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30088 discussions

small difference in recon-all for Ubuntu 11.10 and Centos 5.7
by Knut J Bjuland 06 Apr '12

06 Apr '12

Hi I used recon-all on two different system one with Ubuntu 11.10 and a cluster with Centos 5.7. When I compare the recon-all of these two recon-all run I see that there is a small difference. Is this difference caused by difference in math libraries, and difference in the way floating point is handle? Is there any way to get around this problem and get Freesurfer to behave is similar way on Centos 5.7 system as it did on the Ubuntu 11.10. Knut J

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aseg.mgz looks worse after longitudinal processing on 5.1
by Brain Apprentice 05 Apr '12

05 Apr '12

Hi Surfers, I have done some Longitudinal Processing on a bunch of subjects and although the pial and white surfaces are looking good after the Longitudinal Processing, the aseg segmentation for each subject is often looking much worse. I have attached a sample screen grab to show you what I mean. The images on top show the Longitudinal Processed views. The images on bottom are of the same subject before the Longitudinal Processing has occurred. It is possible I am doing something wrong. I just thought I would throw it out to the experts to see if they are having similar experiences or if there are suggestions on things that I should do. Thanks very much, B.A.

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Error on Step 3 of longitudinally process
by Brain Apprentice 05 Apr '12

05 Apr '12

Hi, I was wondering if I am doing something wrong when doing step 3 of the longitudinally process. The error I get is: ERROR: Template/base ID cannot be the same as a time point ID (in /shared/subjects/subjects/a-aut-v510/10022/base-tps) Here is the environment: -------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer510 FSFAST_HOME /usr/local/freesurfer510/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer510/subjects MNI_DIR /usr/local/freesurfer510/mni FSL_DIR /usr/local/fsl418 ---------- FreeSurfer variables reset ---------- SUBJECTS_DIR /shared/subjects/subjects/a-aut-v510 FSLOUTPUTTYPE NIFTI_GZ The command I am running is: recon-all -long 10022--01-24-06--0470 10022 -all The base-tps file is: 10022--01-24-06--0470 10022--03-14-06--0441 10022--04-14-08--0463 10022--04-25-06--0442 10022--07-25-06--0462 10022--08-26-10--0555 10022--10-21-06--0461 10022--11-20-08--0412 The <tpNid> is: 10022--01-24-06--0470 The <templateid> is: 10022 I am trying to follow the format listed on http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing however it still does not seem to work. Does anyone have any idea on what I need to do differently? Thank You in advance for any suggestions you might have. B.A.

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Cortical Thickness
by Nooshin Zadeh 05 Apr '12

05 Apr '12

Dear Freesurfer group I want to get cortical thickness, and I am confused between using these two command lines: mris_anatomical_stats -t subjid/surf<http://ads.clicksor.com/search.php?q=surf>/lh.thickness -b subjid lh that gives following information number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 110852 71971 0 0.000 0.000 0.168 0.133 5368 529.3 /Users/christine/Result_FS_Corrected/N219c/surf/lh.white and mris_anatomical_stats -t subjid/label/lh.cortex.label -b subjid lh that gives following information number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 110852 71971 0 0.000 0.000 0.168 0.133 5368 529.3 /Users/christine/Result_FS_Corrected/N219c/surf/lh.white. Can you please guide me which one is the right one for measuring cortical thickness? Why for both of them (mean+-STD) is zero? Thanks in advance. Best Regards --------------------------------------------------- Nooshin N. Zadeh Graduate Assistant Departments of Electrical Engineering and Neurology University of Miami ** * * * *

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Re: [Freesurfer] white matter hyper intensities
by Gregory Kirk 05 Apr '12

05 Apr '12

interestingly, in this case i think there may even be reason why white matter hyper intensities could be more common in our insular region of interest where we detected thinning. The disease is HIV and activated monocytes invade the perivascular spaces where they can cause inflamation, which the lit. seems to say can cause white matter hyper intensities. these virchow robin spaces are prominent around the insula and may in fact this may be the etiology of the changes there. so i guess i should try and tease apart which it is, maybe add flair imaging. thanks for the comments greg On 04/05/12, Bruce Fischl wrote: > Hi Greg, > > yes, that can happen where they are hyper-intense on T2 and hypo-intense on T1 and thus look like GM on the T1. It's not that common since they are usually deeper, but we have seen it. > > sorry > Bruce > > > On Wed, 4 Apr 2012, Gregory Kirk wrote: > > >a collaborator just got a grant review that claimed > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > >There's a possibility that changes in cortical thickness in > >the insula might be a consequence of lesions (MR-hyperintensities) in the white > >matter. > > > > > >i would think that white matter hyper intensities would tend to enhance freesurfers ability > >to detect the white matter/grey matter boundary rather than cause an error. > > > > > >any comments as to the correctness of my thinking would be appreciated. > > > > > >thank you > > > > > >greg > > > >_______________________________________________ > >Freesurfer mailing list > >Freesurfer(a)nmr.mgh.harvard.edu > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > _______________________________________________ > 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.

1 0

lobar WM volumes
by Inês Violante 05 Apr '12

05 Apr '12

Dear all, I need to obtain the white matter volume per lobe for a given numer of subjects. I started by using the following: mri_annotation2label --subject <subjid> --hemi rh --lobesStrict lobe mri_aparc2aseg --s <subjid> --labelwm --annot lobe and now I have a lobe+aseg.mgz file. How can I create a stats file containing the wm volume for each lobe? Thank you, ines

4 8

Qdec issue
by sonya kaur 05 Apr '12

05 Apr '12

Hi everyone, I realize I'm quickly becoming an annoyance, but I'm having trouble loading my data file into qdec. I keep getting the error: QdecDataTable::Load failed to tokenize string: on line 88 of HTN_FMRI_Qdec. HTN_FMRI_Qdec is the name of my data file. I do not even have a line 88 as I have only 86 subjects and 4 variables. Thank you! Sonya -- Sonya Kaur Clinical Psychology Graduate Student Department of Psychology The University of Texas, Austin 1 University Station, A8000 Austin, TX 78712 SEA 4.110E <sonya_kaur(a)mail.utexas.edu> sonya_kaur(a)mail.utexas.edu

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How to flatten time course on the cortex
by Kaveh Kohan 05 Apr '12

05 Apr '12

Hi FreeSurfer Users, I am new to the Freesurfer, I have a question regarding mapping of the resting state fMRI time courses on the cortex area. I apologise in case my question is naive. please bear with me: Is it possible to have time-courses sampled from cortex? I mean how can I get corresponding time-course for each vertex on the cortex ? I know that FreeSurfer can produce mask for cortex are but I would like to have time-courses on the flattened (2D) map; ie assuming that cortex is flattened, each pixel of the 2D flattened image which resides in the cortex (I guess it corresponds to a vertex on the cortex manifold?) is time-series. I have ran recon-all on the T1. All of those operation were done using a third party packages that uses freesurfer namely CMTK (http://cmtk.org) I do not exactly know how to use "bbregister" to register the parcellation on the resting-state fMRI image? I would be thankful if you can help. Thanks

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white matter hyper intensities
by Gregory Kirk 05 Apr '12

05 Apr '12

a collaborator just got a grant review that claimed There's a possibility that changes in cortical thickness in the insula might be a consequence of lesions (MR-hyperintensities) in the white matter. i would think that white matter hyper intensities would tend to enhance freesurfers ability to detect the white matter/grey matter boundary rather than cause an error. any comments as to the correctness of my thinking would be appreciated. thank you greg

3 2

Stylus Input for Cortical Edits
by Jeff Stout 05 Apr '12

05 Apr '12

Hi All, We have a large number of subjects that need minor edits (orbital frontal cortex/eye issues subcortical parcellation etc.). To speed up the process I was wondering if a stylus input would help with the editing. Do the graphics tablets (stylus input) work with freesurfer editing? Do they end up being useful or is it not worth investing in? And if so, could someone recommend a brand (wacom?) that would work with Ubuntu 10.04 (or just linux in general). Thank you, Jeff Stout

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