Freesurfer October 2014

freesurfer@nmr.mgh.harvard.edu

129 participants
187 discussions

Re: [Freesurfer] rawfunc2surf-sess with a limited set of surface files
by Reza Rajimehr 09 Oct '14

09 Oct '14

Hi Doug, Removing -i fmc did not help, and I still get the same error. By looking at the rawfunc2surf-sess script, it looks like specifying an argument for -surfreg makes ExpKeyNeeded = 1. Can I just specify something for -expkey? Is this something that is used only in the name of log file? Thanks, Reza Try it without -i fmc On 10/08/2014 04:38 AM, Reza Rajimehr wrote: > One more question: > > I tried to run: > > rawfunc2surf-sess -s oz_fparc -i fmc -trgsubject F99 -surfreg > iter05.sphere.reg -fwhm 2 -per-session > > And I got this: > > ERROR: experts key needed (-expkey) > > Not sure what this flag is. > > Reza

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Re: [Freesurfer] Surface Viewer Issue.
by Jamie Hanson 09 Oct '14

09 Oct '14

Hi Greg, Is this simply an image viewing problem or does the data actually need to be re-processed? (I'm working with ~500 subjects, so I figured I would check before taxing the servers I had access to). Thanks much! Best, Jamie. On Thu, Oct 9, 2014 at 12:00 PM, <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: Surface Viewer Issue. (Gregory Kirk) > 2. Re: Mismatched dimensions with T1 and Flair inputs {Disarmed} > (Vilde) > 3. Re: v5.1 control point mri_ca_normalize bug (Marx, Gabe) > 4. Re: v5.1 control point mri_ca_normalize bug (Bruce Fischl) > 5. Re: rawfunc2surf-sess with a limited set of surface files > (Douglas N Greve) > 6. functional correlation (Brian Donley) > 7. Re: rawfunc2surf-sess with a limited set of surface files > (Reza Rajimehr) > 8. mri_thickness & mri_make_surfaces (Seung-Goo KIM) > 9. Re: WM & Pial Segmentation Errors (Varjabedian, Ani) > 10. "deployed" (compiled) MATLAB scripts path manipulation > (slehar(a)nmr.mgh.harvard.edu) > 11. 8 spots remain in the FreeSurfer course (Allison Stevens) > 12. excluding labels (Adam, Ruth) > 13. FSGD Format Error (Retzepi, Kallirroi) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 08 Oct 2014 14:47:27 -0500 > From: Gregory Kirk <gkirk(a)wisc.edu> > Subject: Re: [Freesurfer] Surface Viewer Issue. > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <76a0cbb215b316.54354e7f(a)wiscmail.wisc.edu> > Content-Type: text/plain; CHARSET=US-ASCII > > i saw this problem on one redhat installation, not on any others, seems > something with the X library orientation > information and openGL > > greg > > On 10/08/14, Jamie Hanson wrote: > > Hi Freesurfer List, > > > > > > I had a (hopefully quick) question about surface viewers and data > orientation in tksurfer v. freeview. > > > > > > I processed all my data in freesurfer v5.3.0 (on a linux cluster) and > noticed something odd when I viewed surfaces. For tksurfer, the surfaces > were upside down when I opened them (see attached pic: tksurfer.png); for > freeview, the data looked fine (see attached pic: freeview.png). > > > > > > I believe the orientation of the images is correct (judging by the > freeview axes), but wondered if this was something others had run into? I > uploaded an example subject to the Martinos Center FileDrop (link: > http://gate.nmr.mgh.harvard.edu/filedrop2/?p=9491zcnivqw) > > > > > > Any thoughts are greatly appreciated! Thanks much! > > > > > > Best, > > Jamie. > > > > > > > > -- > > Jamie L. Hanson > > Postdoctoral Fellow, Carolina Consortium on Human Development > > Duke University > > 417 Chapel Drive > > Duke West Campus > > Sociology-Psychology Building, Room 07A > > Durham, NC 27710 > > Email: jamielarshanson(a)gmail.com > > Website: http://jamiehanson.org/ > > > ------------------------------ > > Message: 2 > Date: Wed, 8 Oct 2014 22:01:06 +0200 > From: Vilde <vildeskard(a)hotmail.com> > Subject: Re: [Freesurfer] Mismatched dimensions with T1 and Flair > inputs {Disarmed} > To: <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <DUB122-W3321C71B2BEC2FA5D6BE4CD2A30(a)phx.gbl> > Content-Type: text/plain; charset="iso-8859-1" > > I will try that. > > Have a good day! > > Date: Wed, 8 Oct 2014 14:07:38 -0400 > From: fischl(a)nmr.mgh.harvard.edu > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Mismatched dimensions with T1 and Flair inputs > > you would have to first run recon-all -all on the T1 > On Wed, 8 Oct 2014, > Vilde wrote: > > > Thank you Bruce! > > > > If I understand you correctly, would the command be > > > > Recon-all -s subj_name -FLAIRpial.nii ? > > > > Or would I first have to do recon-all with only T1 as input and then do > > another command after it has finished running? And in that case, what > would > > that command be? > > > > Best, > > Vilde > > > > Date: Wed, 8 Oct 2014 11:56:51 -0400 > > From: fischl(a)nmr.mgh.harvard.edu > > To: freesurfer(a)nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] Mismatched dimensions with T1 and Flair inputs > > > > Hi Vilde > > > > no, you can't give recon-all a flair directly, it needs a T1 do do the > > recon on. You use the flair at the end to do a post-hoc deformation using > > -flairpial I believe > > > > cheers > > Bruce > > > > > > On Wed, 8 Oct 2014, Vilde wrote: > > > > > Dear mailing list, > > > I am trying to do a recon-all with two nifti inputs: A T1 and a Flair, > for > > > pial surface refinement. This results in an error message saying the > > > dimensions are mismatched. (The third dimension of the T1 and Flair are > > > different by one slice. ) I do not, however, have a problem running > > > recon-all with only one T1 input. I am using Freesurfer v 5.1 . > > > > > > I read in the release notes that in version 5.2 you can use the flag > -FLAI > > R > > > when you are using a flair image as input. I suppose this will not run > in > > an > > > earlier version? > > > Would it be correct to use the following command : > > > > > > recon-all -s [subject] -i T1.nii -i flair.nii -all > > > > > > Kind regards, > > > Vilde > > > > > > > > > > > > > _______________________________________________ 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. > > > > > > _______________________________________________ > 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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Study design for qdec or command line group analysis
by Sneha Pandya 09 Oct '14

09 Oct '14

Dear freesurfers, I have a study in which we want to perform group analysis to find the effect of age on cortical thickness between patients and controls. We have 11 patients with age group from 45-75 years and the mean of 53. We shall age match our controls with respect to similar age range and mean. However our patient scans are from both 1.5T and 3.0T scanner, hence I have few questions about designing our study. A) Can we treat certain discrete factors as continuous variables, like gender (male with value 1 and female with value 2), and scanner (1.5T with value 1 and 3.0T with value 2) to make group analysis qdec-able in case of 3 discrete factors? I tried to look into mailing archive to figure out the answer, but so far found confounding answers. B) If what asked above is possible can you please suggest which design I should opt for? Design 1) Three discrete factors, each with 2 levels: (i) gender (male and female) (ii) groups (healthy and patients) (iii) scanner (1.5T and 3.0T), Continuous variable: (i) age OR Design 2) Two discrete factors, each with 2 levels (i) gender (male and female) (ii) groups (healthy and patients) Continuous variables: (i) age (ii) scanner (1.5T as 1, and 3.0T as 0) >From literature we are not expecting any effect of gender and scanner on change of cortical thickness with age between groups, however I guess we need to control for it right? Should I implement design 1 with mri_glmfit command line, as it has 3 discrete factors or design 2 in qdec? B) We are expecting some change in cortical thickness with age between groups. Hence we shall be using DODS model to perform the analysis. In this case I should demean my ages right (subtract grand mean of age from combined healthy and patient groups and subtract from every individual age)? Thanks, Sneha

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excluding labels
by Adam, Ruth 09 Oct '14

09 Oct '14

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lgi mris_preproc
by Lars M. Rimol 09 Oct '14

09 Oct '14

Hi, In the wiki page on the gyrification index it says that to sample the results to ico, use recon-all -s my_subject_id -qcache -measure pial_lgi If I prefer not to use qudec, can I instead use mris_preproc to do the registration to atlas and concatenate the files and then use mri_surf2sruf to smooth? And then proceed with inferential statistics? Thank you! ----------------------------------------------------------- from the wiki: The primary output file is ?h.pial_lgi, which can be viewed as an overlay in tksurfer or freeview: tksurfer my_subject_id lh inflated -overlay lh.pial_lgi To perform a vertex-wise analysis in QDEC of the lgi surface data, first sample the results to the average template subject 'fsaverage': recon-all -s my_subject_id -qcache -measure pial_lgi Do this for each of the subjects in your group -- yours, Lars M. Rimol, PhD Norwegian University of Technology and Science (NTNU) Trondheim, Norway

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FSGD Format Error
by Retzepi, Kallirroi 09 Oct '14

09 Oct '14

Hi all, I have been struggling with my .fsgd file. Its header is the following (a total of 119 subjects): GroupDescriptorFile 1 Title Patients_vs_Controls MeasurementName thickness Class PxMale Class PxFemale Class ConMale Class ConFemale Class PxMPRAGE Class PxSPGR Class ConMPRAGE Class ConSPGR Class MaleMPRAGE Class MaleSPGR Class FemaleMPRAGE Class FemaleSPGR Variables Age Input FS_1 PxFemale PxMPRAGE FemaleMPRAGE 51 ..............(rest of subjects) I think something is up with my Class declaration, since the error message I get is the following: ERROR: gdfReadV1: Input line 1, subjid = FS_1 Found 3 variables, expected. 1 FSGDF Format Error: file = /group_stats/Px_vs_Con_A.fsgd, tag=Input Any help would be greatly appreciated!! Thank you!

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8 spots remain in the FreeSurfer course
by Allison Stevens 09 Oct '14

09 Oct '14

Hello everyone, We have 8 spots remaining in our upcoming FreeSurfer course happening on October 27-29. We will accept late registrations up to the course date; however, since the payment deadline has passed, payment is due immediately upon registration. Details on the course and a link to the registration page can be found here: https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription Note: This course is the only one where we are currently able to accept credit card. This likely won't be an option for future courses. Allison

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"deployed" (compiled) MATLAB scripts path manipulation
by slehar＠nmr.mgh.harvard.edu 09 Oct '14

09 Oct '14

I have been following the directions on this site to "deploy" (compile) my MATLAB script so as to be able to run it on launchpad without worrying about MATLAB licenses. https://nmr.mgh.harvard.edu/martinos/itgroup/deploytool.html They say that the deployed script cannot do path manipulations such as addpath() or path(path,xxx), so the script should use isdeployed to make sure that such path commands are only executed if isdeployed == 0. % Only add path if not deployed if isdeployed==0; addpath ~nummenma/matlab/work/connectome/HCP_preproc_tools; end but then I need to add the path back in again so it can access the functions on that path. In the deploytool GUI I click Settings (the little gear icon), and in the upper window "Additional Parameters passed to MCC:" I inserted ======[ Additional Parameters passed to MCC: ]====== -I ~nummenma/matlab/work/connectome/HCP_preproc_tools mris_gradient_nonlin__unwarp_volume__batchmode_HCPS.m ==================================================== (A web site I found said you need a path to the m-file itself, not just to the directory that contains it, and you separate the path and file) Then I found I had to circumvent more path(path,xxx) commands in my startup.m file too ======[ startup.m ]====== % If script is not deployed add paths if isdeployed==0; %------------ FreeSurfer -----------------------------% fshome = getenv('FREESURFER_HOME'); fsmatlab = sprintf('%s/matlab',fshome); if (exist(fsmatlab) == 7) path(path,fsmatlab); end clear fshome fsmatlab; %-----------------------------------------------------% %------------ FreeSurfer FAST ------------------------% fsfasthome = getenv('FSFAST_HOME'); fsfasttoolbox = sprintf('%s/toolbox',fsfasthome); if (exist(fsfasttoolbox) == 7) path(path,fsfasttoolbox); end clear fsfasthome fsfasttoolbox; %-----------------------------------------------------% end ========================= Now at least it compiles without error. But when I run it I get this: Set up FreeSurfer environment -------- freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 FSFAST_HOME /usr/local/freesurfer/stable5_3_0/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /space/ficus/4/users/SNEF_subjects MNI_DIR /usr/local/freesurfer/stable5_3_0/mni FSL_DIR /usr/pubsw/packages/fsl/current ./run_unwarpone.sh /cluster/matlab/8.2 /space/ficus/4/users/SLOTS_sessions_Step/SLOTS010/aahscout/001/001.mgz /space/ficus/4/users/SLOTS_sessions_unwarp/SLOTS010/aahscout/001/001.mgz /space/ficus/4/users/SLOTS_sessions_Step/SLOTS010/unwarpscout001.log ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/cluster/matlab/8.2/runtime/glnxa64:/cluster/matlab/8.2/bin/glnxa64:/cluster/matlab/8.2/sys/os/glnxa64 The file '/usr/local/freesurfer/stable5_3_0/matlab/load_nifti.m' is not in the application's expanded CTF archive at '/homes/6/slehar/.mcrCache8.2/unwarp2'. This is typically caused by calls to ADDPATH in your startup.m or matlabrc.m files. Please see the compiler documentation and use the ISDEPLOYED function to ensure ADDPATH commands are not executed by deployed applications. An error occurred while trying to determine whether "load_nifti" is a function name. MATLAB:err_while_looking_up_function Error:An error occurred while trying to determine whether "load_nifti" is a function name. Error:Error in mclFreeStackTrace. Any idea what the problem is now? load_nifti is presumably a FreeSurfer function -- do I now have a problem with my paths to FreeSurfer? I searched my script code and found no explicit call to "load_nifti", I presume that is called deep inside some other function. Should I add the FreeSurfer paths also through the deploytool GUI and not call "nmrenv"? (from my .cshrc file... alias nmrenv 'source /usr/local/freesurfer/nmr-stable53-env' )

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mri_thickness & mri_make_surfaces
by Seung-Goo KIM 09 Oct '14

09 Oct '14

Hi all, I’m trying to compute cortical thickness using mris_thickness (stable 5), but getting slightly different results from the recon-all 5.1.0-amd64-2.13 (mri_make_surfaces, stable 5). Hinted from an old thread: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg05994.html, I set the switch “-N 20", but it returns different values: 50% of vertices have identical values with the cross-correlation of about 0.98 and RMS of 0.08 mm, which is of course very high, but a bit odd while I was expecting nearly identical results. When I checked the scatter plots, the mris_thickness returns a bit smaller values for many vertices than the standard result. Is this somewhat expected difference between mri_make_surfaces and mris_thickness? Also I found that mri_thickness reads “?h.gray”, not “?h.pial”. As I assumed that it reads “?h.pial” and “?h.white” to compute thickness, so I just linked “?h.pial” to “?h.gray”. Is this assumed input for mris_thickness? Best regards, -- Seung-Goo KIM

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functional correlation
by Brian Donley 08 Oct '14

08 Oct '14

Hello Freesurfers A bit new to the program, so I hope the following makes sense. We would like to do a bottom-up vertex-by-vertex analysis to see where functional activation correlates with thickness. We've done our functional analyses through SPM and can get those maps into tksurfer. Most of the tutorials and information I see has to do with, for example, defining a ROI based on functional data and extracting the thickness measures "under" that ROI. But this would be a little different Does this make sense, and is this doable in freesurfer? If so, could someone point me to the relevant tutorial or commands? I appreciate your help

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Freesurfer October 2014