but it displays on the server side, not the client. This is definitely some issue relating to X11 (I have X11forwarding set to yes) but I just cant seem to figure it out the exact setting needed to get it to display on the client side. Of course neither of these replicates your error... In your case the image window opens, but the image window is blank (white). If anyone one the list has experienced something similar I would interested to discover what if any remedy exists. -Zeke On 06/11/2013 12:53 PM, Jon Wieser wrote: > thanks zeke > > ----- Original Message ----- > From: "Z K" <zkaufman(a)nmr.mgh.harvard.edu> > To: "Jon Wieser" <wieser(a)uwm.edu> > Cc: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu> > Sent: Tuesday, June 11, 2013 11:30:50 AM > Subject: Re: [Freesurfer] tkmedit on ssh remote machine error > > Hi Jon, > > I myself have not been able successful running tkmedit over an ssh > session using Mac as both client and server... But I know it can be > done. There's a lot of factors involved, many to do with > Xwindows/Xforwarding/XQuartz/ssh and have nothing to do with freesurfer. > So its been a bit of a challenge to debug. Ill follow up as soon as I > reasonable can. > > -Zeke > > On 06/11/2013 10:28 AM, Jon Wieser wrote: >> hi Zeke, >> were you able to find a solution to my problem with running tkmedit on a remote machine? >> thanks >> Jon >> >> ----- Original Message ----- >> From: "Z K" <zkaufman(a)nmr.mgh.harvard.edu> >> To: "Jon Wieser" <wieser(a)uwm.edu> >> Sent: Thursday, May 30, 2013 1:42:41 PM >> Subject: Re: [Freesurfer] tkmedit on ssh remote machine error >> >> Hmm that is a very strange error you are encountering. Im trying to >> duplicate the issue on my end. I only have one Mac 10.6 and one Mac 10.7 >> machine but Ill let you know what I find and hopefully I can come up >> with a solution. >> >> -Zeke >> >> On 05/30/2013 02:37 PM, Jon Wieser wrote: >>> both machines have Mac OS X 10.6.8 >>> >>> the tkmedit works fine when not logged in remotely >>> there is no error and the brain image is there >>> Jon >>> >>> ----- Original Message ----- >>> From: "Z K" <zkaufman(a)nmr.mgh.harvard.edu> >>> To: "Jon Wieser" <wieser(a)uwm.edu> >>> Cc: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu> >>> Sent: Thursday, May 30, 2013 12:16:55 PM >>> Subject: Re: [Freesurfer] tkmedit on ssh remote machine error >>> >>> Jon, >>> >>> I have not seen or heard of this error before... are both machines Mac >>> OSX 10.6.8? Also, will the same command will produce a brain image when >>> not logged in remotely? >>> >>> -Zeke >>> >>> On 05/30/2013 12:43 PM, Jon Wieser wrote: >>>> >>>> hi freesurfer folks >>>> >>>> I'm ssh'ing to from one MAc to another >>>> X11 is on both machines >>>> MAC OS X 10.6.8 >>>> >>>> When I start TKmedit with: (freesurfer files are in the freesurfer directory) >>>> >>>> tkmedit freesurfer brainmask.mgz -aux T1.mgz >>>> >>>> >>>> I get the errors: >>>> Thu May 30 11:34:50 cerebrum.uwm.edu tkmedit.bin[78500] <Error>: kCGErrorIllegalArgument: _CGSFindSharedWindow: WID 349 >>>> Thu May 30 11:34:50 cerebrum.uwm.edu tkmedit.bin[78500] <Error>: kCGErrorFailure: Set a breakpoint @ CGErrorBreakpoint() to catch errors as they are logged. >>>> Thu May 30 11:34:50 cerebrum.uwm.edu tkmedit.bin[78500] <Error>: kCGErrorIllegalArgument: CGSSetWindowSendExposed: Invalid window 0x15d >>>> Thu May 30 11:34:50 cerebrum.uwm.edu tkmedit.bin[78500] <Error>: unknown error code: invalid drawable >>>> error: xp_attach_gl_context returned: 2 >>>> >>>> >>>> >>>> tkmedit GUI opens and the image window opens, but the image window is blank (white) , (no image of the brain) >>>> >>>> >>>> >>>> >>>> i have set X11forwarding to yes in the /etc/sshd_config file >>>> so xeyes works ok remotely >>>> Jon >>>> >>>> >>> _______________________________________________ >>> 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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Fwd: mri_nu_correct.mni options
by Cristian Paz 12 Jun '13

12 Jun '13

Dear Freesurfer List! Does anyone know what the purpose of the flag: mri_nu_correct.mni --i T1.nii --o nuT1.nii *--no-float* as opposed to: mri_nu_correct.mni --i T1.mgz --o nuT1.mgz *--n 2 *? Thank you! Cris ---------- Forwarded message ---------- From: Cristian Paz <pazcristian99(a)gmail.com> Date: 2013/6/12 Subject: Re: [Freesurfer] mri_nu_correct.mni options To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> OK, I understand. I am planning to replicate the methods of a study that used mri_nu_correct.mni (probably only on T1) About mri_nu_correct.mni - what is the purpose with the flag: mri_nu_correct.mni --i T1.nii --o nuT1.nii --no-float as opposed to: mri_nu_correct.mni --i T1.mgz --o nuT1.mgz --n 2 ? Thank you! Cris 2013/6/12 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > they are different. nu_correct is much gentler and doesn't allow for user > intervention in the way that specifying control points does. You'll need to > mess around to see what is best > > Bruce > On Wed, 12 Jun 2013, Cristian Paz wrote: > > Hi Bruce! >> Thank you! >> >> So I should rather use mri_normalize instead of mri_nu_correct.mni to >> correct for intensity non-uniformity? >> >> >> >> Cheers, >> Cristian >> >> >> >> 2013/6/12 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> Hi Cristian >> >> you can use mri_normalize directly on the T1, but it won't work for >> the T2 unless you specify control points and >> tell it to only use them. There are other (more esoteric) options >> in mri_normalize that you could use. Look at the >> recon-all code for the T2-based dura correction >> >> cheers >> Bruce >> On Wed, 12 Jun 2013, Cristian Paz wrote: >> >> Dear FS'ers. >> >> If I want to do bias correction of T1 and T2 images, without >> necessarily doing a recon-all - >> what are the different options/parameters I can add in the >> command line? >> >> Right now I have been testing : >> >> mri_nu_correct.mni --i <input> --o <output> >> >> and unfortunately the output looks worse than the input. >> >> this wiki page was not too informative with regards to >> options: >> http://ftp.nmr.mgh.harvard.**edu/fswiki/mri_nu_correct.mni<http://ftp.nmr.mgh.harvard.edu/fswiki/mri_nu_correct.mni> >> . >> >> Thanks in advance! >> >> Kind regards >> Cris >> >> >> >> >> >> >> 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<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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Base Pial Surface Edits
by David Tate 12 Jun '13

12 Jun '13

We have recently run a set of longitudinal data (FreeSurfer5.3) and are making edits to the base pial surfaces. It is clear that there are two different ways of doing pial edits including: 1. editing the brainmask.mgz and 2. the brain.finalsurfs.mgz. I recognize that they are specific ways to deal with different issues in the surface reconstruction. My question is will the following command (recon-all -base <ID> -autorecon2-pial -autorecon3) pick up both edits in the -base rerun or will you need to make the brainmask.mgz edits, rerun the -base recon command the make brain.finalsufs.mgz edits, rerun the -base command? Thanks, David

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