Re: [Freesurfer] rawfunc2surf-sess with a limited set of surface files
One more question: I tried to run: rawfunc2surf-sess -s oz_fparc -i fmc -trgsubject F99 -surfreg iter05.sphere.reg -fwhm 2 -per-session And I got this: ERROR: experts key needed (-expkey) Not sure what this flag is. Reza ___ 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] Comparison of surface and euclidean distances of fsaverage
Please remove this mail. This problem was already solved. On Tue, 7 Oct 2014 16:55:16 +0200 pfannmo...@uni-greifswald.de wrote: Dear FreeSurfer experts, I computed distances on the cortex surface of fsaverage using mris_pmake. The exact syntax of the distance computation was: mris_pmake --subject fsaverage --hemi lh/rh --surface0 smoothwm --curv0 sulc --curv1 sulc --mpmOverlay euclidean --mpmProg pathFind --mpmArgs startVertex:X,endVertex:X . Subsequently, the euclidean distance was computed using the MNI coordinates displayed by tksurfer if the startVertex and the stopVertex are selected: distance_euc = sqrt[(startMNI_x-stopMNI_x)^2+(startMNI_y-stopMNI_y)^2+(startMNI_z-stopMNI_z)^2] . The in-surface distance must be larger or equal to the euclidean distance. However, in ~50% of the cases investigated the opposite is computed. Typical distances calculated are in the range of 7 mm. Do you have an explanation for this outcome and a possible solution? How can it be corrected? I am using FreeSurfer 5.3 and did not encounter any other problems in data evaluation. Any help us highly appreciated! Sincerely yours pfannmoe ___ 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] WM Pial Segmentation Errors
Hi Bruce, Do I not have permission to transfer files to the remote machine? I can login fine as an anonymous user but when I attempt to use the put command it says it could not create the file. On 10/7/14, 7:33 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Michael sure, the T2 can help if you have it (although you'll need to download some updated binaries), but it is impossible to tell from these images what is going on. Looks either the intensity normalization, mri_segment or mris_make_surfaces failed. You can try the expert options for each one to prespecify the range of allowable intensities for gray and white matter. If you upload the subject to our ftp site (the whole subject directory tarred and gzipped) we will take a look cheers Bruce On Mon, 6 Oct 2014, Smith, Michael wrote: Hi, I¹ve been having trouble on a few of our subjects with getting the white matter and pial surface files to ³line up² correctly with the volume files. I¹ve attached a screenshot of what is happening: the pial surface is in red and the white matter surface file is in yellow. I have also attached an example of a ³good² subject for comparison. I¹ve tried looking through the tutorials online but didn¹t see anything that was really related to my issue and I was wondering what the best way to correct this. We have T2 weighted images for several subjects is well if that helps. Not sure if Freesurfer can use T2 images instead of T1 in the reconall script but I thought I would mention it. Thank you very much in advance! Best, Michael S. ___ 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] WM Pial Segmentation Errors
can you send us the details of your ftp command? On Wed, 8 Oct 2014, Smith, Michael wrote: Hi Bruce, Do I not have permission to transfer files to the remote machine? I can login fine as an anonymous user but when I attempt to use the put command it says it could not create the file. On 10/7/14, 7:33 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Michael sure, the T2 can help if you have it (although you'll need to download some updated binaries), but it is impossible to tell from these images what is going on. Looks either the intensity normalization, mri_segment or mris_make_surfaces failed. You can try the expert options for each one to prespecify the range of allowable intensities for gray and white matter. If you upload the subject to our ftp site (the whole subject directory tarred and gzipped) we will take a look cheers Bruce On Mon, 6 Oct 2014, Smith, Michael wrote: Hi, I¹ve been having trouble on a few of our subjects with getting the white matter and pial surface files to ³line up² correctly with the volume files. I¹ve attached a screenshot of what is happening: the pial surface is in red and the white matter surface file is in yellow. I have also attached an example of a ³good² subject for comparison. I¹ve tried looking through the tutorials online but didn¹t see anything that was really related to my issue and I was wondering what the best way to correct this. We have T2 weighted images for several subjects is well if that helps. Not sure if Freesurfer can use T2 images instead of T1 in the reconall script but I thought I would mention it. Thank you very much in advance! Best, Michael S. ___ 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] cortical and subcortical masks in txt
Hi Stefano, what would the format of the txt file be? Probably your best bet would be to do it in matlab Bruce On Tue, 7 Oct 2014, std...@virgilio.it wrote: Hi list, I need to extract the cortical and subcortical masks created by using recon-all as .txt. I would work on the txt to import FS masks in Brain Voyager Qx which does not accept .nii.gz but only .par/.rec format. Thanks Best regards, Stefano ___ 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] WM Pial Segmentation Errors
See attached On 10/8/14, 10:46 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: can you send us the details of your ftp command? On Wed, 8 Oct 2014, Smith, Michael wrote: Hi Bruce, Do I not have permission to transfer files to the remote machine? I can login fine as an anonymous user but when I attempt to use the put command it says it could not create the file. On 10/7/14, 7:33 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Michael sure, the T2 can help if you have it (although you'll need to download some updated binaries), but it is impossible to tell from these images what is going on. Looks either the intensity normalization, mri_segment or mris_make_surfaces failed. You can try the expert options for each one to prespecify the range of allowable intensities for gray and white matter. If you upload the subject to our ftp site (the whole subject directory tarred and gzipped) we will take a look cheers Bruce On Mon, 6 Oct 2014, Smith, Michael wrote: Hi, I¹ve been having trouble on a few of our subjects with getting the white matter and pial surface files to ³line up² correctly with the volume files. I¹ve attached a screenshot of what is happening: the pial surface is in red and the white matter surface file is in yellow. I have also attached an example of a ³good² subject for comparison. I¹ve tried looking through the tutorials online but didn¹t see anything that was really related to my issue and I was wondering what the best way to correct this. We have T2 weighted images for several subjects is well if that helps. Not sure if Freesurfer can use T2 images instead of T1 in the reconall script but I thought I would mention it. Thank you very much in advance! Best, Michael S. ___ 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] WM Pial Segmentation Errors
Hi Michael you need to follow the directions on this page: http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange in particular, make sure you change directories before trying to put cheers Bruce On Wed, 8 Oct 2014, Smith, Michael wrote: See attached On 10/8/14, 10:46 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: can you send us the details of your ftp command? On Wed, 8 Oct 2014, Smith, Michael wrote: Hi Bruce, Do I not have permission to transfer files to the remote machine? I can login fine as an anonymous user but when I attempt to use the put command it says it could not create the file. On 10/7/14, 7:33 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Michael sure, the T2 can help if you have it (although you'll need to download some updated binaries), but it is impossible to tell from these images what is going on. Looks either the intensity normalization, mri_segment or mris_make_surfaces failed. You can try the expert options for each one to prespecify the range of allowable intensities for gray and white matter. If you upload the subject to our ftp site (the whole subject directory tarred and gzipped) we will take a look cheers Bruce On Mon, 6 Oct 2014, Smith, Michael wrote: Hi, I¹ve been having trouble on a few of our subjects with getting the white matter and pial surface files to ³line up² correctly with the volume files. I¹ve attached a screenshot of what is happening: the pial surface is in red and the white matter surface file is in yellow. I have also attached an example of a ³good² subject for comparison. I¹ve tried looking through the tutorials online but didn¹t see anything that was really related to my issue and I was wondering what the best way to correct this. We have T2 weighted images for several subjects is well if that helps. Not sure if Freesurfer can use T2 images instead of T1 in the reconall script but I thought I would mention it. Thank you very much in advance! Best, Michael S. ___ 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] v5.1 control point mri_ca_normalize bug
Hi Gabe this wasn't really a bug per-se, just induced some behavior that people didn't like. You can't skip the mri_ca_normalize step or the aseg won't be accurate. The aseg patch I believe just starts autorecon2-cp after the aseg hs been created, but Nick or Zeke can correct me if I'm wrong. cheers Bruce On Mon, 6 Oct 2014, Marx, Gabe wrote: Hello Freesurfer experts, I had a question regarding the v5.1 control point mri_ca_normalize bug. I read the release notes and know that this bug can be worked around by adding the –nocanorm flag to my recon-all however I have become worried about the ramifications of skipping mri_ca_normalize in my pipeline. Would someone be able to give me a better description as to what mri_ca_normalize is doing and what I am sacrificing by taking it out of my pipeline? Furthermore, in regards to the patch for the recon-all script to fix this bug, what is the patch doing exactly? If I had some data in which I used the –nocanorm flag and other data in which I used the patch would I still be able to make valid analysis if I merged them? Would there be significant inconsistencies? Thanks! Best, Gabe ___ 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] Mismatched dimensions with T1 and Flair inputs
Dear mailing list, I am trying to do a recon-all with two nifti inputs: A T1 and a Flair, for pial surface refinement. This results in an error message saying the dimensions are mismatched. (The third dimension of the T1 and Flair are different by one slice. ) I do not, however, have a problem running recon-all with only one T1 input. I am using Freesurfer v 5.1 . I read in the release notes that in version 5.2 you can use the flag -FLAIR when you are using a flair image as input. I suppose this will not run in an earlier version? Would it be correct to use the following command : recon-all -s [subject] -i T1.nii -i flair.nii -all Kind regards,Vilde ___ 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] Mismatched dimensions with T1 and Flair inputs
Hi Vilde no, you can't give recon-all a flair directly, it needs a T1 do do the recon on. You use the flair at the end to do a post-hoc deformation using -flairpial I believe cheers Bruce On Wed, 8 Oct 2014, Vilde wrote: Dear mailing list, I am trying to do a recon-all with two nifti inputs: A T1 and a Flair, for pial surface refinement. This results in an error message saying the dimensions are mismatched. (The third dimension of the T1 and Flair are different by one slice. ) I do not, however, have a problem running recon-all with only one T1 input. I am using Freesurfer v 5.1 . I read in the release notes that in version 5.2 you can use the flag -FLAIR when you are using a flair image as input. I suppose this will not run in an earlier version? Would it be correct to use the following command : recon-all -s [subject] -i T1.nii -i flair.nii -all Kind regards, Vilde ___ 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] WM Pial Segmentation Errors
Ah, sorry for some reason it just wasn’t clicking before. I was able to upload a dataset. Thanks! On 10/8/14, 10:59 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Michael you need to follow the directions on this page: http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange in particular, make sure you change directories before trying to put cheers Bruce On Wed, 8 Oct 2014, Smith, Michael wrote: See attached On 10/8/14, 10:46 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: can you send us the details of your ftp command? On Wed, 8 Oct 2014, Smith, Michael wrote: Hi Bruce, Do I not have permission to transfer files to the remote machine? I can login fine as an anonymous user but when I attempt to use the put command it says it could not create the file. On 10/7/14, 7:33 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Michael sure, the T2 can help if you have it (although you'll need to download some updated binaries), but it is impossible to tell from these images what is going on. Looks either the intensity normalization, mri_segment or mris_make_surfaces failed. You can try the expert options for each one to prespecify the range of allowable intensities for gray and white matter. If you upload the subject to our ftp site (the whole subject directory tarred and gzipped) we will take a look cheers Bruce On Mon, 6 Oct 2014, Smith, Michael wrote: Hi, I¹ve been having trouble on a few of our subjects with getting the white matter and pial surface files to ³line up² correctly with the volume files. I¹ve attached a screenshot of what is happening: the pial surface is in red and the white matter surface file is in yellow. I have also attached an example of a ³good² subject for comparison. I¹ve tried looking through the tutorials online but didn¹t see anything that was really related to my issue and I was wondering what the best way to correct this. We have T2 weighted images for several subjects is well if that helps. Not sure if Freesurfer can use T2 images instead of T1 in the reconall script but I thought I would mention it. Thank you very much in advance! Best, Michael S. ___ 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] Mismatched dimensions with T1 and Flair inputs
Thank you Bruce! If I understand you correctly, would the command be Recon-all -s subj_name -FLAIRpial.nii ? Or would I first have to do recon-all with only T1 as input and then do another command after it has finished running? And in that case, what would that command be? Best, Vilde Date: Wed, 8 Oct 2014 11:56:51 -0400 From: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Mismatched dimensions with T1 and Flair inputs Hi Vilde no, you can't give recon-all a flair directly, it needs a T1 do do the recon on. You use the flair at the end to do a post-hoc deformation using -flairpial I believe cheers Bruce On Wed, 8 Oct 2014, Vilde wrote: Dear mailing list, I am trying to do a recon-all with two nifti inputs: A T1 and a Flair, for pial surface refinement. This results in an error message saying the dimensions are mismatched. (The third dimension of the T1 and Flair are different by one slice. ) I do not, however, have a problem running recon-all with only one T1 input. I am using Freesurfer v 5.1 . I read in the release notes that in version 5.2 you can use the flag -FLAIR when you are using a flair image as input. I suppose this will not run in an earlier version? Would it be correct to use the following command : recon-all -s [subject] -i T1.nii -i flair.nii -all Kind regards, Vilde ___ 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] sequence advice for GE 750 8-channel coil
Hello Lee - thanks so much for your response. I looked into the document you referred me to and found a section on GE protocols here (page 3): http://martinos.org/~andre/FreeSurfer_recommended_morphometry_protocols.pdf I would appreciate your input on a few details. First, the document indicates min (9150ms) for the TR value. However, the minimum TR is about 8 ms when I prescribe a similar IR-FSPGR sequence. I may be missing something obvious, but: a) Would that be 9.15 ms instead? (actually, the TR is not selectable when prescribing this 3D sequence). Also, we are mostly interested in getting good whole-brain segmentation and, from what I gather, the document mentions that multiecho FLASH is the way to go for this. b) Would the GE IR-FSPGR sequence specified in the protocol document still be OK for getting reliable whole-brain segmentation? c) I take it then that there is no GE-version for the multiecho FLASH, correct? Thanks again, Antonio ___ 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] Running GCA atlas, problem with talairach
Hi Freesurfers, I am trying to make an atlas using the GCA algorithm and the error message I just got is asking for the talairach.xfm file. The scans I am using were originally run through freesurfer 3.1 and talairach processing was not done. What do you suggest I do to use these scans in my new atlas? Kind regards, Alexarae ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Surface Viewer Issue.
i saw this problem on one redhat installation, not on any others, seems something with the X library orientation information and openGL greg On 10/08/14, Jamie Hanson wrote: Hi Freesurfer List, I had a (hopefully quick) question about surface viewers and data orientation in tksurfer v. freeview. I processed all my data in freesurfer v5.3.0 (on a linux cluster) and noticed something odd when I viewed surfaces. For tksurfer, the surfaces were upside down when I opened them (see attached pic: tksurfer.png); for freeview, the data looked fine (see attached pic: freeview.png). I believe the orientation of the images is correct (judging by the freeview axes), but wondered if this was something others had run into? I uploaded an example subject to the Martinos Center FileDrop (link: http://gate.nmr.mgh.harvard.edu/filedrop2/?p=9491zcnivqw). Any thoughts are greatly appreciated! Thanks much! Best, Jamie. -- Jamie L. Hanson Postdoctoral Fellow, Carolina Consortium on Human Development Duke University 417 Chapel Drive Duke West Campus Sociology-Psychology Building, Room 07A Durham, NC 27710 Email: jamielarshan...@gmail.com Website: http://jamiehanson.org/ ___ 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] Mismatched dimensions with T1 and Flair inputs {Disarmed}
I will try that. Have a good day! Date: Wed, 8 Oct 2014 14:07:38 -0400 From: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Mismatched dimensions with T1 and Flair inputs you would have to first run recon-all -all on the T1 On Wed, 8 Oct 2014, Vilde wrote: Thank you Bruce! If I understand you correctly, would the command be Recon-all -s subj_name -FLAIRpial.nii ? Or would I first have to do recon-all with only T1 as input and then do another command after it has finished running? And in that case, what would that command be? Best, Vilde Date: Wed, 8 Oct 2014 11:56:51 -0400 From: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Mismatched dimensions with T1 and Flair inputs Hi Vilde no, you can't give recon-all a flair directly, it needs a T1 do do the recon on. You use the flair at the end to do a post-hoc deformation using -flairpial I believe cheers Bruce On Wed, 8 Oct 2014, Vilde wrote: Dear mailing list, I am trying to do a recon-all with two nifti inputs: A T1 and a Flair, for pial surface refinement. This results in an error message saying the dimensions are mismatched. (The third dimension of the T1 and Flair are different by one slice. ) I do not, however, have a problem running recon-all with only one T1 input. I am using Freesurfer v 5.1 . I read in the release notes that in version 5.2 you can use the flag -FLAI R when you are using a flair image as input. I suppose this will not run in an earlier version? Would it be correct to use the following command : recon-all -s [subject] -i T1.nii -i flair.nii -all Kind regards, Vilde ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] v5.1 control point mri_ca_normalize bug
Hi Bruce, I appreciate the response! I am sorry, I am a bit confused. The release notes state: An option is to disable the running of mri_ca_normalize when re-running the -autorecon2 or -autorecon2-cp stage after adding control points by adding the flag -nocanorm to the end of recon-all. We will continue to investigate a more automated solution to detection of this problem. The more permanent workaround for v5.1 users is to edit their recon-all script making the following change, which will disable usage of control points with ca_norm: # find these lines: set cmd = (mri_ca_normalize) if($UseControlPoints) set cmd = ($cmd -f $ControlPointsFile) # and comment-out the second line like this: set cmd = (mri_ca_normalize) #if($UseControlPoints) set cmd = ($cmd -f $ControlPointsFile) # then re-run your subjects with the flags: -autorecon2 -autorecon3 -clean-aseg Are you saying the -nocanorm flag will result in inaccurate data? Thanks! Gabe -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Wednesday, October 08, 2014 8:12 AM To: Freesurfer support list Subject: Re: [Freesurfer] v5.1 control point mri_ca_normalize bug Hi Gabe this wasn't really a bug per-se, just induced some behavior that people didn't like. You can't skip the mri_ca_normalize step or the aseg won't be accurate. The aseg patch I believe just starts autorecon2-cp after the aseg hs been created, but Nick or Zeke can correct me if I'm wrong. cheers Bruce On Mon, 6 Oct 2014, Marx, Gabe wrote: Hello Freesurfer experts, I had a question regarding the v5.1 control point mri_ca_normalize bug. I read the release notes and know that this bug can be worked around by adding the –nocanorm flag to my recon-all however I have become worried about the ramifications of skipping mri_ca_normalize in my pipeline. Would someone be able to give me a better description as to what mri_ca_normalize is doing and what I am sacrificing by taking it out of my pipeline? Furthermore, in regards to the patch for the recon-all script to fix this bug, what is the patch doing exactly? If I had some data in which I used the –nocanorm flag and other data in which I used the patch would I still be able to make valid analysis if I merged them? Would there be significant inconsistencies? Thanks! Best, Gabe ___ 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] v5.1 control point mri_ca_normalize bug
I don't think you want to run with -nocanorm. Just commenting out the addition of the -f $ControlPointsFile should be sufficient. Right Nick? On Wed, 8 Oct 2014, Marx, Gabe wrote: Hi Bruce, I appreciate the response! I am sorry, I am a bit confused. The release notes state: An option is to disable the running of mri_ca_normalize when re-running the -autorecon2 or -autorecon2-cp stage after adding control points by adding the flag -nocanorm to the end of recon-all. We will continue to investigate a more automated solution to detection of this problem. The more permanent workaround for v5.1 users is to edit their recon-all script making the following change, which will disable usage of control points with ca_norm: # find these lines: set cmd = (mri_ca_normalize) if($UseControlPoints) set cmd = ($cmd -f $ControlPointsFile) # and comment-out the second line like this: set cmd = (mri_ca_normalize) #if($UseControlPoints) set cmd = ($cmd -f $ControlPointsFile) # then re-run your subjects with the flags: -autorecon2 -autorecon3 -clean-aseg Are you saying the -nocanorm flag will result in inaccurate data? Thanks! Gabe -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Wednesday, October 08, 2014 8:12 AM To: Freesurfer support list Subject: Re: [Freesurfer] v5.1 control point mri_ca_normalize bug Hi Gabe this wasn't really a bug per-se, just induced some behavior that people didn't like. You can't skip the mri_ca_normalize step or the aseg won't be accurate. The aseg patch I believe just starts autorecon2-cp after the aseg hs been created, but Nick or Zeke can correct me if I'm wrong. cheers Bruce On Mon, 6 Oct 2014, Marx, Gabe wrote: Hello Freesurfer experts, I had a question regarding the v5.1 control point mri_ca_normalize bug. I read the release notes and know that this bug can be worked around by adding the –nocanorm flag to my recon-all however I have become worried about the ramifications of skipping mri_ca_normalize in my pipeline. Would someone be able to give me a better description as to what mri_ca_normalize is doing and what I am sacrificing by taking it out of my pipeline? Furthermore, in regards to the patch for the recon-all script to fix this bug, what is the patch doing exactly? If I had some data in which I used the –nocanorm flag and other data in which I used the patch would I still be able to make valid analysis if I merged them? Would there be significant inconsistencies? Thanks! Best, Gabe ___ 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] rawfunc2surf-sess with a limited set of surface files
Try it without -i fmc On 10/08/2014 04:38 AM, Reza Rajimehr wrote: One more question: I tried to run: rawfunc2surf-sess -s oz_fparc -i fmc -trgsubject F99 -surfreg iter05.sphere.reg -fwhm 2 -per-session And I got this: ERROR: experts key needed (-expkey) Not sure what this flag is. Reza ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] functional correlation
Hello Freesurfers A bit new to the program, so I hope the following makes sense. We would like to do a bottom-up vertex-by-vertex analysis to see where functional activation correlates with thickness. We've done our functional analyses through SPM and can get those maps into tksurfer. Most of the tutorials and information I see has to do with, for example, defining a ROI based on functional data and extracting the thickness measures under that ROI. But this would be a little different Does this make sense, and is this doable in freesurfer? If so, could someone point me to the relevant tutorial or commands? I appreciate your help ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] rawfunc2surf-sess with a limited set of surface files
Hi Doug, Removing -i fmc did not help, and I still get the same error. By looking at the rawfunc2surf-sess script, it looks like specifying an argument for -surfreg makes ExpKeyNeeded = 1. Can I just specify something for -expkey? Is this something that is used only in the name of log file? Thanks, Reza Try it without -i fmc On 10/08/2014 04:38 AM, Reza Rajimehr wrote: One more question: I tried to run: rawfunc2surf-sess -s oz_fparc -i fmc -trgsubject F99 -surfreg iter05.sphere.reg -fwhm 2 -per-session And I got this: ERROR: experts key needed (-expkey) Not sure what this flag is. Reza ___ 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.
