[Freesurfer] freesurfer install
Hi freesurfer， I ?installed the package of freesurfer according to the intruction of freesurfer website. But when I checked whether it was installed successfully, I inputed?the commands following: 1)?tksurfer bert rh pial? Couldn't create output file .xdebug_tksurfersubject is bert hemiis rh surface is pial surfer: current subjects dir: /usr/local/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /usr/local/freesurfer/bin surfer: can't create file surfer.log in cwd surfer: surfer.log created in /tmp surfer: session root data dir ($session) reset to: surfer: /tmp Reading image info (/usr/local/freesurfer/subjects/bert) Reading /usr/local/freesurfer/subjects/bert/mri/orig.mgz surfer: Reading header info from /usr/local/freesurfer/subjects/bert/mri/orig.mgz 2) tkmedit bert orig.mgz?Couldn't create output file .xdebug_tkmedit === ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to freesurfer@nmr.mgh.harvard.edu : : Now exiting... : 3) ?qdec?qdec.bin: error while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or directory yxk-ThinkStation-D30:/usr/local/freesurfer/bin> ? Thus, I want to know the reason why these problems occurred, and the solution to these problems. Thank you very much Meng___ 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] convert labels to volumetric masks
Dear FreeSurfers, I want to convert cortical labels to volumetric masks, and I run the following commands: 1. tkregister2 �Cmov sub/mri/rawavg.mgz �Cnoedit �Cs sub �Cregheader �Creg ./register.dat 2. mri_label2vol �Clabel ./lh.entorhinal.label �Ctemp sub/mri/rawavg.mgz �Csubject sub �Chemi lh �Co sub_lh_entorhinal.nii.gz �Cproj frac 0 1 .1 �Cfillthresh .3 �Creg ../mri/register.dat if I do not run the recon-all command, could I change the rawavg.mgz to sub.nii (original data)? The second problem is that when I convert the annotation file to volumetric mask, whether I should convert the file to labels using mri_annotation2label first, then run the commands as decribed above, or there is a way that could convert the annotation file to volumetric mask directly? The last problem is that how to convert the .curv file and .w file to volumetic mask? Any help will be very appreciated. Best wishes, Meng___ 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] convert labels to volumetric masks
Hi Doug, Thanks for your reply. The mask created is used to register with the normalized functional data and to define the roi, so could I run the following command? tkregister2 -mov sub/func.nii -noedit -s fsaverage -regheader -reg ./register.dat/ and the func.nii has been normalized (sub.nii) to the MNI space. The .w file I download from http://ltl.tkk.fi/wiki/Atlas, indicates the maximum probability map. Best wishes, Meng Dear FreeSurfers, I want to convert cortical labels to volumetric masks, and I run the following commands: 1. /tkregister2 -mov sub/mri/rawavg.mgz -noedit -s sub -regheader -reg ./register.dat/ 2. /mri_label2vol -label ./lh.entorhinal.label -temp sub/mri/rawavg.mgz -subject sub -hemi lh -o sub_lh_entorhinal.nii.gz -proj frac 0 1 .1 -fillthresh .3 -reg ../mri/register.dat/ if I do not run the recon-all command, could I change the rawavg.mgz to sub.nii (original data)? What is sub.nii? The second problem is that when I convert the annotation file to volumetric mask, whether I should convert the file to labels using mri_annotation2label first, then run the commands as decribed above, or there is a way that could convert the annotation file to volumetric mask directly? You can use the same label2vol command above but spec --annot instead of --label The last problem is that how to convert the .curv file and .w file to volumetic mask? mri_surf2vol should work for the curv file. Why do you have a .w file? BTW, for our standard annotations (aparc and aparc.a2009s) you will probably be happier with the results if you use mri_label2vol with --seg aparc+aseg.mgz or --seg aparc.a2009s+aseg.mgz. Otherwise, there are some holes that are created if you use the surface labels. doug___ 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] convert labels to volumetric masks
Dear FreeSurfers, I want to convert cortical labels to volumetric masks, the mask created are used to register with the normalized functional data and to define the roi, so could I run the following command? tkregister2 -mov sub/func.nii -noedit -s fsaverage -regheader -reg ./register.dat/ and the func.nii has been normalized (sub.nii) to the MNI space. And if the command is wrong, which command should I use? Best wishes, Meng___ 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] convert labels to volumetric masks
Hi Doug, Thanks for your reply. I have downloaded some freesurfer files (.annot, .label, .curv, .w) about the specific regions. And I want to convert this files to volumetric masks, then the masks are used to overlay the normalized functional data, and according to the mask to define the specific region as roi. Thus, the problem is that, how I can achieve this goal, and which commands should I use. Thanks a lot. Best wishes, Meng Date: Mon, 29 Apr 2013 17:30:14 -0400 From: Douglas N Greve Subject: Re: [Freesurfer] convert labels to volumetric masks To: freesurfer@nmr.mgh.harvard.edu Message-ID: <517ee666.8050...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=UTF-8; format=flowed Hi Meng, I don't understand what you are trying to do. Can you elaborate? That command will simply check a registration that already exists. doug On 04/29/2013 10:36 AM, limengsecret wrote: Dear FreeSurfers, I want to convert cortical labels to volumetric masks, the mask created are used to register with the normalized functional data and to define the roi, so could I run the following command? tkregister2 -mov sub/func.nii -noedit -s fsaverage -regheader -reg ./register.dat/ and the func.nii has been normalized (sub.nii) to the MNI space. And if the command is wrong, which command should I use? Best wishes, Meng___ 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] convert labels to volumetric masks
Hi Doug, The relative freesurfer files were downloaded from http://ltl.tkk.fi/wiki/Atlas about the retinotopic visual areas. And I want to convert the files to volumetric masks to use for my own data. The functional data have been preprocessed with slice-timing, realignment, and normalization. And the masks overlay the functional data created above to define the retinotopic visual areas. Thank you! Meng 发件人： Douglas N Greve 发送时间： 2013-05-02 02:02 收件人： limengsecret 抄送： freesurfer 主题： Re: [Freesurfer] convert labels to volumetric masks Hi Meng, On 04/30/2013 09:53 PM, limengsecret wrote: > Hi Doug, > Thanks for your reply. > I have downloaded some freesurfer files (.annot, .label, .curv, .w) > about the specific regions. what do you mean you downloaded them? where did they come from exactly? Are they your own data? > And I want to convert this files to volumetric masks, then the masks > are used to overlay the normalized functional data, and according to > the mask to define the specific region as roi. How was your functional data normalized? Specifically what atlas was used? > Thus, the problem is that, how I can achieve this goal, and which > commands should I use. > Thanks a lot. > Best wishes, > Meng > Date: Mon, 29 Apr 2013 17:30:14 -0400 > From: Douglas N Greve > Subject: Re: [Freesurfer] convert labels to volumetric masks > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <517ee666.8050...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=UTF-8; format=flowed > Hi Meng, > I don't understand what you are trying to do. Can you > elaborate? That command will simply check a registration that already > exists. > doug > On 04/29/2013 10:36 AM, limengsecret wrote: > Dear FreeSurfers, > I want to convert cortical labels to volumetric masks, the mask > created are used to register with the normalized functional data and > to define the roi, so could I run the following command? > tkregister2 -mov sub/func.nii -noedit -s fsaverage -regheader -reg > ./register.dat/ > and the func.nii has been normalized (sub.nii) to the MNI space. And > if the command is wrong, which command should I use? > Best wishes, > Meng > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ 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] determine the peak vertex
Hi freesurfer, I have a label and each vertex in this label has a probability value. My problem is that how to determine the peak vertex (or the center of gravity) of this label and get the coordinates. And I also want to know, in the tksurfer interface, whether the vertex index has a correspondence to the vertex RAS. Thanks a lot! Best wishes, Meng___ 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.
