Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30093 discussions

FS 5.1 MNI305 aparc+aseg registration with FSL MNI152
by raij＠nmr.mgh.harvard.edu 13 Mar '13

13 Mar '13

Dear fellow Surfers, I am trying to overlay FreeSurfer 5.1 MNI305 (=fsaverage) aparc+aseg.mgz 3D volumes (caudate, putamen, pallidum, etc) onto FSL MNI152 2mm resolution volume. I first extract the nuclei from MNI305 aparc+aseg.mgz, for example: mri_extract_label $FREESURFER_HOME/subjects/fsaverage/mri/aparc+aseg.mgz 11 MNI305_3D_masks/mask_lh_caudate.nii I then try to resample the extracted volume into FSL MNI152 2mm space, using the registration that comes with FS 5.1 (.dat format): mri_vol2vol --mov MNI305_3D_masks/mask_lh_caudate.nii --targ $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat --o MNI152_3D_masks/mask_lh_caudate.nii Unfortunately, caudate appears in a clearly incorrect location, both when checking the result with tkmedit2, and when viewing the volumes with freeview. Adding --inv does not fix this either. However, if I simply overlay the volume extracted from MNI305 aparc+aseg on the FSL MNI152 2 mm volume, the location looks just fine. It therefore appears that MNI305 and MNI152 are in the same space, and mri_vol2vol is not needed. Is this correct? Or am I just using an incorrect register.dat file? Thanks! Tommi Details: On machine ernie nmr-std-env (5.1.0 stable) $FSLDIR = /usr/pubsw/packages/fsl/current/ $FREESURFER_HOME = /usr/local/freesurfer/stable5_1_0/ --- Tommi Raij, MD, PhD TMS Core Director MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.

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Re: [Freesurfer] bbregister error
by Anastasia Yendiki 13 Mar '13

13 Mar '13

Hi Salil - I'm cc-ing Doug who may be able to help. The error happens when bbregister invokes fslregister, in this particular line of fslregister: set refvol = `stem2fname $SUBJECTS_DIR/$subjid/mri/$fsvol` When run on brainmask.mgz, it returns "ERROR: could not determine file". a.y On Wed, 6 Mar 2013, Salil Soman wrote: > > Thank you for your email. Changing the mask option got me past the error I > was having initially, but now I get these new errors: > > mri_convert ERROR: could not determine file for > /mnt/glusterfs/salsoman/output/FS/WCA_0226_T1_FS/mri/ERROR:/mnt/glusterfs/salsoman/output/TRACULA/WCA_0226_T1_FS/dmri/xfms/tmp.bbregis > ter.30396/fslregister/refvol.fslregister.nii > mri_convert ERROR: could not determine file for > /mnt/glusterfs/salsoman/output/FS/WCA_0226_T1_FS/mri/ERROR:/mnt/glusterfs/salsoman/output/TRACULA/WCA_0226_T1_FS/dmri/xfms/tmp.bbregis > ter.30396/fslregister/refvol.fslregister.nii > > Thank you for your consideration. > > Best wishes, > > -S > > On Wed, Mar 6, 2013 at 1:15 PM, Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi Salil - The problem is that you've set dob0 = 1 but you haven't set > b0mlist and b0plist, so it doesn't know where to find your field maps to do > the B0 unwarping. > > a.y > > >

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is ftp server down?
by Kristina Nalbandian 13 Mar '13

13 Mar '13

Hello, I am trying to download these files for Surface-Based Interhemispheric R egistration: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/surfregftp://… However, the links are not working. I've tried accessing the links through both IE and Firefox and neither work. Thank you for your help, Kristina Nalbandian

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Divisions for "anterior" and "posterior" insula?
by Maleki, Nasim 13 Mar '13

13 Mar '13

Hi all, I have a hard time relating the boundaries of the insula defined by Freesurfer (Destrieux a2009s) with what is out there in the literature. Most of what is out there is described in terms of anterior and posterior insula, and I'm not sure if most of them match well with what is described in Destrieux et al. paper (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2937159/?tool=pubmed) as the "anterior" and "posterior" insula as described below: "The central sulcus of the insula ran antero-inferiorly from the superior segment of the circular segment of the insula. It was a small sulcus that was not always visible on its whole course on the inflated views. It divided the insula in two parts: the short insular gyri [G_insular_short, 18] (anterior) and the long insular gyrus (posterior). Due to their small size, the central sulcus of the insula and the long insular gyri were grouped in the same label [G_Ins_lg_and_S_cent_ins, 17]." Based on these definitions, would it be fair to say: Anterior insula = "G_insular_short" and "S_circular_insula_ant" Posterior insula = "G_Ins_lg_and_S_cent_ins" and "S_circular_insula_inf" Thank you for your help, Nasim

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FS 5.2 tkmedit X11 - Xquartz Snow-Leopard
by Garikoitz Lerma-Usabiaga 13 Mar '13

13 Mar '13

Hi FS experts, I just installed 5.2 for Snow Leopard in a machine who already had 5.1. When running tkmedit in 5.1 X11 works well, but when running it from 5.2 it gives the following error: BRODMANN80:~ glerma$ tkmedit bert T1.mgz dyld: Library not loaded: /opt/X11/lib/libGLU.1.dylib Referenced from: /Users/glerma/Apps/freesurfer/tktools/tkmedit.bin Reason: image not found Trace/BPT trap I've seen in the mail list that when this happens, Xquartz should be installed. But, is it a requirement for freesurfer 5.2 in Snow Leopard to run with Xquartz? Should I remove X11 and install Xquartz then? (it may affect other programs and I am reluctant to do it...) Many thanks, Gari

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mean thickness covariate, mean area covariate, & mri_anatomical_stats for multiple subjects
by Laura M. Tully 12 Mar '13

12 Mar '13

Hello freesurfers, It appears that prior discussions on the listserv have recommended using mean cortical thickness (rather than ICV) as a covariate for thickness analyses (predominantly recommended by Michael Harms). I have three questions about this: 1. Is there a paper that I could cite that recommends using mean cortical thickness rather than ICV? 2. Would the same logic be applied to surface area analyses? i.e. would it make more sense to use mean surface area as a covariate in surface area analyses? If so, which mean surface area calculation should be used? mri_anatomical_stats can produce both pial and white matter mean surface area stats. 3. Is there a way to run mri_anatomical_stats on multiple subjects at once and write to a tablefile (similar to asegstats2table output)? Thanks! Laura. -- -- Laura M. Tully, MA Social Neuroscience & Psychopathology, Harvard University Center for the Assessment and Prevention of Prodromal States, UCLA Semel Institute of Neuroscience ltully(a)mednet.ucla.edu ltully(a)fas.harvard.edu 310-267-0170 -- Follow me on Twitter: @tully_laura

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nu_correct: Command not found error
by Sinead Kelly 12 Mar '13

12 Mar '13

Dear all, I am currently running cortical thickness analysis using Freesurfer v5.2 on a high performance computing cluster however, when I run the 'recon_all' command I get the following error Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0 INFO: SUBJECTS_DIR is /home/users/kellys37/CT_TEST/CON3140 Actual FREESURFER_HOME /home/support/tcin/apps/freesurfer/5.2.0 Linux tcin-n02.cluster 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:20:03 EST 2012 x86_64 x86_64 x86_64 GNU/Linux nu_correct: Command not found. #-------------------------------------------- #@# MotionCor Thu Mar 7 11:44:10 GMT 2013 Found 1 runs /home/users/kellys37/CT_TEST/CON3140/001/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /home/users/kellys37/CT_TEST/CON3140/001/mri/orig/001.mgz /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz /home/users/kellys37/CT_TEST/CON3140/001 mri_convert /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz --conform mri_convert /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.9997, 0.0244327, -0.00148148) j_ras = (0.0239203, 0.987991, 0.152651) k_ras = (-0.00519336, -0.15257, 0.988279) Original Data has (0.898438, 0.898438, 0.9) mm size and (256, 256, 180) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz... mri_add_xform_to_header -c /home/users/kellys37/CT_TEST/CON3140/001/mri/transforms/talairach.xfm /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Mar 7 11:44:32 GMT 2013 /home/users/kellys37/CT_TEST/CON3140/001/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux tcin-n02.cluster 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:20:03 EST 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 001 exited with ERRORS at Thu Mar 7 11:44:38 GMT 2013 For more details, see the log file /home/users/kellys37/CT_TEST/CON3140/001/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I had did not encounter this error when using an older version of Freesurfer on our clusters. Do you know if there is any way to resolve this problem? Any advice would be appreciated. Kind regards, Sinead -- Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8

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R: Re: R: Re: Question on tracula and dwi-T1 overlap
by stdp82＠virgilio.it 12 Mar '13

12 Mar '13

I got it from mri directory but I'm understanding that this directory isn't ok.I'm attacking the image from dlabel/diff/aparc+aseg.bbr.nii Stefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 12-mar-2013 17.19 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: Question on tracula and dwi-T1 overlap Can you please answer my question? I can't really tell if the issue is due poor dwi-aseg overlap unless you tell me where you got that aseg volume from. On Tue, 12 Mar 2013, stdp82(a)virgilio.it wrote: > Thank you Anastasia. What do you think about the issue in the file attacked > (I'm noting that same subjects are lacking of same > tracts or same tracts are incomplete) > > > Stefano > > > ----Messaggio originale---- > Da: ayendiki(a)nmr.mgh.harvard.edu > Data: 12-mar-2013 17.02 > A: <stdp82(a)virgilio.it> > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] Question on tracula and dwi-T1 overlap > > > Hi Stefano - Where did you get the aseg.nii.gz from? Anything that's in > the dlabel/diff/ directory has been mapped to the same space as the DWI, > so those are the volumes that can be compared directly to dwi.nii.gz. > > a.y > > On Tue, 12 Mar 2013, stdp82(a)virgilio.it wrote: > > > Hi list, > > > > I have two questions, please. > > > > I'm using version 5.1 to complete my analysis. > > > > 1- I have attacked two images from aseg.nii.gz and dwi.nii.gz of the same > > subject (figure 1 and 3). You can note the dwi do not overlap to the aseg. > > How can I resolve this issue? > > > > 2-After TRACULA analysis, I'm noting that same subjects are lacking of > same > > tracts or same tracts are incomplete (figure 3). > > > > Could it depends from the issue in question 1? I'm thinking to rerun all > > using version 5.2 but before starting new analyses, I'd like to ask you > > which is the possible error. > > > > > > Stefano > > > >_______________________________________________ > 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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Re: [Freesurfer] does mkcontrast-sess correct for multiple comparisons?
by Douglas Greve 12 Mar '13

12 Mar '13

Hi Rosa, the sig maps are uncorrected at the individual level. To correct them, run selxavg3-sess with the -fwhm option. This will compute the FWHM of the residuals. When that is done, look for the fwhm.dat file and get its contents. Did you run this in the subject's native space? If so, then you will need to run a simulation. Let me know and I'll tell you how If you can the analysis in the fsaverage space, then run mri_surfcluster --in sig.nii.gz --thmin TT --sign abs --subject fsaverage --hemi lh --annot aparc \ --csd $FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/cortex/fwhmXX/abs/th20/mc-z.csd \ --vwsig vwsig.nii.gz --cwsig cwsig.nii.gz --fwhm fwhm.dat --mask mask.nii.gz --sum sum.dat Where TT is the voxel-wise threshold (cluster forming threshold), --sign abs means take positive or negative, XX is the FWHM (rounded up to next integer). The output vwsig is the volume corrected for voxel-wise significance, cwsig is the clusteriwise significance. doug On 3/12/13 8:35 PM, Rosa Lafer-Sousa wrote: > Hi Doug, I am analyzing data for two monkeys and I am under the > impression that I should be correcting each independently for every > contrast I generate. I also run stxgrinder-sess after I run > mkcontrast to generate the contrasts. Are the significance maps > yielded by these two steps constructed from uncorrected p-values? I > want to make sure I correct for multiple comparisons within each > voxel, and I assumed this was being taken care of internally by these > steps... if it is not, how would you suggest I go about doing so? > > thanks, > Rosa > > On Tue, Mar 12, 2013 at 3:26 PM, Douglas Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > Hi Rosa, it does not. Usually correction is done at the group > level. Do you need to do it on an individual? > doug > > > On 3/12/13 6:27 PM, Rosa Lafer-Sousa wrote: >> Hi freesurfers! >> >> I am curious about corrections for multiple comparisons. I use >> mkcontrast to generate my statistical maps and am curious if the >> function provides any internal corrections for multiple comparisons >> >> Does mkcontrast-sess correct for multiple comparisons? If so, how? >> >> thank you, >> Rosa >> >> -- >> Rosa Lafer-Sousa >> Lab Manager, Conway Lab >> Wellesley College - Neuroscience >> 106 Central Street >> Wellesley, MA >> >> Harvard Medical School -Neurobiology >> 220 Longwood Ave >> WAB Rm 215 >> Boston, MA 02115 >> >> 210-325-3185 >> rlaferso(a)wellesley.edu <mailto:rlaferso@wellesley.edu> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@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. > > > > > -- > Rosa Lafer-Sousa > Lab Manager, Conway Lab > Wellesley College - Neuroscience > 106 Central Street > Wellesley, MA > > Harvard Medical School -Neurobiology > 220 Longwood Ave > WAB Rm 215 > Boston, MA 02115 > > 210-325-3185 > rlaferso(a)wellesley.edu <mailto:rlaferso@wellesley.edu>

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does mkcontrast-sess correct for multiple comparisons?
by Rosa Lafer-Sousa 12 Mar '13

12 Mar '13

Hi freesurfers! I am curious about corrections for multiple comparisons. I use mkcontrast to generate my statistical maps and am curious if the function provides any internal corrections for multiple comparisons Does mkcontrast-sess correct for multiple comparisons? If so, how? thank you, Rosa -- Rosa Lafer-Sousa Lab Manager, Conway Lab Wellesley College - Neuroscience 106 Central Street Wellesley, MA Harvard Medical School -Neurobiology 220 Longwood Ave WAB Rm 215 Boston, MA 02115 210-325-3185 rlaferso(a)wellesley.edu

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