Freesurfer May 2014

freesurfer@nmr.mgh.harvard.edu

139 participants
206 discussions

Coomand not found
by Francesca Strappini 14 May '14

14 May '14

Hi, I'm just starting out with freesurfer. I downloaded CentOS6_x86_64 and I have Ubuntu 12.04 LTS. I have set up the licence file and configured freesurfer: tcsh setenv FREESURFER_HOME /media/Shared_Data/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh -------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /media/Shared_Data/freesurfer FSFAST_HOME /media/Shared_Data/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /media/Shared_Data/freesurfer/subjects MNI_DIR /media/Shared_Data/freesurfer/mni When I try to run any type of command, like tkmedit bert orig.mgz, I get this error: command not found. Thanks for the help! Francesca

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problems about extracting specific vertex thickness value and getting a average thickness for a specific mask
by charujing 13 May '14

13 May '14

Hi FS experts and users I have done the each subjects' surface regestration on fsaverage surface, and merge all of them into a *.mgh. Group analysis is also completed. Now I have two questions: 1,I want to extract the VtxMax vertex number thickness for all subjects. The VtxMax vertex number can be got in the *.sig.cluster.summary file. And it represents the most significant vertex in that cluster. I search my question in google and find these scripts which maybe helpful for me: for i in `seq 1 $numsubject` do mri_convert --frame $i y.mgh $SUBJECTS_DIR/fsaverage/surf/lh.$i.mgh mris_convert -c $i.mgh $SUBJECTS_DIR/fsaverage/surf/lh.inflated lh.$i.asc done I got the lh.*.asc file and open it. There are five columes in this file. I guess that: first colume is vertex number, the 2nd-4th columes represent MNI305 coordinates in surface, and the 5th colume is thickness of this vertex. If I want to deal with my 1st question, all I need to get the lh.*.asc file and search the specific vertex number in this file. All of above, is there anything wrong? 2, I created a surface mask, and want to extract the average thickness value in this mask for every subject. How can I complete it? Can I extract all vertex thickness in that mask, and average them in each subject? If so, however, it will be a bot of inconvenience. I want to some simple codes to deal with it. Any reply will be highly appreaciated. Thanks All the best. Rujing Zha 2014-05-10 charujing

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freeview segmentation fault
by Mark D. Strohm 13 May '14

13 May '14

Hello- We’re having a problem with our Freesurfer 5.3 install: freeview exits with a Segmentation fault. No windows open, and there is no other other output. strohm::funcserv1:=>freeview Segmentation fault All I have been able to find is that it appears to be making an inappropriate ioctl call to the freeview script. This is freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 on openSUSE 12.3. Any help would be appreciated Thank you. -Mark- 8011 open("/space/raid/fmri/freesurfer/bin/freeview", O_RDONLY) = 3 8011 dup2(3, 16) = 16 8011 close(3) = 0 8011 read(16, "#!/bin/tcsh -ef\nsource $FREESURFER_HOME/bin/tcl_setup\nsource $FREESURFER_HOME/bin/vtk_setup\nsource $FREESURFER_HOME/bin/qt_setup\nif($#argv > 0) then\n if(\"$argv[1]\" == \"-tkmedit\") then\n tkmeditfv $argv[2-$#argv]\n exit 0\n endif\nendif\nfreeview.bin $argv\n", 8192) = 259 8011 lseek(16, 0, SEEK_CUR) = 259 8011 ioctl(16, SNDCTL_TMR_TIMEBASE or SNDRV_TIMER_IOCTL_NEXT_DEVICE or TCGETS, 0x7fffe2b9a2f0) = -1 ENOTTY (Inappropriate ioctl for device) […] 8011 ioctl(16, SNDCTL_TMR_TIMEBASE or SNDRV_TIMER_IOCTL_NEXT_DEVICE or TCGETS, 0x7fffe2b9a480) = -1 ENOTTY (Inappropriate ioctl for device) 8011 write(17, "Segmentation fault\n", 19) = 19 8011 exit_group(139) = ? 8011 +++ exited with 139 +++ -- Mark D. Strohm, Ph.D. System Administrator, UCLA, Semel Institute & Department of Psychology Center for Cognitive Neuroscience (CCN) & Functional Neuroimaging Core (FUNC) 2567D Franz Hall, 1-310-206-5618, mstrohm(a)ucla.edu

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distance comparisons across subjects in fsaverage group sphere
by Milde, Christopher 13 May '14

13 May '14

Dear Freesurfers, In Fischl et al. 1999 it is highlighted, that the topological structure of the original surface is preserved in the spherical space and due to the nature of a sphere, computations (distance, area) measures are easy to make. My question now, concerns the comparability of distance measures between subjects in the group fsaverage sphere. My aim is to compare distances between peak voxels coordinates of two study populations, to figure out if a systematic difference exist between the peak voxel distances of the two study populations. Can I compare the distances between peak voxels (vertices) between different subjects based on the fsaverage group sphere? So, is the comparability of distances between vertexes of individually spheres preserved in group fsaverage space? Ps: I know that the distances in spherical space are not Euclidian but still geodesic Best wishes and thanks in advance, Christopher Milde, M.Sc. Biol. Institute for Cognitive and Clinical Neuroscience Central Institute of Mental Health Square J 5 68159 Mannheim, Germany Christopher Milde, M.Sc. Biol. Institute for Cognitive and Clinical Neuroscience Central Institute of Mental Health Square J 5 68159 Mannheim, Germany Phone: +49-621-1703-6313 E-mail: christopher.milde(a)zi-mannheim.de Homepage: http://www.zi-mannheim.de/ Office: Forschungs- und Verwaltungsgebäude, Room 230

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Freeview/Freesurfer Version Compatibility
by Sarah Blankenship 13 May '14

13 May '14

During the Spring Freesurfer workshop the newest version of Freeview was used as the primary viewing tool. Are there compatibility issues with using the newest version of Freeview while running analyses in an older version of Freesurfer (v5.1.0)? That is, if you run recon-all through v5.1.0, can you view and make manual edits using the newest release of Freeview (11 May 2014 build) or should you only use the Freeview build that is specific to your Freesurfer version (22 May 2011 build for 5.1.0)? Thank you, Sarah Blankenship Graduate Research Assistant Neuroscience and Cognitive Science Program University of Maryland, College Park

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Re: [Freesurfer] nonlinear models in longitudinal analysis
by Jodie Davies-Thompson 13 May '14

13 May '14

Hi Martin, Thanks for your reply. I'm not entirely sure what you mean (sorry - I'm new to this!). Do you mean something like this? For examining an increase between timepoint 1 and 2, but the same between timepoint 2 and 3? fsid fsid-base years years-to-years Day1 base 0 0.4 Day2 base 0.4 0.4 Day3 base 0.8 0 All the best, Jodie Message: 6 Date: Fri, 09 May 2014 16:52:25 -0400 From: Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] nonlinear models in longitudinal analysis To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <536D4009.7030907(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Jodie, 'years' should contain the real time between time points (usually, unless you have test-retest where time is irrelevant, or different task that can be ordered as you like). For what you are trying to do you should use linear mixed effects models with a piecewise linear setup. This will allow you to estimate a slope before and after timepoint 2 and compare those slopes. Your design matrix would probably have the column of 1, years and a column with years-years(at tp2 of that subject) if that value is positive 0 otherwise Testing if the coef of the 3rd column is > 0 is asking if the slope increases in the second interval. Not exactly what you want, but close and of course you can test if the slope in interval 1 is different from zero (second column) and if the slope in interval 2 is different from zero ( 0 1 1, ie the sum of the last two columns). Best, Martin On 05/08/2014 03:48 PM, Jodie Davies-Thompson wrote: > Dear Freesurfer experts, > > I am attempting to do a longitudinal analysis of cortical thickness with 3 timepoints. So far, I have successfully completed the analysis for long_mris_slopes comparing timepoint 1 to timepoint 2, timepoint 2 to timepoint 3, and a linear increase for timepoint 1 to 2 to 3. > > However, I am primarily interested in finding regions which show a) an increase between timepoint 1 and 2, but no difference between 2 and 3, and b) no difference between timepoint 1 and 2, but an increase between 2 and 3. > > Would the correct way of 'modelling' these two in the qdec file be: > > a) > fsid fsid-base years > day1 base 0 > day2 base 3 > day3 base 3 > > and b) > fsid fsid-base years > day1 base 0 > day2 base 0 > day3 base 3 > > All the best, > Jodie > > - > --- > Jodie Davies-Thompson, Postdoctoral Fellow > Department of Ophthalmology & Visual Sciences > UBC/VGH Eye Care Centre > 2550 Willow Street > Vancouver, BC, V5Z 3N9 > Canada > Tel: 604-875-4111 ext 69003 > - --- Jodie Davies-Thompson, Postdoctoral Fellow Department of Ophthalmology & Visual Sciences UBC/VGH Eye Care Centre 2550 Willow Street Vancouver, BC, V5Z 3N9 Canada Tel: 604-875-4111 ext 69003

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Re: [Freesurfer] Viewing functional data on the inflated brain
by Sherryse Corrow 13 May '14

13 May '14

Hi Douglas, I don’t receive any emails from anyone, I only receive the the digest which is what I “reply” to. So I am not sure what you mean by “try responding to the email that I sent.” This is why I attempted to email you directly as I thought that is what you were asking for. I hope to have straightened things out by finding each part of our conversation and pasting them below (in reverse order). If you have further questions, please let me know. Sincerely, Sherryse Message: 9 Date: Fri, 09 May 2014 17:36:36 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Viewing functional data on the inflated brain To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <536D4A64.5000400(a)nmr.mgh.harvard.edu<mailto:536D4A64.5000400@nmr.mgh.harvard.edu>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed both of what? Sorry, it looks like the thread was garbled below or somehow the digest got into it. Try responding to the email that I sent to keep things in order On 05/09/2014 05:09 PM, Sherryse Corrow wrote: Thanks Douglas. Yes, both of those exist. Douglas N Greve<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:…> Wed, 07 May 2014 12:51:02 –0700<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:…> It is looking for subject P143 in /usr/local/freesurfer/subjects Does it exist? If so, does /usr/local/freesurfer/subjects/P143/mri/brainmask.mgz Exist? Sherryse Corrow<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:…> Wed, 07 May 2014 11:00:54 -0700<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:…> Thanks Douglas. We tried that . . . The registration matrix that we need is not created. Here is the output log file (attached). I am a bit new to this so I am hoping it has the information you need. After taking a quick glance at the log file, we noticed there are errors in the log file. Step by step, this is what we did after we ran recon-all: Reg-feat2anat ‹feat OurFeatDirectory.feat ‹subject P143 When we open the folder experiment.feat/reg/freesurfer, there is no anat2exf.register.dat file. However, there is a file called: anat2exf.register.dat.init. Thanks, Sherryse Douglas Greve<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:…> Mon, 05 May 2014 19:58:31 –0700<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:…> Run reg-feat2anat. If that does not work, then send the command line and terminal output. Just saying that something does not work will not get you closer to a solution. We need to know what you did and what happened Doug Sherryse Corrow<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:…> Mon, 05 May 2014 16:56:58 –0700<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:…> Hi all, Earlier today, I posted the message listed below. However, we discovered part of our issue. When we run reg-feat2anat, there is no anat2exf.register.dat file created. Therefore, we have no registration matrix to use. Before, we were inadvertently using the anat2std file instead. Any suggestions on how to get the anat2exf.register.dat file created? Thanks, Sherryse Douglas Greve<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:…> Mon, 05 May 2014 19:50:18 –0700<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:…> Can you tell us specifically what you have done? I mean command lines … doug Sherryse Corrow<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:…> Mon, 05 May 2014 15:58:35 -0700<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:…> Dear FreeSurfer community, We are having some issues registering our functional data (or masks) from FSL to an inflated brain in FreeSurfer. Some of our masks, when registered to the inflated brain and viewed in FreeSurfer, are not showing up on the cortical surface. We have followed web-tutorials for registration but are still having the issue. Any suggestions?

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mri_surf2surf
by Caka 13 May '14

13 May '14

Dear Doug and All, I want to register the individual subject surface into the fsaverage surface. I used mdi_surf2surf command. But one error occurred. Could you please help me with this. Here are the scripts: ————————————————————————————————————————————————————————— [root@localhost sub001]# mri_surf2surf --hemi lh --srcsubject sub001 --srcsurfval thickness --src_type curv --trgsubject fsaverage --trgsurfval ./sub001-thickness-lh.img srcsubject = sub001 srcval = thickness srctype = curv trgsubject = fsaverage trgval = ./sub001-thickness-lh.img trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /disk250/data_analysis/data_female_male_140/sub001/surf/lh.sphere.reg Loading source data Reading curvature file /disk250/data_analysis/data_female_male_140/sub001/surf/lh.thickness Reading target surface reg /disk250/data_analysis/data_female_male_140/fsaverage/surf/lh.sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (132230) Reverse Loop had 21224 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 146822, nTrgMulti = 17020, MnTrgMultiHits = 2.247 nSrc121 = 93121, nSrcLost = 0, nSrcMulti = 39109, MnSrcMultiHits = 2.35099 Saving target data Saving to ./sub001-thickness-lh.img ANALYZE FORMAT ERROR: ncols 163842 in volume exceeds 32768 ————————————————————————————————————————————————————————————— Thank you very much! Qiongmin

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Subcortical volume calculation from aparc+aseg.mgz?
by Schreiber, Stefanie 13 May '14

13 May '14

Dear all, For the evaluation of the subcortical volumes we executed ‘mri_segstats’ on ‘aseg.mgz’ and for comparison on ‘aparc+aseg.mgz’ in a number of individuals. Apparently the volume of subcortical structures, like the hippocampus, is calculated as the same values if calculated (without partial volume correction) from ‘aseg.mgz’ and ‘aparc+aseg.mgz’. However, when partial volume correction is applied, the resulting values for e.g. hippocampal volumes differ between the ‘mri_segstats’ calculation for ‘aseg.mgz’ and ‘aparc+aseg.mgz’. How could those differences resulting from the partial volume correction in these cases be explained? The command used to calculate the subcortical volumes with partial volume correction was: mri_segstats --seg ./mri/aparc+aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --excludeid 0 --sum ./stats/my.test.stats --pv ./mri/norm.mgz Previously we have been using the subcortical volumes from ‘aseg.stats’, which, as I understand it, is generated by recon-all from ‘aseg.mgz’ via ‘mri_segstats’ (with partial volume correction). From your experience, would it be also valid to use subcortical volumes generated by applying ‘mri_segstats’ (with partial volume correction) on ‘aparc+aseg.mgz’, even though the resulting values might differ from the values in aseg.stats? Thank you very much in advance, Steffi Schreiber

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Fwd: extracting rois for connectivity analysis
by Jutta Ernst 13 May '14

13 May '14

Dear Freesurfer's I draw a roi to extract the cortical thickness for my two groups and that worked fine. Now I'm trying to export the very same roi to use it for further connectivity analysis. Can anyone please help me and tell me how to do it? Thanks in advance!! :-) Cheers Jutta

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Freesurfer May 2014