Re: [Freesurfer] Recon-all with mris_fix_topology error
Hi Bruce, What I included on te previous e-mail was the content of the recon-all.error. I thought that this would be sufficient. I think that this is the error that you're asking me about. CORRECTING DEFECT 60 (vertices=8674, convex hull=4036) normal vector of length zero at vertex 111480 with 0 faces vertex 111480 has 0 face Numerical result out of range Thank you :) On Tue, Jun 28, 2011 at 6:12 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Jordi, what is the error? You didn't include it Bruce On Tue, 28 Jun 2011, Jordi Casals wrote: 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. 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/**compliancelinehttp://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] MRI_Convert error on recon-all process
Hi Bruce, The machine is a 3T Philips Achieva. On Tue, Jun 28, 2011 at 6:10 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: 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 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 volume padding in pipeline
Good day everyone, I received a Freesurfer processed MRI volume from a college and would like to compare it to the unprocessed data. Alas Freesurfer padded the MRI volume from [384 384 256] to [385 385 385]. I would like to revert this padding! Can someone please be kind enough to tell me in which way the pads are added, ie. how much is added on each side of each dimension. Thanks a lot, Lukas ___ 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] SupraTentorial Volume question
Dear Freesurfer experts, I posted one week ago a question about the SupraTentorial Volume that is indicated in the aseg.stats but unfortunately did not receive any suggestions as yet. 1. SupraTentorial Vol. is defined as Cortex + CorticalWhiteMatter + SubCortGray (http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats) but when I sum up these columns myself from the aseg.stats I do not arrive at the exact value of SupraTentorial Vol that is indicated in the same aseg.stats. For some of my subjects this value is higher, for some it is lower. What could be the reason for these differences? Is CSF and ventricle volume already subtracted from the SupraTentorial Volume? 2. Is it possible to exclude lesions from the volume-based measures by incorporating a self-defined lesion mask for each subject? Any help or suggestions is very much appreciated! Ruthger Righart (PhD) Institute for Stroke and Dementia Research (ISD) Klinikum der Universität München Max-Lebsche-Platz 30 81377 Munich | Germany ruthger.righ...@med.uni-muenchen.de ___ 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] Recon-all with mris_fix_topology error
usually that means that the partition you are working on ran out of space. Can you check? cheers Bruce On Wed, 29 Jun 2011, Jordi Casals wrote: Hi Bruce, What I included on te previous e-mail was the content of the recon-all.error. I thought that this would be sufficient. I think that this is the error that you're asking me about. CORRECTING DEFECT 60 (vertices=8674, convex hull=4036) normal vector of length zero at vertex 111480 with 0 faces vertex 111480 has 0 face Numerical result out of range Thank you :) On Tue, Jun 28, 2011 at 6:12 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Jordi, what is the error? You didn't include it Bruce On Tue, 28 Jun 2011, Jordi Casals wrote: 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. 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] MRI_Convert error on recon-all process
and the dicoms are right off the machine? Hmmm. Can you send us a set so we can see what went wrong? cheers Bruce On Wed, 29 Jun 2011, Jordi Casals wrote: Hi Bruce, The machine is a 3T Philips Achieva. On Tue, Jun 28, 2011 at 6:10 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: 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 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 volume padding in pipeline
Hi Lukas, try: mri_convert -rl rawavg.mgz orig.mgz orig.rawavg.mgz or replace orig.mgz with whatever volume you want to convert cheers Bruce On Wed, 29 Jun 2011, Lukas Fiederer wrote: Good day everyone, I received a Freesurfer processed MRI volume from a college and would like to compare it to the unprocessed data. Alas Freesurfer padded the MRI volume from [384 384 256] to [385 385 385]. I would like to revert this padding! Can someone please be kind enough to tell me in which way the pads are added, ie. how much is added on each side of each dimension. Thanks a lot, Lukas ___ 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] SupraTentorial Volume question
Hi Ruthger I'll leave 1 for Nick or Doug. As for 2, the easiest thing to do is the put your lesion mask directly into the aseg.mgz and rerun the segstats. You can find the appropriate label in FreeSurferColorLUT.txt and just replace the voxels values in aseg.mgz that correspond to your mask with the lesion value. cheers Bruce On Wed, 29 Jun 2011, Righart, Ruthger Dr. wrote: Dear Freesurfer experts, I posted one week ago a question about the SupraTentorial Volume that is indicated in the aseg.stats but unfortunately did not receive any suggestions as yet. 1. SupraTentorial Vol. is defined as Cortex + CorticalWhiteMatter + SubCortGray (http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats) but when I sum up these columns myself from the aseg.stats I do not arrive at the exact value of SupraTentorial Vol that is indicated in the same aseg.stats. For some of my subjects this value is higher, for some it is lower. What could be the reason for these differences? Is CSF and ventricle volume already subtracted from the SupraTentorial Volume? 2. Is it possible to exclude lesions from the volume-based measures by incorporating a self-defined lesion mask for each subject? Any help or suggestions is very much appreciated! Ruthger Righart (PhD) Institute for Stroke and Dementia Research (ISD) Klinikum der Universität München Max-Lebsche-Platz 30 81377 Munich | Germany ruthger.righ...@med.uni-muenchen.de ___ 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] registration with Melodic
Hi all, I have manually registered fMRI data that I want to run ICA on, and I want Melodic to use my register.dat file, not re-register the data using its own algorithm. Since there doesn't seem to be any way to use the register.dat file as an input, I've been trying to figure out a way to apply the registration info to the .nii file and then simply uncheck the registration options in Melodic. I used a bit of code I found in the forum archives to try this, which created, using the f.nii and register.dat file, a file called f.anat.nii. But when I tried to use this as the 4D input for Melodic I got the error 'Child process exited abnormally.' I used the following to perform the transformation into f.anat.nii: mri_vol2vol --mov f.nii --reg register.dat --fstarg --o f.anat.nii Any thoughts on how to create an input that Melodic will accept so that it will use my registration? Thanks much, Kat ___ 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 with Tkmedit
Hi Antonella what video card are you using? Did you try updating your video driver? cheers Bruce On Wed, 29 Jun 2011, Antonella Kis wrote: Good morning, Thank you very much Bruce. I attached the tiff file and I am posting my message again on the list: I am having problem with tksurfer. When I run: tksurfer lh inflated for NPI002, 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 tiff image for the lh inflated for the NPI002 case after running tksurfer. I get similar image for the bert's data included as a freesurfer sample data. 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.
Re: [Freesurfer] Freesurfer Digest, Vol 88, Issue 86
Good afternoon Bruce, I am not sure what video card I am using (and I am not sure how to do the updating for my video driver) but I could see these surfaces on the same computer while using an old Freesurfer version V.5.0. I saved this old version on my computer under freesurfer_backup and I re-installed the new version V.5.1.0. (my FREESURFER_HOME directory is directed to the new version v.5.1.0). I wonder if this maybe the reason or there maybe some problem with my insatllation? Many thanks for helping. Antonella From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of freesurfer-requ...@nmr.mgh.harvard.edu [freesurfer-requ...@nmr.mgh.harvard.edu] Sent: Wednesday, June 29, 2011 12:00 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 88, Issue 86 Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-requ...@nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-ow...@nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than Re: Contents of Freesurfer digest... Today's Topics: 1. Re: Error with Tkmedit (Bruce Fischl) -- Message: 1 Date: Wed, 29 Jun 2011 10:49:56 -0400 (EDT) From: Bruce Fischl fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Error with Tkmedit To: Antonella Kis ator...@yahoo.com Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.lrh.2.00.1106291049290.8...@gate.nmr.mgh.harvard.edu Content-Type: text/plain; charset=iso-8859-15 Hi Antonella what video card are you using? Did you try updating your video driver? cheers Bruce On Wed, 29 Jun 2011, Antonella Kis wrote: Good morning, Thank you very much Bruce. I attached the tiff file and I am posting my message again on the list: I am having problem with tksurfer. When I run: ?tksurfer lh inflated for NPI002, 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 tiff? image for the lh inflated for the NPI002 case after running tksurfer. I get similar image for the bert's data included as a freesurfer sample data. Thank you! Antonella -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer End of Freesurfer Digest, Vol 88, Issue 86 ** 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. 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
Re: [Freesurfer] Freesurfer Digest, Vol 88, Issue 86
hmmm, not sure what's up with that. Nick and Krish: any ideas? On Wed, 29 Jun 2011, Antonella Kis wrote: Good afternoon Bruce, I am not sure what video card I am using (and I am not sure how to do the updating for my video driver) but I could see these surfaces on the same computer while using an old Freesurfer version V.5.0. I saved this old version on my computer under freesurfer_backup and I re-installed the new version V.5.1.0. (my FREESURFER_HOME directory is directed to the new version v.5.1.0). I wonder if this maybe the reason or there maybe some problem with my insatllation? Many thanks for helping. Antonella From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of freesurfer-requ...@nmr.mgh.harvard.edu [freesurfer-requ...@nmr.mgh.harvard.edu] Sent: Wednesday, June 29, 2011 12:00 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 88, Issue 86 Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-requ...@nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-ow...@nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than Re: Contents of Freesurfer digest... Today's Topics: 1. Re: Error with Tkmedit (Bruce Fischl) -- Message: 1 Date: Wed, 29 Jun 2011 10:49:56 -0400 (EDT) From: Bruce Fischl fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Error with Tkmedit To: Antonella Kis ator...@yahoo.com Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.lrh.2.00.1106291049290.8...@gate.nmr.mgh.harvard.edu Content-Type: text/plain; charset=iso-8859-15 Hi Antonella what video card are you using? Did you try updating your video driver? cheers Bruce On Wed, 29 Jun 2011, Antonella Kis wrote: Good morning, Thank you very much Bruce. I attached the tiff file and I am posting my message again on the list: I am having problem with tksurfer. When I run: ?tksurfer lh inflated for NPI002, 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 tiff? image for the lh inflated for the NPI002 case after running tksurfer. I get similar image for the bert's data included as a freesurfer sample data. Thank you! Antonella -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer End of Freesurfer Digest, Vol 88, Issue 86 ** 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. 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] Over-smoothing of pial surface
Hi, I am trying to extract the pial surface for one of my subjects using freesurfer. Unfortunately, the last couple times that I ran recon-all, it generated a surface that was overly smoothed. I suspect this is due to a poor contrast in my MRI images. I tried to edit them via matlab and run them again. First, I got a talairach transform error and when I re-ran it with the -notal-check flag, I got a global region empty error. I was wondering if there is a way to enhance the mri images in freesurfer to obtain better contrast for a more accurate pial surface. Please let me know what is the best way to tackle this problem. I do not think it's the version of freesurfer, because the pial surface was created fine for some of the other subjects. Thank you, YP ___ 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 recon-all function
Hi, I am currently trying to use the recon-all function. It works fine on an older computer, but my group is attempting to get freesurfer up and running on a newer computer. The subject data is located in a folder called 2645166 as shown in the following command. When I run the command: recon-all -s 2645166 -all I get the following error after the script runs for about a minute: ERROR: avi2talxfm failed, see transforms/talairach_avi.log Linux dell3 2.6.35.6-45.fc14.x86_64 #1 SMP Mon Oct 18 23:57:44 UTC 2010 x86_64 x86_64 x86_64 GNU/Linux The output of your bugr script gives: FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 RedHat release: Fedora release 14 (Laughlin) Kernel info: Linux 2.6.35.6-45.fc14.x86_64 x86_64 A brief internet search found nothing regarding this avi2talxfm function. Any suggestions and/or help would be greatly appreciated. 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.
Re: [Freesurfer] error using recon-all function
Hi Ryan, what is in transforms/talairach_avi.log? cheers Bruce On Wed, 29 Jun 2011, Ryan Hutten wrote: Hi, I am currently trying to use the recon-all function. It works fine on an older computer, but my group is attempting to get freesurfer up and running on a newer computer. The subject data is located in a folder called 2645166 as shown in the following command. When I run the command: recon-all -s 2645166 -all I get the following error after the script runs for about a minute: ERROR: avi2talxfm failed, see transforms/talairach_avi.log Linux dell3 2.6.35.6-45.fc14.x86_64 #1 SMP Mon Oct 18 23:57:44 UTC 2010 x86_64 x86_64 x86_64 GNU/Linux The output of your bugr script gives: FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 RedHat release: Fedora release 14 (Laughlin) Kernel info: Linux 2.6.35.6-45.fc14.x86_64 x86_64 A brief internet search found nothing regarding this avi2talxfm function. Any suggestions and/or help would be greatly appreciated. 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.
Re: [Freesurfer] SupraTentorial Volume question
Hi Ruthger, you won't get the exact number because the aseg.stats file is computed with partial volume correction. doug On 6/29/11 9:14 AM, Bruce Fischl wrote: Hi Ruthger I'll leave 1 for Nick or Doug. As for 2, the easiest thing to do is the put your lesion mask directly into the aseg.mgz and rerun the segstats. You can find the appropriate label in FreeSurferColorLUT.txt and just replace the voxels values in aseg.mgz that correspond to your mask with the lesion value. cheers Bruce On Wed, 29 Jun 2011, Righart, Ruthger Dr. wrote: Dear Freesurfer experts, I posted one week ago a question about the SupraTentorial Volume that is indicated in the aseg.stats but unfortunately did not receive any suggestions as yet. 1. SupraTentorial Vol. is defined as Cortex + CorticalWhiteMatter + SubCortGray (http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats) but when I sum up these columns myself from the aseg.stats I do not arrive at the exact value of SupraTentorial Vol that is indicated in the same aseg.stats. For some of my subjects this value is higher, for some it is lower. What could be the reason for these differences? Is CSF and ventricle volume already subtracted from the SupraTentorial Volume? 2. Is it possible to exclude lesions from the volume-based measures by incorporating a self-defined lesion mask for each subject? Any help or suggestions is very much appreciated! Ruthger Righart (PhD) Institute for Stroke and Dementia Research (ISD) Klinikum der Universität München Max-Lebsche-Platz 30 81377 Munich | Germany ruthger.righ...@med.uni-muenchen.de ___ 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 ___ 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, I believe the mri_segstats program is exactly what you're looking for here. Best, Michael On Tue, Jun 28, 2011 at 5:12 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Over-smoothing of pial surface
Send us the dataset and we will take a look Bruce On Jun 29, 2011, at 12:34 PM, Yagna Pathak y...@cornell.edu wrote: Hi, I am trying to extract the pial surface for one of my subjects using freesurfer. Unfortunately, the last couple times that I ran recon-all, it generated a surface that was overly smoothed. I suspect this is due to a poor contrast in my MRI images. I tried to edit them via matlab and run them again. First, I got a talairach transform error and when I re-ran it with the -notal-check flag, I got a global region empty error. I was wondering if there is a way to enhance the mri images in freesurfer to obtain better contrast for a more accurate pial surface. Please let me know what is the best way to tackle this problem. I do not think it's the version of freesurfer, because the pial surface was created fine for some of the other subjects. Thank you, YP ___ 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 Anatasia, Thank you for the response. I've reformatted the files and -prep ran fine. I'm receiving a similar error to some other users upon running -bedp Where bedpostx fails immediately I wanted to point out, and wonder if other folks have had any luck, that if I try running bedpostx from FSL directly on the dmri folder, it starts normally. I can then kill the bedpostx process, and relaunch trac-all -bedp -c ... and things seem to be continuing... It still returns the unexpected operator errors that other users have reported but it does not break to a command prompt anymore, and instead beings return the 0 slices processed ... iterating message. I'm curious, has anyone else had luck navigating around this bedpostx error? Or would it be best to just run bedpostx separately in FSL and return to trac-all after the bedpostx processing is complete? Thanks again! Jared On Jun 28, 2011, at 3:24 PM, Anastasia Yendiki wrote: 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 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
