Freesurfer November 2018

freesurfer@nmr.mgh.harvard.edu

121 participants
189 discussions

Coordinates' annotations question
by 王子谦 08 Nov '18

08 Nov '18

External Email - Use Caution Hi developers, thank for your amazing program, it’s really helpful. After using it for a short time, I met a question in the middle of my research. I have thousands sets of coordinates in MNI space. And I wanna get the information about where these coordinates locate in Destrieux atlas. Namely, the annotations of these coordinates. As I know, fsl has this command ‘atlasquery’. Do we have something like it?? Thank you very much. Any suggestion would be helpful. best regards, Ziqian Wang

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Re: [Freesurfer] Basic question in testing installation by 4 examples
by fsbuild 07 Nov '18

07 Nov '18

External Email - Use Caution Hello Zainab, The first 2 commands you list are, export FREESURFER_HOME=/usr/local/freesurfersource $FREESURFER_HOME/SetUpFreeSurfer.sh .... and the output from the source command shows you what has been setup in your environment... FREESURFER_HOME   /usr/local/freesurferFSFAST_HOME       /usr/local/freesurfer/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /usr/local/freesurfer/subjectsMNI_DIR           /usr/local/freesurfer/mni Now there should be no need to run more export commands, i.e.,  SUBJECTS_DIR is already set correctly.    But the next export command you type, export SUBJECTS_DIR=path to subject directory - changed the setting of SUBJECTS_DIR from "/usr/local/freesurfer/subjects" to "path to subject directory" which is a path that does not exist You only need to run the export and source commands once in your current shell before runningany/all subsequent freesurfer commands. Zainab Albar November 7, 2018 at 19:29         External Email - Use Caution        Hello Freesurfer expert, I am brand new to Freesurfer, my apology for the basic question, I kept trying to figure out my mistake in installation for last week and could not find a solution to it. Here is my output, my problem with subject_DIR keeps changing and recon command is not found. it worked only once with me till I reach example 4 when I had an output that libpng12.so.0 not found. Thank you for help in advance, zhbar@DESKTOP-V43QKHC:~$ export FREESURFER_HOME=/usr/local/freesurferzhbar@DESKTOP-V43QKHC:~$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /usr/local/freesurferFSFAST_HOME       /usr/local/freesurfer/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /usr/local/freesurfer/subjectsMNI_DIR           /usr/local/freesurfer/mnizhbar@DESKTOP-V43QKHC:~$ export SUBJECTS_DIR=path to subject datazhbar@DESKTOP-V43QKHC:~$ sudo cp $FREESURFER_HOME/subjects/sample-001.mgz .[sudo] password for zhbar:zhbar@DESKTOP-V43QKHC:~$ mri_convert sample-001.mgz sample-001.nii.gzmri_convert.bin sample-001.mgz sample-001.nii.gz$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from sample-001.mgz...TR=7.25, TE=3.22, TI=600.00, flip angle=7.00i_ras = (-0, -1, -0)j_ras = (-0, 0, -1)k_ras = (-1, 0, 0)writing to sample-001.nii.gz...zhbar@DESKTOP-V43QKHC:~$ export SUBJECTS_DIR=path to subject directoryzhbar@DESKTOP-V43QKHC:~$ recon-all -i sample-001.nii.gz -s bert -allERROR: SUBJECTS_DIR path does not exist.zhbar@DESKTOP-V43QKHC:~$ sudo recon-all -i sample-001.nii.gz -s bert -allsudo: recon-all: command not foundzhbar@DESKTOP-V43QKHC:~$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------Setting up environment for FreeSurfer/FS-FAST (and FSL)WARNING: path does not existFREESURFER_HOME   /usr/local/freesurferFSFAST_HOME       /usr/local/freesurfer/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      pathMNI_DIR           /usr/local/freesurfer/mni _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Basic question in testing installation by 4 examples
by Zainab Albar 07 Nov '18

07 Nov '18

External Email - Use Caution Hello Freesurfer expert, I am brand new to Freesurfer, my apology for the basic question, I kept trying to figure out my mistake in installation for last week and could not find a solution to it. Here is my output, my problem with subject_DIR keeps changing and recon command is not found. it worked only once with me till I reach example 4 when I had an output that libpng12.so.0 not found. Thank you for help in advance, zhbar@DESKTOP-V43QKHC:~$ export FREESURFER_HOME=/usr/local/freesurfer zhbar@DESKTOP-V43QKHC:~$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni zhbar@DESKTOP-V43QKHC:~$ export SUBJECTS_DIR=path to subject data zhbar@DESKTOP-V43QKHC:~$ sudo cp $FREESURFER_HOME/subjects/sample-001.mgz . [sudo] password for zhbar: zhbar@DESKTOP-V43QKHC:~$ mri_convert sample-001.mgz sample-001.nii.gz mri_convert.bin sample-001.mgz sample-001.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from sample-001.mgz... TR=7.25, TE=3.22, TI=600.00, flip angle=7.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) writing to sample-001.nii.gz... zhbar@DESKTOP-V43QKHC:~$ export SUBJECTS_DIR=path to subject directory zhbar@DESKTOP-V43QKHC:~$ recon-all -i sample-001.nii.gz -s bert -all ERROR: SUBJECTS_DIR path does not exist. zhbar@DESKTOP-V43QKHC:~$ sudo recon-all -i sample-001.nii.gz -s bert -all sudo: recon-all: command not found zhbar@DESKTOP-V43QKHC:~$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) WARNING: path does not exist FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR path MNI_DIR /usr/local/freesurfer/mni

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Ventricles segmentation
by Miguel Ángel Rivas Fernández 07 Nov '18

07 Nov '18

External Email - Use Caution Hello Freesurfer devs, Is possible segment the brain ventricles using Freesurfer in terms of mm3 or ml? I would be interested in study the ventricular enlargement. Is possible with Freesurfer or other toolbox. Any help would be appreciated. Thanks in advance. Cheers, -- *Miguel Ángel Rivas Fernández*

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T-value in QDEC or FREESURFER
by Vikas Bandalli 07 Nov '18

07 Nov '18

External Email - Use Caution Dear freesurfer team. I am running an analysis betweene two groups Normal and Patients. Here is an example of my particular design diagnosis :- Normal vs Bipolar Co-variate :- Age Nuisance factor :- Total_Intra cranial volume I would please like to know a couple of things related to QDEC 1.I am looking for difference in volume between patients and controls and the analysis. For correcting for multiple comparisons I ran Monte carlo - Z simulation at threshold of 1.3 My understanding is the analysis overall runs a two-tailed t-test first and then when we select to run MC-z simulation it iterates for multiple comparisions (by repeating the saem say 1000 times ) and gives out 'clusterwise p-value' Is my understanding correct? 2.I would like to extract T-values for the same . Are we getting cluster wise T-value similar to cluster wise p-value ? in the terminal 3. Where would I find t-values for the analysis ??? 4.Are there any methods to extract T-values in qdec or freesurfer . If so,please specify. I am enclosing screenshots from my analysis for the same . Kindly request you to please have a look please help me out with this ?? Thanking You, Yours sincerely , Dr.Vikas Bandalli -- Bangalore Medical College and Research Institute (BMCRI), Bangalore,India, Ph : +918904286825

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How to combine and divide surface-based fMRI data?
by Zhi Li 07 Nov '18

07 Nov '18

External Email - Use Caution Hello FreeSurfer experts, May I ask how can I modify the surface-based fMRI data, such as combing two independent sessions into one or dividing one 4D into a series of 3D surface-based fMRI files in which each one denotes a single volume/TR? Thank you very much. Best wishes, Zhi

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MatrixReadTxT: could not scan value [1][1]
by Anwar Shatil 07 Nov '18

07 Nov '18

External Email - Use Caution Hello Doug: My dti_recon is getting stuck at the "Fitting Tensor" stage. I was wondering if there is any solution to the problem "MatrixReadTxT: could not scan value [1][1]". My log file is attached here and the problem can be found right at the bottom. Is this a bug? What is the solution? There were similar reports on this earlier but nobody answered. https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subj… I am using FS 6.0 in MacOS. Best, Anwar

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Re: [Freesurfer] GLM
by Greve, Douglas N.,Ph.D. 07 Nov '18

07 Nov '18

Sounds like you need an F-test, eg, create a contrast like 1 1 -1 -1 0 0 0 0 0 0 0 0 1 1 0 0 -1 -1 0 0 0 0 0 0 This tests the null hypothesis that p1==p2==control On 11/07/2018 10:11 AM, 13181786167 wrote: > > External Email - Use Caution > > Thanks for your reply. Using the first one, We can obtain the sig.mgh > among 3 groups. If I want to obtain the results simultaneously between > patient 1 and 2, patient 1 and control, patient 2 and control. What > should I do. > > Sincerely, > Zheng > > > > > 郑凤莲 > 邮箱：13181786167(a)163.com > > <https://maas.mail.163.com/dashi-web-extend/html/proSignature.html?iconUrl=h…> > > > 签名由网易邮箱大师 <https://mail.163.com/dashi/dlpro.html?from=mail88> > 定制 > > On 11/07/2018 22:57, Greve, Douglas N.,Ph.D. > <mailto:DGREVE@mgh.harvard.edu> wrote: > Use the first one. Not sure what you mean by your multiple > comparisons > question > > On 11/01/2018 11:20 PM, 郑凤莲 wrote: > > > > External Email - Use Caution > > > > Hi experts, > > > > I am using FS 6.0 for analyzing the cortical thickness > difference > > between 3 groups: patient1, patient2 and control. In DODS > model, I > > need to creat 2 files, FSDG and mtx file. And we have > 3 variables: > > age, gender and cortical thickness. > > 1. The FSDG file is: > > GroupDescriptorFile 1 > > Title Tutorial > > Class patient1-male > > Class patient1-female > > Class patient2-male > > Class patient2-female > > Class control-male > > Class control-female > > Variables age > > Input subject1 patient1-female 20 > > Input subject2 patient1-male 33 > > Input subject3 patient2-female 40 > > Input subject4 patient2-male 50 > > Input subject5 control-male 30 > > Input subject6 control-female 35 > > And there is another way: > > GroupDescriptorFile 1 > > Title Tutorial > > Class patient1 > > Class patient2 > > Class control > > Variables sex age > > Input subject1 patient1 1 20 > > Input subject2 patient1 2 33 > > Input subject3 patient2 1 40 > > Input subject4 patient2 2 50 > > Input subject5 control 2 30 > > Input subject6 control 1 35 > > What I want to confirm is that if I want to adjust for sex > and age, > > which one is right? > > Another question is that is there any way to get the multiple > > comparisons between groups simultaneously? > > I am looking forward to your reply. Thanks very much. > > > > Sincerely, > > Zheng > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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Mapping a custom measure to the pial surface of fsaverage
by ts+ml＠rcmd.org 07 Nov '18

07 Nov '18

External Email - Use Caution Dear FreeSurfer experts, I have created a custom measure on the pial surface of a number of subjects, and I would like to map the data to the fsaverage subject. (By custom measure I mean something like 'area' or 'curv', i.e., one scalar value per surface vertex.) I have already done the same for the white surfaces, and it was pretty straight-forward: 1) Save the per-vertex data in a curv-format file in SUBJECTS_DIR/<subject>/surf/?h.<measure> 2) Run 'recon-all -s <subject> -qcache -measure <measure>' This will map the data to fsaverage and create files named ?h.<measure>.fwhm<n>.fsaverage.mgh in the surf/ directories as expected (where <n> is 0, 5, .., 25). My question is: how can I do the same for my data from the pial surface? Are there any command line options for 'recon-all' (or maybe for mris_preproc) that can do this? I already tried to put the pial per-vertex data into files named SUBJECTS_DIR/<subject>/surf/?h.pial.<measure>, but they are not handled by the recon-all command listed above: no fsaverage files show up for them. Thanks in advance, Tim -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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Extracting values from a single vertex
by Nillo, Ryan Michael R 07 Nov '18

07 Nov '18

External Email - Use Caution Hi FreeSurfer users, I want to extract thickness values at a single vertex. I searched on the support list and found an mris_convert command to use. However, the file I want to extract values from is a volume with multiple frames. When I try to use mris_convert on it, I only got the value at a vertex on the first frame. The goal is to set that vertex as a seed point and use the values as a regressor for glm. Is there a way to do this with FreeSurfer's commandline tools, or should I do this in Matlab? Mahalo, Ryan M Nillo Staff Research Associate I UCSF Department of Radiology and Biomedical Imaging

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Freesurfer November 2018