Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

Problems with tkmedit
by Esteve Cervantes Martin 15 May '14

15 May '14

Hi, I'm Esteve Cervantes an student from UPC. I'm trying to install Freesurferfrom the source and I'm having some problems with tkmedit. I previously had some problems with recon-all because I got segmentation faults. After installing the mni.srcbuilt.tgz from source and some fixes it runs ok. But when I wanted to run tkmedit to view my volumes I got only one window with the picture, but a blank window for the tools. Then I tried to install the tcltkticblt-8.4.6.tgz and after building again freesrufer, now I get nothing. The output is: ecervantes@v3:~/opt/freesurfer1/tktools>> vglrun tkmedit 002_S_0295 brainmask.mgz -surfs [VGL] NOTICE: Automatically setting VGL_CLIENT environment variable to [VGL] 192.168.1.31, the IP address of your SSh client. Converting main surface: 100% done. Converting main surface: 100% done. Converting pial surface: 100% done. Converting main surface: 100% done. Converting main surface: 100% done. Converting pial surface: 100% done. ecervantes@v3:~/opt/freesurfer1/tktools>> It starts and sudenly ends without showing any window... I'm out of ideas any help will be appreciated. Thank you, Esteve

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Tksurfer will not accept key input in Ubuntu 14.04
by Knut J Bjuland 15 May '14

15 May '14

Bug report I am unable to enter number using the keyboard when using Tksurfer under Ubuntu 14.04. I have tried to enter a number in overlay configuration and smooth overlay. Is there any workaround? I have this bug on two different system with Ubuntu 14.04. Best regards Knut J Bjuland

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BrainMask Edits
by David Tate 15 May '14

15 May '14

Question regarding the use of skull stripping errors. I am wondering if it is possible to correct (use the -wsthresh or -gcut) in longitudinal processed data or would these types of edits be required in the earlier processing steps (initial FreeSurfer recon-all)? Thanks in advance for any help with this. David F. Tate, Ph.D.

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white matter surface (tkmedit -surfs) vs wm.mgz
by Mayer Kristina 15 May '14

15 May '14

Dear all I am segmenting data of 2 year olds and as freesurfer fails on segmneting inferior parts of the temporal lobe, I try to edit this manually using tkmedit (protocol from fswiki: WhiteMatterEdits_tktools, PialEdits_tktools, ControlPoints_tktools). I first add control points, with successfull amelioration of brainmask volumes. As this leads to integration of too much tissue in the white matter surface (displayed as tkmedit brainmask.mgz -surfs), i tried to manually edit wm.mgz. When I edit wm.mgz, there is no change in -surfs. When looking at the data in tkmedit (tkmedit subjid wm.mgz -surfs), total WM surface (-surfs), and wm.mgz are not the same. Where is the file generated that is shown in tkmedit as -surfs and which volume/file do I have to edit to ameliorate output of -surfs? Best, Kristina

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Cannot allocate memory
by Mayer Kristina 15 May '14

15 May '14

Hi there, I am using freesurfer on MRI data of children. In one dataset I have following error appearing, I did not find described before. MRISalloc(41043678, 76): could not allocate faces Cannot allocate memory Linux cs2.kispi.int 3.13.5-103.fc19.x86_64 #1 SMP Mon Mar 3 18:46:36 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux Waht do I have to check or edit manually? Thanks! Best, Kristina

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Frontal WM volume
by Yang, Daniel 14 May '14

14 May '14

Dear FreeSurfer group, If I want to extract frontal WM volume, is it something doable in FreeSurfer? Much obliged, Daniel

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Measuring cortical thickness at a specific location
by pfotiad＠nmr.mgh.harvard.edu 14 May '14

14 May '14

Hi FS experts, I was wondering whether it would be possible to measure the average cortical thickness at a specific slice (either axial, coronal, or sagittal). I read in Bruce's paper: "Measuring the thickness of the human cerebral cortex from magnetic resonance images" that "Measuring the thickness from the coronal slice at the point indicated by the green cross would result in an estimate in excess of 1 cm." Is that always the case, or has there been a way to bypass that issue? Thank you for your time, Panos

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Registration and Surface flatten
by Caka 14 May '14

14 May '14

Dear Doug and all, I have already done two things: (1) 'recon-all’ to the segmentation for 140 subjects; (2) surface registration to fsaverage template for 1 subject using: mri_surf2surf --hemi lh --srcsubject sub001 --srcsurfval thickness --src_type curv --trgsubject fsaverage --trgsurfval ./sub001-thickness-lh.mgz Now I have got the 'sub001-thickness-lh.mgz' file. I have two questions: (1) Is this 'sub001-thickness-lh.mgz’ a surface file or a volume file? How can I read it? I used ‘freeview sub001-thickness-lh.mgz’ to read it, but a dark scene was shown, nothing can be found. I also used ‘mris_convert -c $SUBJECTS_DIR/sub001/sub001-thickness-lh.mgz $SUBJECTS_DIR/sub001/surf/lh.orig lh.thickness.asc’, an error occurred like ‘ERROR: number of vertices in /disk250/data_analysis/sub001/sub001-thickness-lh.mgz does not match surface (163842, 132230)’. (2) After the registration, I want to flatten the surface of curvature or thickness into a full plane. The wiki says we should first specify 5 vertices and cut the whole area without the midline region, then ‘kris_flatten’ can be used. Indeed, this procedure requires quite a lot manually operation. I am wondering if there are some automatically commands that can do this flatten projects for 140 subject? Any reply would be really appreciated! Qiongmin

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Coomand not found
by Francesca Strappini 14 May '14

14 May '14

Hi, I'm just starting out with freesurfer. I downloaded CentOS6_x86_64 and I have Ubuntu 12.04 LTS. I have set up the licence file and configured freesurfer: tcsh setenv FREESURFER_HOME /media/Shared_Data/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh -------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /media/Shared_Data/freesurfer FSFAST_HOME /media/Shared_Data/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /media/Shared_Data/freesurfer/subjects MNI_DIR /media/Shared_Data/freesurfer/mni When I try to run any type of command, like tkmedit bert orig.mgz, I get this error: command not found. Thanks for the help! Francesca

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problems about extracting specific vertex thickness value and getting a average thickness for a specific mask
by charujing 13 May '14

13 May '14

Hi FS experts and users I have done the each subjects' surface regestration on fsaverage surface, and merge all of them into a *.mgh. Group analysis is also completed. Now I have two questions: 1,I want to extract the VtxMax vertex number thickness for all subjects. The VtxMax vertex number can be got in the *.sig.cluster.summary file. And it represents the most significant vertex in that cluster. I search my question in google and find these scripts which maybe helpful for me: for i in `seq 1 $numsubject` do mri_convert --frame $i y.mgh $SUBJECTS_DIR/fsaverage/surf/lh.$i.mgh mris_convert -c $i.mgh $SUBJECTS_DIR/fsaverage/surf/lh.inflated lh.$i.asc done I got the lh.*.asc file and open it. There are five columes in this file. I guess that: first colume is vertex number, the 2nd-4th columes represent MNI305 coordinates in surface, and the 5th colume is thickness of this vertex. If I want to deal with my 1st question, all I need to get the lh.*.asc file and search the specific vertex number in this file. All of above, is there anything wrong? 2, I created a surface mask, and want to extract the average thickness value in this mask for every subject. How can I complete it? Can I extract all vertex thickness in that mask, and average them in each subject? If so, however, it will be a bot of inconvenience. I want to some simple codes to deal with it. Any reply will be highly appreaciated. Thanks All the best. Rujing Zha 2014-05-10 charujing

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