[Freesurfer] saving adjustments under different names
Dear all, I have run the recon-all process on my subject im01. Now I am checking for errors and found some. I also found the solution steps. However, as far as I understand it, every time I make a change, this will be permanently done. Is there a way to keep the steps I have done so far and to same further changes to a new subject file, e.g. im01_skullcorrected. I would just like to backup the steps I have done in case I worsen the solution so far and in case I want to compare them. Also, is there a way that the results from recon-all are saved under a different name? Thanks, Maria -- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522 ___ 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] saving adjustments under different names
There isn't a way to have the new or old results automatically saved under a different name. I would suggest making copies of the files before edits and after edits but before rerunning if you want to keep track of the changes. Depending on what you are making edits to, you would likely need to make copies of brainmask.mgz, wm.mgz, lh.pial, rh.pial, lh.white, rh.white. Allison On Mon, 17 Oct 2011, Maria Felber wrote: Dear all, I have run the recon-all process on my subject im01. Now I am checking for errors and found some. I also found the solution steps. However, as far as I understand it, every time I make a change, this will be permanently done. Is there a way to keep the steps I have done so far and to same further changes to a new subject file, e.g. im01_skullcorrected. I would just like to backup the steps I have done in case I worsen the solution so far and in case I want to compare them. Also, is there a way that the results from recon-all are saved under a different name? Thanks, Maria ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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] Hanging or running at 'SubCort Seg'?
hmmm, looks like it is almost finished with mri_cc but doesn't complete. It usually only takes like 2 minutes for this process, so something must be wrong. Can you send me aseg.auto_noCCseg.mgz and norm.mgz for this subject? You can probably just email them. cheers Bruce On Mon, 17 Oct 2011, Irwin, William wrote: Hi Bruce- It is still running, but the recon-all.log as it stands is attached. Thanks for your help. Regards, Wil From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Sunday, October 16, 2011 6:27 PM To: Irwin, William Cc: freesurfer@nmr.mgh.harvard.edu; Irwin, William Subject: Re: [Freesurfer] Hanging or running at 'SubCort Seg'? Hi Wil Can you send us the full recon-all.log? Cheers Bruce On Oct 16, 2011, at 3:53 PM, Irwin, William wir...@memory.ucsf.edu wrote: Hi- I?m a bit stumped by a cased. The input volume looks very good. The first error was the Talairach transform would not complete, so I used the ?-notal-check? flag. As I have been focused on other things, I just let the job run, but after 2 weeks, it is stuck (I assume) as indicated. It is running on a fast processor with plenty of memory, so system constraints are not the issue #@# SubCort Seg Sun Oct 9 16:41:44 PDT 2011 mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2008-03-26.gca as eg.auto_noCCseg.mgz mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz ?lta /media/ClusterData2/data/localdata2/FreeSurfer/wirwin/wirwin_subject s/FT047-5/mri/transforms/cc_up.lta FT047-5 Any suggestions as to what might be the problem? Thanks much, Wil ___ 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] saving adjustments under different names
Hi Maria, you have to make a copy of the subject dir for this. cheers Bruce On Mon, 17 Oct 2011, Maria Felber wrote: Dear all, I have run the recon-all process on my subject im01. Now I am checking for errors and found some. I also found the solution steps. However, as far as I understand it, every time I make a change, this will be permanently done. Is there a way to keep the steps I have done so far and to same further changes to a new subject file, e.g. im01_skullcorrected. I would just like to backup the steps I have done in case I worsen the solution so far and in case I want to compare them. Also, is there a way that the results from recon-all are saved under a different name? Thanks, Maria ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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] First-level analysis with continuous covariate
Hi Emily, I think the parametric modulation should work. In the example, there is a ShockOffset and ShockSlope as conditions 1 and 2. In your case, you would have 4 conditions. 1. IndoorsOffset 2. Indoors-OpennessSlope 3. OutdoorsOffset 4. Outdoors-OpennessSlope You would then create a contrast of 2 vs 4 to test the interaction. doug Emily Ward wrote: How does one execute a first-level (subject-level) analysis with a continuous covariate? For example, in an event-related experiment presenting pictures of scenes, I have two conditions: environment (indoors/outdoors) and openness (a continuous rating obtained independently). I am interested in the environment x openness interaction, so I need to model them together. The parametric modulation paradigm file seems close to what I need, but in the example, there is no discrete variable to consider. Is there a way to model both discrete and continuous variables together? If so, can this method also be used to model out nuisance regressors, like trial performance? Thank you, Emily ___ 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 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
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
[Freesurfer] implementation on Neurodebian
Dear Freesurfer developer(s), Is there a way to get Freesurfer run faster on Neurodebian. While the package produces some truly out of the world segmentations and labels for the cortical surface, it seems to take time. For eg: Defect correction and retesellation takes an hour, other steps take longer..I'm not sure if it's the original dataset, the OS platform (i.e Virtual Machine, Neurodebian) or original computational engine itself. Would be happy in efforts and hints to make this run faster. Best regards, Cartik Sharma ___ 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] Hanging or running at 'SubCort Seg'?
Hi Bruce- We'll this was insightful: The norm.mgz file was empty and when I looked at the original input after (after MRI convert) the sagittal view was rotate by 90 degrees. I'm not sure what caused this, as the input is correctly oriented. The discrepancy between input and conversion to .mgz seem likely to explain why the Talairach transform failed. Suggested on what would cause this glitch? Thanks, Wil |-Original Message- |From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] |Sent: Monday, October 17, 2011 6:27 AM |To: Irwin, William |Cc: freesurfer@nmr.mgh.harvard.edu |Subject: RE: [Freesurfer] Hanging or running at 'SubCort Seg'? | |hmmm, looks like it is almost finished with mri_cc but doesn't complete. |It usually only takes like 2 minutes for this process, so something must be |wrong. Can you send me aseg.auto_noCCseg.mgz and norm.mgz for this |subject? You can probably just email them. | |cheers |Bruce | | |On Mon, 17 Oct 2011, Irwin, |William wrote: | | | Hi Bruce- | | | | It is still running, but the recon-all.log as it stands is attached. | | | | Thanks for your help. | | | | Regards, | | Wil | | | | From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] | Sent: Sunday, October 16, 2011 6:27 PM | To: Irwin, William | Cc: freesurfer@nmr.mgh.harvard.edu; Irwin, William | Subject: Re: [Freesurfer] Hanging or running at 'SubCort Seg'? | | | | Hi Wil | | Can you send us the full recon-all.log? | | Cheers | | Bruce | | | On Oct 16, 2011, at 3:53 PM, Irwin, William wir...@memory.ucsf.edu |wrote: | | Hi- | | | | I?m a bit stumped by a cased. The input volume looks very good. The first |error was the Talairach transform would not complete, so I used the | ?-notal-check? flag. As I have been focused on other things, I just let the |job run, but after 2 weeks, it is stuck (I assume) as indicated. It | is running on a fast processor with plenty of memory, so system | constraints are not the issue | | | | #@# SubCort Seg Sun Oct 9 16:41:44 PDT 2011 | | | | mri_ca_label -align -nobigventricles norm.mgz | transforms/talairach.m3z | /usr/local/freesurfer/average/RB_all_2008-03-26.gca as | | eg.auto_noCCseg.mgz | | | | mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz ?lta | /media/ClusterData2/data/localdata2/FreeSurfer/wirwin/wirwin_subject | | s/FT047-5/mri/transforms/cc_up.lta FT047-5 | | | | Any suggestions as to what might be the problem? | | | | Thanks much, | | Wil | | ___ | 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] Hanging or running at 'SubCort Seg'?
what is your input format? Is it analyze? On Mon, 17 Oct 2011, Irwin, William wrote: Hi Bruce- We'll this was insightful: The norm.mgz file was empty and when I looked at the original input after (after MRI convert) the sagittal view was rotate by 90 degrees. I'm not sure what caused this, as the input is correctly oriented. The discrepancy between input and conversion to .mgz seem likely to explain why the Talairach transform failed. Suggested on what would cause this glitch? Thanks, Wil |-Original Message- |From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] |Sent: Monday, October 17, 2011 6:27 AM |To: Irwin, William |Cc: freesurfer@nmr.mgh.harvard.edu |Subject: RE: [Freesurfer] Hanging or running at 'SubCort Seg'? | |hmmm, looks like it is almost finished with mri_cc but doesn't complete. |It usually only takes like 2 minutes for this process, so something must be |wrong. Can you send me aseg.auto_noCCseg.mgz and norm.mgz for this |subject? You can probably just email them. | |cheers |Bruce | | |On Mon, 17 Oct 2011, Irwin, |William wrote: | | | Hi Bruce- | | | | It is still running, but the recon-all.log as it stands is attached. | | | | Thanks for your help. | | | | Regards, | | Wil | | | | From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] | Sent: Sunday, October 16, 2011 6:27 PM | To: Irwin, William | Cc: freesurfer@nmr.mgh.harvard.edu; Irwin, William | Subject: Re: [Freesurfer] Hanging or running at 'SubCort Seg'? | | | | Hi Wil | | Can you send us the full recon-all.log? | | Cheers | | Bruce | | | On Oct 16, 2011, at 3:53 PM, Irwin, William wir...@memory.ucsf.edu |wrote: | | Hi- | | | | I?m a bit stumped by a cased. The input volume looks very good. The first |error was the Talairach transform would not complete, so I used the | ?-notal-check? flag. As I have been focused on other things, I just let the |job run, but after 2 weeks, it is stuck (I assume) as indicated. It | is running on a fast processor with plenty of memory, so system | constraints are not the issue | | | | #@# SubCort Seg Sun Oct 9 16:41:44 PDT 2011 | | | | mri_ca_label -align -nobigventricles norm.mgz | transforms/talairach.m3z | /usr/local/freesurfer/average/RB_all_2008-03-26.gca as | | eg.auto_noCCseg.mgz | | | | mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz ?lta | /media/ClusterData2/data/localdata2/FreeSurfer/wirwin/wirwin_subject | | s/FT047-5/mri/transforms/cc_up.lta FT047-5 | | | | Any suggestions as to what might be the problem? | | | | Thanks much, | | Wil | | ___ | 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] open-access article on TRACULA now available
Hi all - Since a few of you have inquired about a TRACULA reference in the past, here's one: http://www.frontiersin.org/neuroinformatics/10.3389/fninf.2011.00023/abstract There's a link on the right where you can download the PDF. Happy reading! a.y ___ 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] reg-feat2anat failure
How are you generating the masks? doug Michelle Umali wrote: Hi Freesurfers, I've run reg-feat2anat on several subjects in order to generate binary masks to use in an FSL ppi. For 3 subjects, this completely failed. When I looked at the fsl's own registration of fsl feat 2 standard (via tkregister2), the registration is fine, but after running reg-feat2anat, the registration of the feat to the freesurfer anatomical and the feat to standard are completely off. I manually fixed and saved the registration edits via reg-feat2anat --manual, but when I generated the masks again, they were totally wrong still. When looking at freesurfer's feat to standard registration, it looks like all the brains weren't tall enough in the saggital view. Am I supposed to stretch the feat brain to fit? How can I fix this so that the masks are accurate? Thanks. Michelle ___ 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 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] Incorrect pial surface
We've uploaded the file as 30193retry.tar.gz Jordan Pierce ___ 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] Incorrect pial surface
Okay, I'll take a look. Allison On Mon, 17 Oct 2011, Jordan Pierce wrote: We've uploaded the file as 30193retry.tar.gz Jordan Pierce ___ ___ 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] QDec questions
Hi, just wondering if anyone has any advice on the following questions: I'm using QDEC to analyze cortical thickness differences between groups and I have a few questions: 1) There are a few variables that I need to control for. First variable is scanner - I used two different scanners of different field strengths (1.5T GE and 3T Siemens) so I wanted to control for scanner. I also wanted to control for age and gender. Here's my ideal design setup: discrete variables - groups, scanner, gender nuisance variable - age contrast would be 1 -1 0 0 0 0 I realize that scanner, gender, and group are all discrete variables, and that age would be a continuous one. However, in the design tab, I am not able to select all 3 discrete variables (groups, scanner, and gender). Should I designate scanner or gender as a nuisance variable instead? Would it matter which one I use as the nuisance variable? Possible setup: discrete vars - groups, scanner nuisance vars - age, gender contrast - 1 -1 0 0 (Correct?) 2) If I use DODS, should I demean the ages if age is a nuisance variable? 3) If I use a smoothing kernel during the analysis, then create an ROI and map that ROI to each individual subject, will the resulting .stats file in each subjects stats folder reflect the smoothed data or does mapping onto each ROI just extract the raw unsmoothed data from each vertex? Thanks! Krista ___ 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 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
[Freesurfer] label transformation to MNI space
Hi all, I am trying to transform some labels from the aparc to masks in MNI space. Ideally, I would like to do this for each subject in my study individually (using their own rawavg.mgz and labels), but for now I started out with fsaverage. I first converted the label file into a nifti: mri_label2vol --label ./fsaverage/label/lh.entorhinal.label --subject fsaverage --temp ./fsaverage/mri/brainmask.mgz --o lh_entorhinal.nii.gz --identity And then put the nifti file containing the label into MNI space: mri_vol2vol --mov lh_entorhinal.nii.gz --targ MNI152_T1_2mm.brain.nii.gz --o lh_entorhinal_MNI.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat But when I open lh_entorhinal_MNI.nii.gz with fslview, the location is completely wrong. I checked the location with tkregister as well: tkregister2 --mov lh_entorhinal_MNI.nii.gz --reg /$FREESURFER_HOME/average/mni152.register.dat But here the entorhinal was also in the wrong place. Do you know how to fix this? Thanks, -- Linda Douw, PhD. ___ 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] aparc+aspec to T1
Dear experts, I would like to move my aparc+aseg.mgz image back to the native T1 space (rawavg.mgz). I tried: mri_convert -rl rawavg.mgz -rt nearest aparc+aseg.mgz ./subj001_aparc+aseg2raw.nii.gz However, it there a way that I don't change the value within the original aparc+aseg.mgz, so that I can use the LUT to define ROIs for additional processes? Thanks. Monica ___ 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] aparc+aspec to T1
Hi Monica I'm not sure what that means, but adding segmentation labels requires manual labeling and retraining etc cheers Bruce On Mon, 17 Oct 2011, Hsiao-Ying (Monica) Wey wrote: Dear experts, I would like to move my aparc+aseg.mgz image back to the native T1 space (rawavg.mgz). I tried: mri_convert -rl rawavg.mgz -rt nearest aparc+aseg.mgz ./subj001_aparc+aseg2raw.nii.gz However, it there a way that I don't change the value within the original aparc+aseg.mgz, so that I can use the LUT to define ROIs for additional processes? Thanks. Monica ___ 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] aparc+aspec to T1
See http://www.freesurfer.net/fswiki/FsAnat-to-NativeAnat doug Hsiao-Ying (Monica) Wey wrote: Dear experts, I would like to move my aparc+aseg.mgz image back to the native T1 space (rawavg.mgz). I tried: mri_convert -rl rawavg.mgz -rt nearest aparc+aseg.mgz ./subj001_aparc+aseg2raw.nii.gz However, it there a way that I don't change the value within the original aparc+aseg.mgz, so that I can use the LUT to define ROIs for additional processes? Thanks. Monica ___ 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 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] reg-feat2anat failure
Hi Doug, I am using reg-feat2anat on the feat directory of each run. reg-feat2anat --feat feadir.feat --subject XX Then I checked and adjusted the registration with: reg-feat2anat --feat featdir.feat --manual Next I checked and adjusted the registration to the standard with: reg-feat2anat --feat featdir.feat --manxfm func2std To generate cortical binary masks I used: aparc2feat --feat featdir.feat --annot BA fslmaths featdir.feat/reg/freesurfer/lh.BA.nii.gz -thr 10 -uthr 10 featdir.feat/reg/freesurfer/V1_l.nii.gz To generate subcortical binary masks I did: aseg2feat --feat featdir.feat --aseg aparc+aseg fslmaths featdir.feat/reg/freesurfer/aparc+aseg.nii.gz -thr 54 -uthr 54 featdir.feat/reg/freesurfer/amygdala_r.nii.gz When I looked at the masks in FSLview and checked the masks against the other atlases, everything was off even after painstakingly editing the registrations. Is there something I am doing wrong? Thanks. Michelle On Mon, Oct 17, 2011 at 1:36 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: How are you generating the masks? doug Michelle Umali wrote: Hi Freesurfers, I've run reg-feat2anat on several subjects in order to generate binary masks to use in an FSL ppi. For 3 subjects, this completely failed. When I looked at the fsl's own registration of fsl feat 2 standard (via tkregister2), the registration is fine, but after running reg-feat2anat, the registration of the feat to the freesurfer anatomical and the feat to standard are completely off. I manually fixed and saved the registration edits via reg-feat2anat --manual, but when I generated the masks again, they were totally wrong still. When looking at freesurfer's feat to standard registration, it looks like all the brains weren't tall enough in the saggital view. Am I supposed to stretch the feat brain to fit? How can I fix this so that the masks are accurate? Thanks. Michelle --**--** __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html 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.
