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30132 discussions

Gradient Inhomogeneity Correction in Bay3
by Chinappen, Dhinakaran Maheswaran 06 Mar '19

06 Mar '19

Dear Freesurfer community, We acquired images in Bay3 and would like to know where the gradient inhomogeneity correction files would be on cluster, if any. We are familiar with the Bay4 procedure for correcting for inhomogeneity and were also wondering if similar steps would be followed for images acquired in Bay3. Thank you! Dhinakaran. -- Dhinakaran M. Chinappen Clinical Research Coordinator Neurology Department Massachusetts General Hospital m: 1-267-257-1224

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mri_segstats issue with hippocampal subfields
by Daniel Callow 06 Mar '19

06 Mar '19

External Email - Use Caution Hello, I am trying to extract stats from the hippocampal subfield volumes that I have warped to diffusion space. mri_vol2vol --mov /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./lowb.nii.gz --targ /Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/mri/lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz --inv --interp nearest --o /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./lhipp2diff.nii.gz --reg /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./register.dat --no-save-reg Then I run mri_segstats --seg /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./lhipp2diff.nii.gz --ctab /Applications/freesurfer/FreeSurferColorLUT.txt --id 550 --id 552 --id 556 --id 557 --id 558 --i /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./fa-masked.nii.gz --sum ${SUBJECTS_DIR}/${subj}.${cond}./stats/lhipp.fa.stats using the --i id# from FreeSurferColorLUT.txt. However, looking at the values of the hippocampal subfield volume I see that the Id's are all in the 200's? Is there a txt file that has the labelings like in FreeSurferColorLUT.txt for these hippocampal subfields? Thank you for any help you can provide! *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

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extracting cortical parcellation
by Atena Rezaei 06 Mar '19

06 Mar '19

External Email - Use Caution Hello, I am trying to extract the cortical parcellation(atlas) file from freesurfer with all the labels. I found the lh.aparc.annot file in label folder. Should I use mri_annotation2label to create labels? or how can I extract the whole file? Thanks for ur help! BR, Atena

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(no subject)
by Jahan, Bushra 06 Mar '19

06 Mar '19

Hello - I'm wondering how to generate a label in FreeSurfer from peak activation in a cluster? Is there a specific command?

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Whitening/weighting matrix in FSFAST
by Zhi Li 06 Mar '19

06 Mar '19

External Email - Use Caution Hello Freesurfer Experts, May I ask if there is a whitening/weighting matrix used to give weighted least squares estimates (WLS) and whiten the data during the 1st-level model estimation in FSFAST? If so, how could I get it? Many thanks and kind regards, Lizhi

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Group analysis
by Hengameh Marzbani 06 Mar '19

06 Mar '19

External Email - Use Caution Hi Freesurfers, I want to do group analysis on four groups and use the volume values in aseg,stats. 1- Is it correct that each subcortical segmentation is based on a "volumetric segmentation atlas" created by Freesurfer? 2- Are the volume values expressed in the space of this atlas? 3- Can I compare these absolute values between 4 groups ? 4- Should I apply correction to the volume measures by eTIV (also called ICV)? Thanks you in advance! Best regards, Hengameh

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citing freesurfer
by Daniel Callow 06 Mar '19

06 Mar '19

External Email - Use Caution Hello, How should I go about properly citing freesurfer if I am using dt_recon for dti analysis? Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

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Choroid plexus analysis
by Benjamin Luerweg 06 Mar '19

06 Mar '19

External Email - Use Caution Dear community, anyone out there who can give me some information regarding how valid a volume detection of the choroid plexus is? I used fs 6.0. Kind regards, Ben

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curved reformat image....
by Gonzalo Rojas Costa 06 Mar '19

06 Mar '19

External Email - Use Caution Hi: How can I get in an automatic way curved reformat images (for example, see paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5009174/) Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl http://www.aribrain.info https://scholar.google.com/citations?user=LO7LZ3oAAAAJ https://www.researchgate.net/profile/Gonzalo_Rojas2 https://cl.linkedin.com/in/gonzalorojascosta

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mris_ca_label: assignment of emty surface to wrong label
by Jörg Stadler 06 Mar '19

06 Mar '19

External Email - Use Caution Hi, I transfered the SPM Anatomy Toolbox (http://www.fz-juelich.de/inm/inm-1/DE/Forschung/_docs/SPMAnatomyToolbox/SPM…) from Collin space to fsaverage using Wu J, Ngo GH, Greve DN, Li J, He T, Fischl B, Eickhoff SB, Yeo BTT. *Accurate nonlinear mapping between MNI volumetric and FreeSurfer surface coordinate systems* <http://people.csail.mit.edu/ythomas/publications/2018VolSurfMapping-HBM.pdf>, /Human Brain Mapping/ 39:3793–3808, 2018. mris_seg2annot --seg rh_Anatomy_v22c.nii.gz --ctab-auto Anatomy_v22c --s fsaverage --hemi rh --o rh.anat_v22c mris_seg2annot --seg lh_Anatomy_v22c.nii.gz --ctab-auto Anatomy_v22c --s fsaverage --hemi lh --o lh.anat_v22c This gave me the annot files for fsaverage (annotation.png) and a template for the color lookup table. Training of the classifier: mris_ca_train -t Anatomy_v22c_LUT.txt lh lh.sphere.reg anat_v22c.annot fsaverage lh.Anatomy_v22c.gcs mris_ca_train -t Anatomy_v22c_LUT.txt rh rh.sphere.reg anat_v22c.annot fsaverage rh.Anatomy_v22c.gcs Transfer to individual subject fsaverage: mris_ca_label fs_average lh sphere.reg lh.Anatomy_v22c.gcs Anatomy_v22c.annot mris_ca_label fs_average rh sphere.reg rh.Anatomy_v22c.gcs Anatomy_v22c.annot Now the miracle occurred and the whole surface got labeled. (mris_ca_label.png) How can a keep unassigned regions unlabeled? Joerg

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