Freesurfer August 2013

freesurfer@nmr.mgh.harvard.edu

145 participants
268 discussions

Re: [Freesurfer] Different results in surface and volume analyses
by Emily Boeke 08 Aug '13

08 Aug '13

Hi Doug, Thanks for the response. Is this masking out of the cortical regions in the volume analysis a newer aspect of the processing stream? Previously I have seen this activation in the volume. It would be great if you could let me know the flags to see the full volume analysis. Thanks! Emily Message: 41 Date: Wed, 07 Aug 2013 19:29:33 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Different results in surface and volume analyses To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <5202D85D.1090808(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Emily, the processing stream is designed to mask out cortical regions from the volume analysis. The volume analysis is used for subcortical structures. To make sure that the same voxels are not analyzed twice, the cortical surface is masked out of the mni305 analysis. doug ps. If you really want to see the full volume analysis, then there are some flags that will do this. Message: 14 Date: Wed, 7 Aug 2013 13:15:37 -0400 From: Emily Boeke <eboeke01(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Different results in surface and volume analyses To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <948E8FDF-754A-4AE0-A0C9-86D848F1438A(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=us-ascii Hello everyone, I am looking at a visual stimulus vs fixation contrast in my individual subjects' data to make sure we are seeing normal activation there. If I look at the surface data in tksurfer, I see activation in the occipital cortex, but in the mni305 analysis, there is no activation in this region. These are the preprocess , mkanalysis, and selxavg commands I used for the surface vs. mni305: preproc-sess -s amur_dss -df sesspar -per-run -fwhm 5 -sliceorder down -surface fsaverage lhrh -mni305-2mm -fsd cond mkanalysis-sess -fsd cond -surface fsaverage lh -fwhm 5 -paradigm Fear_Gen_Cond.par -event-related -TR 3 -nconditions 3 -polyfit 4 -spmhrf 0 -refeventdur 6 -analysis cond.sm05.lh -per-run -nskip 4 -stc down mkanalysis-sess -fsd cond -surface fsaverage rh -fwhm 5 -paradigm Fear_Gen_Cond.par -event-related -TR 3 -nconditions 3 -polyfit 4 -spmhrf 0 -refeventdur 6 -analysis cond.sm05.rh -per-run -nskip 4 -stc down mkanalysis-sess -fsd cond -mni305 2 -fwhm 5 -paradigm Fear_Gen_Cond.par -event-related -TR 3 -nconditions 3 -polyfit 4 -spmhrf 0 -refeventdur 6 -analysis cond.sm05.mni305 -per-run -nskip 4 -stc down selxavg3-sess -s amur_dss -df sesspar -analysis cond.sm.lh selxavg3-sess -s amur_dss -df sesspar -analysis cond.sm.rh selxavg3-sess -s amur_dss -df sesspar -analysis cond.sm.mni305 Why might we be seeing this activation on the surface map but not the volume one? Thanks! Emily

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(no subject)
by aqureshi＠nmr.mgh.harvard.edu 08 Aug '13

08 Aug '13

Hi Dr. Fischl, I had a couple subjects that failed recon-all. Although the error log said recon-all failed at mri_watershed it looks like the root problem is a couple steps earlier, because the nu.mgz looks too dark. This was discussed in a previous thread from 2008. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07293.html. You wrote, "p.s. are the 001.mgz and 002.mgz dark? The orig.mgz? Sometimes nu_correct can create very dark images, and there are some switches you can loo through to correct them. Alternatively if it is the 001.mgz, mri_convert has a scale option you can use." On my subject 001.mgz looks good (there was no 002.mgz file). It is only nu.mgz that looks too dark. It looks like the solution you gave then was for a problematic 001.mgz file, but from your response it looks as if the problem was nu.mgz the solution would be different. What are the switches you can loop through to correct the nu.mgz. Thanks, Abid

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monte carlo results differences between qdec and glmfit
by Marie Farstad Høvik 08 Aug '13

08 Aug '13

Dear Freesurfer experts, We are using mri_glmfit and wanted to compare our results to qdec to decide which method we prefer for group analysis. The results are consistent between the two methods, except for the monte carlo results. When we run mri_glmfit-sim to do the monte carlo simulations there are no significant clusters. We are not surprised by this as when we apply a FDR corrections all of our clusters go away. However, when we are using the monte carlo method in qdec we get a large significant cluster (in the csd summary file there are two large significant clusters, but using the image in qdec we only see one of them). The model is the same for both methods. We are (or think) we are using the exact same parameters as qdec. Is there a reason why the simulation results are so different? Which result should we use? The following are two of the simulation commands we have tried using v5.1: mri_glmfit-sim --glmdir glm/lh.asrs_sex_age.thickness.glmdir/ --sim mc-z 100 4 mc-z.unsigned --sim-sign abs --cwpvalthresh 0.01 --overwrite mri_glmfit-sim --glmdir glm/lh.asrs_sex_age.thickness.glmdir/ --sim mc-z 100 2 mc-z.unsigned --sim-sign abs --cwpvalthresh 0.01 --overwrite For the following command, we saw three clusters (they are inconsistent with the qdec ones), but none of them significant (p-values=.2): mri_glmfit-sim --glmdir glm/lh.asrs_sex_age.thickness.glmdir/ --sim mc-z 100 4 mc-z.unsigned --sim-sign abs --cwpvalthresh 0.995 --overwrite We haven't run 10 000 simulations yet, because we wanted to see if there were any significant clusters there at all before running that many simulations. Any advice would be very helpful. Thank you for your time, Marie

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CC mask
by Joao Pedro Battistella Nadas 08 Aug '13

08 Aug '13

> Hello, > > I am working with freesurfer to segment MRI images and I need to obtain a binary mask of the Corpus Callosum. Using the aseg.mgz file I was able to identify it segmented into 5 different structures (labels 251 to 255). However when looking at the mask of the union of those 5 labels, the CC does not look like the shape it should have (it looks like it is just the central part of it). I am trying to obtain this mask for the example patient "bert", and later on I will apply it to my own cases. > Any help would be much appreciated, > thank you > João Pedro B. Nadas

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mri_cvs_register for EPI
by Marcel Falkiewicz 08 Aug '13

08 Aug '13

Hello, I'm trying to use mri_cvs_register (whose registration accuracy is, by the way, jaw-dropping) for EPI images. However, the descriptions which I've found on the web do not make the task easier. My goal is to get functional images in cvs_avg35_inMNI152 space, resampled to 3mm isotropic resoluton (for subsequent ICA analysis). I'm taking following steps: 1. recon-all on anatomical data (obvious) 2. mri_cvs_register (mri_cvs_register --targ cvs_avg35_inMNI152 --mov subject) I do not understand what the files stored in cvs folder are needed for. As far as I understand the normalization process, I need a file which stores the subject -> template warp. Which file is it? Do I need to use the --nocleanup option in mri_cvs_register to get the aforementioned file? In the wiki page a following command line is recommended to reconstruct this warp when the --nocleanup options was not used: createMorph --out fullCVSmorph.tm3d --template template.mgz \ - --subject movingvol.mgz --in gcam nlalign-afteraseg-norm.m3z \ morph el_reg_toTEMPLATE.tm3d However, there is no single *.tm3d file in my cvs directory... Here are the files that are present: el_reg_tocvs_avg35_inMNI152.affine.mgz el_reg_tocvs_avg35_inMNI152_aseg.mgz el_reg_tocvs_avg35_inMNI152.mgz final_CVSmorphed_tocvs_avg35_inMNI152_aseg.mgz final_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz final_CVSmorph_tocvs_avg35_inMNI152.m3z lh.dbg_surf.pial lh.dbg_surf.white lh.resample.aparc.annot lh.resample.pial lh.resample.white nlalign-afteraseg-norm.mgz nlalign-aseg.mgz rh.dbg_surf.pial rh.dbg_surf.white rh.resample.aparc.annot rh.resample.pial rh.resample.white step1_CVSmorphed_tocvs_avg35_inMNI152_aseg.mgz step1_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz summary.AC1004_to_cvs_avg35_inMNI152.mri_cvs_register.1308031447.log transform.txt In my particular case, which images should be entered as arguments to --template and --subject ? 3. standard EPI pre-processing, which results in motion-correction parameters and realigned images 4. coregistration of EPI to anatomical data with BBR. The transformation is stored as register.dof6.dat, which contain the mapping EPI -> anatomical I understand that the next step is combining the registrations from step (2) and (4) in order to get EPI images in cvs_MNI space. This can be accomplished with mri_vol2vol. However, I do not understand which files should be used for this registration. Sorry for the lenghty post, but I'm quite new to freesurfer and I'm a bit confused:) Best regards, Marcel

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Re: [Freesurfer] (no subject)
by Bruce Fischl 08 Aug '13

08 Aug '13

you could try using --scale <scale factor> to scale the intensities of the 001.mgz up On Wed, 7 Aug 2013, Abid Qureshi wrote: > I'm using 4.5.0. The earliest subjects were done using 4.5.0 so for consistency we are sticking with 4.5.0. - > Abid > > > On Wed, Aug 7, 2013 at 6:52 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > Hi Abid > > what version of FS are you using? > Bruce > On Wed, 7 Aug 2013, aqureshi(a)nmr.mgh.harvard.edu wrote: > > Hi Dr. Fischl, > > I had a couple subjects that failed recon-all. Although the error log said > recon-all failed at mri_watershed it looks like the root problem is a > couple steps earlier, because the nu.mgz looks too dark. This was > discussed in a previous thread from 2008. > > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07293.html. > > You wrote, "p.s. are the 001.mgz and 002.mgz dark? The orig.mgz? Sometimes > nu_correct can create very dark images, and there are some switches you > can loo through to correct them. Alternatively if it is the 001.mgz, > mri_convert has a scale option you can use." > > On my subject 001.mgz looks good (there was no 002.mgz file). It is only > nu.mgz that looks too dark. It looks like the solution you gave then was > for a problematic 001.mgz file, but from your response it looks as if the > problem was nu.mgz the solution would be different. What are the switches > you can loop through to correct the nu.mgz. > > Thanks, > Abid > > _______________________________________________ > 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. > > > > > -- > WARNING: E-mail sent over the Internet is not secure. Information sent by e-mail may not remain confidential. > > DISCLAIMER: This e-mail is intended only for the individual to whom it is addressed. It may be used only in > accordance with applicable laws. If you received this e-mail by mistake, notify the sender and destroy the > e-mail > >

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Group analysis
by Marcos Martins da Silva 08 Aug '13

08 Aug '13

Hi, FreeSurfers. Is it possible to use FreeSurfer's group analysis tools to investigate surface deformation instead of thickness? I guess it would be interesting for subcortical structures like putamen, amygdala or hippocampus. Let's say you get the putamen data from 15 subjects and compare it to putamen data from fsaverage, After correct registration, I guess we can detect regions of contraction and expansion leading to changes in the putamen contour. I imagined it could be done if we calculate the signed Euclidean distances between the corresponding points of for each subject's putamen and fsaverage, with positive and negative values indicating, for example, the presence of an outward or inward surface deformation. After all calculation I guess we can get a similar result to the pictures we can see at http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis but showing only a putamen and the colors meaning surface deformation instead of thickness. This way, you can notice morphological differences among subjects even if they have the same volume. Thanks in advance, Marcos

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cvs_register then mri_vol2vol
by Barron, Daniel S 08 Aug '13

08 Aug '13

Hi Freesurfers (Lilla), I'm running v5.1.0 on a Mac trying to apply a cvs morph via the following function: mri_vol2vol --targ cvs_avg35_inMNI152 --m3z $SUBJECTS_DIR/NC001/cvs_avg35_inMNI152/combined_tocvs_avg35_inMNI152_elreg_afteraseg-norm.m3z --noDefM3zPath --mov $SUBJECTS_DIR/NC001/labels/lh.hipp.nii.gz --o $SUBJECTS_DIR/NC001/labels2cvs/lh.hipp2cvsMNI152.nii.gz --interp nearest --no-save-reg Using the m3z file as it is; no assumed location. movvol /media/users/barrond/NYU/Freesurfer/NC001/labels/lh.hipp.nii.gz targvol cvs_avg35_inMNI152 outvol /media/users/barrond/NYU/Freesurfer/NC001/labels2cvs/lh.hipp2cvsMNI152.nii.gz invert 0 tal 0 talres 2 regheader 0 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Morphing InvertMorph 0 Synth 0 SynthSeed 1375994175 corRead(): can't open file /media/users/barrond/NYU/Freesurfer/cvs_avg35_inMNI152/COR-.info I don't know what "COR-.info" is or how to make it. Could someone please point me in the right direction? Cheers, Daniel

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Re: [Freesurfer] trac-all inquiry
by Soto, David 08 Aug '13

08 Aug '13

Hi - further to my prior email find attached please a clean version of the log file - without the append of previous attempts as you can see there are no errors in the log although as i said the last line in the Terminal said Segmentation fault (core dumped) cheers ds http://www1.imperial.ac.uk/medicine/people/d.soto/ ________________________________________ From: Soto, David Sent: 07 August 2013 23:47 To: Anastasia Yendiki Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: RE: [Freesurfer] trac-all inquiry Hi Anastasia, I checked the becs and bvals files, there was a bug in the transposition of the columns into 3 rows in the bvecs. But i still have problems.. I rerun trac-all -prep and seemed fine but ended with a Segmentation fault (core dumped) which however is not present in the last line of the trac-all.log (Attached). Writing output files to /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_* Writing spline volume to /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_cpts_5.nii.gz Segmentation fault (core dumped) Just in case I tried trac-all -bedp complains like these below, any advise appreciated, cheers - ds /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/diffree/tracula02ST.txt -bedp INFO: SUBJECTS_DIR is /home/dsoto/Documents/fmri/rsdtianawmgui INFO: Diffusion root is /home/dsoto/Documents/fmri/rsdtianawmgui Actual FREESURFER_HOME /usr/local/freesurfer WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri /usr/local/freesurfer/bin/bedpostx_mgh: 131: /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected http://www1.imperial.ac.uk/medicine/people/d.soto/ ________________________________________ From: Anastasia Yendiki [ayendiki(a)nmr.mgh.harvard.edu] Sent: 07 August 2013 17:22 To: Soto, David Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: RE: [Freesurfer] trac-all inquiry Hi David - Every time you run trac-all, the results get appended to this file, so you need to look for error messages only in the more recent invocation of trac-all. The first error there seems to be: Error: bvecs and bvals don't have the same number of entries Do you have the same number of b-values and gradient vectors and volumes in your DWI series? a.y On Tue, 6 Aug 2013, Soto, David wrote: > hi > > I upgraded to FS 5.3 but still encountering issues with > trac-all prep. > > The log is attached, things I noted after inspecting it > > 1) INFO: FreeSurfer build stamps do not match > Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 > Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 > > 2) Error: input image /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb not valid > 3) Image Exception : #22 :: ERROR: Could not open image /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb_brain > 4) Image Exception : #22 :: ERROR: Could not open image > /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/diff/White-Matter++. > 5) ERROR: Could not read /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dtifit_FA.nii.gz > but despite all this it says: > trac-preproc finished without error at Tue Aug 6 21:27:30 BST 2013 > > thanks for your help > > cheers > ds > > http://www1.imperial.ac.uk/medicine/people/d.soto/ > > > > > ________________________________________ > From: Anastasia Yendiki [ayendiki(a)nmr.mgh.harvard.edu] > Sent: 06 August 2013 19:30 > To: Soto, David > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] trac-all inquiry > > I see, you're using the old version of tracula (from freesurfer 5.1). In > that version, you had to define the number of low-b images in the > configuration file. I strongly recommend updating to freesurfer 5.3. A lot > of things have improved in tracula since then. > > Also, in the future please attach any log files as separate attachments > instead of pasting them into the body of your email - this causes the body > of the email to exceed the limit allowable on the list. > > Thanks, > a.y > > > 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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surface upside down, wrong hemis, nouveau error
by Dewitt, Iain (NIH/NIDCD) [F] 07 Aug '13

07 Aug '13

Dear FreeSurfer community, I have a newly installed version of FreeSurfer: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 running on Red Hat Enterprise Linux 6.4. When I load a surface in tksurfer, eg: tksurfer fsaverage5 lh smoothwm the wrong hemisphere loads and the surface is upside down (see attached image). Further, when I try to select a vertex on the surface, there is no alignment between the pointer and the vertex ultimately selected. For instance, as seen in the attached image, when I click on STG, the vertex highlighted is in the central sulcus. Terminal output is below. I get similar behavior for other surfaces and other pre-installed subjects. The only error message I am getting is: libGL error: failed to load driver: nouveau libGL error: Try again with LIBGL_DEBUG=verbose for more details. Nouveau appears to be installed: [31] /sbin/lspci -v -s `/sbin/lspci | awk '/VGA/{print $1}'` 05:00.0 VGA compatible controller: NVIDIA Corporation GF116 [GeForce GTX 550 Ti] (rev a1) (prog-if 00 [VGA controller]) Subsystem: eVga.com. Corp. Device 1559 Flags: bus master, fast devsel, latency 0, IRQ 30 Memory at f8000000 (32-bit, non-prefetchable) [size=32M] Memory at d8000000 (64-bit, prefetchable) [size=128M] Memory at d4000000 (64-bit, prefetchable) [size=64M] I/O ports at ec00 [size=128] Expansion ROM at f7f80000 [disabled] [size=512K] Capabilities: <access denied> Kernel driver in use: nouveau Kernel modules: nouveau, nvidiafb Any thoughts on what else I should check or what might be going wrong? cheers Iain [20] tksurfer fsaverage5 lh smoothwm subject is fsaverage5 hemi is lh surface is smoothwm surfer: current subjects dir: /home/dewitt/mrdata/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/dewitt checking for nofix files in 'smoothwm' Reading image info (/home/dewitt/mrdata/freesurfer/subjects/fsaverage5) Reading /home/dewitt/mrdata/freesurfer/subjects/fsaverage5/mri/orig.mgz surfer: Reading header info from /home/dewitt/mrdata/freesurfer/subjects/fsaverage5/mri/orig.mgz surfer: vertices=10242, faces=20480 surfer: single buffered window surfer: tkoInitWindow(fsaverage5) libGL error: failed to load driver: nouveau libGL error: Try again with LIBGL_DEBUG=verbose for more details. surfer: using interface /home/dewitt/apps/freesurfer/tktools/tksurfer.tcl Reading /home/dewitt/apps/freesurfer/tktools/tkm_common.tcl Reading /home/dewitt/apps/freesurfer/tktools/tkm_wrappers.tcl Reading /home/dewitt/apps/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /home/dewitt/apps/freesurfer/tktools/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... % ----------------------------------- selected vertex 6123 out of 10242 current -47.84 -8.78 45.57 orig -49.76 -9.85 46.75 pial 0.00 0.00 0.00 white -49.73 -9.60 46.90 inflated 0.00 0.00 0.00 normals -0.68 -0.66 0.32 nneighbors 6 ripflag 0 surfer: dmin=1.2521, vno=6123, x=-47.8367, y=-8.7830, z=45.5727 surfer: curv=0.000000, fs=0.000000 surfer: val=0.000000, val2=0.000000 surfer: amp=0.000000, angle=0.000000 deg (0.000000) surfer: vertex 6123 marked (curv=0.000000, stat=0.000000) x = (-47.8, -8.8, 45.6), n = (-0.7, -0.7, 0.3).

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Freesurfer August 2013