[Freesurfer] Fsaverage for ROI analysis of children
Hello all, I have been conducting an ROI analysis and following the cortical thickness ROI tutorial found here: https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness. After going through this tutorial with a few of my subjects I’ve noticed the ROI when registered to the fsaverage template is not in the correct position. I’m guessing this is due to the nature of my subjects (children ranging from 8months-11 years old). Is there a better template I should use for this analysis? Also, when I run mri_segstats to get the cortical thickness for my ROI, will these numbers be inaccurate too? Thanks in advance! It is worth noting I am running Darwin-lion-stable-pub-v5.3.0 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] Fsaverage for ROI analysis of children
Can you back up and tell us what it is you are trying to do? Where did the ROI come from and how did you create it? doug On 11/3/14 8:56 AM, Smith, Michael wrote: Hello all, I have been conducting an ROI analysis and following the cortical thickness ROI tutorial found here: https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness. After going through this tutorial with a few of my subjects I've noticed the ROI when registered to the fsaverage template is not in the correct position. I'm guessing this is due to the nature of my subjects (children ranging from 8months-11 years old). Is there a better template I should use for this analysis? Also, when I run mri_segstats to get the cortical thickness for my ROI, will these numbers be inaccurate too? Thanks in advance! It is worth noting I am running Darwin-lion-stable-pub-v5.3.0 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] Fsaverage for ROI analysis of children
Hi Doug, We are trying to look at the cortical thickness of a few different ROIs (primary auditory cortex) and see how these areas relate to the EEG ERPs we collected on these subjects as a function of age and development. I created the ROIs using the mri_annotation2label command per hemisphere then mri_label2vol to create a binary volume file for each ROI in each hemisphere. Does that sound correct or would you recommend doing it a different way? Best, Michael S. From: Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Monday, November 3, 2014 at 9:31 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fsaverage for ROI analysis of children Can you back up and tell us what it is you are trying to do? Where did the ROI come from and how did you create it? doug On 11/3/14 8:56 AM, Smith, Michael wrote: Hello all, I have been conducting an ROI analysis and following the cortical thickness ROI tutorial found here: https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness. After going through this tutorial with a few of my subjects I’ve noticed the ROI when registered to the fsaverage template is not in the correct position. I’m guessing this is due to the nature of my subjects (children ranging from 8months-11 years old). Is there a better template I should use for this analysis? Also, when I run mri_segstats to get the cortical thickness for my ROI, will these numbers be inaccurate too? Thanks in advance! It is worth noting I am running Darwin-lion-stable-pub-v5.3.0 Best, Michael S. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://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] Fsaverage for ROI analysis of children
Did you make the from the ?h.aparc.annot of fsaverage? If so, why not make the label from the ?h.aparc.annot from the individual subject and then calculate the thickness from that? doug On 11/3/14 9:44 AM, Smith, Michael wrote: Hi Doug, We are trying to look at the cortical thickness of a few different ROIs (primary auditory cortex) and see how these areas relate to the EEG ERPs we collected on these subjects as a function of age and development. I created the ROIs using the mri_annotation2label command per hemisphere then mri_label2vol to create a binary volume file for each ROI in each hemisphere. Does that sound correct or would you recommend doing it a different way? Best, Michael S. From: Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Date: Monday, November 3, 2014 at 9:31 AM To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fsaverage for ROI analysis of children Can you back up and tell us what it is you are trying to do? Where did the ROI come from and how did you create it? doug On 11/3/14 8:56 AM, Smith, Michael wrote: Hello all, I have been conducting an ROI analysis and following the cortical thickness ROI tutorial found here: https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness. After going through this tutorial with a few of my subjects I've noticed the ROI when registered to the fsaverage template is not in the correct position. I'm guessing this is due to the nature of my subjects (children ranging from 8months-11 years old). Is there a better template I should use for this analysis? Also, when I run mri_segstats to get the cortical thickness for my ROI, will these numbers be inaccurate too? Thanks in advance! It is worth noting I am running Darwin-lion-stable-pub-v5.3.0 Best, Michael S. ___ Freesurfer mailing list freesur...@nmr.mgh.harvard.eduhttps://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 ___ 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] Fsaverage for ROI analysis of children
I made the ROI on an individual subject basis, not from fsaverage. Not sure if the labels I made came from the .aparc.annot files, what is the default of mri_annotation2label? I used the -outdir flag. From: Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Monday, November 3, 2014 at 10:10 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fsaverage for ROI analysis of children Did you make the from the ?h.aparc.annot of fsaverage? If so, why not make the label from the ?h.aparc.annot from the individual subject and then calculate the thickness from that? doug On 11/3/14 9:44 AM, Smith, Michael wrote: Hi Doug, We are trying to look at the cortical thickness of a few different ROIs (primary auditory cortex) and see how these areas relate to the EEG ERPs we collected on these subjects as a function of age and development. I created the ROIs using the mri_annotation2label command per hemisphere then mri_label2vol to create a binary volume file for each ROI in each hemisphere. Does that sound correct or would you recommend doing it a different way? Best, Michael S. From: Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Monday, November 3, 2014 at 9:31 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fsaverage for ROI analysis of children Can you back up and tell us what it is you are trying to do? Where did the ROI come from and how did you create it? doug On 11/3/14 8:56 AM, Smith, Michael wrote: Hello all, I have been conducting an ROI analysis and following the cortical thickness ROI tutorial found here: https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness. After going through this tutorial with a few of my subjects I’ve noticed the ROI when registered to the fsaverage template is not in the correct position. I’m guessing this is due to the nature of my subjects (children ranging from 8months-11 years old). Is there a better template I should use for this analysis? Also, when I run mri_segstats to get the cortical thickness for my ROI, will these numbers be inaccurate too? Thanks in advance! It is worth noting I am running Darwin-lion-stable-pub-v5.3.0 Best, Michael S. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://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] I got ERROR during recon-all
I'm new on FREESURFER and have tried to run recon-all refer to https://surfer.nmr.mgh.harvard.edu/fswiki/QuickInstall#Practicedata.26commands However, I got an ERROR .. could you tell me how to run it. Last login: Mon Nov 3 23:53:19 on ttys000 freesurfer-Darwin-lion-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni Ngoaks-MacBook-Pro:~ ngoak$ cd /Applications/freesurfer/subjects/1 Ngoaks-MacBook-Pro:1 ngoak$ ls 1.hdr 1.img 1.txt A001.nii Ngoaks-MacBook-Pro:1 ngoak$ recon-all -all -i A001.nii -s subject001 mkdir: /Applications/freesurfer/subjects/subject001: Permission denied mkdir: /Applications/freesurfer/subjects/subject001/scripts: Permission denied mkdir: /Applications/freesurfer/subjects/subject001/scripts: Permission denied cp: /Applications/freesurfer/subjects/subject001/scripts/build-stamp.txt: No such file or directory cat: /Applications/freesurfer/subjects/subject001/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer /Applications/freesurfer/subjects/subject001: No such file or directory. Ngoaks-MacBook-Pro:1 ngoak$ Best Regards Chonnikan Jongkreangkrai ? ___ 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] Question
Hi, I just took the FreeSurfer course. I am using the command reconall -s subj_ID -i t1w -all. Frequently, because I log on remotely to the server and because of the time that it takes, the terminal disconnects and therefore the process is not complete entirely. Can you point me to a way to redo just the steps that have not been done yet. I give an example of the latest files generated, with just a few files missing. How do I direct it to pick up from where it left? Thank you. Here is the list of files generated: drwxrwsr-x 2 ktanev schiz 80 Oct 31 14:06 orig/ drwxrwsr-x 3 ktanev schiz 1.0K Oct 31 21:39 transforms/ -rw-rw-r-- 1 ktanev schiz 258K Oct 31 21:39 aseg.auto.mgz -rw-rw-r-- 1 ktanev schiz 1.6K Oct 31 21:31 aseg.auto_noCCseg.label_intensities.txt -rw-rw-r-- 1 ktanev schiz 257K Oct 31 21:38 aseg.auto_noCCseg.mgz -rw-rw-r-- 1 ktanev schiz 258K Oct 31 21:39 aseg.mgz -rw-rw-r-- 1 ktanev schiz 1.4M Oct 31 21:45 brain.finalsurfs.mgz -rw-rw-r-- 1 ktanev schiz 1.4M Oct 31 14:53 brainmask.auto.mgz -rw-rw-r-- 1 ktanev schiz 1.4M Oct 31 14:53 brainmask.mgz -rw-rw-r-- 1 ktanev schiz 1.4M Oct 31 21:45 brain.mgz -rw-rw-r-- 1 ktanev schiz 395K Oct 31 15:33 ctrl_pts.mgz -rw-rw-r-- 1 ktanev schiz 145K Oct 31 21:49 filled.mgz -rw-rw-r-- 1 ktanev schiz 12K Oct 31 14:12 mri_nu_correct.mni.log -rw-rw-r-- 1 ktanev schiz 5.7K Oct 31 14:08 mri_nu_correct.mni.log.bak -rw-rw-r-- 1 ktanev schiz 1.5M Oct 31 15:33 norm.mgz -rw-rw-r-- 1 ktanev schiz 5.6M Oct 31 14:12 nu.mgz -rw-rw-r-- 1 ktanev schiz 3.6M Oct 31 20:32 nu_noneck.mgz -rw-rw-r-- 1 ktanev schiz 7.8M Oct 31 14:07 orig.mgz -rw-rw-r-- 1 ktanev schiz 5.7K Oct 31 14:08 orig_nu.log -rw-rw-r-- 1 ktanev schiz 7.8M Oct 31 14:08 orig_nu.mgz -rw-rw-r-- 1 ktanev schiz 19M Oct 31 14:07 rawavg.mgz -rw-rw-r-- 1 ktanev schiz 119 Oct 31 21:45 segment.dat -rw-rw-r-- 1 ktanev schiz 5.5M Oct 31 14:16 T1.mgz -rw-rw-r-- 1 ktanev schiz 1.6K Oct 31 16:35 talairach.label_intensities.txt -rw-rw-r-- 1 ktanev schiz 214 Oct 31 15:30 talairach.log -rw-rw-r-- 1 ktanev schiz 214 Oct 31 21:08 talairach_with_skull_2.log -rw-rw-r-- 1 ktanev schiz 214 Oct 31 14:52 talairach_with_skull.log -rw-rw-r-- 1 ktanev schiz 463K Oct 31 21:48 wm.asegedit.mgz -rw-rw-r-- 1 ktanev schiz 464K Oct 31 21:48 wm.mgz -rw-rw-r-- 1 ktanev schiz 507K Oct 31 21:47 wm.seg.mgz ___ 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] Question
You can run it with recon-all -s subject -make all In the future, you can run recon-all with nohup, ie, nohup recon-all -s subject ... ie, put nohup as the first item and as the last item. This will cause it to run in the background and it should continue to run even if you log out doug On 11/3/14 12:50 PM, Tanev, Kaloyan,M.D. wrote: Hi, I just took the FreeSurfer course. I am using the command reconall --s subj_ID -i t1w -all. Frequently, because I log on remotely to the server and because of the time that it takes, the terminal disconnects and therefore the process is not complete entirely. Can you point me to a way to redo just the steps that have not been done yet. I give an example of the latest files generated, with just a few files missing. How do I direct it to pick up from where it left? Thank you. Here is the list of files generated: drwxrwsr-x 2 ktanev schiz 80 Oct 31 14:06 orig/ drwxrwsr-x 3 ktanev schiz 1.0K Oct 31 21:39 transforms/ -rw-rw-r-- 1 ktanev schiz 258K Oct 31 21:39 aseg.auto.mgz -rw-rw-r-- 1 ktanev schiz 1.6K Oct 31 21:31 aseg.auto_noCCseg.label_intensities.txt -rw-rw-r-- 1 ktanev schiz 257K Oct 31 21:38 aseg.auto_noCCseg.mgz -rw-rw-r-- 1 ktanev schiz 258K Oct 31 21:39 aseg.mgz -rw-rw-r-- 1 ktanev schiz 1.4M Oct 31 21:45 brain.finalsurfs.mgz -rw-rw-r-- 1 ktanev schiz 1.4M Oct 31 14:53 brainmask.auto.mgz -rw-rw-r-- 1 ktanev schiz 1.4M Oct 31 14:53 brainmask.mgz -rw-rw-r-- 1 ktanev schiz 1.4M Oct 31 21:45 brain.mgz -rw-rw-r-- 1 ktanev schiz 395K Oct 31 15:33 ctrl_pts.mgz -rw-rw-r-- 1 ktanev schiz 145K Oct 31 21:49 filled.mgz -rw-rw-r-- 1 ktanev schiz 12K Oct 31 14:12 mri_nu_correct.mni.log -rw-rw-r-- 1 ktanev schiz 5.7K Oct 31 14:08 mri_nu_correct.mni.log.bak -rw-rw-r-- 1 ktanev schiz 1.5M Oct 31 15:33 norm.mgz -rw-rw-r-- 1 ktanev schiz 5.6M Oct 31 14:12 nu.mgz -rw-rw-r-- 1 ktanev schiz 3.6M Oct 31 20:32 nu_noneck.mgz -rw-rw-r-- 1 ktanev schiz 7.8M Oct 31 14:07 orig.mgz -rw-rw-r-- 1 ktanev schiz 5.7K Oct 31 14:08 orig_nu.log -rw-rw-r-- 1 ktanev schiz 7.8M Oct 31 14:08 orig_nu.mgz -rw-rw-r-- 1 ktanev schiz 19M Oct 31 14:07 rawavg.mgz -rw-rw-r-- 1 ktanev schiz 119 Oct 31 21:45 segment.dat -rw-rw-r-- 1 ktanev schiz 5.5M Oct 31 14:16 T1.mgz -rw-rw-r-- 1 ktanev schiz 1.6K Oct 31 16:35 talairach.label_intensities.txt -rw-rw-r-- 1 ktanev schiz 214 Oct 31 15:30 talairach.log -rw-rw-r-- 1 ktanev schiz 214 Oct 31 21:08 talairach_with_skull_2.log -rw-rw-r-- 1 ktanev schiz 214 Oct 31 14:52 talairach_with_skull.log -rw-rw-r-- 1 ktanev schiz 463K Oct 31 21:48 wm.asegedit.mgz -rw-rw-r-- 1 ktanev schiz 464K Oct 31 21:48 wm.mgz -rw-rw-r-- 1 ktanev schiz 507K Oct 31 21:47 wm.seg.mgz ___ 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] registering coronal images
Dear all, I have some T1 images which are originally in coronal view and the in-plane resolution is 0.5x0.5mm and slice thickness is 2mm. The matrix size is 512x512. I need to segment the left and right hemisphers. As the head is tilted I also need to register the images. Which atlas you recommend to use for this case ? Does MIN152_T1_0.5mm work better or MIN152_T1_2mm ? Thank you, Mahmoud ___ 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] registering coronal images
is this the only T1-weighted image you have, or do you also have something more isotropic? On Mon, 3 Nov 2014, Mahmoud wrote: Dear all, I have some T1 images which are originally in coronal view and the in-plane resolution is 0.5x0.5mm and slice thickness is 2mm. The matrix size is 512x512. I need to segment the left and right hemisphers. As the head is tilted I also need to register the images. Which atlas you recommend to use for this case ? Does MIN152_T1_0.5mm work better or MIN152_T1_2mm ? Thank you, Mahmoud ___ 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] registering coronal images
Dear Bruce, Unfortunately, this is the only thing I have. Mahmoud On Mon, Nov 3, 2014 at 2:44 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: is this the only T1-weighted image you have, or do you also have something more isotropic? On Mon, 3 Nov 2014, Mahmoud wrote: Dear all, I have some T1 images which are originally in coronal view and the in-plane resolution is 0.5x0.5mm and slice thickness is 2mm. The matrix size is 512x512. I need to segment the left and right hemisphers. As the head is tilted I also need to register the images. Which atlas you recommend to use for this case ? Does MIN152_T1_0.5mm work better or MIN152_T1_2mm ? Thank you, Mahmoud ___ 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] registering coronal images
I see. You can try running it through recon-all, but the 2mm is at the edge of what will work On Mon, 3 Nov 2014, Mahmoud wrote: Dear Bruce, Unfortunately, this is the only thing I have. Mahmoud On Mon, Nov 3, 2014 at 2:44 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: is this the only T1-weighted image you have, or do you also have something more isotropic? On Mon, 3 Nov 2014, Mahmoud wrote: Dear all, I have some T1 images which are originally in coronal view and the in-plane resolution is 0.5x0.5mm and slice thickness is 2mm. The matrix size is 512x512. I need to segment the left and right hemisphers. As the head is tilted I also need to register the images. Which atlas you recommend to use for this case ? Does MIN152_T1_0.5mm work better or MIN152_T1_2mm ? Thank you, Mahmoud ___ 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] Fwd: Underinclusion of Gray Matter
Hi Christina it's tough to tell from just a single image, but it looks to me like you are missing a bunch of white matter. Can you tell us more about the scan? The typical way you would fix this is by setting some thresholds in mris_make_surfaces using the expert options. Probably max_csf should be lower. If you upload the subject we will take a look cheers Bruce On Mon, 3 Nov 2014, Christina Chen wrote: Hi, Are there any ways to fix underinclusion of gray matter cortical edges when the white matter is fine? Attached is a picture. Thanks, Christina ___ 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] mri_watershed -brain_atlas undocumented?
Hi all, I noticed that during skull stripping the standard recon-all pipeline uses option -brain_atlas in the routine mri_watershed. However documentation of this argument cannot be found in the help section or on the website. mri_watershed --help | less -p atlas https://surfer.nmr.mgh.harvard.edu/fswiki/mri_watershed?highlight=(atlas) Is this an undocumented flag or simply a synonym for -atlas. Does the -brain_atlas flag take an extra argument to specify the atlas? Thanks, Tom Specs: Mac OS X 10.8.5 freesurfer-Darwin-lion-stable-pub-v5.3.0 mri_watershed --version stable5 ___ 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] Fwd: Underinclusion of Gray Matter
dear all, i am new on Mac and freeSusrfer. I have installed freesurfer through the tutorial. Is there any tutorial how to run on Mac. Is there any method to extract stats on excel or spps? The .mgz file shows the brain radiologically (r/l) or vice versa John Papatriantafyllou On Mon, Nov 3, 2014 at 11:58 PM, Christina Chen che...@usc.edu wrote: Hi, Are there any ways to fix underinclusion of gray matter cortical edges when the white matter is fine? Attached is a picture. Thanks, Christina ___ 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.
