Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

TRACULA problems
by Koubiyr, Ismail 01 Jul '16

01 Jul '16

Hi everyone, It’s been two weeks that I’ve been facing some issues with Tracula. I hope you could help me with that. I run trac-all -prep -c on some DICOM files but I had the following error : WARNING: file /Users/ismailkoubiyr/Documents/PFE/Tracula/dti/SER_5/MR.1.2.826.0.1.3680043.6.8878.22551.20150806120704.648.1017 does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header I also tried to de-mosiac the DICOMs, it gave me the same error. Then I converted the DICOMs into NIFTI, which allowed me not to get this error but something else weird happened. Now I get : ERROR: fMRIframe: frame >= nframes I checked the bvecs and bvals files, they seem normal, no additional space, but when the new bvecs and bvals are created, they seem messed up. I will attach you all the bvecs and bvals I used and the ones I get too. Ideally, the DICOMs should work fine but I have no idea why I get these errors. The bvecs and bvals are obtained from dcm2nii and then corrected to avoid any additional space. Thank you in advance for your help. Best, Ismail P.S : 3T2_bvecs.txt and 3T2_bvals.txt are the original files used.

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dynamic monitor: freesurfer jobs on the Open Science Grid
by Krieger, Donald N. 01 Jul '16

01 Jul '16

For those who are interested, we have deployed a crude dynamic monitor for freesurfer jobs running on the Open Science Grid. It can be viewed at http://xd-login.opensciencegrid.org/scratch/donkri/fsurfPoll.html . The display information is in addition to that which is currently accessible via "fsurf list" . Each job runs in a sequence of three steps. The second step runs in parallel as two separate OSG jobs. These are your "recon-all -autorecon2" jobs. At the lower right corner of the webpage, the number of jobs for each user at each step is listed. Best - Don

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Intensity normalization issues leading to improper segmentation
by Elodie Cauvet 01 Jul '16

01 Jul '16

Dear Freesurfer list, Maybe I am hoping for a miracle with my question, but I am bit desperate after unsuccessfully trying things around for over a year. In a nutshell, I need advice on the intensity normalization options. We have T1 data from twins (8-25years) acquired on a 3T MR750 GE scanner with a 32 channel coil (IR-FSPGR 3D volume). This coil has a huge problem in a field inhomogeneity resulting in strong occipital hypersignal and frontal hyposignal, from which I believe all my problems originate. - The standard pipeline provide an incomplete temporal and frontal segmentation (white and pial surfaces do not include enough) while over including in occipital and parietal. - We tried using the watershed 40 value from the skulltrip to get more of the occipital (we had a few subjects having holes in occipital within the brain segmentation). This option changed also the segmentation resulting in better segmentation for temporal and frontal but worse in parietal and occipital. - We tried control points as well, without success (as you can imagine due to the fronto-occipital inhomogeneity). We also tried manually removing extra voxels from the white surface to correct it. But unfortunately, this is not an option because we have about 200 scans to process. - We tried using N4 intensity bias correction on the raw images before feeding it to freesurfer, but the segmentation did not run through for all participants (stuck in fixing topology for more than a week) and for those working, the pial surface did not include enough grey matter. I am now thinking about playing with the option of intensity normalization (mri_ca_normalize) within freesurfer but would like to have your expert opinion on that before roaming. Any advice on how to set up mri_ca_normalize to retrieve a good white matter homogeneity? Or any other functions I should be playing around with? Thanks a lot in advance for your help, Kind regards, Élodie Élodie CAUVET | PhD Karolinska Institutet Center of Neurodevelopmental Disorders (KIND) Gävlegatan 22B, floor 8 | 113 30 Stockholm +46 (0)8 514 527 10 | +46 (0)728 774 058 elodie<https://email.ki.se/owa/redir.aspx?C=IoHR3hOTXk-47Iiqw9Fmhe3QF6jM79EIy3qtnp…>.cauvet(a)ki.se<https://email.ki.se/owa/redir.aspx?C=IoHR3hOTXk-47Iiqw9Fmhe3QF6jM79EIy3qtnp…> http://ki.se/en/kind/startpage<https://email.ki.se/owa/redir.aspx?C=IoHR3hOTXk-47Iiqw9Fmhe3QF6jM79EIy3qtnp…> http://elodiecauvet.wordpress.com/<https://email.ki.se/owa/redir.aspx?C=IoHR3hOTXk-47Iiqw9Fmhe3QF6jM79EIy3qtnp…> Karolinska Institutet – a medical university

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Re: [Freesurfer] FSFAST- Cerebellum
by Thomas Yeo 01 Jul '16

01 Jul '16

Hi Sabin, The idea is to use the freesurfer left and right cerebellar masks to make the Buckner parcellation. Your steps seem roughly correct but the names of your variables seem to change from one section to another, so I can't be sure. Regards, Thomas On Friday, 1 July 2016, Sabin Khadka <mr.sabinkhadka(a)gmail.com> wrote: > Hi Thomas- Thanks for reply. > > Sorry for not being clear on the previous email. I want extract values > from Buckner et al 2011 defined 7 regions (network) for left and right > hemisphere separately. Wondering if I am in correct direction if I do > **** > mri_binarize --i FSSub/mri/aparc.a2009s+aseg.mgz --match 8 --o > cerebellum_left_mask_FSSub.nii.gz : For left regions > & > mri_binarize --i FSSub/mri/aparc.a2009s+aseg.mgz --match 47 --o > cerebellum_right_mask_FSSub.nii.gz : For right regions > ***** > fslmaths Buckner2011_atlas_FSSub.nii.gz -mas > cerebellum_mask_FSSub_m8.nii.gz Buckner_atlas_FSSub_m8 # For left > fslmaths Buckner2011_atlas_FSSub.nii.gz -mas > cerebellum_mask_FSSub_m47.nii.gz Buckner_atlas_FSSub_m47 # For right > ***** > and use > mri_segstats --seg Buckner_atlas_FSSub_m8.nii.gz --ctab > $FREESURFER_HOME/average/YeoJNeurophysiol11_MNI152/Yeo2011_7Networks_ColorLUT.txt > --excludeid 0 --i fmcpr.anat.nii.gz --avgwf Cerebellum_networks_L.txt > mri_segstats --seg Buckner_atlas_FSSub_m47.nii.gz --ctab > $FREESURFER_HOME/average/YeoJNeurophysiol11_MNI152/Yeo2011_7Networks_ColorLUT.txt > --excludeid 0 --i fmcpr.anat.nii.gz --avgwf Cerebellum_networks_R.txt > > to extract values. > > Again, thanks for all your help and input. > > Cheers, > Sabin Khadka > > On Thu, Jun 30, 2016 at 3:40 PM, Thomas Yeo <ythomas(a)csail.mit.edu > <javascript:_e(%7B%7D,'cvml','ythomas(a)csail.mit.edu');>> wrote: > >> Hi Sabin, >> >> You can try to combine with FreeSurfer's segmentation of left and right >> cerebellum. >> >> --Thomas >> >> On Thu, Jun 30, 2016 at 7:59 PM, Sabin Khadka <mr.sabinkhadka(a)gmail.com >> <javascript:_e(%7B%7D,'cvml','mr.sabinkhadka(a)gmail.com');>> wrote: >> >>> Hi Thomas, >>> >>> Yes, I think I got it working. I forgot to put --seg in my command line >>> which is my the ERROR: segmentation volume needed to be specified error. I >>> did following and gave me average time series from each region (or Network) >>> mri_segstats --seg Buckner_atlas_FSSub.nii.gz --ctab >>> $FREESURFER_HOME/average/YeoJNeurophysiol11_MNI152/Yeo2011_17Networks_ColorLUT.txt >>> --excludeid 0 --i fmcpr.anat.nii.gz --avgwf test.txt >>> >>> >>> Yes, I did overlay Buckner_atlas_FSSub.nii.gz over subject's >>> aparc.a2009s+aseg.mgz and I assumed it looked fine. Please see below for >>> freeview screenshot below (with and without overlay) >>> >>> However, I have a followup question. If I want to get the network values >>> separately for >>> >>> mri_binarize --i FSSub/mri/aparc.a2009s+aseg.mgz --match 8 --o >>> cerebellum_left_mask_FSSub.nii.gz : For left regions >>> & >>> mri_binarize --i FSSub/mri/aparc.a2009s+aseg.mgz --match 47 --o >>> cerebellum_right_mask_FSSub.nii.gz : For right regions >>> >>> and follow other steps for each mask? >>> >>> >>> >>> >>> without overlay >>> >>> [image: Inline image 1] >>> with overlay >>> >>> [image: Inline image 2] >>> >>> >>> Thanks for your help. >>> >>> >>> Cheers, >>> Sabin Khadka >>> >>> On Thu, Jun 30, 2016 at 11:29 AM, Thomas Yeo <ythomas(a)csail.mit.edu >>> <javascript:_e(%7B%7D,'cvml','ythomas(a)csail.mit.edu');>> wrote: >>> >>>> Hi Sabin, >>>> >>>> I think fslmeants should work. But you might need to first run >>>> mri_binarize to convert Buckner_atlas_FSSub.nii.gz into individual >>>> ROIs. >>>> >>>> Also can you tell us which step generated the error "ERROR: must >>>> specify a segmentation volume"? Is this the final step? Have you tried >>>> overlaying Buckner_atlas_FSSub.nii.gz onto your individual subject in >>>> freeview to check that the previous steps have worked? >>>> >>>> Thanks, >>>> Thomas >>>> >>>> On Mon, Jun 27, 2016 at 6:53 PM, Sabin Khadka <mr.sabinkhadka(a)gmail.com >>>> <javascript:_e(%7B%7D,'cvml','mr.sabinkhadka(a)gmail.com');>> wrote: >>>> > Hi Thomas- On second thought is it valid to simply do if I want >>>> average time >>>> > series of the cerebellum regions? >>>> > >>>> > fslmeants -i fmcpr.anat.nii.gz -m Buckner_atlas_FSSub.nii.gz >> >>>> > avgCerebellum.txt >>>> > >>>> > Is this correct? >>>> > >>>> > >>>> > Cheers, >>>> > Sabin Khadka >>>> > >>>> > On Mon, Jun 27, 2016 at 11:36 AM, Sabin Khadka < >>>> mr.sabinkhadka(a)gmail.com >>>> <javascript:_e(%7B%7D,'cvml','mr.sabinkhadka(a)gmail.com');>> >>>> > wrote: >>>> >> >>>> >> Hi Thomas and Doug- >>>> >> >>>> >> Thanks for you suggestions. Per your suggestions I performed >>>> following >>>> >> >>>> >> recon-all -i >>>> >> >>>> $FREESURFER_HOME/average/Yeo_JNeurophysiol11_MNI152/FSL_MNI152_FreeSurferConformed_1mm.nii.gz >>>> >> -subjid Yeo2011_MNI152_FS >>>> >> >>>> >> recon-all -no-isrunning -autorecon-all -subjid Yeo2011_MNI152_FS >>>> >> >>>> >> mri_vol2vol --mov >>>> >> >>>> $FREESURFER_HOME/average/Buckner_JNeurophysiol11_MNI152/Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz >>>> >> \ >>>> >> --s Yeo2011_MNI152_FS --targ $FREESURFER_HOME/average/mni305.cor.mgz >>>> --m3z >>>> >> talairach.m3z --o BucknerAtlas1mm_FSL.nii.gz --nearest >>>> >> >>>> >> mri_vol2vol --mov $SUBJECTS_DIR/FSSub/mri/norm.mgz --s FSSub --targ >>>> >> BucknerAtlas1mm_FSL.nii.gz --m3z talairach.m3z --o >>>> >> Buckner2011_atlas_FSSub.nii.gz --nearest --inv-morph >>>> >> >>>> >> mri_binarize --i FSSub/mri/aparc.a2009s+aseg.mgz --match 8 --match >>>> 47 --o >>>> >> cerebellum_mask_FSSub.nii.gz >>>> >> >>>> >> fslmaths Buckner2011_atlas_FSSub.nii.gz -mas >>>> cerebellum_mask_FSSub.nii.gz >>>> >> Buckner_atlas_FSSub >>>> >> >>>> >> mri_vol2vol --mov fmcpr.nii.gz --fstarg --reg register.dof6.dat --o >>>> >> fmcpr.anat.nii.gz >>>> >> >>>> >> mri_segstats --i Buckner_atlas_FSSub.nii.gz --i fmcpr.anat.nii.gz >>>> --avgwf >>>> >> test.txt >>>> >> >>>> >> However, I got the following error >>>> >> ERROR: must specify a segmentation volume >>>> >> >>>> >> Am I doing anything wrong here. Do you have any suggestions/fixes? >>>> >> >>>> >> >>>> >> Cheers, >>>> >> Sabin Khadka >>>> >> >>>> >> On Fri, Jun 24, 2016 at 6:30 AM, Thomas Yeo <ythomas(a)csail.mit.edu >>>> <javascript:_e(%7B%7D,'cvml','ythomas(a)csail.mit.edu');>> wrote: >>>> >>> >>>> >>> Hi Doug, thanks. >>>> >>> >>>> >>> Hi Sabin, you can use the following steps to transform the Buckner >>>> >>> cerebellum atlas to your subject's native anatomical space and then >>>> >>> follow Doug's instructions (taken and adapted from another user >>>> >>> Bronwyn's email): >>>> >>> >>>> >>> 1. Run MNI152 1mm template through recon-all >>>> >>> recon-all -i FSL_MNI152_FreeSurferConformed_1mm.nii -subjid >>>> >>> Yeo2011_MNI152_FS >>>> >>> >>>> >>> 2. Warp the Buckner_atlas1mm.nii.gz (use the LooseMask) to >>>> freesurfer >>>> >>> nonlinear volumetric space >>>> >>> mri_vol2vol --mov BucknerAtlas1mm.nii --s Yeo2011_MNI152_FS --targ >>>> >>> $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o >>>> >>> BucknerAtlas1mm_FSI.nii.gz --nearest >>>> >>> >>>> >>> 3. warp the BucknerAtlas1mm_FSI.nii.gz from freesurfer nonlinear >>>> >>> volumetric space to each subject: >>>> >>> mri_vol2vol --mov $SUBJECTS_DIR/subjID/mri/norm.mgz --s subjID >>>> --targ >>>> >>> BucknerAtlas1mm_FSI.nii.gz --m3z talairach.m3z --o >>>> >>> Buckner2011_atlas_subjID.nii.gz --nearest --inv-morph >>>> >>> >>>> >>> 4. Create a cerebellum gray matter mask in the native subject's >>>> space >>>> >>> by applying mri_binarize to aparc+aseg.mgz of the subject >>>> >>> mri_binarize --i subjID/mri/aparc+aseg.mgz --match 8 --match 47 --o >>>> >>> cerebellum_mask_subjID.nii.gz >>>> >>> >>>> >>> 5. Using this mask to mask the Buckner cerebellum parcellations >>>> >>> fslmaths Buckner2011_atlas_subjID.nii.gz -mas >>>> >>> cerebellum_mask_subjID.nii.gz Buckner_atlas_subjID_mask.nii.gz >>>> >>> >>>> >>> Regards, >>>> >>> Thomas >>>> >>> >>>> >>> On Fri, Jun 24, 2016 at 4:47 PM, Douglas Greve >>>> >>> <greve(a)nmr.mgh.harvard.edu >>>> <javascript:_e(%7B%7D,'cvml','greve(a)nmr.mgh.harvard.edu');>> wrote: >>>> >>> > yes >>>> >>> > >>>> >>> > >>>> >>> > >>>> >>> > On 6/24/16 9:19 AM, Thomas Yeo wrote: >>>> >>> >> >>>> >>> >> Hi Doug, >>>> >>> >> >>>> >>> >> Would your mri_segstats command work if instead of aseg.mgz, >>>> Sabin >>>> >>> >> passed in the cerbellum parcellation in the same anatomical >>>> space as >>>> >>> >> aseg? >>>> >>> >> >>>> >>> >> --Thomas >>>> >>> >> >>>> >>> >> On Thu, Jun 23, 2016 at 11:28 PM, Douglas Greve >>>> >>> >> <greve(a)nmr.mgh.harvard.edu >>>> <javascript:_e(%7B%7D,'cvml','greve(a)nmr.mgh.harvard.edu');>> wrote: >>>> >>> >>> >>>> >>> >>> After you run preproc-sess, there will be a file called >>>> >>> >>> register.dof6.dat. >>>> >>> >>> Map fmri into the anatomical space, something like >>>> >>> >>> >>>> >>> >>> mri_vol2vol --mov fmcpr.nii.gz --fstarg --reg register.dof6.dat >>>> --o >>>> >>> >>> fmcpr.anat.nii.gz >>>> >>> >>> >>>> >>> >>> Then use mri_segstats with --seg aseg.mgz --i fmcpr.anat.nii.gz >>>> >>> >>> >>>> >>> >>> However, I don't think that the aseg has those cerebellum >>>> >>> >>> parcellations. >>>> >>> >>> >>>> >>> >>> On 6/21/16 5:52 PM, Sabin Khadka wrote: >>>> >>> >>> >>>> >>> >>> Hi Yeo- Thanks very much for your answer. Yes the data is in >>>> mni305 >>>> >>> >>> space. I >>>> >>> >>> process my fmri data with >>>> >>> >>> >>>> >>> >>> preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh >>>> -mni305 >>>> >>> >>> -fwhm 6 >>>> >>> >>> -per-run -stc odd >>>> >>> >>> and then to extract ROI time series values I did >>>> >>> >>> >>>> >>> >>> mri_segstats --annot fsaverage rh aparc --i >>>> >>> >>> rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz --excludeid >>>> 2000 >>>> >>> >>> --excludeid 2004 --avgwf CorticalTimeSeries_rh.txt >>>> >>> >>> >>>> >>> >>> and for cortical time series >>>> >>> >>> >>>> >>> >>> mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab >>>> >>> >>> /opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id 12 >>>> --id >>>> >>> >>> 13 >>>> >>> >>> --id >>>> >>> >>> 17 --id 18 --id 26 --id 49 --id 50 --id 51 --id 52 --id 53 --id >>>> 54 >>>> >>> >>> --id >>>> >>> >>> 58 >>>> >>> >>> --i rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz --avgwf >>>> >>> >>> subCorticalTimeSeries.txt >>>> >>> >>> >>>> >>> >>> Now I am not sure as how to extract cerebellum ROIs (time >>>> series as >>>> >>> >>> described in Buckner et.al 2011)? If there are any other >>>> additional >>>> >>> >>> steps >>>> >>> >>> I >>>> >>> >>> need to perform ? or if I have to use some other scripts >>>> commands >>>> >>> >>> (other >>>> >>> >>> than mri_segstats). >>>> >>> >>> >>>> >>> >>> >>>> >>> >>> Cheers, >>>> >>> >>> Sabin Khadka >>>> >>> >>> >>>> >>> >>> On Mon, Jun 20, 2016 at 10:20 PM, Thomas Yeo < >>>> ythomas(a)csail.mit.edu >>>> <javascript:_e(%7B%7D,'cvml','ythomas(a)csail.mit.edu');>> >>>> >>> >>> wrote: >>>> >>> >>>> >>>> >>> >>>> Hi Sabin, >>>> >>> >>>> >>>> >>> >>>> The structures 601-628 FreeSurferCololLUT.txt correspond to >>>> >>> >>>> anatomical >>>> >>> >>>> substructures of the cerebellum (e.g., Crus I, etc). Is that >>>> what >>>> >>> >>>> you >>>> >>> >>>> want? Or are you looking to use the functional parcels defined >>>> in >>>> >>> >>>> Buckner 2011? >>>> >>> >>>> >>>> >>> >>>> In addition, I do not know how mri_segstats works, so I cannot >>>> >>> >>>> verify >>>> >>> >>>> how you call the command is correct. Maybe others can provide >>>> >>> >>>> feedback >>>> >>> >>>> here. >>>> >>> >>>> >>>> >>> >>>> However, the Buckner cerebellar parcellations in >>>> >>> >>>> $FREESURFER_HOME/average/Buckner_JNeurophysiol11_MNI152/ is in >>>> >>> >>>> MNI152 >>>> >>> >>>> space. From your command, I assume your data is in MNI305 >>>> space. So >>>> >>> >>>> you might need to transform the parcellation from MNI152 to >>>> MNI305. >>>> >>> >>>> >>>> >>> >>>> Thanks, >>>> >>> >>>> Thomas >>>> >>> >>>> >>>> >>> >>>> On Sat, Jun 18, 2016 at 8:49 AM, Sabin Khadka >>>> >>> >>>> <mr.sabinkhadka(a)gmail.com >>>> <javascript:_e(%7B%7D,'cvml','mr.sabinkhadka(a)gmail.com');>> >>>> >>> >>>> wrote: >>>> >>> >>>>> >>>> >>> >>>>> Hi all, >>>> >>> >>>>> >>>> >>> >>>>> I am trying to extract mean time series BOLD data using >>>> FSFAST from >>>> >>> >>>>> Cortical >>>> >>> >>>>> ROIs + sub cortical ROIs and cerebellum. >>>> >>> >>>>> >>>> >>> >>>>> preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh >>>> -mni305 >>>> >>> >>>>> -fwhm >>>> >>> >>>>> 6 >>>> >>> >>>>> -per-run -stc odd mri_segstats --annot fsaverage lh aparc >>>> --i >>>> >>> >>>>> rest210/bold/001/fmcpr.odd.sm6.fsaverage.lh.nii.gz >>>> --excludeid 1000 >>>> >>> >>>>> --excludeid 1004 --avgwf CorticalTimeSeries_lh.txt >>>> >>> >>>>> mri_segstats --annot fsaverage rh aparc --i >>>> >>> >>>>> rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz >>>> --excludeid 2000 >>>> >>> >>>>> --excludeid 2004 --avgwf CorticalTimeSeries_rh.txt >>>> >>> >>>>> >>>> >>> >>>>> and for cortical time series >>>> >>> >>>>> >>>> >>> >>>>> mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab >>>> >>> >>>>> /opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id >>>> 12 --id >>>> >>> >>>>> 13 >>>> >>> >>>>> --id >>>> >>> >>>>> 17 --id 18 --id 26 --id 49 --id 50 --id 51 --id 52 --id 53 >>>> --id 54 >>>> >>> >>>>> --id >>>> >>> >>>>> 58 >>>> >>> >>>>> --i rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz --avgwf >>>> >>> >>>>> subCorticalTimeSeries.txt >>>> >>> >>>>> >>>> >>> >>>>> But I am not sure on how exactly to extract time series from >>>> >>> >>>>> cerebellar >>>> >>> >>>>> regions. So if I want to extract time series from regions as >>>> >>> >>>>> described >>>> >>> >>>>> in >>>> >>> >>>>> Buckner et.al 2011. Could I just use mri_segstats for the >>>> labels >>>> >>> >>>>> 601-628 >>>> >>> >>>>> in >>>> >>> >>>>> FreeSurferCololLUT.txt? If not could you please direct me to >>>> >>> >>>>> processes >>>> >>> >>>>> that >>>> >>> >>>>> I can use. >>>> >>> >>>>> >>>> >>> >>>>> Cheers, >>>> >>> >>>>> Sabin Khadka >>>> >>> >>>>> >>>> >>> >>>>> _______________________________________________ >>>> >>> >>>>> Freesurfer mailing list >>>> >>> >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> <javascript:_e(%7B%7D,'cvml','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 >>>> <javascript:_e(%7B%7D,'cvml','Freesurfer(a)nmr.mgh.harvard.edu');> >>>> >>> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>> >>> >>>> >>> >>> >>>> >>> >>> >>>> >>> >>> >>>> >>> >>> _______________________________________________ >>>> >>> >>> Freesurfer mailing list >>>> >>> >>> Freesurfer(a)nmr.mgh.harvard.edu >>>> <javascript:_e(%7B%7D,'cvml','Freesurfer(a)nmr.mgh.harvard.edu');> >>>> >>> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>> >>> >>>> >>> >>> >>>> >>> >>> >>>> >>> >>> _______________________________________________ >>>> >>> >>> Freesurfer mailing list >>>> >>> >>> Freesurfer(a)nmr.mgh.harvard.edu >>>> <javascript:_e(%7B%7D,'cvml','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 >>>> <javascript:_e(%7B%7D,'cvml','Freesurfer(a)nmr.mgh.harvard.edu');> >>>> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >> >>>> >> >>>> > >>>> >>> >>> >> >

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Freeview recon button
by Walid Yassin 30 Jun '16

30 Jun '16

Hello freesurfers, I downloaded freesurfer v5.3.0. & I am using freeview, but it doesn't have the Recon edit button. I saw that someone asked about this questions twice in the archive but was never answered. There was a note in the wiki page that reads "*Note*: Recon edit mode is only available in the most recent release of freeview". I thought that the most recent release of freeview comes with the most recent release of freesurfer. Can someone please let me know if there is a separate download link to the recent release of freeview? Thank you in advance, Also If someone can answer my previous question regarding the Gyrification i would really really appreciate it. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg47883.html Thank you again, Best regards, Walid

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Re: [Freesurfer] qdec load error missing BLT
by Antonin Skoch 30 Jun '16

30 Jun '16

Dear Joshua, we had the same problem with freeSurfer 5.3.0 on Debian GNU/Linux 8.3 (jessie). In our case this was warning, the qdec launched, however the fsgd plot functionality (interactive vertex-wise GLM plot display) did not work. It seems that the error is caused by interference of tk/blt libraries packaged with freeSurfer with those installed on the system. We were able to resolve this issue by uninstalling following installed packages: tk8.6-blt2.5 blt If this do not help to you, try to run strace -f qdec and inspect, which libraries are loaded during initialization on your system before the error is issued. Regards, Antonin Skoch

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REPOST: Skull Strip and Bad Surfaces
by Katherine Reiter 30 Jun '16

30 Jun '16

Dear FreeSurfer experts, I am working on a data set and am having particular difficulty with one subject. It appeared the skull strip was mistakenly removing occipital regions. These regions were absent from the brainmask, T1, and resulting surfaces. I attempted to solve this in 2 different ways. I first adjusted the watershed and reran the recon-all -autorecon2 in order to redraw the surfaces. Adjusting the watershed worked to include these regions in both the brainmask and T1 but the resulting surfaces hugely inaccurate (see the attached screenshot '4003_badsurfs_parietal_cerebellum2'; Oddly enough, the frontal surfaces are largely accurate but the parietal regions include gray matter in the white surface and even large amounts of the cerebellum, while excluding occipital regions. I then reran it from the raw dicoms and had the same issue with occipital regions being excluded so I adjusted the watershed and tried to manually fix the surfaces, but this resulted in similar inaccurate surfaces. See the second attached screenshot '4003_badsurfs'. ll surfaces are fairly messy, but some regions are more accurage, where the appears to distinguish between gray and white and other areas are over inclusive, but cerebellar and some superior and medial regions are excluded. Any and all help would be much appreciated. Thanks in advance! Kate Katherine Reiter, M.S. Clinical Psychology Doctoral Student Marquette University Phone: (414) 288-3807 Email: katherine.reiter(a)marquette.edu

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REPOST: Longitudinal Stream: Recon-all and template
by Tamara Tavares 30 Jun '16

30 Jun '16

Hello All, I am planning to run the longitudinal stream on my data set and I have a few questions: 1) When I run the data cross sectionally using "recon-all -all" should I specify all my subject's T1 volumes (using the -file1.nii -1file2.nii) or can I run each of my subject's T1 volumes individually through recon-all? My understanding is that some motion correction will occur if I specify more than one T1 which may alter the results versus if I specify one T1? 2) What input files should I use to create my base templates? Are the input files the norm.mgz files from each subject? Thank you in advance for your help! Best, Tamara

2 1

mean cortical thickness not equal to averaged ROIs cortical thickness
by Nabin Koirala 30 Jun '16

30 Jun '16

Hi freesurfer team, I extracted the cortical thickness values using aparcstats2table command and I got the cortical thickness values for 34 regions and mean cortical thickness for each hemisphere. But when I averaged the cortical thickness from those 34 regions regions it was different than the mean cortical thickness obtained by aparcstats2table. I would expect it to be the same or very close but I checked it for more than 100 subjects and they are significantly different. Am I missing something silly here ? Thank you. Regards, Nabin

3 5

Get a given point's ROI
by Yuan Lin 29 Jun '16

29 Jun '16

Dear FreeSurfer experts, I am a beginner to learn to use FreeSurfer. Now I have a question to be solved. I have gotten the reconstruction results of a subject after using the command recon-all. How can I know a given point belongs to which region of interest? For example, how can I know whether a give point belongs to the superior frontal or inferior temporal? Which commands should I use? Thank you so much. Best, Lin

2 3

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