Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

A question on mis-classified cortical gray matter
by caoaize 21 Jul '10

21 Jul '10

Hello FreeSurfer Experts, I met a problem on cortex gray matter segmentation. In my case, a small part of gray matter is lost, i.e. they are classifed as CSF but not gray matter. I attached a picture here, where the problem area is highlighted by blue circle. Does someone have experience on how to check and improve cortex area segmentation? Can I manually editing? Any feedback will be very appreciated. Aize _________________________________________________________________ MSN十年回馈，每位用户可免费获得价值25元的卡巴斯基反病毒软件2010激活码，快来领取！ http://kaba.msn.com.cn/?k=1

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Creating aparc.a2009s+aseg.mgz for the averaged data
by liang wang 19 Jul '10

19 Jul '10

Hi, When I use make_average_subject to generate an average data, I can't find aparc.a2009s+aseg.mgz within the new average/mri. To get common parcellation to all subjects, I need to create this file. I understand that " mri_aparc2aseg --s average --a2009s " enable to perform what I want. However, when running this command, a error message shows up "ERROR: cannot find /drive3/Stammer/Thickness/average/mri/ribbon.mgz". As displayed by this message, I did not find the ribbon.mgz file. I don't konw how to figure out this problem. Any suggestions? By the way, my make_average_surface file is updated by Nick's new one. And it does not include ribbon.mgz before updating. Liang -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wanglbit(a)gmail.com

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2009 Destrieux Parcellation on pre 4.5 recons
by Michael Waskom 19 Jul '10

19 Jul '10

Hi Experts, Is there any reason one should not generate the 2009 Destriuex parcellation for brains that were recon-ned with earlier versions of Freesurfer? (ie using recon-all with -cortparc2 and -parcstats2 while in the 4.5 environment) Thanks! Cheers, Mike

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Grey matter discrepancy between mris_anatomical_stats and sum of lh/rh.aparc.stats
by Matthew Ku 19 Jul '10

19 Jul '10

Dear Freesurfer Experts, When in the process of analyzing grey matter volumes, I have found that the totals from the summing of the lh.aparc.stats and rh.aparc.stats do not match with the total grey matter volume found from the mris_anatmoical_stats command. Does anyone know which value is more accurate in terms of grey matter volume? Thanks, _________________________________________ Matthew Ku University of Pennsylvania School of Engineering Class of 2013 (845) 596-3840 mattku(a)seas.upenn.edu

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ROI with mri_label2vol
by Arslan, Ali 19 Jul '10

19 Jul '10

Hi, I'm trying to create a ROI of V1 from the labels (for each hemisphere) I defined. I was able to create an volume with the command below mri_label2vol --label $SUBJ/label/lh.v1.ali.label --label $SUBJ/label/rh.v1.ali.label --temp $SUBJ/mri/T1.mgz --reg $SUBJ/stats/register.dat --fillthresh 0.5 --o $SUBJ/ROI/test_v1_T_000.bshort What I want are these 1) This command gives me an ROI which includes the gray matter but I want a smoother ROI which also has some nearby white matter voxels so that I make sure ROI doesn't leave any V1 voxel out for my functional analysis later on. I looked at the --proj flag for this but couldn't find any explanation about it. Would it help me about this? Where can I find more information about it? Would changing --labvoxvol make sense? 2) The resulting ROI is not binary and I would like to make it so (actually left and right hemispheres are in different densities, e.g. one seems lighter and the other one is darker in my viewer). Can I output the volume as binary from mri_label2vol or should I convert it later on (and how)? Best, Ali

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fsaverage label into MNI mask
by Esther Walton 19 Jul '10

19 Jul '10

Hi, I want to turn a fsaverage-label (lh.DLPFC.label) into a mask (nifti) in MNI space and used these two commands: 1) To turn the label into a volume (within $SUBJECTS_DIR): mri_label2vol --label lh.DLPFC.label --subject fsaverage --temp ./fsaverage/mri/brainmask.mgz --o left_DLPFC_july19b.nii.gz --identity 2) To turn the DLPFC nifti into MNI space: mri_vol2vol --mov left_DLPFC_july19b.nii.gz --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --o left_DLPFC_MNI_july19b.nii.gz --interp nearest --reg $FREESURFER_HOME/average/mni152.register.dat However, even though the final output file is in MNI, the ROI doesn't align with the MNI152 brain. Could it be that the FSL and the FS MNI152 brain are not the same and therefore the registration file is not the right one to use? Thanks for your help, Esther _________________________________________________________________ The New Busy think 9 to 5 is a cute idea. Combine multiple calendars with Hotmail. http://www.windowslive.com/campaign/thenewbusy?tile=multicalendar&ocid=PID2…

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Extracting fMRI time course and computing correlations among them
by liang wang 19 Jul '10

19 Jul '10

Hi, Does anyone know one of studies which uses the parcellations (aparc or aparc.a2009s) Freesurfer provides to extract fMRI time course from each subject's fMRI data. Reading the instructions in Freesurfer Wiki, I know how to do that. However, I am not sure whether I should use the parcellations from the average output (obtained from make_average_subject), or the parcellations based on each subject. I would next compute functional connectivity between these regions. I am appreciated for any suggestions. Liang -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wanglbit(a)gmail.com

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Any suggestions for imaging parameters on a GE 3T with 8 channel head coil
by Mira Michelle Raman 19 Jul '10

19 Jul '10

Hi Freesurfers, We would like to optimize the 'Freesurferability' of images for a new project involving fidgety young children. Ideally, the structural scan time will be under 5 minutes. We have a GE Signa 3T MR750, with an 8-channel head coil. Preliminary experiments have found two short structural scan options, but both require some intervention after autorecon2 in the Freesurfer pipeline. Does anyone have a suggestion for a sequence that a) runs in under 5 minutes b) freesurfs with minimal intervention and c) that they would be kind enough to share. Thank you in advance, Mira ____________________________________________________ Mira Michelle Raman Scientific Programmer Center for Interdisciplinary Brain Sciences Research Stanford University 401 Quarry Rd. Stanford, CA 94305 (650)498-4620

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recon-all -make all -s (subject) ERROR
by aekairys＠umich.edu 19 Jul '10

19 Jul '10

Hi freesurfers, I just got this error while continuing processing of a subject: mri_average: MRIread(/PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/cor-2.img) failed Linux titan 2.6.18-128.el5 #1 SMP Wed Dec 17 11:41:38 EST 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Mon Jul 19 09:52:39 EDT 2010 make: *** [/PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/rawavg.mgz] Error 1 Any suggestions would be greatly appreciated thanks best, Anson K. (freesurfer rookie)

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unknown region in aparc+aseg
by Deniz Ozgen 19 Jul '10

19 Jul '10

Hello All, Looking at aparc+aseg of some subjects we see some regions of the cortex labeled as "unknown" especially in the medial region / temporal lobe, close to amygdala. Additionally, around these regions there are some regions of the cortex that are not labeled at all. We see this on images acquired on both 1.5T and 3T magnets, with poor and good SNR. I was wondering what this "unknown" regions refer to, and if there is a way to fix this (using control points, or manual editing etc.) Thanks in advance. Deniz

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