Freesurfer

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30088 discussions

Re: [Freesurfer] fixing hippocampus segmentation
by Bruce Fischl 27 Feb '11

27 Feb '11

Hi Tetiana, I think what you're seeing are just the consequences of a voxel-based segmentation. The borders have to be voxelated. Note that much of this will be corrected in the volume calculation that performs a partial-volume correction. cheers Bruce On Wed, 23 Feb 2011, Tetiana Dadakova wrote: > Dear Bruce, dear all, > > I attach several images to show where I would like to manually > interfere into segmentation process. > > img1: Hippocampus' volume covers part of amygdala and parahippocampal > area. The intensity in these non-hippocampal regions are between > 75-95. > > img2: Segmentation of brain stem (problem point are shown by arrows). > This problem repeats more or less for every subject. > > img3: Edges of thalamus are too "pixelated". I mean, shouldn't the > line be smoother? Can this cause overestimation of thalamus' volume? > > Manual correction (drawing) of all the mis-segmented parts would take > a lot of time, so I would like to find out other way of controlling > the segmentation process. (Something like "putting control points" > would be perfect). > > Thank you, > Tanja. > > > On Mon, Feb 21, 2011 at 2:56 PM, Bruce Fischl > <fischl(a)nmr.mgh.harvard.edu> wrote: >> Hi Tanja, >> Can you send us an image? Is parahippocampal white matter significantly darker than 110? >> Bruce >> >> >> >> On Feb 21, 2011, at 6:41 AM, Tetiana Dadakova <tetiana.d(a)gmail.com> wrote: >> >>> Dear Freesurfer users, >>> >>> For some of my subjects Freesurfer strongly overestimates hippocampus' >>> volume. Is there any way to fix the segmentation of hippocampus by >>> e.g. adding some control points (like for white matter here >>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints)? >>> >>> Thank you, >>> Tanja. >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> >

2 3

installation problem
by Liukarl 26 Feb '11

26 Feb '11

Hello, Freesurfer experts: I emailed some installation problems a couple days ago, but haven’t answered yet. I am new to freesurfer and try to install the newest version of freesurfer in Ubuntu system. I closely followed the instructions, and the only difference is that I installed it in my Documents, instead of local folder. Below is the output after “source $FREESURFER_HOME/SetUpFreeSurfer.sh” -------- freesurfer-Linux-centos4-stable-pub-v5.0.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/jie/Documents/freesurfer/ FSFAST_HOME /home/jie/Documents/freesurfer//fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /home/jie/Documents/freesurfer//subjects MNI_DIR /home/jie/Documents/freesurfer//mni Everything seems fine and I also added the .license file to the freesurfer folder. But when I test it by “tkmedit bert orig.mgz”, it reponds “Illegal instruction” If I type in “recon-all”, it will show “ Required Arguments: -subjid <subjid> -<process directive>…... ” and the other arguments. How to fix the problem and make Fressurfer run? Any help is appreciated. Thanks a lot! PS: my Ubuntu is 32-bit and choose the 32-bit version Freesurfer. Jie

2 6

qdec problems
by 汪贵宏 26 Feb '11

26 Feb '11

Hi all, I want to analyse the thickness difference between patients and normals,but I can not understand the results that I got from qdec-analysis .I hope someone can help me. Firstly,as the papers says, the Cortical (surface-based) Analysis measures the Distance between white and pial surfaces , get One value per vertex in result.And also,there are 33 areas when we choose to analyses,and we can only get the thickness of these 33 areas per hemisphere,so,my question is why it has just one thickness value in such a large area on the hemisphere? Secondly,in my opinion,there will be red or green in a large scale if it does exist thickness differences between the patients and normals in one areas,such as "lh_bankssts_thickness",but,the results seems not in that way,why? Do I explain my questions clearly? Thanks, wang

3 2

tutorial course
by Pom Sailasuta 25 Feb '11

25 Feb '11

Hello, Is it too late to register for the April tutorial course at MGH? thanks -- Pom

2 1

mni is already installed
by Pom Sailasuta 25 Feb '11

25 Feb '11

Hi Dr. Greve, mni is already installed, (came with freesurfer software) in /usr/local/freesurfer/mni. thank you -- Pom

2 4

more errors
by Pom Sailasuta 25 Feb '11

25 Feb '11

Hi Bruce, Thank you so much. I got new error as follow ////////////////////////////// Pom@pom-PC subjects]$ recon-all -s 211-1029-MKA_elan -all Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.0.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.0.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer Linux pom-PC.SME 2.6.35.6-45.fc14.i686 #1 SMP Mon Oct 18 23:56:17 UTC 2010 i686 i686 i386 GNU/Linux nu_correct: Command not found. #-------------------------------------------- #@# MotionCor Fri Feb 25 09:46:49 PST 2011 Found 1 runs /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri//001.mgz WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri//001.mgz /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri/rawavg.mgz /usr/local/freesurfer/subjects/211-1029-MKA_elan mri_convert /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri/rawavg.mgz /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri/orig.mgz --conform mri_convert /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri/rawavg.mgz /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri/orig.mgz --conform $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri/rawavg.mgz... TR=4083.33, TE=14.00, TI=0.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, -1, 0) k_ras = (-0, -0, 1) Original Data has (1.0156, 1.0156, 3) mm size and (256, 256, 60) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri/orig.mgz... mri_add_xform_to_header -c /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri/transforms/talairach.xfm /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri/orig.mgz /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Nu Intensity Correction Fri Feb 25 09:47:00 PST 2011 mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.12 2009/12/16 20:15:41 greve Exp $ Linux pom-PC.SME 2.6.35.6-45.fc14.i686 #1 SMP Mon Oct 18 23:56:17 UTC 2010 i686 i686 i386 GNU/Linux Fri Feb 25 09:47:00 PST 2011 nu_correct: Command not found. tmpdir is ./tmp.mri_nu_correct.mni.17383 /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.17383/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.17383/nu0.mnc -odt float $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from orig.mgz... TR=4083.33, TE=14.00, TI=0.00, flip angle=90.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.17383/nu0.mnc... -------------------------------------------------------- Iteration 1 Fri Feb 25 09:47:03 PST 2011 nu_correct -clobber ./tmp.mri_nu_correct.mni.17383/nu0.mnc ./tmp.mri_nu_correct.mni.17383/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.17383/0/ nu_correct: Command not found. ERROR: nu_correct Linux pom-PC.SME 2.6.35.6-45.fc14.i686 #1 SMP Mon Oct 18 23:56:17 UTC 2010 i686 i686 i386 GNU/Linux recon-all -s 211-1029-MKA_elan exited with ERRORS at Fri Feb 25 09:47:03 PST 2011 //////////////////////////////////////////// There is nu_correct in /usr/local/freesurfer/mni/bin as follows: [Pom@pom-PC subjects]$ which nu_correct /usr/local/freesurfer/mni/bin/nu_correct thanks again. -- Pom

2 1

mri_convert error
by Pom Sailasuta 25 Feb '11

25 Feb '11

Hello, I got an error below using mri_convert, please help /////////////////////////////////////////// [Pom@pom-PC mri]$ mri_convert -it dicom -ot mgz /orig/i399386.MRDC.1 001.mgz mri_convert -it dicom -ot mgz /orig/i399386.MRDC.1 001.mgz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /orig/i399386.MRDC.1... Starting DICOMRead2() ERROR: file /orig/i399386.MRDC.1 does not exist. /////////////////////////////////// I am in /usr/local/freesurfer/subjects/211-1029-MKA_elan/mri folder and there is subfolder orig and definitely contains the first GE DICOM file i399386.MRDC.1 and all users has permission to red and write in the subjects dir. thanks for your input. pom

2 1

Re: [Freesurfer] aparcstats2table error
by Alex Hanganu 25 Feb '11

25 Feb '11

Thank you for your quick answer. Chris - it's "/stats/" in the address. Doug - Thanks, mris_anatomical_stats works. For this it was also necessary to copy the .label file in each subjects - "/label/" directory Alex --- En date de : Jeu 24.2.11, Chris Hyatt <Chyatt(a)harthosp.org> a écrit : De: Chris Hyatt <Chyatt(a)harthosp.org> Objet: Re: [Freesurfer] aparcstats2table error À: "FS Mailing List" <Freesurfer(a)nmr.mgh.harvard.edu>, "Alex Hanganu" <hanganu.alexandru(a)yahoo.de> Date: Jeudi 24 février 2011, 18h48 You have /stat/ rather than /stats/ in the address. Have you checked that? >>> Alex Hanganu <hanganu.alexandru(a)yahoo.de> 2/24/2011 12:22 PM >>> Dear Chris, Doug, We created a ROI in qdec (EXMPL.label) and tried to measure it's thickness. The cmd used: aparcstats2table --hemi ?h --subjects 1 2 3 --parc .../DIR/EXMPL.label --meas thickness --t ROI.txt ERROR: cannot find .../freesurfer/subjects/SUBJECT_NAME/stat/EXMPL.label.statsqdec/DIR Can you please tell us what might be the problem ? Sincerely, Alex.

2 1

Subcortical segmentation of a skull-stripped Analyze-formatted image
by andrewkrause＠ucla.edu 24 Feb '11

24 Feb '11

Hello, I'm a complete newbie to FreeSurfer, so I appreciate any and all help you can provide. I am trying to use FreeSurfer to automatically create some masks of subcortical structures, but am having trouble getting the whole process started. When I run "recon-all -autorecon1 -noskullstrip -s FAD" (where FAD is my subject name) it quits with the error "ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)" I am trying to do this to a skull-stripped brain originally in Analyze format (there are no DICOMs since it's actually an average of many skull-stripped scans), to which I've already registered all of the scans I want to study. I used mri_convert to convert the .img file into a .mgz file, but compared to the bert example, the background (non-brain area) is a light gray instead of black. I don't know if this is where the error is occuring, and if it is, how to correct it. If it helps, the scan I'm trying to create masks from has been registered to the ICBM brain template. Let me know what other information you need and thanks for the help, -- Andrew

4 13

Mapping label to subjects
by John Richey 24 Feb '11

24 Feb '11

Dear freesurfer experts, I have what I think is a fairly straighforward task, but the steps are not exactly clear to me. I wish to create a new label on the cortical surface and then map this label to each individual subject in order to extract roi data. I've successfully made my label on the cortical surface for the subject 'fsaverage', however it's not clear to me how to map this back to individual space (that is, to create the corresponding file in SUBJECTS_DIR/$SUBJ/labels/ ) Thanks in advance, any help would be greatly appreciated.

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