Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

lGI value is aberrantly high
by Wayne Su 28 Jun '11

28 Jun '11

Hello, I am using FS 5.1 to measure lGI (local Gyrification Index). Only one particular scan failed. Here are some messages: ³... remeasuring lGI value for vertex iV = 65101. It may take a few minutes. WARNING -- Problem for vertex iV = 65101, lGI value is aberrantly high (lGI=56.5472)... ...lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface.² ³mris_euler_number ../surf/lh.orig \n euler # = v-e+f = 2g-2: 143555 - 430659 + 287106 = 2 --> 0 holes F =2V-4: 287106 = 287110-4 (0) 2E=3F: 861318 = 861318 (0) total defect index = 0² ³mris_euler_number ./lh.pial-outer-smoothed ================= euler # = v-e+f = 2g-2: 65560 - 196674 + 131116 = 2 --> 0 holes F =2V-4: 131116 = 131120-4 (0) 2E=3F: 393348 = 393348 (0) total defect index = 0² I re-run the recon-all -s 01_097_Y0 -hemi lh -autorecon2 autorecon3 and recon-all -s 01_097_Y0 -localGI It stopped at the same vertex. Could you please let me know anything I can do to overcome this issue? Thank you very much. Wayne

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surface reconstruction of neonatal brain
by Antonis Makropoulos 28 Jun '11

28 Jun '11

Hello everybody, I would like to ask you about the topology correction algorithm of freesurfer. I have produced the tissue segmentation for a number of neonatal brains, but as they are not topologically accurate, I would like to try your algorithm to fix the surfaces. As I can see, the mris_fix_topology step requires the brain.mgz volume, but I am not sure how to produce it. I have read the paper "A METHODOLOGY FOR ANALYZING CURVATURE IN THE DEVELOPING BRAIN FROM PRETERM TO ADULT" where the different tissues are substituted by uniform intensities recognised by freesurfer, but I would like to use the original image information if possible. Is there any way to make use of the T1/T2 images (transform them) in the mris_fix_topology step? Thank you very much for your time. With kind regards, Antonis

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rtview and color bar
by Michelle Umali 28 Jun '11

28 Jun '11

Hi Freesurfers! I ran rtview, and I couldn't find a color bar/legend. I'm just wondering how thow the colors get assigned. Is each color a position of wedge stimulus? I'm trying to define V1/V2/V3 boundaries and was wondering how to get the horizontal and vertical meridians. Any help would be most welcome. Thanks. Michelle

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FNIRT and fslregister
by marco battaglini 28 Jun '11

28 Jun '11

Hi all, regarding the VolumeRoiCorticalThickness pipeline, is it possible to apply non linear transformation as obtained by FNIRT, instead of linear transformation as obtained by FLIRT? If yes, in which way? By using fslregister? Thank you marco

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recommended voxel size
by Jessica Liu 27 Jun '11

27 Jun '11

Hi all, I know that freesurfer recommends an isotropic voxel size, but I found that a voxel size of 1.2x1.2x1.6 at 1.5T actually gives a better resolution for my data. Would the different voxel size significantly affect the outcome of the volumetric segmentation? Thanks! Jessica

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Problems with Tkmedit
by Antonella Kis 27 Jun '11

27 Jun '11

Hi, I have some problems with tkmedit. The recon-all finished without problems, but when using tkmedit the following error occured: /usr/local/freesurfer//tktools/tkmedit.bin: error while loading shared libraries: libXmu.so.6: cannot open shared object file: No such file or directory I was running: tkmedit NPI002 brainmask.mgz \-aux T1.mgz -surfs \-segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt Please help. Thank you. Antonella

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Hippocampal subfield segmentations
by newfei＠nmr.mgh.harvard.edu 27 Jun '11

27 Jun '11

Hi, I have a couple of questions about hippocampal subfield segmentations generated using the kvlQuantifyHippocampalSubfieldSegmentations.sh script (recons performed using version 5.1). The volumes obtained for each individual subfield are systematically larger than the total hippocampal segmentation volume generated by the recon-all. These volumes are also larger than the volumes in the paper (van Leemput, 2009) where CA1: 537-935 mm^3 and CA4/DG: 526 mm^3. For example in the dataset that I am working on , a typical subfield volume in the right hippocampus would be 2270 mm^3; CA2-3: 6477 mm^3; CA4-DG: 3796 mm^3.The sum of all subfields is 24437 mm^3. c.f. hippocampal volume obtained from aseg.stats:3688 mm^3 First, are my values correct? Second, are the discrete subfield volumes supposed to match up with the hippocampal volume from aseg.stats? Thanks, New Fei

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Freeview Overlay
by iacono＠nmr.mgh.harvard.edu 27 Jun '11

27 Jun '11

Hi all, I haven't had any answer to my post, so I give another try. Hope it doesn't bother you. I am trying to overlay a map on a specific subcortical structure (the caudate). -I obtained the surface of the structure using the command: mri_tessellate structure.nii.gz 1 lh.structure.surf -then I projected my map on the surface using: mri_vol2surf --mov map.nii --regheader structure --hemi lh --surf structure.surf --projdist 0 --fwhm 5 --out projected_map.mgz --interp trilinear Everything seems to work properly. I am able to see the result using tksurfer. However, when I try to overlay projected_map.mgz on lh.structure.surf using freeview I experience a segmentation fault issue. It seems that the software looks for the WM, the pial, the curv, etc surfaces. Obviously I don't have these information, since I am projecting the map only on the caudate nucleus. Is it mandatory to have these inputs? Could you give me an advice about that? Thanks Maria

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Help with tkmedit
by Sandy Goncalves 27 Jun '11

27 Jun '11

Hello, I am brand new to this software (and command for that matter) and need some help. After installing all the software, when I enter tkmedit in the xterminal, I receive an error message that looks like this: X Error of failed request: BadRequest (invalid request code or no such operation) Major opcode of failed request: 128 (Apple-DRI) Minor opcode of failed request: 1 () Serial number of failed request: 16 Current serial number in output stream: 16 Interestingly, when I type in tksurfer, this works. So I'm not sure what I should do in order to get tkmedit to work! Any help would be great! Thanks, Sandy

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Error while loading shared libraries: libXmu.so.6
by Antonella Kis 27 Jun '11

27 Jun '11

Dear Freesurfer experts, I am trying to visualize the volumes and surfaces but I got an error wile using tkmedit. I will appreciate any help, suggestions. This is from bugr: FREESURFER_HOME: /usr/local/freesurfer/ Build stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 RedHat release: Fedora release 12 (Constantine) Kernel info: Linux 2.6.32.23-170.fc12.x86_64 x86_64 Here is what I was running. It also shows the error: [root@EW-LNX3 elysa]# tcsh setenv FREESURFER_HOME /usr/local/freesurfer/ setenv SUBJECTS_DIR $FREESURFER_HOME/subjects/june2011/_orig_/ tkmedit NPI002 brainmask.mgz \-aux T1.mgz -surfs \-segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt /usr/local/freesurfer//tktools/tkmedit.bin: error while loading shared libraries: libXmu.so.6: cannot open shared object file: No such file or directory Is this because I use a licence from the same version but installed on another computer? Thank you very much! Antonella

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