Freesurfer

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Re: [Freesurfer] Desikan Atlas in volume space (ece ulug)
by Mcnorgan, Christopher 09 Nov '18

09 Nov '18

External Email - Use Caution Hi Ece, I believe you will find a walkthrough of the steps to do exactly what you want done on my lab wiki: http://ccnlab.psy.buffalo.edu/wiki/index.php/Annotation_Coordinates Hope this helps, Chris /********************************************** * Chris McNorgan * Assistant Professor * Department of Psychology * University at Buffalo, * The State University of New York * http://ccnlab.buffalo.edu/ * Office: 716.645.0236 * Lab: 716.645.0222 **********************************************/ On Nov 6, 2018, at 12:00 PM, freesurfer-request(a)nmr.mgh.harvard.edu<mailto:freesurfer-request@nmr.mgh.harvard.edu> wrote: Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu<mailto:freesurfer-request@nmr.mgh.harvard.edu> You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu<mailto:freesurfer-owner@nmr.mgh.harvard.edu> When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Ynt: Ynt: ?lt: Desikan Atlas in volume space (ece ulug) From: ece ulug <eceulug77(a)hotmail.com<mailto:eceulug77@hotmail.com>> Subject: [Freesurfer] Ynt: Ynt: İlt: Desikan Atlas in volume space Date: November 6, 2018 at 6:37:17 AM EST To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> External Email - Use Caution Exactly. I cannot find in this file but i found lh.aparc.label and lh.aparc.annot files in freesurfer/subjects/fsaverage/label. Actually i told in my previous message. I need coordinates for generate caudalanteriorcingulate mask in coordinate system. ________________________________ Gönderen: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu>> adına freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> Gönderildi: 6 Kasım 2018 Salı 00:45 Kime: Freesurfer support list Konu: Re: [Freesurfer] Ynt: İlt: Desikan Atlas in volume space I don't think there is an lh.aparc.label file - I don't know what it would be if it existed. Maybe we can take a step back and you can let us know what you are trying to achieve? On Mon, 5 Nov 2018, ece ulug wrote: > > External Email - Use Caution > > Thanks for your reply doctor. Actually I want to access Desikan K. Atlas coordinates as x, y, z. > (each regions. for example caudalanteriorcingulate). > > > In that case, one expert said that ; the closest to what you want is probably > $FREESURFER_HOME/subjects/fsaverage/surf/lh.aparc.label. You can open it with a text editor. Then > you should cross-check with $FREESURFER_HOME/subjects/fsaverage/surf/lh.aparc.annot for the actual > labels of those vertices. The .annot file can be opened in Matlab with the read_annotation command > from FreeSurfer. > > > What do you recommend? > Ece > > ____________________________________________________________________________________________________ > Gönderen: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu>> adına freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> > <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> > Gönderildi: 5 Kasım 2018 Pazartesi 20:18 > Kime: Freesurfer support list > Konu: Re: [Freesurfer] İlt: Desikan Atlas in volume space > Hi Ece > > for a given subject the Desikan parcellation is sampled into the volume > alread in the file aparc+aseg.mgz in the subject's mri dir. Is that what > you are looking for? > > cheers > Bruce > > On Mon, 5 Nov 2018, ece ulug wrote: > > > > > External Email - Use Caution > > > > Dear Experts, > > > > > > I am very beginner in Freesurfer, and I want to use 'read_annotation' > > function but i don't know what is the next step. I added the Matlab > > screenshoot. > > > > > > Additionally; 'read_curv' function don't work in Matlab. I added it. > > > > > > Thanks in advance > > > > Ece > > > > > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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回复： ?????? Recon-all run error
by 1013364183 09 Nov '18

09 Nov '18

External Email - Use Caution Dear Bruce Fischl: We ran two images of about 500MB, but stopped at a certain step for a few days, we would like to ask what is the reason, the attachment has a recon-all.log file at runtime. Thanks in advance yours yujunjie ------------------ 原始邮件 ------------------ 发件人: "Bruce Fischl"<fischl(a)nmr.mgh.harvard.edu>; 发送时间: 2018年11月7日(星期三) 凌晨2:42 收件人: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu>; 主题: Re: [Freesurfer] ?????? Recon-all run error does it occur if you run it outside of recon-all? Do you have enough free ram? If so, you can filedrop us the dataset and we can try to replicate and fit ix. On Tue, 6 Nov 2018, 1013364183 wrote: > > External Email - Use Caution > > Dear Bruce, > I found the error location in the recon-all.log folder. Here is the place where it went wrong??I > don't think it's the reason for insufficient memory.. > ''mri_convert.bin: putget.c:322: fill_NC_var: Assertion `chunksz % 4 == 0' failed.'' > This data is ok when we run with versions prior to freesurfer 6.0. But after we run the 6.0 > version and set the expert file, this error will occur.Do I need to step through the instructions to > see the problem? How should this error be solved? > > Thanks in advance > > yours yujunjie > > ------------------ ???????? ------------------ > ??????: "Bruce Fischl"<fischl(a)nmr.mgh.harvard.edu>; > ????????: 2018??11??6??(??????) ????9:40 > ??????: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu>; > ????: Re: [Freesurfer] Recon-all run error > > that certainly looks like something is running out of ram. Can you run > the command that failed directly on the command line and see if it works? > Was anything else running on the machine at the time? We do report total > and free memory at the start of the recon in the recon-all.log file > > cheers > Bruce > On Tue, > 6 Nov 2018, 1013364183 wrote: > > > > > External Email - Use Caution > > > > Dear FS, > > When we run ??recon-all?? with a 5GB high-resolution image, core dumped appears when the > mri_convert > > command is executed. The specific errors are as follows: > > /opt/el7/pkgs/freesurfer/freesurfer_6.0/bin/mri_convert: line 3: 29235 Aborted (core dumped) > > mri_convert.bin "$@" > > ERROR: converting to minc > > We want to know if our high resolution image is too large for freesurfer to handle, or our > computer > > memory (64GB running memory) is limited. > > > > Thanks a lot in advance! > > yours sincerely, > > yu junjie > > > > > > > _______________________________________________ > 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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Fornix in TRACULA
by Hayek, Dayana 09 Nov '18

09 Nov '18

External Email - Use Caution Dear all, In my research work, I am using Freesurfer for both grey and white matter segmentation. However, I am restricted in the white matter analysis since my studies and related to memory function and I am mainly interested in the Fornix. I read in one of the threads that TRACULA will include soon an Atlas with the Fornix. Any news regarding this issue? Do you have any timeline of the progress of this atlas? Thank you so much for your help! ------------------------------------------------------------ Dayana Hayek, MSc.-Bio, cand dr.rer.nat Universitätsmedizin Greifswald | Klinik und Poliklinik für Neurologie AG Kognitive Neurologie Ferdinand-Sauerbruch-Straße | D-17475 Greifswald [Intern: W.-Rathenau-Str. 49 | Whg. 6.5] E-Mail: dayana.hayek(a)stud.uni-greifswald.de

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Cerelellar parcellation labels Request
by dongnandi1 09 Nov '18

09 Nov '18

External Email - Use Caution Hi Freesurfer experts, The cerebellar 7 and 17 networks parcellation cannot be downloaded. The link to cerebellar parcellation in SUIT is out of date too. so, if you can kindly share the cerebellar 17-network parcellation and their anatomy labels, I would be particularly grateful! Best wishes Fan 2018/11/08

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dcmunpack Error
by Maryam Tayebi 08 Nov '18

08 Nov '18

External Email - Use Caution Hello Freesurfer Developers, I was going to reconstruct MPRAGE images from GE 3T machine. First I used this command: *dcmunpack -src . -scanonly scan.log* It made just *scan.log* file for me. Then I used this command: *unpacksdcmdir -src /<my dicoms pathways> -targ <my output directory> -scanonly scan.log* However, it made 3 files for me; dicomdir.sumfile, parse.status and unpack.log, but they were 0 bites. Furthermore, the following message also appeared on the terminal: *ERROR: parsing /hpc/mtay316/tutorial4/practice_with_data/dicoms/ See logfile /hpc/mtay316/tutorial4/practice_with_data//unpack.log for more details* I used this command for SIEMENS data and it worked. Apparently this code just works on SIEMENS data not GE. So now what is the code that I can use for GE dcm images? 1) FREESURFER Version: freesurfer-x86_64-unknown-linux-gnu-stable6-20170118 2) Platform: Ubuntu 16.04 LTS 3) unpack.log : see attached Regards -- *Maryam Tayebi* PhD Candidate of Bioengineering Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand MSc of Medical Imaging University of Manchester, Manchester, UK

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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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