Freesurfer July 2014

freesurfer@nmr.mgh.harvard.edu

163 participants
257 discussions

problems with Surface-based Interhemispheric Registration
by angela.favaro＠unipd.it 07 Jul '14

07 Jul '14

Hi all, I have a problem with 'Surface-based Interhemispheric Registration' I followed the instructions and all seem to work, but the command: 'surfreg --s $subject --t fsaverage_sym --lh --xhemi' finish with the error below (indeed in the xhemi/label directory, there is no file) What can I do? Thank you for any help! Angela #@# Cortical Parc rh Mon Jun 30 17:44:52 CEST 2014 /Users/angelafavaro/Desktop/risonanze/studyfree/subj024/xhemi/scripts \n mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 subj024/xhemi rh ../surf/rh.sphere.reg /Applications/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot \n No such file or directory mris_ca_label: could not open label file ../label/rh.cortex.label No such file or directory No such file or directory Darwin host-001.homenet.telecomitalia.it 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 recon-all -s subj024/xhemi exited with ERRORS at Mon Jun 30 17:44:52 CEST 2014

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neonatal processing stream?
by Alexopoulos, Dimitrios 07 Jul '14

07 Jul '14

Several months ago someone mentioned the possibility of a neonatal processing stream. Is this in development, and if so is there an approximate time frame for release. Thanks Jim The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email.

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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

2 1

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

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Freesurfer July 2014