Freesurfer August 2018

freesurfer@nmr.mgh.harvard.edu

104 participants
167 discussions

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

3 7

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

3 4

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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Confusion about MRI_GLMFIT
by Funk, Quentin 10 Aug '18

10 Aug '18

External Email - Use Caution Freesurfer experts, I'm trying to figure out what values I get from mri_glmfit as in the tutorial.<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> In particular, I'm interested in how I can compare these values to what I get from QDEC. In that tutorial, the software does a linear regression for each gender and then computes a F_ratio for the two two fits. (How does this relate to the average in the contrast listed?) The F_ratio then gives a way to get P-values (under certain assumptions)--so then from the F_ratio, pvals are computed--this leads to sig.mgh. But what are the other files? The descriptions are a bit too vague for me to understand, unfortunately. The ones I'm interested in primarily are: pcc.mgh -- partial (pearson) correlation coefficient (surface overlay) z.mgh -- z-stat that corresponds to the significance (surface overlay) The z-stat should be some sort of standard score--so a standard score of significance (so p-value?) compared to what distribution? Second, what if I were interested in a different categorical variable--say I had a group of Alzheimer's patients and a group of Healthy patients. In QDEC, I click "diagnosis" as the variable to do the analysis on. What contrast does this correspond to? What type of linear fit is being compared--the slope of the regression with respect to age? If I leave out nuisance variables (like age), I should conceivably get an F-test between the two constant models, which should be more or less similar to a voxelwise t-test? Any help here is appreciated! Quentin Funk, PhD Houston Methodist Research Institute 713-363-9003<tel:713-363-9003> Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas for patient care. Houston Methodist is nationally ranked in 8 specialties and is designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Correlations on QDEC
by Avi Gharehgazlou 10 Aug '18

10 Aug '18

External Email - Use Caution Hi experts, I have examined the relation between LGI and a behavioural continuous scale (SCQ) on QDEC while controlling for sex, age and surface area in my model. When I want to do another analysis, doing exactly this but also controlling for diagnosis as well, QDEC gives the following error: ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit.bin --y /d/mjt/9/users/avideh/data/recon/qdec/lh_LGI_RBS_overallscore_NDDs_controlling_SexAgeSA_fhwm0/y.mgh --fsgd /d/mjt/9/users/avideh/data/recon/qdec/lh_LGI_RBS_overallscore_NDDs_controlling_SexAgeSA_fhwm0/qdec.fsgd dods --glmdir /d/mjt/9/users/avideh/data/recon/qdec/lh_LGI_RBS_overallscore_NDDs_controlling_SexAgeSA_fhwm0 --surf fsaverage lh --label /d/mjt/9/users/avideh/data/recon/fsaverage/label/lh.aparc.label --C /d/mjt/9/users/avideh/data/recon/qdec/lh_LGI_RBS_overallscore_NDDs_controlling_SexAgeSA_fhwm0/contrasts/lh-Avg-Intercept-pial_lgi.mat --C /d/mjt/9/users/avideh/data/recon/qdec/lh_LGI_RBS_overallscore_NDDs_controlling_SexAgeSA_fhwm0/contrasts/lh-Avg-pial_lgi-RBS-Cor.mat --C /d/mjt/9/users/avideh/data/recon/qdec/lh_LGI_RBS_overallscore_NDDs_controlling_SexAgeSA_fhwm0/contrasts/lh-Diff-ADHD-ASD-Intercept-pial_lgi.mat --C /d/mjt/9/users/avideh/data/recon/qdec/lh_LGI_RBS_overallscore_NDDs_controlling_SexAgeSA_fhwm0/contrasts/lh-Diff-ADHD-ASD-Cor-pial_lgi-RBS.mat --C /d/mjt/9/users/avideh/data/recon/qdec/lh_LGI_RBS_overallscore_NDDs_controlling_SexAgeSA_fhwm0/contrasts/lh-Diff-M-F-Intercept-pial_lgi.mat --C /d/mjt/9/users/avideh/data/recon/qdec/lh_LGI_RBS_overallscore_NDDs_controlling_SexAgeSA_fhwm0/contrasts/lh-Diff-M-F-Cor-pial_lgi-RBS.mat --C /d/mjt/9/users/avideh/data/recon/qdec/lh_LGI_RBS_overallscore_NDDs_controlling_SexAgeSA_fhwm0/contrasts/lh-X-Dx-Sex-Intercept-pial_lgi.mat --C /d/mjt/9/users/avideh/data/recon/qdec/lh_LGI_RBS_overallscore_NDDs_controlling_SexAgeSA_fhwm0/contrasts/lh-X-Dx-Sex-Cor-pial_lgi-RBS.mat 2. The FSGD file (if using one) 3. And the design matrix above Attempting to diagnose further SumSq: Min=0.488835 (col 11), Max=3.834060 (col 6) ... could not determine the cause of the problem My understanding is that QDEC allows for controlling for 2 discrete variables, thus I don't know what I am doing wrong if I also control for diagnosis (in addition to sex)? I would really appreciate your help, Thanks so much, Avi

2 1

mri_volcluster not recognize --mindistance
by Yagmur Ozdemir 19 10 Aug '18

10 Aug '18

External Email - Use Caution Hello FreeSurfer experts, I am trying to run mri_volcluster with the following command to later create masks of clustered regions from functional data. I get an error saying that the option --mindistance is not recognized, even though this option is shown in mri_volcluster --help and the FS wiki page. Any idea what might be causing this? mri_volcluster --in thresh_highres.nii.gz --sum volcluster.txt --ocn clustered_thresh_highres.nii.gz --thmin 1.5 --sign pos --regheader <subject> --mindistance 10 --minsizevox 800 --fwhm 3 ERROR: Option --mindistance unknown Best Idil

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Freesurfer August 2018