Re: [Freesurfer] Problems with hippocampal subfield segmentation
Hi Juergen, This looks like an error very early in the hippocampal subfield segmentation routines. Could you please send me the file hippo-subfields.log (found in the scripts subdirectory of the subject in question), and ideally the files nu.mgz, aseg.mgz, and transforms/talairach.xfm files (found in the mri subdirectory)? Thanks, Koen 2011/6/24 Jürgen Hänggi j.haen...@psychologie.uzh.ch: Dear FS experts We have some problems with the segmentation of hippocampal subfields. The recon-all finished without problems, but when using GEMS the following error occured: nan nan nan nan nan nan nan nan nan Singular: 0 m_BoundingBoxSize: [94, 66,144] minimalMappedCoordinate: [3.40282e+38, 3.40282e+38,3.40282e+38] maximalMappedCoordinate: [1.17549e-38, 1.17549e-38,1.17549e-38] Cropping with min [-1932735280 -1932735280 -1932735280] and max [-214748367 -214748367 -214748367] /Applications/freesurfer/bin/kvlSegmentHippocampalSubfields.sh: line 18: 58718 Segmentation fault kvlSegmentWithoutGUI configurationFileDeformableRegistration.txt failed to do kvlSegmentWithoutGUI configurationFileDeformableRegistration.txt Darwin Reinhard-Drobetzs-iMac.local 10.7.0 Darwin Kernel Version 10.7.0: Sat Jan 29 15:17:16 PST 2011; root:xnu-1504.9.37~1/RELEASE_I386 i386 recon-all -s 13716099 exited with ERRORS at Fri Jun 24 00:12:30 CEST 2011 I guess the problem occurred due to the NANs in the matrix, isn't it? Thanks in advance Regards Jürgen Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] long_mris_slopes
Hi Martin, That worked! Thanks a lot, Seán On 23 June 2011 18:22, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Sean, I think the --out... names need to be without the ending (mgh) so for example --out-avg=long23.thickness-avg Maybe that'll fix it. Best, Martin On Thu, 2011-06-23 at 09:12 -0700, Seán Froudist Walsh wrote: Dear FreeSurfers, I am looking for a little help comparing longitudinal data. I have three timepoints on each patient and have been able to get individual spc-thickness maps using the long_mris_slopes command where my table included all three time points. I would however like to compare different timepoints with each other: tp3-tp2 and tp2-tp1. I was hoping it would be as simple as specifying a new qdec table including (for example) only tp3 and tp2, and giving new output names using the following command long_mris_slopes --qdec ./qdec/long.qdec.tableTP23.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --out-avg=long23.thickness-avg.mgh --out-rate=long23.thickness-rate.mgh --out-pc1=long23.thickness-pc1.mgh --out-spc=long23.thickness-spc.mgh --out-stack=long23.thickness-stack.mgh --out-label=long23.cortex --time scan --qcache fsaverage but I get the following error: mris_calc: Sorry, but I seem to have encountered an error. While making backup of internal data arrays, it seems that some of the backups already exist. I'm not really sure what the internal data arrays are, and would greatly appreciate any help. Many thanks in advance and all the best, Seán ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Error while loading shared libraries: libXmu.so.6
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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Freeview Overlay
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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Help with tkmedit
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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Freeview Overlay
Hi Maria, I've tested the files you sent me and were able to replicate the problem. Will work on it asap. Sorry about the delay. Ruopeng On 06/27/2011 12:13 PM, iac...@nmr.mgh.harvard.edu wrote: 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Freeview Overlay
Hi Maria, The fix is done and should be available in tomorrow's dev build. Ruopeng On 06/27/2011 12:13 PM, iac...@nmr.mgh.harvard.edu wrote: 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Hippocampal subfield segmentations
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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Hippocampal subfield segmentations
Hi New Fei, The subfield volume estimates are given in number of voxels of size 0.5mm isotropic - you'd need to divide by a factor of 8 to obtain measurments in mm^3. The sum of the subfield volumes will not be the same as the total hippocampal volume in aseg.stats because the used computational methods are different. They should be close, though. Hope this helps, Koen On Mon, Jun 27, 2011 at 1:25 PM, new...@nmr.mgh.harvard.edu wrote: 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Problems with Tkmedit
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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] lGI value is aberrantly high
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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] recommended voxel size
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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] recommended voxel size
Hi Jessica, what do you mean by better resolution for my data? Bruce On Mon, 27 Jun 2011, Jessica Liu wrote: 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
