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mris_divide_parcellation for white matter
by Corinna Bauer 07 Jul '14

07 Jul '14

hello, I was wondering if it was possible to use mris_divide_parcellation on white matter labels. Thanks, Corinna

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longitudinal freesurfer error
by Salil Soman 07 Jul '14

07 Jul '14

Hi, I have followed the steps in the longitudinal qdec tutorial ( https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel) but when I try to analyze longitudinal features such as long.thickness-rate I get an error: Error in analyze: Couldn't open /SUBJECTS_DIR/SUBJECT_ID/surf/lh.long.thickness-rate.fwhm10.fsaverage.mgz or .mgh file Any suggestions on what I am doing incorrectly? Best wishes, Sal -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System

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how to edit extracted masks
by Brianna Damadian 07 Jul '14

07 Jul '14

Hello, I used the mri_label2vol command to extract my aseg.mgz to patient native space (output=aseg-in-rawavg.mgz). I then used the mri_extract_label command as follows to create a mask of the ventricles: mri_extract_label aseg-in-rawavg.mgz 4 5 14 15 43 44 72 ventricles.img When I open this mask on top of the rawavg.mgz volume to look at quality, it seems there are some pieces that are clearly ventricle missing from the mask (see attached). Is there a way to edit this mask or the segmentation to include those areas in the ventricle mask as well as the segmentation volume output for the ventricles? Thanks, Brianna

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Problem of Volumes differ in dimension in Longitudinal pipeline
by wang kangcheng 07 Jul '14

07 Jul '14

Dear experts Today, I conduct the longitudinal analysis according to tutorials of freesurfer (https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing) But, when I do recon-all -base <templateid> -tp <tp1id> -tp <tp2id> ... -all, it report the error: --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- mri_diff --notallow-pix /Users/wangkangcheng/Desktop/long_fs_test/long/s12002_MRI2/mri/rawavg.mgz /Users/wangkangcheng/Desktop/long_fs_test/long/s12002_MRI1/mri/rawavg.mgz \n Volumes differ in dimension v1dim 176 256 256 1 v2dim 176 184 200 1 \n******************************************************************************* WARNING: Image geometries differ across time, maybe due to aquisition changes? This can potentially bias a longitudinal study! Will continue in 10s. ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- When I check the raw data and find that the structural data of s12002_MRI1 was the file which was converted by the command of dcm2nii and begin with "co". However, data of s12002_MRI2 was the file which begin with "o". But, when I used the file which begin with "co", they did not have same dimension. How could I solve the problem? (PS: have processed hundreds of data for subject of MRI1) Thank you Wang Kangcheng

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Using the Longitudinal Pipeline
by Alfred Ochs 07 Jul '14

07 Jul '14

Colleagues, We are preparing to perform longitudinal pilot studies a group of subjects and controls under far less than ideal conditions. The initial MRI scans were done clinically on a 1.5T Siemens scanner using the ADNI Siemens scanning protocol. The follow-up scans need to be done on a 3.0T Phillips (research, i.e., gratis) scanner using the ADNI Phillips protocol. Am I correct in assuming that the FreeSurfer longitudinal pipeline will somewhat iron out the inherent segmentation & parcellation differences between MRIs taken on these two machines? Thank you, Alfred Ochs

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mris__label__calc intersect error in longitudinal qcache
by Michael Kranz 07 Jul '14

07 Jul '14

Hi, I'm having trouble figuring out following problem: For one subject (out of 200), I get the following error (this error only persists for the right hemisphere-- left hemisphere works fine for this subject). mris_label_calc intersect /SUBJECTS_DIR/sub2.long.subt/label/rh.cortex.label /SUBJECTS_DIR/subt/label/rh.long.cortex.label /SUBJECTS_DIR/subt/label/rh.long.cortex.label ERROR -11 : mris_label_calc intersect did not work? *subt is base and sub2 is second time point .* Do you guys have any experience with this error and problems that it may have been caused by? I've tried re-running the longitudinal stream from scratch and the error still persists. I've visually checked the images and all segmentations were accurate. Thanks, Mike Kranz

2 1

Categorical covariates with more than two levels on qdec
by Isotalus, Hanna 07 Jul '14

07 Jul '14

Dear Freesurfer experts, I am doing an analysis on a large data set gathered from eight different imaging centres. In my analysis I would like to covary for the imaging site but qdec only allows me to covary for categorical variables if they have two levels (and I have eight). I am also using age (continuous) and gender (categorical, two levels) as covariates. Is there a way of using the imaging site as a covariate using qdec? Do you have any suggestions on how I should proceed? Is treating imaging site as a continuous variable acceptable? Best wishes, Hanna?

3 2

Extracting polar angle and eccentricity from vertices
by Jackie Lam 07 Jul '14

07 Jul '14

Hello all, I’ve just finished retinotopy analysis following http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis…. Now I’m wondering, is it possible to get quantitative values of polar angle and eccentricity for each vertex from, say, an ROI I’ve drawn out? If so, how would I go about doing that? Which files would I use? Thank you in advance, Jack

2 1

Get mean thickness after qdec monte-carlo simulation.
by June k. 07 Jul '14

07 Jul '14

Dear surfers. I’ve analyzed 2 group comparison data using qdec gui. I got some significant clusters after Monte-carlo simulation with 1.3, absolute. However, I have no idea to get thickness value of each group in the significant areas. Is there any way to extract mean (and S.D. if possible) thickness of the area shown in gui analysis after monte-carlo simulation? -Sincerely, June.

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Overlay onto surf file
by Paul Quigley 07 Jul '14

07 Jul '14

Hello, Could anyone give me some insight into how freeview projects an overlay onto a surface? For example, I have an overlay generated though mri_vol2surf for subject pq, call it stats.nii. Opening the nifti in MATLAB, I see that the image it stores is a single, flat vector (had about 130,000 entries). I can overlay stats.nii onto a variety of surf files (e.g. sphere.lh, inflated.lh). So it seems clear that each surf file has its own method for translating the indices in the vector to points on the surface... Is there any way to extract this information from the surf file? Basically, my goal is to figure out how I can translate coordinates on sphere.?h (theta, phi or x,y,z doesn't matter) to subscripts on my T1. Any help would be greatly appreciated! Thank you, Paul

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