Re: [Freesurfer] Coregistration to MNI
It looks like cvs failed. Can you send the log? Also, please remember to post to the list and not us personally. On 7/30/2020 11:13 AM, Camargo, Aldo wrote: External Email - Use Caution Hi Douglas, I was able to run the script to create the cvs folder and its files but still I can not run the script that does the coregistration of the Pet image to the MNI space. I am getting the following error: (base) acamargo@acamargo-System-Product-Name:~/PET/MPRAGE/2006-09-27_14_15_46.0/S19445/subj1/mri$ mri_vol2vol --gcam /home/acamargo/PET/ADNI_Brain_PET__Raw/2006-11-01_11_56_37.0/I28835/meanPET.nii.gz register.dof6.lta $SUBJECS_DIR/subj1/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z $FREESURFER_HOME/subject/cvs_avg35_inMNI152/mri.2mm/register.lta 0 1 pet.cvs.2mm.sm00.ni.gz Loading mov /home/acamargo/PET/ADNI_Brain_PET__Raw/2006-11-01_11_56_37.0/I28835/meanPET.nii.gz Loading source LTA register.dof6.lta Loading GCAM /subj1/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z ERROR: cannot find or read /subj1/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z *From:* Douglas N. Greve *Sent:* Wednesday, July 29, 2020 10:39 AM *To:* Camargo, Aldo ; Freesurfer support list *Subject:* Re: [Freesurfer] Coregistration to MNI Here is the command mri_cvs_register --mov $subject --mni --openmp N This command can take a very long time to run. The --openmp N indicates the number of processors to use if you have a multiprocessor system. Even with N=3, it can take 18 hours. On 7/29/2020 12:35 AM, Camargo, Aldo wrote: External Email - Use Caution Hi Douglas, I don't have the folder cvs and I don't have the files bellow: cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/register.lta How can I get these files, Aldo *From:* Camargo, Aldo <mailto:acama...@som.umaryland.edu> *Sent:* Monday, July 27, 2020 11:46 PM *To:* Douglas N. Greve <mailto:dgr...@mgh.harvard.edu> *Subject:* Re: [Freesurfer] Coregistration to MNI Thanks a lot Douglas for your great input, Aldo *From:* freesurfer-boun...@nmr.mgh.harvard.edu <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <mailto:dgr...@mgh.harvard.edu> *Sent:* Monday, July 27, 2020 10:46 AM *To:* freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject:* Re: [Freesurfer] Coregistration to MNI This command will allow you to have a registration file and sample into MNI152 2mm space mri_vol2vol --gcam pet.nii.gz register.dof6.lta $SUBJECTS_DIR/$subject/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/register.lta 0 1 pet.cvs.2mm.sm00.nii.gz you can get the registration file with mri_coreg --mov pet.nii.gz --s $subject --reg register.dof6.lta On 7/26/2020 9:19 AM, Zollei, Lilla,Ph.D. wrote: Hi Aldo, If you have a recon-ned structural MRI corresponding to your PET scan then the answer is yes. Lilla *From:* freesurfer-boun...@nmr.mgh.harvard.edu <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Camargo, Aldo <mailto:acama...@som.umaryland.edu> *Sent:* Saturday, July 25, 2020 12:19 AM *To:* Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject:* [Freesurfer] Coregistration to MNI External Email - Use Caution Hi Freesurfer experts, I want to coregister a PET image to the MNI space, can I use mri_cvs_register ? Thanks a lot, Aldo Camargo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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] Coregistration to MNI
Here is the command mri_cvs_register --mov $subject --mni --openmp N This command can take a very long time to run. The --openmp N indicates the number of processors to use if you have a multiprocessor system. Even with N=3, it can take 18 hours. On 7/29/2020 12:35 AM, Camargo, Aldo wrote: External Email - Use Caution Hi Douglas, I don't have the folder cvs and I don't have the files bellow: cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/register.lta How can I get these files, Aldo *From:* Camargo, Aldo *Sent:* Monday, July 27, 2020 11:46 PM *To:* Douglas N. Greve *Subject:* Re: [Freesurfer] Coregistration to MNI Thanks a lot Douglas for your great input, Aldo *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* Monday, July 27, 2020 10:46 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Coregistration to MNI This command will allow you to have a registration file and sample into MNI152 2mm space mri_vol2vol --gcam pet.nii.gz register.dof6.lta $SUBJECTS_DIR/$subject/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/register.lta 0 1 pet.cvs.2mm.sm00.nii.gz you can get the registration file with mri_coreg --mov pet.nii.gz --s $subject --reg register.dof6.lta On 7/26/2020 9:19 AM, Zollei, Lilla,Ph.D. wrote: Hi Aldo, If you have a recon-ned structural MRI corresponding to your PET scan then the answer is yes. Lilla *From:* freesurfer-boun...@nmr.mgh.harvard.edu <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Camargo, Aldo <mailto:acama...@som.umaryland.edu> *Sent:* Saturday, July 25, 2020 12:19 AM *To:* Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject:* [Freesurfer] Coregistration to MNI External Email - Use Caution Hi Freesurfer experts, I want to coregister a PET image to the MNI space, can I use mri_cvs_register ? Thanks a lot, Aldo Camargo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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
Re: [Freesurfer] Coregistration to MNI
This command will allow you to have a registration file and sample into MNI152 2mm space mri_vol2vol --gcam pet.nii.gz register.dof6.lta $SUBJECTS_DIR/$subject/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/register.lta 0 1 pet.cvs.2mm.sm00.nii.gz you can get the registration file with mri_coreg --mov pet.nii.gz --s $subject --reg register.dof6.lta On 7/26/2020 9:19 AM, Zollei, Lilla,Ph.D. wrote: Hi Aldo, If you have a recon-ned structural MRI corresponding to your PET scan then the answer is yes. Lilla *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Camargo, Aldo *Sent:* Saturday, July 25, 2020 12:19 AM *To:* Freesurfer support list *Subject:* [Freesurfer] Coregistration to MNI External Email - Use Caution Hi Freesurfer experts, I want to coregister a PET image to the MNI space, can I use mri_cvs_register ? Thanks a lot, Aldo Camargo ___ 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
Re: [Freesurfer] Coregistration to MNI
Hi Aldo, If you have a recon-ned structural MRI corresponding to your PET scan then the answer is yes. Lilla From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Camargo, Aldo Sent: Saturday, July 25, 2020 12:19 AM To: Freesurfer support list Subject: [Freesurfer] Coregistration to MNI External Email - Use Caution Hi Freesurfer experts, I want to coregister a PET image to the MNI space, can I use mri_cvs_register ? Thanks a lot, Aldo Camargo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Coregistration to MNI
External Email - Use Caution Hi Freesurfer experts, I want to coregister a PET image to the MNI space, can I use mri_cvs_register ? Thanks a lot, Aldo Camargo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] coregistration - FA to Freesurfer
Thanks Doug! It worked! Joana 2011/10/17 Douglas N Greve gr...@nmr.mgh.harvard.edu No, use the register.dat that you manually created as the input to bbregister with the --init-reg. You could move your register.dat to regidster.man.dat and set the output to be register.dat. doug Joana Braga Pereira wrote: Hi Doug, Thanks for the reply. I'm not sure i understand how to solve it. Are you suggesting to re-run bbregister using the --init-reg option and the register.dat files that were previously created for the badly-registered subjects? Joana 2011/10/17 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto: gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu Those almost surely failed because of a bad initialization. You can usually tell this by looking at the first value in the mincost file. For these, the mincost is something like .9. The mincost will be a value bet 0 and 1.1, with 0 being perfect. Looks at your good subjects to get an idea of what range to expect for well-registered subjects. You should be able to use the registrations you created as input to bbregister (with the --init-reg option), and bbregister should do fine after that. doug Joana Braga Pereira wrote: Hi Doug, I made quite a few changes, including translations and rotations (not scaling changes), to 10 out of 24 subjects. Here are a few of the bbregister log.files from subjects in which the registration didn't go well. Thanks for the help! Joana 2011/10/17 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu Hi Joana, how big were the changes that you made? Sometimes the initialization routine won't get it close enough, then bbregister fails. Can you send the bbregister log file? doug Lilla Zollei wrote: Even though it is not ideal, manual adjustments can be useful. I would use manual registration in a small number of cases though. If most of your data requires it, I would try to play with the automatic registration parameters more. --Lilla On Sun, 16 Oct 2011, Joana Braga Pereira wrote: Dear Lilla and Ed, Thanks a lot for your suggestions, they were really really helpful! I did the analyses as you suggested. After bbregister i checked the results with tkregister2 and saw that most subjects were well coregistered. However in a few of them my lowb images were out of place with respect to the target and so i made manual adjustments using bbregister interface tools.. I was just wondering whether this is the normal procedure as manual adjustments can be quite subjective and i would prefer not to introduce such a bias in the analyses. Thanks a lot for your valuable help! Joana 2011/10/15 Ed Gronenschild ed.gronensch...@np.unimaas.nl mailto:ed.gronenschild@np.**unimaas.nled.gronensch...@np.unimaas.nl mailto:ed.gronenschild@np.**unimaas.nled.gronensch...@np.unimaas.nl mailto:ed.gronenschild@np.**unimaas.nled.gronensch...@np.unimaas.nl Dear Joana, Two things: 1. You should be very careful to use fslswapdim since it may result in an unintended left-right flipping. It's better to use fslreorient2std. 2. The tool dt-recon computes the coregistration of the lowb volume to the anatomical volume, see register.dat. You can then use the following to coregister FA: mri_vol2vol --reg register.dat --mov fa.nii --o fa-ana.nii -targ subject/mri/T1.mgz where subject is the output folder generated by the recon-all command. You should not forget to set the global variable SUBJECTS_DIR Cheers, Ed On 14 Oct, 2011, at 18:00, freesurfer-requ...@nmr.mgh.**harvard.edufreesurfer-requ...@nmr.mgh.harvard.edu mailto:freesurfer-request@**nmr.mgh.harvard.edufreesurfer-requ...@nmr.mgh.harvard.edu
Re: [Freesurfer] coregistration - FA to Freesurfer
Even though it is not ideal, manual adjustments can be useful. I would use manual registration in a small number of cases though. If most of your data requires it, I would try to play with the automatic registration parameters more. --Lilla On Sun, 16 Oct 2011, Joana Braga Pereira wrote: Dear Lilla and Ed, Thanks a lot for your suggestions, they were really really helpful! I did the analyses as you suggested. After bbregister i checked the results with tkregister2 and saw that most subjects were well coregistered. However in a few of them my lowb images were out of place with respect to the target and so i made manual adjustments using bbregister interface tools.. I was just wondering whether this is the normal procedure as manual adjustments can be quite subjective and i would prefer not to introduce such a bias in the analyses. Thanks a lot for your valuable help! Joana 2011/10/15 Ed Gronenschild ed.gronensch...@np.unimaas.nl Dear Joana, Two things: 1. You should be very careful to use fslswapdim since it may result in an unintended left-right flipping. It's better to use fslreorient2std. 2. The tool dt-recon computes the coregistration of the lowb volume to the anatomical volume, see register.dat. You can then use the following to coregister FA: mri_vol2vol --reg register.dat --mov fa.nii --o fa-ana.nii -targ subject/mri/T1.mgz where subject is the output folder generated by the recon-all command. You should not forget to set the global variable SUBJECTS_DIR Cheers, Ed On 14 Oct, 2011, at 18:00, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Dear Bruce and Anastasia, Thanks for the quick reply! I tried the bbregister as you suggested but when i visualize the target and dti image they don't look registered at all. This is the comand i used: bbregister --s CN01 --mov /home/joana/FA/CN01/dti_FA.nii.gz --reg /home/joana/FA/CN01/register.dat --init-fsl --dti --template-out /home/joana/FA/CN01/template.nii.gz --fslmat /home/joana/FA/CN01/flirt.tmx I tried to use the bbregister tools to align them but I didn't get very far... Did i miss something? I read in another mail something about using the register.dat created in bbregister and do mri_label2vol but i'm not sure how to do it. Thanks, Joana ___ 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] coregistration - FA to Freesurfer
Hi Joana, how big were the changes that you made? Sometimes the initialization routine won't get it close enough, then bbregister fails. Can you send the bbregister log file? doug Lilla Zollei wrote: Even though it is not ideal, manual adjustments can be useful. I would use manual registration in a small number of cases though. If most of your data requires it, I would try to play with the automatic registration parameters more. --Lilla On Sun, 16 Oct 2011, Joana Braga Pereira wrote: Dear Lilla and Ed, Thanks a lot for your suggestions, they were really really helpful! I did the analyses as you suggested. After bbregister i checked the results with tkregister2 and saw that most subjects were well coregistered. However in a few of them my lowb images were out of place with respect to the target and so i made manual adjustments using bbregister interface tools.. I was just wondering whether this is the normal procedure as manual adjustments can be quite subjective and i would prefer not to introduce such a bias in the analyses. Thanks a lot for your valuable help! Joana 2011/10/15 Ed Gronenschild ed.gronensch...@np.unimaas.nl Dear Joana, Two things: 1. You should be very careful to use fslswapdim since it may result in an unintended left-right flipping. It's better to use fslreorient2std. 2. The tool dt-recon computes the coregistration of the lowb volume to the anatomical volume, see register.dat. You can then use the following to coregister FA: mri_vol2vol --reg register.dat --mov fa.nii --o fa-ana.nii -targ subject/mri/T1.mgz where subject is the output folder generated by the recon-all command. You should not forget to set the global variable SUBJECTS_DIR Cheers, Ed On 14 Oct, 2011, at 18:00, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Dear Bruce and Anastasia, Thanks for the quick reply! I tried the bbregister as you suggested but when i visualize the target and dti image they don't look registered at all. This is the comand i used: bbregister --s CN01 --mov /home/joana/FA/CN01/dti_FA.nii.gz --reg /home/joana/FA/CN01/register.dat --init-fsl --dti --template-out /home/joana/FA/CN01/template.nii.gz --fslmat /home/joana/FA/CN01/flirt.tmx I tried to use the bbregister tools to align them but I didn't get very far... Did i miss something? I read in another mail something about using the register.dat created in bbregister and do mri_label2vol but i'm not sure how to do it. Thanks, Joana ___ 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 -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] coregistration - FA to Freesurfer
Those almost surely failed because of a bad initialization. You can usually tell this by looking at the first value in the mincost file. For these, the mincost is something like .9. The mincost will be a value bet 0 and 1.1, with 0 being perfect. Looks at your good subjects to get an idea of what range to expect for well-registered subjects. You should be able to use the registrations you created as input to bbregister (with the --init-reg option), and bbregister should do fine after that. doug Joana Braga Pereira wrote: Hi Doug, I made quite a few changes, including translations and rotations (not scaling changes), to 10 out of 24 subjects. Here are a few of the bbregister log.files from subjects in which the registration didn't go well. Thanks for the help! Joana 2011/10/17 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Hi Joana, how big were the changes that you made? Sometimes the initialization routine won't get it close enough, then bbregister fails. Can you send the bbregister log file? doug Lilla Zollei wrote: Even though it is not ideal, manual adjustments can be useful. I would use manual registration in a small number of cases though. If most of your data requires it, I would try to play with the automatic registration parameters more. --Lilla On Sun, 16 Oct 2011, Joana Braga Pereira wrote: Dear Lilla and Ed, Thanks a lot for your suggestions, they were really really helpful! I did the analyses as you suggested. After bbregister i checked the results with tkregister2 and saw that most subjects were well coregistered. However in a few of them my lowb images were out of place with respect to the target and so i made manual adjustments using bbregister interface tools.. I was just wondering whether this is the normal procedure as manual adjustments can be quite subjective and i would prefer not to introduce such a bias in the analyses. Thanks a lot for your valuable help! Joana 2011/10/15 Ed Gronenschild ed.gronensch...@np.unimaas.nl mailto:ed.gronensch...@np.unimaas.nl Dear Joana, Two things: 1. You should be very careful to use fslswapdim since it may result in an unintended left-right flipping. It's better to use fslreorient2std. 2. The tool dt-recon computes the coregistration of the lowb volume to the anatomical volume, see register.dat. You can then use the following to coregister FA: mri_vol2vol --reg register.dat --mov fa.nii --o fa-ana.nii -targ subject/mri/T1.mgz where subject is the output folder generated by the recon-all command. You should not forget to set the global variable SUBJECTS_DIR Cheers, Ed On 14 Oct, 2011, at 18:00, freesurfer-requ...@nmr.mgh.harvard.edu mailto:freesurfer-requ...@nmr.mgh.harvard.edu wrote: Dear Bruce and Anastasia, Thanks for the quick reply! I tried the bbregister as you suggested but when i visualize the target and dti image they don't look registered at all. This is the comand i used: bbregister --s CN01 --mov /home/joana/FA/CN01/dti_FA.nii.gz --reg /home/joana/FA/CN01/register.dat --init-fsl --dti --template-out /home/joana/FA/CN01/template.nii.gz --fslmat /home/joana/FA/CN01/flirt.tmx I tried to use the bbregister tools to align them but I didn't get very far... Did i miss something? I read in another mail something about using the register.dat created in bbregister and do mri_label2vol but i'm not sure how to do it. Thanks, Joana ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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
Re: [Freesurfer] coregistration - FA to Freesurfer
Hi Doug, Thanks for the reply. I'm not sure i understand how to solve it. Are you suggesting to re-run bbregister using the --init-reg option and the register.dat files that were previously created for the badly-registered subjects? Joana 2011/10/17 Douglas N Greve gr...@nmr.mgh.harvard.edu Those almost surely failed because of a bad initialization. You can usually tell this by looking at the first value in the mincost file. For these, the mincost is something like .9. The mincost will be a value bet 0 and 1.1, with 0 being perfect. Looks at your good subjects to get an idea of what range to expect for well-registered subjects. You should be able to use the registrations you created as input to bbregister (with the --init-reg option), and bbregister should do fine after that. doug Joana Braga Pereira wrote: Hi Doug, I made quite a few changes, including translations and rotations (not scaling changes), to 10 out of 24 subjects. Here are a few of the bbregister log.files from subjects in which the registration didn't go well. Thanks for the help! Joana 2011/10/17 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto: gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu Hi Joana, how big were the changes that you made? Sometimes the initialization routine won't get it close enough, then bbregister fails. Can you send the bbregister log file? doug Lilla Zollei wrote: Even though it is not ideal, manual adjustments can be useful. I would use manual registration in a small number of cases though. If most of your data requires it, I would try to play with the automatic registration parameters more. --Lilla On Sun, 16 Oct 2011, Joana Braga Pereira wrote: Dear Lilla and Ed, Thanks a lot for your suggestions, they were really really helpful! I did the analyses as you suggested. After bbregister i checked the results with tkregister2 and saw that most subjects were well coregistered. However in a few of them my lowb images were out of place with respect to the target and so i made manual adjustments using bbregister interface tools.. I was just wondering whether this is the normal procedure as manual adjustments can be quite subjective and i would prefer not to introduce such a bias in the analyses. Thanks a lot for your valuable help! Joana 2011/10/15 Ed Gronenschild ed.gronensch...@np.unimaas.nl mailto:ed.gronenschild@np.**unimaas.nled.gronensch...@np.unimaas.nl Dear Joana, Two things: 1. You should be very careful to use fslswapdim since it may result in an unintended left-right flipping. It's better to use fslreorient2std. 2. The tool dt-recon computes the coregistration of the lowb volume to the anatomical volume, see register.dat. You can then use the following to coregister FA: mri_vol2vol --reg register.dat --mov fa.nii --o fa-ana.nii -targ subject/mri/T1.mgz where subject is the output folder generated by the recon-all command. You should not forget to set the global variable SUBJECTS_DIR Cheers, Ed On 14 Oct, 2011, at 18:00, freesurfer-requ...@nmr.mgh.**harvard.edufreesurfer-requ...@nmr.mgh.harvard.edu mailto:freesurfer-request@**nmr.mgh.harvard.edufreesurfer-requ...@nmr.mgh.harvard.edu wrote: Dear Bruce and Anastasia, Thanks for the quick reply! I tried the bbregister as you suggested but when i visualize the target and dti image they don't look registered at all. This is the comand i used: bbregister --s CN01 --mov /home/joana/FA/CN01/dti_FA.**nii.gz --reg /home/joana/FA/CN01/register.**dat --init-fsl --dti --template-out /home/joana/FA/CN01/template.**nii.gz --fslmat /home/joana/FA/CN01/flirt.tmx I tried to use the bbregister tools to align them but I didn't get very far... Did i miss something? I read in another mail something about using the register.dat created in bbregister and do mri_label2vol but i'm not sure how to do it. Thanks, Joana __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** freesurfer
Re: [Freesurfer] coregistration - FA to Freesurfer
No, use the register.dat that you manually created as the input to bbregister with the --init-reg. You could move your register.dat to regidster.man.dat and set the output to be register.dat. doug Joana Braga Pereira wrote: Hi Doug, Thanks for the reply. I'm not sure i understand how to solve it. Are you suggesting to re-run bbregister using the --init-reg option and the register.dat files that were previously created for the badly-registered subjects? Joana 2011/10/17 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Those almost surely failed because of a bad initialization. You can usually tell this by looking at the first value in the mincost file. For these, the mincost is something like .9. The mincost will be a value bet 0 and 1.1, with 0 being perfect. Looks at your good subjects to get an idea of what range to expect for well-registered subjects. You should be able to use the registrations you created as input to bbregister (with the --init-reg option), and bbregister should do fine after that. doug Joana Braga Pereira wrote: Hi Doug, I made quite a few changes, including translations and rotations (not scaling changes), to 10 out of 24 subjects. Here are a few of the bbregister log.files from subjects in which the registration didn't go well. Thanks for the help! Joana 2011/10/17 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Hi Joana, how big were the changes that you made? Sometimes the initialization routine won't get it close enough, then bbregister fails. Can you send the bbregister log file? doug Lilla Zollei wrote: Even though it is not ideal, manual adjustments can be useful. I would use manual registration in a small number of cases though. If most of your data requires it, I would try to play with the automatic registration parameters more. --Lilla On Sun, 16 Oct 2011, Joana Braga Pereira wrote: Dear Lilla and Ed, Thanks a lot for your suggestions, they were really really helpful! I did the analyses as you suggested. After bbregister i checked the results with tkregister2 and saw that most subjects were well coregistered. However in a few of them my lowb images were out of place with respect to the target and so i made manual adjustments using bbregister interface tools.. I was just wondering whether this is the normal procedure as manual adjustments can be quite subjective and i would prefer not to introduce such a bias in the analyses. Thanks a lot for your valuable help! Joana 2011/10/15 Ed Gronenschild ed.gronensch...@np.unimaas.nl mailto:ed.gronensch...@np.unimaas.nl mailto:ed.gronensch...@np.unimaas.nl mailto:ed.gronensch...@np.unimaas.nl Dear Joana, Two things: 1. You should be very careful to use fslswapdim since it may result in an unintended left-right flipping. It's better to use fslreorient2std. 2. The tool dt-recon computes the coregistration of the lowb volume to the anatomical volume, see register.dat. You can then use the following to coregister FA: mri_vol2vol --reg register.dat --mov fa.nii --o fa-ana.nii -targ subject/mri/T1.mgz where subject is the output folder generated by the recon-all command. You should not forget to set the global variable SUBJECTS_DIR Cheers, Ed On 14 Oct, 2011, at 18:00, freesurfer-requ...@nmr.mgh.harvard.edu mailto:freesurfer-requ...@nmr.mgh.harvard.edu mailto:freesurfer-requ...@nmr.mgh.harvard.edu mailto:freesurfer-requ...@nmr.mgh.harvard.edu wrote: Dear Bruce and Anastasia, Thanks for the quick reply! I tried the bbregister as you suggested but when i visualize the target and
Re: [Freesurfer] coregistration - FA to Freesurfer
Dear Lilla and Ed, Thanks a lot for your suggestions, they were really really helpful! I did the analyses as you suggested. After bbregister i checked the results with tkregister2 and saw that most subjects were well coregistered. However in a few of them my lowb images were out of place with respect to the target and so i made manual adjustments using bbregister interface tools.. I was just wondering whether this is the normal procedure as manual adjustments can be quite subjective and i would prefer not to introduce such a bias in the analyses. Thanks a lot for your valuable help! Joana 2011/10/15 Ed Gronenschild ed.gronensch...@np.unimaas.nl Dear Joana, Two things: 1. You should be very careful to use fslswapdim since it may result in an unintended left-right flipping. It's better to use fslreorient2std. 2. The tool dt-recon computes the coregistration of the lowb volume to the anatomical volume, see register.dat. You can then use the following to coregister FA: mri_vol2vol --reg register.dat --mov fa.nii --o fa-ana.nii -targ subject/mri/T1.mgz where subject is the output folder generated by the recon-all command. You should not forget to set the global variable SUBJECTS_DIR Cheers, Ed On 14 Oct, 2011, at 18:00, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Dear Bruce and Anastasia, Thanks for the quick reply! I tried the bbregister as you suggested but when i visualize the target and dti image they don't look registered at all. This is the comand i used: bbregister --s CN01 --mov /home/joana/FA/CN01/dti_FA.nii.gz --reg /home/joana/FA/CN01/register.dat --init-fsl --dti --template-out /home/joana/FA/CN01/template.nii.gz --fslmat /home/joana/FA/CN01/flirt.tmx I tried to use the bbregister tools to align them but I didn't get very far... Did i miss something? I read in another mail something about using the register.dat created in bbregister and do mri_label2vol but i'm not sure how to do it. Thanks, Joana ___ 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] coregistration - FA to Freesurfer
Dear Joana, Two things: 1. You should be very careful to use fslswapdim since it may result in an unintended left-right flipping. It's better to use fslreorient2std. 2. The tool dt-recon computes the coregistration of the lowb volume to the anatomical volume, see register.dat. You can then use the following to coregister FA: mri_vol2vol --reg register.dat --mov fa.nii --o fa-ana.nii -targ subject/mri/T1.mgz where subject is the output folder generated by the recon-all command. You should not forget to set the global variable SUBJECTS_DIR Cheers, Ed On 14 Oct, 2011, at 18:00, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Dear Bruce and Anastasia, Thanks for the quick reply! I tried the bbregister as you suggested but when i visualize the target and dti image they don't look registered at all. This is the comand i used: bbregister --s CN01 --mov /home/joana/FA/CN01/dti_FA.nii.gz --reg /home/joana/FA/CN01/register.dat --init-fsl --dti --template-out /home/joana/FA/CN01/template.nii.gz --fslmat /home/joana/FA/CN01/ flirt.tmx I tried to use the bbregister tools to align them but I didn't get very far... Did i miss something? I read in another mail something about using the register.dat created in bbregister and do mri_label2vol but i'm not sure how to do it. Thanks, Joana ___ 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] coregistration - FA to Freesurfer
Dear Bruce and Anastasia, Thanks for the quick reply! I tried the bbregister as you suggested but when i visualize the target and dti image they don't look registered at all. This is the comand i used: bbregister --s CN01 --mov /home/joana/FA/CN01/dti_FA.nii.gz --reg /home/joana/FA/CN01/register.dat --init-fsl --dti --template-out /home/joana/FA/CN01/template.nii.gz --fslmat /home/joana/FA/CN01/flirt.tmx I tried to use the bbregister tools to align them but I didn't get very far... Did i miss something? I read in another mail something about using the register.dat created in bbregister and do mri_label2vol but i'm not sure how to do it. Thanks, Joana 2011/10/13 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Joana, try bbregister. cheers Bruce On Thu, 13 Oct 2011, Joana Braga Pereira wrote: Dear FreeSurfers, I'm trying to coregister FA images pre-processed with FSL to Freesurfer, however i'm having a few problems and was wondering if someone could help me out. These are the steps that i carried out: mri_convert subj_01/mri/brain.mgz brain.nii.gz fslswapdim brain.nii.gz x z -y brain_swap.nii.gz flirt -ref brain_swap.nii.gz -in nodif_brain.nii.gz -out XXX.nii.gz -omat XXX.mat -cost corratio -dof 6 -interp trilinear flirt -in myFA.nii.gz -ref XXX.nii.gz -out myFA_coregistered.nii.gz -applyxfm -init XXX.mat Unfortunately myFA_coregistered.nii.gz was not as good as i expected since I want to extract the mean FA values of a subcortical ROI from freesurfer and to do that you need quite good coregistration. Does anyone know a better way to do this? Many thanks, Joana 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] coregistration - FA to Freesurfer
Hi Joana, You should use the lowb volume as the moving volume for the registration and then apply the output registration matrix to your FA volume. You can also add the --o flag to your below command so that the resampled and registered volume gets written out at the end. You would want that and your template to be in alignment. --Lilla On Fri, 14 Oct 2011, Joana Braga Pereira wrote: Dear Bruce and Anastasia, Thanks for the quick reply! I tried the bbregister as you suggested but when i visualize the target and dti image they don't look registered at all. This is the comand i used: bbregister --s CN01 --mov /home/joana/FA/CN01/dti_FA.nii.gz --reg /home/joana/FA/CN01/register.dat --init-fsl --dti --template-out /home/joana/FA/CN01/template.nii.gz --fslmat /home/joana/FA/CN01/flirt.tmx I tried to use the bbregister tools to align them but I didn't get very far... Did i miss something? I read in another mail something about using the register.dat created in bbregister and do mri_label2vol but i'm not sure how to do it. Thanks, Joana 2011/10/13 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Joana, try bbregister. cheers Bruce On Thu, 13 Oct 2011, Joana Braga Pereira wrote: Dear FreeSurfers, I'm trying to coregister FA images pre-processed with FSL to Freesurfer, however i'm having a few problems and was wondering if someone could help me out. These are the steps that i carried out: mri_convert subj_01/mri/brain.mgz brain.nii.gz fslswapdim brain.nii.gz x z -y brain_swap.nii.gz flirt -ref brain_swap.nii.gz -in nodif_brain.nii.gz -out XXX.nii.gz -omat XXX.mat -cost corratio -dof 6 -interp trilinear flirt -in myFA.nii.gz -ref XXX.nii.gz -out myFA_coregistered.nii.gz -applyxfm -init XXX.mat Unfortunately myFA_coregistered.nii.gz was not as good as i expected since I want to extract the mean FA values of a subcortical ROI from freesurfer and to do that you need quite good coregistration. Does anyone know a better way to do this? Many thanks, Joana The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] coregistration - FA to Freesurfer
Dear FreeSurfers, I'm trying to coregister FA images pre-processed with FSL to Freesurfer, however i'm having a few problems and was wondering if someone could help me out. These are the steps that i carried out: mri_convert subj_01/mri/brain.mgz brain.nii.gz fslswapdim brain.nii.gz x z -y brain_swap.nii.gz flirt -ref brain_swap.nii.gz -in nodif_brain.nii.gz -out XXX.nii.gz -omat XXX.mat -cost corratio -dof 6 -interp trilinear flirt -in myFA.nii.gz -ref XXX.nii.gz -out myFA_coregistered.nii.gz -applyxfm -init XXX.mat Unfortunately myFA_coregistered.nii.gz was not as good as i expected since I want to extract the mean FA values of a subcortical ROI from freesurfer and to do that you need quite good coregistration. Does anyone know a better way to do this? Many thanks, Joana ___ 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] coregistration - FA to Freesurfer
Hi Joana - You can try our in-house tool for within-subject registration, bbregister, with the --dti option. a.y On Thu, 13 Oct 2011, Joana Braga Pereira wrote: Dear FreeSurfers, I'm trying to coregister FA images pre-processed with FSL to Freesurfer, however i'm having a few problems and was wondering if someone could help me out. These are the steps that i carried out: mri_convert subj_01/mri/brain.mgz brain.nii.gz fslswapdim brain.nii.gz x z -y brain_swap.nii.gz flirt -ref brain_swap.nii.gz -in nodif_brain.nii.gz -out XXX.nii.gz -omat XXX.mat -cost corratio -dof 6 -interp trilinear flirt -in myFA.nii.gz -ref XXX.nii.gz -out myFA_coregistered.nii.gz -applyxfm -init XXX.mat Unfortunately myFA_coregistered.nii.gz was not as good as i expected since I want to extract the mean FA values of a subcortical ROI from freesurfer and to do that you need quite good coregistration. Does anyone know a better way to do this? Many thanks, Joana ___ 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] coregistration - FA to Freesurfer
Hi Joana, try bbregister. cheers Bruce On Thu, 13 Oct 2011, Joana Braga Pereira wrote: Dear FreeSurfers, I'm trying to coregister FA images pre-processed with FSL to Freesurfer, however i'm having a few problems and was wondering if someone could help me out. These are the steps that i carried out: mri_convert subj_01/mri/brain.mgz brain.nii.gz fslswapdim brain.nii.gz x z -y brain_swap.nii.gz flirt -ref brain_swap.nii.gz -in nodif_brain.nii.gz -out XXX.nii.gz -omat XXX.mat -cost corratio -dof 6 -interp trilinear flirt -in myFA.nii.gz -ref XXX.nii.gz -out myFA_coregistered.nii.gz -applyxfm -init XXX.mat Unfortunately myFA_coregistered.nii.gz was not as good as i expected since I want to extract the mean FA values of a subcortical ROI from freesurfer and to do that you need quite good coregistration. Does anyone know a better way to do this? Many thanks, Joana ___ 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] coregistration of MRI and MEG
Hello, I am interested in coregistering mri images with MEG (elekta neuromag 306) data in order to do Dynamic Imaging of Coherent Sources (DICS analysis) using fieldtrip. I have installed freesurfer and have been able to open the mri files. How do I proceed next? Under what title will I be able to find the necessary info on Wiki? Thank you very much in advance for your help. best, sameer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Coregistration?
Nate Parks wrote: Does AFNI have an automated coregistration tool? I thought you could only do manual coreg in AFNI. AFNI coregistration program is 3dvolreg. See docs: http://afni.nimh.nih.gov/pub/dist/doc/program_help/3dvolreg.html And if you are having trouble finding which AFNI program does what, you might like my all afni helps on one page: http://www.grahamwideman.com/gw/brain/afni/alldocs_afni.htm Graham ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Coregistration?
Title: Re: [Freesurfer] Coregistration? The AFNI program 3dvolreg does coregistration only for volumes acquired with the same kind of pulse sequence and consequently the same tissue signal values. Use it for coregistering different EPI volumes to each other or different T1-weighted structural scans to each other. I think what Nate was asking about was coregistering EPI data to the structural scans. The AFNI program 3dAnatNudge can help with this to some extent. It uses simple iterative translational movements to find the best fit between a skull-stripped anatomy volume and an EPI volume. No rotation or resizing is done. To use this program you remove the skull and other non-brain voxels from the anatomy volume. The AFNI programs 3dIntracranial and a newer program called 3dSkullStrip both do this. Jeff From: Graham Wideman [EMAIL PROTECTED] Date: Wed, 12 Oct 2005 11:57:15 -0700 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Coregistration? Nate Parks wrote: Does AFNI have an automated coregistration tool? I thought you could only do manual coreg in AFNI. AFNI coregistration program is 3dvolreg. See docs: http://afni.nimh.nih.gov/pub/dist/doc/program_help/3dvolreg.html And if you are having trouble finding which AFNI program does what, you might like my all afni helps on one page: http://www.grahamwideman.com/gw/brain/afni/alldocs_afni.htm Graham ___ 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
Re: [Freesurfer] Coregistration?
Just in case someone hasn't mentioned it yet, try 3dWarpDrive or convert to analyze and use the AIR suite. Graham is correct. There are past posts about this on the AFNI forum that would be helpful to you. Good luck. Brian -- Brian C. Schweinsburg, Ph.D. Assistant Adjunct Professor of Psychiatry University of California, San Diego Office: 858-552-8585 x6109 Cell: 858-354-3756 From: Graham Wideman [EMAIL PROTECTED] Date: Wed, 12 Oct 2005 13:56:19 -0700 To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Coregistration? Sorry all -- my mistake. I thought our folks here were regularly registering functional to anatomical scans, and I thought it was done with 3dvolreg. Just now checking, apparently not. And if 3dAnatNudge can't do rotation, not so helpful (though lack of resize should not be a problem). It would be interesting to see what 3dvolreg would do if the anatomy was resampled to the same grid as that functional scans or vice versa... but starts to look like a research topic. For Nate: It might be worth posting on the AFNI forum to see what other AFNI-sters position on this topic is... doubtless it's been thought about a lot more than by me! Graham Jeff Binder wrote: The AFNI program 3dvolreg does coregistration only for volumes acquired with the same kind of pulse sequence and consequently the same tissue signal values. Use it for coregistering different EPI volumes to each other or different T1-weighted structural scans to each other. I think what Nate was asking about was coregistering EPI data to the structural scans. The AFNI program 3dAnatNudge can help with this to some extent. It uses simple iterative translational movements to find the best fit between a skull-stripped anatomy volume and an EPI volume. No rotation or resizing is done. To use this program you remove the skull and other non-brain voxels from the anatomy volume. The AFNI programs 3dIntracranial and a newer program called 3dSkullStrip both do this. Jeff ___ 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
Re: [Freesurfer] Coregistration?
You can use spmregister (front end for spm) or fsl_rigid_register (uses fsl). Neither spm nor fsl will accept BRIKS, but I think the wrappers will as they will convert the input to analyze using mri_convert. If not, then you'll have to convert them youself. You should also use tkregister2 to check the registrations (run with --help :). doug Nate Parks wrote: Hello, I was wondering if anybody has any insight into the best way to coregister functionals with anatomicals in Freesurfer. I am looking for an automated method of coregistration. I noticed the spm_coregister command, but I am working with AFNI BRIK files, and I assume this requires Analyze format. Any suggestions? Thanks. Nate Parks ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Coregistration?
Hello, I was wondering if anybody has any insight into the best way to coregister functionals with anatomicals in Freesurfer. I am looking for an automated method of coregistration. I noticed the spm_coregister command, but I am working with AFNI BRIK files, and I assume this requires Analyze format. Any suggestions? Thanks. Nate Parks ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Fw: Re: [Freesurfer] coregistration
I have a image xAD1378-T1.img with spm format. after I converted it to COR with mri_convert xAD1378-T1.img AD1378/mri/orig and run FLIRT as Xiao suggests, I found that the anterior and posterior parts of tranformed image was inversed. Xiao thinks it is due to mri_convert, Does anyone know how to fix it? thx, Antao -- Forwarded message -- From: Xiao Han [EMAIL PROTECTED] Date: Mon, 22 Aug 2005 16:03:46 -0400 (EDT) Subject: Re: [Freesurfer] coregistration It has nothing to do with fsl_register. It's because of the conversion from .img to COR format. That's why I suggested you to convert all your data to COR or mgz first before processing. The reason is because Analyze store data in an anterior-to-posterior fashion, but when mri_convert read the data, it assumed posterior-to-anterior (due to a missing .mat file). I dont know how to fix that. You can send an email to freesurfer list. -Xiao On Mon, 22 Aug 2005, [EMAIL PROTECTED] wrote: After I run: fsl_register_new -i AD1378/mri/orig -r average_305.mnc -o AD1378/tmp/orig -dof 9 -cost corratio -ltamat AD1378/mri/transforms/talairach.lta I check the tranformation with: tkmedit -f average_305.mnc -aux AD1378/tmp/orig. I find that the anterior and posterior parts of the image AD1378/tmp/orig are inversed. Do you know why? When I run fsl_register_new with images .img before converting to COR, the result was good. Antao n Mon, 22 Aug 2005 14:16:34 -0400 (EDT) Xiao Han wrote: On Mon, 22 Aug 2005, [EMAIL PROTECTED] wrote: This are the steps I use fsl_register_new: 1) mksubjdir AD1378 2) mri_convert xAD1378-T1.img AD1378/mri/orig 3) fsl_register_new -i AD1378/mri/orig -r average_305.mnc -o AD1378/mri/orig -dof 9 -cost corratio -ltamat AD1378/mri/transforms/talairach.lta I have a question here. Should I replace orig when I run fsl_register_new or I should choose different filename? No, you shouldn't replace the original orig. Use a different name for the -o option. After I run fsl_register_new, I should replace talairach.xfm in recon-all script to talairach.lta and run recon-all. Do I need add -notalairach in stage1? Right, you can replace talariach.xfm with talairach.lta. Also specify -notalairach when you run recon-all. -Xiao ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] coregistration
You may try FLIRT from FSL. http://www.fmrib.ox.ac.uk/fsl/flirt/ -Xiao On Fri, 19 Aug 2005 [EMAIL PROTECTED] wrote: I always have a problem to coregistrate T1 images to Talairach, Is there any way to improve the accuracy of coregistration besides tkregister2? Thanks, Antao ___ 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
