Re: [Freesurfer] lGI value is aberrantly high
Wayne, You can try to rerun the surface reconstruction (recon-all -autorecon2-wm -randomness, in order to change the number of vertices, and then recon-all -autorecon3) and then rerun the lgi process (recon-all -lgi), this should solve the problem. If not, please let me know. Marie On Jun 27, 2011, at 10:32 PM, Wayne Su wrote: Hello, I am using FS 5.1 to measure lGI (local Gyrification Index). Only one particular scan failed. Here are some messages: “... 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.” “mris_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 = 0” “mris_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 = 0” 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 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] FNIRT and fslregister
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 ___ 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] surface reconstruction of neonatal brain
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 ___ 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] long_mris_slopes
Hi Martin and all, I would like to ask you if by comparing tp1 thickness-spc with tp2 (and comparing tp2 with tp3) using the base brain between tp1,2 and 3 (altogether) I have messed up methodologically. I was expecting a rise in cortical thickness in certain areas between tp1 and tp2 followed by a greater rise between tp2 and tp3. I did not expect however a host of other changes which were not seen when viewing spc of tp1, 2 and 3 together. Most of these effects seem to be basically mirror-effects e.g. if there is a rise between tp1 and tp2, there is a drop in thickness in the same area between tp2 and tp3 and vice versa. This happened in several subjects and in variable brain regions. I would like to know if this is because of some methodological flaw. For example, should I run the whole longitudinal stream 2 more times (once to compare tp1 and tp2, and the second time to compare tp2 to tp3)? Also, when viewing the spc of tp1, tp2 and tp3 together are we just looking at the change between timepoints 1 and 3? Many thanks for the help, All the best, Seán On 27 June 2011 11:50, Seán Froudist Walsh froud...@tcd.ie wrote: 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.
Re: [Freesurfer] surface reconstruction of neonatal brain
Hi Antonis, you can try running it with the T2 as the brain.mgz and see how it goes. We do this fairly routinely on ex vivo data (which is T2* weighted) and it does ok. Not as well as in vivo where the contrast is what we expect, but it does produce topologically correct and geometrically reasonable surfaces. cheers Bruce On Tue, 28 Jun 2011, Antonis Makropoulos wrote: 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 ___ 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] lGI value is aberrantly high
Hi Marie: I have the same problem. I am doing LGI on a group of Genetic High Risk (for Schizophrenia) subjects (n=77). Here is what I got for one brain: * WARNING -- Problem for vertex iV = 57001, lGI value is aberrantly high (lGI=47.4609)... ...lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface. ERROR: compute_lgi did not create output file '/usr/local/freesurfer/subjects/HM5103/surf/tmp-mris_compute_lgi-rh.pial/rh.pial_lgi.asc'! Linux NeuroImage-Gamma 2.6.32.26-175.fc12.x86_64 #1 SMP Wed Dec 1 21:39:34 UTC 2010 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Tue Jun 28 06:20:34 EDT 2011* Do I do the same thing that you recommended? thanks, Alan On Tue, Jun 28, 2011 at 4:53 AM, Marie Schaer marie.sch...@unige.ch wrote: Wayne, You can try to rerun the surface reconstruction (recon-all -autorecon2-wm *-randomness*, in order to change the number of vertices, and then recon-all -autorecon3) and then rerun the lgi process (recon-all -lgi), this should solve the problem. If not, please let me know. Marie On Jun 27, 2011, at 10:32 PM, Wayne Su wrote: Hello, I am using FS 5.1 to measure lGI (local Gyrification Index). Only one particular scan failed. Here are some messages: “... 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.” “mris_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 = 0” “mris_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 = 0” 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 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.
Re: [Freesurfer] lGI value is aberrantly high
Hi Alan, If you only have this problem with one or just a few subjects, then I am pretty confident that running recon-all -autorecon2-wm -randomness will solve your problem. Otherwise let me know! Marie On Jun 28, 2011, at 3:48 PM, Alan Francis wrote: Hi Marie: I have the same problem. I am doing LGI on a group of Genetic High Risk (for Schizophrenia) subjects (n=77). Here is what I got for one brain: WARNING -- Problem for vertex iV = 57001, lGI value is aberrantly high (lGI=47.4609)... ...lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface. ERROR: compute_lgi did not create output file '/usr/local/freesurfer/subjects/HM5103/surf/tmp-mris_compute_lgi-rh.pial/rh.pial_lgi.asc'! Linux NeuroImage-Gamma 2.6.32.26-175.fc12.x86_64 #1 SMP Wed Dec 1 21:39:34 UTC 2010 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Tue Jun 28 06:20:34 EDT 2011 Do I do the same thing that you recommended? thanks, Alan On Tue, Jun 28, 2011 at 4:53 AM, Marie Schaer marie.sch...@unige.ch wrote: Wayne, You can try to rerun the surface reconstruction (recon-all -autorecon2-wm -randomness, in order to change the number of vertices, and then recon-all -autorecon3) and then rerun the lgi process (recon-all -lgi), this should solve the problem. If not, please let me know. Marie On Jun 27, 2011, at 10:32 PM, Wayne Su wrote: Hello, I am using FS 5.1 to measure lGI (local Gyrification Index). Only one particular scan failed. Here are some messages: “... 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.” “mris_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 = 0” “mris_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 = 0” 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 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] sourcing freesurfer
I just installed freesurfer on Mac OSX and everything went smoothly in installation. But now I am trying to source it, and it's not working. I typed 'csh' into the terminal to launch c-shell, and then entered: [115-18-41-155-wireles1x:/Applications/freesurfer] Kat% setenv FREESURFER_HOME /Applications/freesurfer [115-18-41-155-wireles1x:/Applications/freesurfer] Kat% source $FREESURFER_HOME/SetUpFreeSurfer.csh And it returns: /SetUpFreeSurfer.csh: No such file or directory. I can see that the SetUpFreeSurfer.csh file is in the freesurfer folder, so I'm really not sure what is causing this error. I've tried doing this from different directories, too. Thanks for any help. ___ 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] sourcing freesurfer
Hi Kat are you including the and in your setenv line? You shouldn't. It should be: setenv FREESURFER_HOME /Applications/freesurfer cheers Bruce On Tue, 28 Jun 2011, Kat Mott wrote: I just installed freesurfer on Mac OSX and everything went smoothly in installation. But now I am trying to source it, and it's not working. I typed 'csh' into the terminal to launch c-shell, and then entered: [115-18-41-155-wireles1x:/Applications/freesurfer] Kat% setenv FREESURFER_HOME /Applications/freesurfer [115-18-41-155-wireles1x:/Applications/freesurfer] Kat% source $FREESURFER_HOME/SetUpFreeSurfer.csh And it returns: /SetUpFreeSurfer.csh: No such file or directory. I can see that the SetUpFreeSurfer.csh file is in the freesurfer folder, so I'm really not sure what is causing this error. I've tried doing this from different directories, too. Thanks for any help. ___ 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] MRI_Convert error on recon-all process
Hello, My name is Jordi Casals. I've been trying to process some subjects with recon-all, but the procees is giving me this error: SUBJECT DFF_082 DATE Tue Jun 28 16:58:40 CEST 2011 USER neuro HOST td547.pic.es PROCESSOR x86_64 OS Linux Linux td547.pic.es 2.6.18-238.9.1.el5 #1 SMP Tue Apr 12 18:53:46 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.313.2.6 2010/08/04 15:50:56 nicks Exp $ /SOFTWR/freesurfer5/bin/recon-all PWD $PATH/DFF_082 CMD mri_convert /DICOM/T13D/DFF_082/DFF_082_0002 $PATH/DFF_082/mri/orig/001.mgz and the recon-all log have the following lines: mri_convert /DICOM/T13D/DFF_082/DFF_082_0002 $PATH/DFF_082/mri/orig/001.mgz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /DICOM/T13D/DFF_082/DFF_082_0002... Starting DICOMRead2() dcmfile = /DICOM/T13D/DFF_082/DFF_082_0002 dcmdir = /DICOM/T13D/DFF_082 WARNING: tag ImageNumber not found WARNING: tag image orientation not found Ref Series No = 301 ERROR: bits = 0 not supported. Send email to freesurfer@nmr.mgh.harvard.edu Linux td547.pic.es 2.6.18-238.9.1.el5 #1 SMP Tue Apr 12 18:53:46 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux recon-all -s DFF_082 exited with ERRORS at Tue Jun 28 16:58:40 CEST 2011 I searched for possible solutions but some of them I don't really understand what I really have to do and the other solutions didn't seem to work. I don't know how to correct the error to reach the complete execution of the process. If someone can help me or guide me to the solution, I would be very grateful. Thank you, Jordi. ___ 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] Recon-all with mris_fix_topology error
Hello FreeSurfer community, I am Jordi Casals, from Barcelona. After few days trying to process a set of modificactions done to a subject (pial, white matter and control points), I still have this error, about mris_fix_topology. I don't know where is the problem, because I have done a lot of subjects in the same way as these one and the other two that give me this error. SUBJECT SRN_005 DATE Wed Jun 22 00:58:31 CEST 2011 USER neuro HOST td560.pic.es PROCESSOR x86_64 OS Linux Linux td560.pic.es 2.6.18-238.9.1.el5 #1 SMP Tue Apr 12 18:53:46 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.133.2.43 2009/04/22 22:34:03 nicks Exp $ /SOFTWR/freesurfer/bin/recon-all PWD $PATH/SRN_005/scripts CMD mris_fix_topology -mgz -sphere qsphere.nofix -ga SRN_005 rh It would be be really great if someone can help me or give me some guides to understand a little bit more the problem and to reach a proper execution. Thank you again, Jordi. ___ 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] MRI_Convert error on recon-all process
Hi Jordi where did your dicoms come from? Bruce On Tue, 28 Jun 2011, Jordi Casals wrote: Hello, My name is Jordi Casals. I've been trying to process some subjects with recon-all, but the procees is giving me this error: SUBJECT DFF_082 DATE Tue Jun 28 16:58:40 CEST 2011 USER neuro HOST td547.pic.es PROCESSOR x86_64 OS Linux Linux td547.pic.es 2.6.18-238.9.1.el5 #1 SMP Tue Apr 12 18:53:46 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.313.2.6 2010/08/04 15:50:56 nicks Exp $ /SOFTWR/freesurfer5/bin/recon-all PWD $PATH/DFF_082 CMD mri_convert /DICOM/T13D/DFF_082/DFF_082_0002 $PATH/DFF_082/mri/orig/001.mgz and the recon-all log have the following lines: mri_convert /DICOM/T13D/DFF_082/DFF_082_0002 $PATH/DFF_082/mri/orig/001.mgz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /DICOM/T13D/DFF_082/DFF_082_0002... Starting DICOMRead2() dcmfile = /DICOM/T13D/DFF_082/DFF_082_0002 dcmdir = /DICOM/T13D/DFF_082 WARNING: tag ImageNumber not found WARNING: tag image orientation not found Ref Series No = 301 ERROR: bits = 0 not supported. Send email to freesurfer@nmr.mgh.harvard.edu Linux td547.pic.es 2.6.18-238.9.1.el5 #1 SMP Tue Apr 12 18:53:46 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux recon-all -s DFF_082 exited with ERRORS at Tue Jun 28 16:58:40 CEST 2011 I searched for possible solutions but some of them I don't really understand what I really have to do and the other solutions didn't seem to work. I don't know how to correct the error to reach the complete execution of the process. If someone can help me or guide me to the solution, I would be very grateful. Thank you, Jordi. ___ 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 using tkmedit
Hello, 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 Thanks for helping. Antonella This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. ___ 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] Tkmedit error
-- Dr.Antonella Kis, PhD Clinical Research Project Coordinator The Hospital for Sick Children (SickKids) Diagnostic Imaging Department Neurosciences and Mental Health Sessional Lecturer Life Sciences, Physics Department University of Toronto at Scarborough Hello, 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 Thanks for helping. Antonella This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. ___ 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] Error using tkmedit
Hi Antonella sorry for the delay. Many of the FS developers have been away at the FS/FSL course and/or HBM. We'll try to get back to you today or tomorrow. Sounds like your linux installation is missing this library though and that you will need to install it. cheers Bruce On Tue, 28 Jun 2011, Antonella Kis wrote: Hello, 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 libra ries: libXmu.so.6: cannot open shared object file: No such file or directory Thanks for helping. Antonella This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. ___ 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] Error using tkmedit
Hi Antonella, I found similar problems in the FreeSurfer mailing list archives: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07366.html http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg03433.html http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07130.html Depending on what installation you have and where the problem occurred, maybe one of the above could help you. Allison On Tue, 28 Jun 2011, Bruce Fischl wrote: Hi Antonella sorry for the delay. Many of the FS developers have been away at the FS/FSL course and/or HBM. We'll try to get back to you today or tomorrow. Sounds like your linux installation is missing this library though and that you will need to install it. cheers Bruce On Tue, 28 Jun 2011, Antonella Kis wrote: Hello, 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 libra ries: libXmu.so.6: cannot open shared object file: No such file or directory Thanks for helping. Antonella This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. ___ 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] mri_volcluster in single direction
Hello All, I've been using fslstats to create a mask of voxels reaching a certain threshold and then using mri_volcluster to reduce the mask down to just clusters above 3 voxels. Now we're trying to filter them down to just those clusters that have more than 3 contiguous voxels in a single direction, rather than total volume. I can't find anything in the help file on this, but I was wondering if there's possibly an undocumented flag in mri_volcluster that would do this? Thanks! - G. William Chapman IV ENG BME 2012 wchap...@bu.edu (617) 383-9042 ___ 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] your mail
Hi Antonella, gzip doesn't recognize your file. Can you just send us a tif? Bruce On Tue, 28 Jun 2011, Antonella Kis wrote: Once again thanks Bruce. I am posting this message also to the list: I am having problem with tksurfer. When I run: tksurfer lh inflated for the Freesurfer data sample called bert, the image is looking totally weird. I don't understand why I cannot get the correct lh inflated since there is no error while running tksurfer. I attached the archive image of the lh inflated for the bert case after running tksurfer. ___ 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] Tracula question: group analysis
Hello Tracula Developers Users, I can follow how to use the diffusion measures from pathstats.overall.txt for each subject to run a group analysis on the tracts. On the other hand I noticed there is also the pathstats.byvoxel.txt which contains various diffusion measures in each voxel along the highest probability path. What are your suggested steps for analyzing this text file for group comparison? I am guessing developers had an analysis method in mind when they decided to print this file out. Thank you in advance for your help. Best, Mary ___ 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] stats on masked functional data
Hello All, Looks like this question slipped through. I have a functional beta value overlay as a .mgh file and a V1 label file and I want to compute the average beta value within that mask for each subject. How do I do this ? Thanks a lot Ri ___ 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] stats on masked functional data
Hi Ri Doug may have something to do this, but if not it would be easy enough in matlab Bruce On Tue, 28 Jun 2011, Ritobrato Datta wrote: Hello All, Looks like this question slipped through. I have a functional beta value overlay as a .mgh file and a V1 label file and I want to compute the average beta value within that mask for each subject. How do I do this ? Thanks a lot Ri ___ 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] Trac-all: using bvecs/bvals from FSL folder
Hi Freesurfer experts, I was wondering if you all had some advice for getting trac-all up and running. I'm trying to work up a trac-all configuration file for a group of subjects, previously processed in FSL. We extracted the Siemens bvec and bval files for the FSL pipeline when importing the dicoms through dicom2nii. I know FSL bval and bvec files are organized in a different matrix shape from what Trac-all wants. Has anyone had sucess with transforming these files? Should/do I need to worry about whether to flip the orientation on bvec files as the images seem to get flipped in the early steps of Trac-all? Also is it possible to feed the configuration file a list of bvec files (for each subject) similar to how we feed it the dicom directory for each subject, or should I create a configuration script for each subject pointing to their bvec file specifically. Thanks in advance for help! Cheers, Jared ___ 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] Tracula question: group analysis
Hi Maryam - You could compare the different measures like FA or MD across subjects along the length of the pathway. There will be a different number of points along the pathway for each subject, so you'd have to interpolate the data points from all your subjects to do a point by point comparison. This can be done in matlab for example, and hopefully there'll be a built-in command for this in the next release! Hope this helps, a.y On Tue, 28 Jun 2011, Maryam Moteabbed wrote: Hello Tracula Developers Users, I can follow how to use the diffusion measures from pathstats.overall.txt for each subject to run a group analysis on the tracts. On the other hand I noticed there is also the pathstats.byvoxel.txt which contains various diffusion measures in each voxel along the highest probability path. What are your suggested steps for analyzing this text file for group comparison? I am guessing developers had an analysis method in mind when they decided to print this file out. Thank you in advance for your help. Best, Mary ___ 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] Trac-all: using bvecs/bvals from FSL folder
Hi Jared - Have you looked at $FREESURFER_HOME/bin/dmrirc.example? You can specify bvecfile, bvalfile, and nb0. Currently these are assumed to be the same for all subjects. The format is 3 columns for bvecs, single column for bvals. Otherwise you shouldn't have to do anything else to them (hopefully! :) a.y On Tue, 28 Jun 2011, Jared Saletin wrote: Hi Freesurfer experts, I was wondering if you all had some advice for getting trac-all up and running. I'm trying to work up a trac-all configuration file for a group of subjects, previously processed in FSL. We extracted the Siemens bvec and bval files for the FSL pipeline when importing the dicoms through dicom2nii. I know FSL bval and bvec files are organized in a different matrix shape from what Trac-all wants. Has anyone had sucess with transforming these files? Should/do I need to worry about whether to flip the orientation on bvec files as the images seem to get flipped in the early steps of Trac-all? Also is it possible to feed the configuration file a list of bvec files (for each subject) similar to how we feed it the dicom directory for each subject, or should I create a configuration script for each subject pointing to their bvec file specifically. Thanks in advance for help! Cheers, Jared ___ 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 in qdec design analyze
Hi Freesurfers, There existed an error Error in Analyze: Couldn't open file /usr/local/freesurfer/subjects/PD1/surf/lh.thickness.fwhm10.fsaverage.mgh, when I clicked on the button Analyze in qdec design. I have only done recon-all with my data (PD-MPR group and Controled-MPR group). Did I miss one step before qdec analysis? Thanks ___ 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.
