Freesurfer

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30071 discussions

Surface Area in Toddlers/Children
by Derek Sayre Andrews 14 Aug '18

14 Aug '18

External Email - Use Caution Dear Freesurfer Developers and Experts, I have been exploring various vertex wise (mass univariate) effects using freesurfer measures of cortical thickness and surface area in a cohort of toddlers/children aged 25-70 months. When looking at the effect of age on surface area using individuals’ measures mapped to fsaverage and smoothed at 15mm fwhm (area.pial. fwhm15.fsaverage.mgh) I observed a widespread negative effect of age (i.e. decreased surface area with age). Given the age group of the cohort this seems implausible. Plotting the sum of each individuals lh+rh.area.pialfsaverage.fwhm15.mgh against age shows the relationship: [cid:image001.png@01D42FCE.C197B360] However, plotting the lh+rh total surface area returned by mris_anatomical_stats reveals a much more plausible relationship between surface area and age: [cid:image002.png@01D42FCE.C197B360] My working hypothesis is that the significantly smaller brain sizes of our cohort compared to fsaverage, and the fact(?) that -qcache does not preserve global surface area, is causing an “over adjustment” in our cohorts smallest brains when mapped to fsaverage. Thus, my questions are three fold 1. Is the mapping of our significantly smaller brains to fsaverage a potential explanation for the results we are seeing in our mass univariate analyses of surface area? 1. If this is the case, would this effect be limited to surface area or also extend to other freesurfer measures including cortical thickness, lGI, sulcal depth etc. 1. How would you recommend approaching vertex wise analyses in a cohort of this age? Create a study specific average subject using make_average_subject to map onto? Thank you for your insight and guidance! Best, Derek PS: All processing was performed using freesurfer v5.1 Derek Sayre Andrews, PhD Postdoctoral Scholar Department of Psychiatry and Behavioral Sciences The M.I.N.D Institute University of California Davis Telephone: +1 916 703 0360 Email: dandrews(a)UCDavis.edu<mailto:dandrews@UCDavis.edu>

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Lobe parcellation without cingulate from --lobesStrict
by Fernanda Hansen P. de Moraes 14 Aug '18

14 Aug '18

External Email - Use Caution Dear FreeSurfer experts, I want to get with mris_anatomical_stats the stats from the four lobes, Frontal, Parietal, Temporal and Occipital as suggest here ( https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation) but without the cingulate. I am trying to use the mri_mergelabels to merge that labels: Rostral Anterior (Frontal) Caudal Anterior (Frontal) Posterior (Parietal) Isthmus (Parietal) in their lobes, but I am facing some difficulties. I am sorry if this is a basic question, but I couldn't find an example that worked for me in the mail archive. I am following these steps: mri_annotation2label --subject PRI002 --hemi lh --lobesStrict lh.lobesStrict.annot mri_mergelabels -i lh.frontal -i lh.rostralanteriorcingulate -i lh.caudalanteriorcingulate -o lh.frontal Is there an easier way to do it? Thank you very much in advance, Fernanda Hansen P. de Moraes -- Fernanda Hansen P. de Moraes Física Médica | Rede D'Or São Luiz Doutoranda em Ciências Médicas | Instituto D'Or de Pesquisa e Ensino

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Re: [Freesurfer] coregistering with bbregister
by Ben M 13 Aug '18

13 Aug '18

External Email - Use Caution Hi Doug, Thank you very much for your response, it helped me a lot. I checked the examples of mri_vol2vol and for functional-to-structural registration I think I should do $ bbregister --t2 --lta /data/bbregister/reg.lta --mov /data/mean_func.nii.gz --s 001 $ mri_vol2vol --lta /data/bbregister/reg.lta --mov /data/mean_func.nii.gz --fstarg --o func2anat.nii.gz --no-resample If I understood correctly, this will align mean_func with the structural image (orig.mgz I think). Is this correct? I have two follow up questions if you don't mind: 1 - I'd like to get the file describing the affine registration of the functional to structural space for subsequent preprocessing. I think this should be the reg.lta (or reg.dat) file from the bbregister step, shouldn't it? This file contains the transformation matrix from functional to structural, is that correct? 2 - does mri_vol2vol actually physically move the -mov image? I think it does, which is the --o func2anat image above. However when I load the mean_func and func2anat images, they don't seem to be different in terms of orientation. I suppose it's because it's difficult to see the transformation with the naked eye? Best, Ben

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Untar and sh files in dev version
by Schumman Resonance 13 Aug '18

13 Aug '18

External Email - Use Caution Hi, Couple of newbie questions. I downloaded the dev version of freesurfer and did: tar xvzf freesurfer-linux-centos6_x86_64-dev.tar.gz to get gzip: stdin: unexpected end of file tar: Unexpected EOF in archive tar: Unexpected EOF in archive tar: Error is not recoverable: exiting now Also, when I ls the folder I couldn't see the SetUpFreesurfer.sh and SurferEnv.sh only the csh files. Any pointers how to solve these would be appreciated. Thanks, S

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Stats2table_bash.sh script
by Schumman Resonance 13 Aug '18

13 Aug '18

External Email - Use Caution Hi, I'm trying to run the Stats2table_bash.sh script from Jamaan Alghamdi & Dr. Vanessa Sluming. And I get This error: File "/Applications/freesurfer/bin/asegstats2table", line 195 print 'ERROR: subjects are not specified (use --subjects SUBJECTS)' ^ SyntaxError: invalid syntax File "/Applications/freesurfer/bin/asegstats2table", line 195 print 'ERROR: subjects are not specified (use --subjects SUBJECTS)' ^ SyntaxError: invalid syntax File "/Applications/freesurfer/bin/aparcstats2table", line 156 print 'ERROR: atleast 1 subject must be provided' . . . This is my set up: _________________________________________________________________ -------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Users/schumman/data MNI_DIR /Applications/freesurfer/mni FSL_DIR /usr/local/fsl _________________________________________________________________ This is the line from SetUpFreeSurfer.sh for my subjects directory ____________________________________________________________ # Set this to your subjects/ dir, usually freesurfer/subjects/ if [ -z $SUBJECTS_DIR ]; then export SUBJECTS_DIR=/Users/schumman/data __________________________________________________ And I modified in their script to my FREESURFER_HOME as below #!/bin/bash path=`dirname $0` sleep 1 cd $path echo "This bash script will create table from ?.stats files" echo "Written by Jamaan Alghamdi & Dr. Vanessa Sluming" echo "University of Liverpool" echo "jamaan.alghamdi(a)gmail.com" echo "http://www.easyneuroimaging.com" echo "20/12/2010 " export FREESURFER_HOME=/Applications/freesurfer sleep 1 source $FREESURFER_HOME/SetUpFreeSurfer.sh sleep 1 export SUBJECTS_DIR=$PWD list="`ls -d */`" asegstats2table --subjects $list --meas volume --skip --statsfile wmparc.stats --all-segs --tablefile wmparc_stats.txt . . . I run the script from my_subject_directory. I suspect this is something very obvious I'm not able to see and I apologize for such a basic question, any help would be much appreciated. Thanks, K

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Outlier voxels after partial volume correction using Petsurfer
by Shane Schofield 13 Aug '18

13 Aug '18

External Email - Use Caution Hello Petsurfers! A few of my subjects ended up with vertices that had outlier PET values after I followed the PetSurfer steps. Most of the binding potentials are in the range of 0 - 3. Looking at the histogram though there are a couple of vertices with values around -30. First of all how can I deal with this? Can these voxels be excluded from the data, and how? Secondly, does this mean that there is something not right with my parameters for mri_gtmpvc? Cheers,Shane

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Cortical surface
by 郑凤莲 12 Aug '18

12 Aug '18

External Email - Use Caution Dear experts, I an using FS 6.0 for cortical reconstructions. I can show whole brain regions (tksurfer...), as shown in the picture. However, I just want to show insular region. Is there any way to complete it? I am looking forward to your reply. Thanks very much. Sincerely, Zheng

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T1 mapping
by Fotiadis, Panagiotis 12 Aug '18

12 Aug '18

Hello, I am interested in doing some T1-mapping analyses on some ex vivo brains. We have collected flash sequences under multiple flip angles (5, 10, 15, 20, 25 and 30). How would you suggest that I proceed? Should I use the mri_ms_fitparms to come up with the T1 maps for each subject and then maybe calculate the signal intensity 1mm into the cortex, or is there another way that you would recommend? Thanks in advance for any advice! Best, Panos Panagiotis Fotiadis Senior Imaging Research Technologist J. P. Kistler Stroke Research Center, Department of Neurology Massachusetts General Hospital, Boston, MA T: (617) 643-3869

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Plotting QDEC results
by Avi Gharehgazlou 12 Aug '18

12 Aug '18

External Email - Use Caution Hi experts, I looked at association between LGI and a behavioural scale on QDEC. after the analysis, to plot the significant clusters/ blobs, I wanted to export LGI values for each subject from each significant blob and based on instructions in previous archives I ran the following command line: mri_glmfit-sim –glmdir (qdec output directory) --cache 1.3 abs which generated a "cache.th13.abs.y.ocn.dat" file. This file contains 3 columns and 36 rows. I'm assuming the values in the three columns correspond to LGI values for each significant blob for each subject? (I had 3 significant blobs and 36 participants) Will you please confirm I am doing (and interpreting) this correctly? Thanks so much, Avi

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Re: [Freesurfer] coregistering with bbregister
by Ben M 12 Aug '18

12 Aug '18

External Email - Use Caution Hi Doug, Thank you for your suggestions, I'll try them. Could you please let me know if my code is actually doing what I intend it to do? Specifically, the idea is to perform functional-to-structural registration. so first I did $ bbregister --t2 --reg /data/bbregister/reg.dat --mov /data/mean_func.nii.gz --s 001 I'm not sure if the --mov image should be the motion-corrected mean functional image or the skull-stripped anatomical image. I think if I want to do functional-to-structural registration it should actually be the anatomical image as --mov right? Or it doesn't matter which one I choose? I then did $ mri_vol2vol --mov /data/bet_structural.nii.gz --targ /data/brain.nii.gz --o /data/coregistered_structural.nii.gz --reg /data/bbregister/reg.dat --inv –-nearest which I thinks applies the transformation matrix to the structural image, am I correct? In this case it would be a structural-to-functional registration I think. So, if I intend to perform functional-to-structural registration I should actually rather do $ bbregister --t2 --reg /data/bbregister/reg.dat --mov /data/bet_structural.nii.gz --s 001 $ mri_vol2vol --mov /data/mean_func.nii.gz --targ /data/brain.nii.gz --o /data/coregistered_functional.nii.gz --reg /data/bbregister/reg.dat --inv –-nearest Could you please confirm if this is correct? Thank you very much, Ben Sometimes the FSL initialization will fail. If you are using FS version 6, then run it without specifying --init-fsl and it will use mri_coreg, which is more robust. If your anatomical and functional were acquired at the same time, you might be able to get away with --init-header instead. On 8/9/18 2:12 PM, Ben M wrote: >>* External Email - Use Caution *>>* Hi, *>* I'm trying to coregister the strucural image to the mean functional *>* image using bbregister, so after reconall I did: *>>* bbregister --t2 --init-fsl --reg /data/bbregister/reg.dat --mov *>* /data/mean_func.nii.gz --s 001 *>>* bet /data/structural.nii.gz /data/bet_structural.nii.gz *>>* #brain.nii.gz is the brain.mgz from reconall output (in freesurfer space) *>* mri_vol2vol --mov /data/bet_structural.nii.gz --targ *>* /data/brain.nii.gz --o /data/coregistered_structural.nii.gz --reg *>* /data/bbregister/reg.dat --inv –-nearest *>>* But when I load the coregistered_structural.nii.gz and the *>* mean_func.nii.gz they are not aligned. I'm sure I'm doing something *>* wrong, could someone help me figure it out please? *>>* Thanks in advance, *>* Ben*

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