Freesurfer May 2012

freesurfer@nmr.mgh.harvard.edu

137 participants
209 discussions

mri_surf2surf source and target annot formats
by Arno Klein 25 May '12

25 May '12

hello! in mri_surf2surf, does anyone know how to specify the source and target formats if --sval is annot without using --sval-annot, as in "--sfmt" or "--tfmt"? cheers, @rno

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trac-all -bedp error
by Gabor Perlaki 25 May '12

25 May '12

Dear all, I've the following error right after starting trac-all -bedp -c configuration_file: Making bedpostx directory structure Queuing preprocessing stages [: 223: NONE: unexpected operator [: 314: NONE: unexpected operator [: 327: xbedpostx_pre: unexpected operator [: 486: x: unexpected operator [: 486: -le: argument expected Queuing parallel processing stage [: 223: NONE: unexpected operator 0 slices processed [: 327: xbedpostx: unexpected operator [: 486: x70: unexpected operator Queuing post processing stage [: 223: NONE: unexpected operator [: 314: NONE: unexpected operator [: 327: xbedpostx_post: unexpected operator [: 486: x: unexpected operator [: 486: -le: argument expected >From the created files it seems that the first error occurs at "preprocid=`${BPDIR}/fsl_sub_seychelles -T 60 -m a -N bedpostx_pre -l ${subjdir}.bedpostX/logs ${FSLDIR}/bin/bedpostx_preproc.sh ${subjdir}`" Any idea how to fix this error? Trac-all -prep finished without error. I've Freesurfer 5.1.0, Ubuntu 11.04 and FSL 4.1.8 installed using Neurodebian and I don't use SGE. I'd appreciate an early answer. Thanks, Gabor

3 3

selxavg3-sess ERROR: analysis XYZ does not exist
by Michael Bannert 25 May '12

25 May '12

Hi all, I'm trying to analyze a retinotopic mapping dataset using FsFast but some things don't seem to work the way they should. When running "selxavg-sess -s ex01s05 -a rtopy.self.lh", I get the following error: "ERROR: analysis rtopy.self.lh does not exist, see mkanalysis-sess" However, I checked that rtopy.self.lh does in fact exist. I also made sure that the folder contains the file analysis.info. Why do I still get this error message? Here is the contents of analysis.info: # FSBUILD freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 # MKAVERSION $Id: mkanalysis-sess,v 1.64.2.1 2011/03/22 16:58:57 greve Exp $ # MKACMD /Users/mbannert/../../Applications/freesurfer/fsfast/bin/mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 3.12 -retinotopy 49.92 -paradigm rtopy.par -funcstem fmcsurfsm5 -fsd bold -nskip 0 -force # DATE Thu May 24 11:50:39 CEST 2012 analysis rtopy.self.lh mcstem fmcpr funcstem fmcsurfsm5 fsd bold TR 3.12 RegDOF 6 RawSpace surface self lh mask brain RawFWHM 0 RawSTC none UseB0DC 0 inorm 100 acfbins 0 fixacf 1 acffwhm 20 acfsvd 0 designtype retinotopy nskip 0 polyfit 2 HPFCutoffHz 0 HeteroGCor 0 parname rtopy.par period 49.92 Any ideas? Thanks for your help! Michael -- Michael Bannert, Dipl.-Psych. Vision & Cognition Lab, Centre for Integrative Neuroscience, Univ. of Tübingen & BCCN Tübingen Otfried-Müller-Str. 25, 72076 Tübingen, Germany Phone: +49 - (0)7071 / 29 - 89031

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Freesurfer 1mm Isotropic standard and the Future
by Joshua Lee 24 May '12

24 May '12

Dear Freesurfers, Over the last years, MR imaging technology hasimproved such that sub 1-mm isotropic scans can be obtained with good signal to noise characteristics. For example, our lab uses 0.7mm isotropic structural MR images. I understand that the Freesurfer pipeline will up-sample these to 1mm isotropic, but it seems a shame that so much information is left unused which could be used to improve the accuracy of sub-cortical and cortical segmentation. My question is whether there are any plans at Freesurfer to change the reference standard resolution from 1mm isotropic, or provide another solution that can help researchers make the most of your technology. Sincerely, Joshua - Joshua

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error longitudinal processing
by Rashmi Singh 24 May '12

24 May '12

Hello, I ran longitudinal processing which exited with errors. I am attaching the output file. Please advise why this error occurred. The recon –all run ran perfectly for all the time points for this subject. My command was as follows: recon-all -base AA510.long -tp AA510.T1 -tp AA510.T2 -tp AA510.T7 -all </dev/null&> FSAA510.long & My all other subjects longitudinal run completed without error. Thanks, Rashmi ________________________________ This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made.

2 1

feat2surf
by Kushal Kapse 24 May '12

24 May '12

hi, i am performing feat2surf after i successfully performed reg-feat2anat.......for some reason it gives me "ERROR: cannot find any .img, .nii, .nii.gz files"....although the stats file is in reg folder.....may i please get suggestion on how to proceed from here thanks kk

2 2

how to save screen shot (using TCL) without X11
by Natalie Han 24 May '12

24 May '12

Hi, I have a tcl script to save multiple tkmedit screen shots, but I wonder if there is a way to suppress the pop out tkmedit windows everytime I want to save the tif. Basically, if I don't have a X11 window when ssh, how can I save the tkmedit screen shots with tcl script? Is there an option in tcl script or tkmedit to render virtually instead of display to the screen? Thanks a lot. -Natalie

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Fwd: fMRI time series in surface space
by Kushal Kapse 24 May '12

24 May '12

----- Forwarded Message ----- From: "Kushal Kapse" <kkapse(a)mail.med.upenn.edu> To: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> Sent: Thursday, May 24, 2012 11:45:14 AM Subject: Re: [Freesurfer] fMRI time series in surface space run preprocessing of FS-FAST and do sampling on surface seems a good way to give a try....i am having confusions with directory structure for FS-FAST....Project/sess01/bold/001/f.nii this is how my anatomical directory structure is originally: data/server/controls/14987_4589/ 14987_4589 is one of the subject in controls folder for me i m confused with following thing around FS-FAST: 1- the "project" directory of FS-FAST is supposed to be within 14987_4589 directory???? because as per the tutorial, "sess01" directory is supposed to be subjects directory with bold folder containing functional runs of that subject called as "sess"....... please let me know thanks kk ----- Original Message ----- From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> To: freesurfer(a)nmr.mgh.harvard.edu Sent: Thursday, May 24, 2012 11:19:21 AM Subject: Re: [Freesurfer] fMRI time series in surface space Why not run the full preprocessing? It will do the sampling (and surface smoothing) for you. Alternatively, you can just use mri_vol2surf, then mris_fwhm to do the surface smoothing (you can also surface smooth in mri_vol2surf so you can do it all with one command). doug On 05/24/2012 08:35 AM, Kushal Kapse wrote: >> Hi Everyone, >> >> I am new to FreeSurfer, and having some issues with what I believe should be a pretty basic operation. >> >> My goal is to register a 4D functional time series to FS average space for further connectivity analysis in Matlab (similar to the recent Yeo et al. J Neurophysiology paper). We have run recon-all without problems on the structural data, but I am having trouble getting the whole functional time series into surface space. When I perform FS-FAST just from pre processing till automatic registration of func-struc, "register.dof6.dat" is produced, which includes input registration matrix. Is their any way to apply this registration matrix to the 4D time series directly, so that the output is in FS average template surface (rather than volumetric) space? >> >> Many thanks, >> kk > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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 Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ 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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Re: [Freesurfer] extract and display several labels using mri_extract_label?
by Martina Papmeyer 24 May '12

24 May '12

Thanks for your help, Bruce! Unfortunately, this also leads to a mgz.file where hippocampus and amygdala are "merged" together so that I can't see anymore what is hippocampus and what is amygdala (both have same value). I tried some other things but nothing appears to work. Any other suggestions? Many thanks, Martina Quoting Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> on Thu, 24 May 2012 08:53:14 -0400 (EDT): > Hi Martina > you can use mri_binarize --match 17 --match 18... to do this. > > cheers > Bruce > > > > On Thu, 24 May 2012, Martina Papmeyer wrote: > >> Hello everyone, >> >> I guess that this might be a simple question but I couldn't find an >> answer to my problem yet. >> >> I would like to extract and visualize four labels from my aseg.mgz >> file for illustration purposes. I tried the following: >> >> mri_extract_label aseg.mgz 17 18 53 54 filename.mgz >> >> (the values correspond to left/right amygdala and left/right >> hippocampus as specified in FreeSurferColorLUT.txt file) >> >> This command unfortunately combines all the four selected labels >> together so that I can't differentiate amygdala and hippocampus >> anymore when I load the filename.mgz file together with my >> FreeSurferColorLUT.txt file in tkmedit. >> >> Is there any other FS tool I can use? >> >> Any form of help would be highly appreciated! >> >> Many thanks and all best wishes, Martina >> >> > > > 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. -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ----- End forwarded message ----- -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Re: [Freesurfer] extract and display several labels using mri_extract_label?
by Bruce Fischl 24 May '12

24 May '12

probably easiest to do in matlab: [v,M,mr] = load_mgh('aseg.mgz'); ind = find(v ~= 17 & v ~= 53 & v ~= 18 & v ~= 54) ; v(ind) = zeros(size(ind)); save_mgh(v, 'aseg.mtl.mgz', M,mr); cheers Bruce On Thu, 24 May 2012, Martina Butt wrote: > Thanks for your help, Bruce! > > Unfortunately, this also leads to a mgz.file where hippocampus and amygdala > are "merged" together so that I can't see anymore what is hippocampus and > what is amygdala (both have same value). I tried some other things but > nothing appears to work. Any other suggestions? > > Many thanks, Martina > > Quoting Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> on Thu, 24 May 2012 > 08:53:14 -0400 (EDT): > >> Hi Martina >> you can use mri_binarize --match 17 --match 18... to do this. >> >> cheers >> Bruce >> >> >> >> On Thu, 24 May 2012, Martina Papmeyer wrote: >> >>> Hello everyone, >>> >>> I guess that this might be a simple question but I couldn't find an >>> answer to my problem yet. >>> >>> I would like to extract and visualize four labels from my aseg.mgz >>> file for illustration purposes. I tried the following: >>> >>> mri_extract_label aseg.mgz 17 18 53 54 filename.mgz >>> >>> (the values correspond to left/right amygdala and left/right >>> hippocampus as specified in FreeSurferColorLUT.txt file) >>> >>> This command unfortunately combines all the four selected labels >>> together so that I can't differentiate amygdala and hippocampus >>> anymore when I load the filename.mgz file together with my >>> FreeSurferColorLUT.txt file in tkmedit. >>> >>> Is there any other FS tool I can use? >>> >>> Any form of help would be highly appreciated! >>> >>> Many thanks and all best wishes, Martina >>> >>> >> >> >> 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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Freesurfer May 2012