Re: [Freesurfer] Problems with quantitative T1 images and Freeview
g466_qMRI_R1.nii.gz https://docs.google.com/file/d/0B_UcVoCKdFenTkh6SUU4MVpxYjA/edit?usp=drive_web Dear Ruopeng, I just had to make sure about data rights issues before sending you the image. No problem there. I have attached the nifti file that I used. There were some attachment size issues, please let me know if you cannot access the file. Thank you for looking into this! Kind regards, Pernille On Mon, Feb 2, 2015 at 3:47 PM, Ruopeng Wang rpw...@nmr.mgh.harvard.edu wrote: Would it be possible to send us an image file that you had problem with? Best, Ruopeng On Feb 2, 2015, at 7:38 AM, Pernille Iversen pern...@drcmr.dk wrote: Dear Freesurfer team, We calculate our T1 images from quantitative sequences. I have tried to process one of these images with the FS pipeline and it finishes apparently without errors. However, when I try to load any of the .mgz files in Freeview, the images appears as a white box. Changing the slider settings for opacity, window, level, min or max does not help. The only way I can get a hint of a brain (including a lot of noise) is to change color map to colorlut, so maybe Freeview has problems with showing these images. Any suggestions how to proceed? Are there any special settings I need for the image generation? Thanks in advance. Pernille ___ 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. -- Pernille Iversen, PhD Manager of Reader Centre Danish Research Centre for Magnetic resonance Center for Functional and Diagnostic Imaging and Research MR-department, 714 Kettegaard Allé 30 tel: 00 45 3862 6205 Hvidovre Hospital fax: 00 45 3862 1620 2650 Hvidovre mail: pern...@drcmr.dk Denmarkwww: www.drcmr.dk/ www.cimbi.dk ___ 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] Problems with quantitative T1 images and Freeview
Dear Freesurfer team, We calculate our T1 images from quantitative sequences. I have tried to process one of these images with the FS pipeline and it finishes apparently without errors. However, when I try to load any of the .mgz files in Freeview, the images appears as a white box. Changing the slider settings for opacity, window, level, min or max does not help. The only way I can get a hint of a brain (including a lot of noise) is to change color map to colorlut, so maybe Freeview has problems with showing these images. Any suggestions how to proceed? Are there any special settings I need for the image generation? Thanks in advance. Pernille ___ 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] pial surface voxel shift
Hi After running several subjects (using trio siemens dicomfiles) with recon-all -all -nowmsa, we have observed an apparent shift of approximately one voxel to the left of the pial surface as compared to the brainmask.mgz in the TkMedit coronal view. This was observed in all of our subjects. Do you have any explanation for this - are there any corrections we need to do to avoid this? Thanks, Pernille ___ 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] Using own atlas - file conversion
Dear all, We have created our own atlas based on several subjects. We have the atlas in analyze volume files and would like to know if we can somehow convert these files into the .gcs format without having to go through all the manual steps of creating a template and labels. Thanks, Pernille Iversen ___ 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] -randomness flag for recon-all
Dear Nick, I have now used version 4.5.0 and the -randomness flag no longer gives errors, however, after 10 parallel runs of a subject with the -randomness flag set, I observe that the stats are completely identical. In the logs I can see that the line setting seed for random number generator to 1234 is no longer there. In the earlier versions where the random initialisation was default I observed differences in the stats when I made the 10 parallel runs on the same subject as I have used this time - so it would seem that the random initialisation is not turned on when I use the flag. Can you please comment on this :) Thanks, Pernille On Sat, Jul 25, 2009 at 12:03 AM, Nick Schmansky ni...@nmr.mgh.harvard.eduwrote: Pernille, My mistake, v4.4.0 still makes use of randomness. The next version, to be released in a couple weeks, with have -norandomness by default. The ReleaseNotes page has been updated. Nick On Thu, 2009-07-23 at 09:52 +0200, Pernille Iversen wrote: Hi, In the release notes for version 4.4.0 it says that The -randomness flag can be used to allow usage of a random seed, however, running the following command: recon-all -all -nowmsa -randomness -subjid f4168_1r gives the following error: ERROR: Flag -randomness unrecognized. Is there another way to reintroduce the randomness? I am using the following version: v 1.133.2.51 2009/06/11 Thanks, Pernille ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Pernille Iversen, PhD Danish Centre for Magnetic resonance MR-department, 340 Kettegaard Allé 30 Hvidovre Hospital tel: 00 45 3632 2978/2885 University of Copenhagen fax: 00 45 3647 0302 2650 Hvidovre mail: pern...@drcmr.dk Denmarkwww: www.drcmr.dk/ www.cimbi.dk ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] -randomness flag for recon-all
Hi, In the release notes for version 4.4.0 it says that The -randomness flag can be used to allow usage of a random seed, however, running the following command: recon-all -all -nowmsa -randomness -subjid f4168_1r gives the following error: ERROR: Flag -randomness unrecognized. Is there another way to reintroduce the randomness? I am using the following version: v 1.133.2.51 2009/06/11 Thanks, Pernille ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
