Re: [Freesurfer] cortical surface area related measures
Regarding Winkler et al.: http://brainder.org/2012/06/02/facewise-brain-cortical-surface-area-scripts-now-available/ On Aug 21, 2012 11:00 PM, Gregory Kirk gk...@wisc.edu wrote: Hi folks, I wanted to make sure i have everything straight w.r.t. the surface area measures. as i see there are 4 ways implemented ( somewhere ) to do cortical surface area analysis. 1. areal expansion 2. Local Gyrification Index 3. direct vertex based true surface area glm, Winkler AM et. al 4. roi based, i.e. based on the surface areas of the parcellation units in lh.aparc.a2009s.stats etc. 1. recent pub, Lisa T. Eyler et. al used the areal expansion method. was this done exactly as would be achived by using the area tab on qdec and setting up a glm ? Dale published surface area specifying some details of implementation but i was not sure if this was exactly what is implemented in qdec ? 2. LGI seems to me this is the ratio of two areas, that of the hull to the area inscribed by projecting the border of the hull onto the grey/white surface. In an e-mail Nick said LGI is a curvature based measure and that confused me a bit. gyrification is of course related to curvature but it seems the quantities actually calculated here are ratios of areas, which gives local info on surface area differences. 3. the winkler stuff is i think not publicly available yet at this time ? 4. straightforward enough not withstanding ICV corrections, etc. any words of clarification before i start trying some analysis on my group ? thank you Greg ___ 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] two Post Doc positions at the Karolinska Institute
Please, observe the announcement of two new post doctoral positions in NeuroImaging and behavior at the Karolinska Institute in Stockholm - https://ki.netrecruiter.se/what:job/jobID:13820/where:4/ -https://ki.netrecruiter.se/what:job/jobID:13880/where:4/ Ivanka Savic MD, PhD ivanka.savic-bergl...@ki.se Associate Professor, senior lecturer in Neurology Dept of Women´s and Children´s Health Karolinska Institute Scheeles väg 3 Karolinska Institute 171 77 Stockholm Ph +4685248 Mo +46709380738 ___ 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] Edits to aparc+aseg.mgz
Doug, Sorry for so many questions, but can I run the autorecon3 command with my previous recon-all -subjid (subject ID) -autorecon-pial or will the autorecon3 have to follow the previous command? Thanks, Cyrus -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Tuesday, August 21, 2012 3:52 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz Run it with -autorecon3 doug On 08/21/2012 10:44 AM, Sarosh, Cyrus wrote: Doug, Thanks for the update and not much time was wasted so no worries. I edited the brainmask.mgz file and ran the new recon-all command with autorecon-pial, which created a new brain.finalsurfs.mgz with the dura edited out and correct surfs. New stat files were created, but no new aparc+aseg.mgz file. Loading this file still shows the segmentation including dura in the cortex and the modification date is the original recon-all date. Is there any way to create a new aparc+aseg.mgz file with this new surf data? Thanks, Cyrus -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Monday, August 20, 2012 2:18 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz Hi Cyrus, my apologies, I told you to edit the wrong file. You should edit brainmask.mgz, not brainmask.finalsurfs.mgz. Sorry about, I hope you did not waste too much time. doug On 08/20/2012 09:31 AM, Sarosh, Cyrus wrote: Doug, I edited the dura from the brain.finalsurfs.mgz file using the command tkmedit (subject ID) brain.finalsurfs.mgz -aux T1.mgz -surfs and going through the necessary slices that need fixing and erase the dura. I then ran this subject with the command recon-all -subjid (subject ID) -autorecon-pial. Looking at the date modified information it appears that new stat files were created, but no new aparc+aseg.mgz file was created. I loaded the brain.finalsurfs.mgz file, which contained a modify date of when I ran the new recon-all command and it looked identical to the original brain.finalsurfs.mgz file, so all of my edits were gone and all of the surfs were incorrect just like before. Also, loading the aparc+aseg.mgz file it looks identical to the previous aparc+aseg.mgz, so no changes were made. Looking at the log it appears my edits were useless because the first step that runs is the -maskbfs step which appears to generate the brain.finalsurfs.mgz file. So, do I need to edit a different file or was my command line incorrect? Thanks, Cyrus -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Tuesday, August 14, 2012 1:43 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz For GM volume and thickness, you will certainly want to fix it. Given how big the PET voxels are, it might not be such a big deal for that. To fix it, you would edit the dura from the brain.finalsurfs.mgz and run recon-all with -autorecon-pial. This will fix aparc+aseg and re-generate the stats files. doug On 08/14/2012 01:40 PM, Sarosh, Cyrus wrote: Doug, Well we want to use the stats information for gray matter volume and thickness of certain vois and we want to use the aparc+aseg file to run PET image analysis to collect data from certain vois. Would performing the given actions correct any incorrect data in the stats files and create a new aparc+aseg.mgz file or will this require separate actions? Thanks, Cyrus -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Tuesday, August 14, 2012 11:28 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz Depending upon how bad it is and what you are going to do with it, it may be a good idea to edit the brain.finalsurfs.mgz to remove the dura, then run recon-all -autorecon-pial ... doug On 08/14/2012 11:18 AM, Sarosh, Cyrus wrote: Doug, I looked at the surface files by using the command -tkmedit (subject ID) brainmask.mgz -surfs -aseg. I also viewed the same surfs using the T1.mgz file. The pial surface (red line) does identify the dura as part of the cortex, but it doesn't look as bad as the aseg.mgz vois made it appear. Cyrus -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Monday, August 13, 2012 4:13 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz Hi Cyrus, this may or may not be a problem. The cortical label in aseg.mgz is not used for this reason. Usually, the
Re: [Freesurfer] Edits to aparc+aseg.mgz
You can run it from the same command line. doug On 8/22/12 8:45 AM, Sarosh, Cyrus wrote: Doug, Sorry for so many questions, but can I run the autorecon3 command with my previous recon-all -subjid (subject ID) -autorecon-pial or will the autorecon3 have to follow the previous command? Thanks, Cyrus -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Tuesday, August 21, 2012 3:52 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz Run it with -autorecon3 doug On 08/21/2012 10:44 AM, Sarosh, Cyrus wrote: Doug, Thanks for the update and not much time was wasted so no worries. I edited the brainmask.mgz file and ran the new recon-all command with autorecon-pial, which created a new brain.finalsurfs.mgz with the dura edited out and correct surfs. New stat files were created, but no new aparc+aseg.mgz file. Loading this file still shows the segmentation including dura in the cortex and the modification date is the original recon-all date. Is there any way to create a new aparc+aseg.mgz file with this new surf data? Thanks, Cyrus -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Monday, August 20, 2012 2:18 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz Hi Cyrus, my apologies, I told you to edit the wrong file. You should edit brainmask.mgz, not brainmask.finalsurfs.mgz. Sorry about, I hope you did not waste too much time. doug On 08/20/2012 09:31 AM, Sarosh, Cyrus wrote: Doug, I edited the dura from the brain.finalsurfs.mgz file using the command tkmedit (subject ID) brain.finalsurfs.mgz -aux T1.mgz -surfs and going through the necessary slices that need fixing and erase the dura. I then ran this subject with the command recon-all -subjid (subject ID) -autorecon-pial. Looking at the date modified information it appears that new stat files were created, but no new aparc+aseg.mgz file was created. I loaded the brain.finalsurfs.mgz file, which contained a modify date of when I ran the new recon-all command and it looked identical to the original brain.finalsurfs.mgz file, so all of my edits were gone and all of the surfs were incorrect just like before. Also, loading the aparc+aseg.mgz file it looks identical to the previous aparc+aseg.mgz, so no changes were made. Looking at the log it appears my edits were useless because the first step that runs is the -maskbfs step which appears to generate the brain.finalsurfs.mgz file. So, do I need to edit a different file or was my command line incorrect? Thanks, Cyrus -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Tuesday, August 14, 2012 1:43 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz For GM volume and thickness, you will certainly want to fix it. Given how big the PET voxels are, it might not be such a big deal for that. To fix it, you would edit the dura from the brain.finalsurfs.mgz and run recon-all with -autorecon-pial. This will fix aparc+aseg and re-generate the stats files. doug On 08/14/2012 01:40 PM, Sarosh, Cyrus wrote: Doug, Well we want to use the stats information for gray matter volume and thickness of certain vois and we want to use the aparc+aseg file to run PET image analysis to collect data from certain vois. Would performing the given actions correct any incorrect data in the stats files and create a new aparc+aseg.mgz file or will this require separate actions? Thanks, Cyrus -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Tuesday, August 14, 2012 11:28 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz Depending upon how bad it is and what you are going to do with it, it may be a good idea to edit the brain.finalsurfs.mgz to remove the dura, then run recon-all -autorecon-pial ... doug On 08/14/2012 11:18 AM, Sarosh, Cyrus wrote: Doug, I looked at the surface files by using the command -tkmedit (subject ID) brainmask.mgz -surfs -aseg. I also viewed the same surfs using the T1.mgz file. The pial surface (red line) does identify the dura as part of the cortex, but it doesn't look as bad as the aseg.mgz vois made it appear. Cyrus -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Monday, August 13, 2012 4:13 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz Hi Cyrus, this
Re: [Freesurfer] mri_segstats error
Hi Doug, Thanks for the quickly reply. The new version of mri_segstats works fine. I noticed after running it though that all the volumes are slightly different than those reported by previous version. I think it might have something to do with the partial volume correction, as the results are the same when I do not use the --pv flag. Is this expected behavior? And if so, is the new version more accurate? Thanks again, -Tyler The material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return 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] mri_segstats error
yes, this is a fix that will be in the next release. The new results are more accurate. doug On 08/22/2012 11:54 AM, Blazey, Tyler wrote: Hi Doug, Thanks for the quickly reply. The new version of mri_segstats works fine. I noticed after running it though that all the volumes are slightly different than those reported by previous version. I think it might have something to do with the partial volume correction, as the results are the same when I do not use the --pv flag. Is this expected behavior? And if so, is the new version more accurate? Thanks again, -Tyler The material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return 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 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] label2vol with yeo annotation - dropping region#17
Hi Anisha, I did make a fix to this program a few months ago. Can you try the new version? I put it here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol doug On 08/22/2012 01:38 PM, Anisha Keshavan wrote: Hello - I'm having trouble using label2vol with the 17 network yeo annotation -- mri_label2vol --annot lh.Yeo2011_17Networks_N1000.SAD_P05.annot --o outfile.nii.gz --hemi lh --subject SAD_P05 --temp /mindhive/xnat/surfaces/sad/SAD_P05/mri/orig.mgz --identity The annotation was created by mri_surf2surf (fsaverage5 -- SAD_P05's surface) and it does have region17. Any idea what's happening? Thanks, Anisha ___ 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] Help removing marking from DICOM/.nii files
Hi Alex, there's no way to erase it in a way that you can recover the underlying signal. I'm surprised that such small things are causing the talairach to crash. If the writing is always the same value and that value does not appear in other parts of the image, you might be able to replace the value with values of nearby voxels. Let me know if you need some instructions on this. doug On 08/22/2012 02:08 PM, Alexandra Tanner wrote: Hi Doug, I'm currently working with 4-6 year old clinical pediatric non-Siemens DICOM files that I'm unpacking and preprocessing in freesurfer. So far we've been able to unpack the DICOMS to .nii format and successfully begin the autorecon process for our first few subjects. We've noticed, when looking at the raw scans for some of our subjects, however, there is writing (probably information from the scan console) included in the images, and in some slices, slightly overlapping with the outer edge of the skull/brain. When attempting to run the autorecon1 on these scans, the command terminates during the talairach transform. We're thinking, since we don't have this issue with all of our subjects, the writing may be what is causing the problem. I'm wondering if you know of any way to remove the writing from the images (I tried seeing if I could erase the lettering in tkmedit but it seems it can't be erased manually). Attached is a screenshot of a coronal slice with the writing. Any suggestions would be greatly appreciated! Thanks, Alex -- 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] Help removing marking from DICOM/.nii files
Hi Doug, Thanks for the quick reply! It seems the value of the writing is much higher than any value elsewhere in the image (over 4000). Instructions on how to replace this value with values of nearby voxels would be great -- hopefully that will allow us to run the autorecon1 command on it. Thanks, Alex Hi Alex, there's no way to erase it in a way that you can recover the underlying signal. I'm surprised that such small things are causing the talairach to crash. If the writing is always the same value and that value does not appear in other parts of the image, you might be able to replace the value with values of nearby voxels. Let me know if you need some instructions on this. doug On 08/22/2012 02:08 PM, Alexandra Tanner wrote: Hi Doug, I'm currently working with 4-6 year old clinical pediatric non-Siemens DICOM files that I'm unpacking and preprocessing in freesurfer. So far we've been able to unpack the DICOMS to .nii format and successfully begin the autorecon process for our first few subjects. We've noticed, when looking at the raw scans for some of our subjects, however, there is writing (probably information from the scan console) included in the images, and in some slices, slightly overlapping with the outer edge of the skull/brain. When attempting to run the autorecon1 on these scans, the command terminates during the talairach transform. We're thinking, since we don't have this issue with all of our subjects, the writing may be what is causing the problem. I'm wondering if you know of any way to remove the writing from the images (I tried seeing if I could erase the lettering in tkmedit but it seems it can't be erased manually). Attached is a screenshot of a coronal slice with the writing. Any suggestions would be greatly appreciated! Thanks, Alex -- 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] Help removing marking from DICOM/.nii files
I'm just shooting from the hip here, but here is what I would do: 1. Create a mask of writing mri_binarize --i 001.mgz --min 4000 --o mask.mgz mri_binarize --i 001.mgz --min 4000 --inv --o mask.inv.mgz 2. Mask out the writing mri_mask 001.mgz mask.inv.mgz 001.masked.mgz 3. Scale the mask to be something near gray/white matter fscalc mask.mgz mul VAL mask.scaled.mgz 4. Create a new image by adding the masked with the scaled mask fscalc 001.masked.mgz add mask.scaled.mgz -o 001.unmasked.mgz 5. Smooth that mri_fwhm --i 001.unmasked.mgz --fwhm 5 --o 001.unmasked.sm05.mgz --smooth-only 6. Mask this to only have writing voxels mri_mask 001.unmasked.sm05.mgz mask.mgz001.unmasked.sm05.masked.mgz 7. Create the final image by adding that to the masked fscalc 001.masked.mgz add 001.unmasked.sm05.masked.mgz -o final.mgz You may have to play around with the amount of smoothing, I was just guessing at 5 good luck doug On 08/22/2012 02:31 PM, Alexandra Tanner wrote: Hi Doug, Thanks for the quick reply! It seems the value of the writing is much higher than any value elsewhere in the image (over 4000). Instructions on how to replace this value with values of nearby voxels would be great -- hopefully that will allow us to run the autorecon1 command on it. Thanks, Alex Hi Alex, there's no way to erase it in a way that you can recover the underlying signal. I'm surprised that such small things are causing the talairach to crash. If the writing is always the same value and that value does not appear in other parts of the image, you might be able to replace the value with values of nearby voxels. Let me know if you need some instructions on this. doug On 08/22/2012 02:08 PM, Alexandra Tanner wrote: Hi Doug, I'm currently working with 4-6 year old clinical pediatric non-Siemens DICOM files that I'm unpacking and preprocessing in freesurfer. So far we've been able to unpack the DICOMS to .nii format and successfully begin the autorecon process for our first few subjects. We've noticed, when looking at the raw scans for some of our subjects, however, there is writing (probably information from the scan console) included in the images, and in some slices, slightly overlapping with the outer edge of the skull/brain. When attempting to run the autorecon1 on these scans, the command terminates during the talairach transform. We're thinking, since we don't have this issue with all of our subjects, the writing may be what is causing the problem. I'm wondering if you know of any way to remove the writing from the images (I tried seeing if I could erase the lettering in tkmedit but it seems it can't be erased manually). Attached is a screenshot of a coronal slice with the writing. Any suggestions would be greatly appreciated! Thanks, Alex -- 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 -- 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.
[Freesurfer] Fw: Convert QDEC clusters on the MNI_152_T1 space
Hi Doug, Many thanks for your help. Can you please take a look and see if this is the correct way to do it. I want to overal in fact my QDEC clusters on the connectivity maps in FSL but I got them by registering on the MNI 152 so I suppose I can just transform or move my QDEC clusters on the MNI space since this is the template I use for my connectivity maps. I am not sure if I need to mention the label of my clusters for example the uncorrected clusters. Should I use the sig.mgh or I just run: mri_label2vol --label lh-precentral --temp MNI152_T1_1mm_brain.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat --fillthresh .5 --o precentral-lh.nii Also what threshold should I use with mri_label2vol if this are my uncorrected clusters? How can I do this if as below I have two clusters in the same region? Contrast: 'lh-Diff-Class1-Class2-Intercept-thickness', 15fwhm, DOF: 69 ClusterNo Max VtxMax Size(mm2) TalX TalY TalZ NVtxs Annotation - --- -- - - -- 1 -3.8743 18231 944.60 -39.8 1.5 14.1 2631 precentral 2 -3.8065 47386 1445.46 -8.2 33.1 33.9 2421 superiorfrontal 3 -2.8630 158749 181.92 -12.7 -12.6 46.4 506 superiorfrontal 4 -2.7960 73670 222.37 -33.7 0.9 8.1 564 insula 5 2.7914 52279 204.80 -9.8 -98.6 4.6 248 pericalcarine 6 -2.7364 43605 173.45 -41.4 -79.2 21.8 288 inferiorparietal 7 -2.6316 17412 301.53 -38.3 5.6 -36.8 439 temporalpole 8 2.6050 150788 64.40 -24.0 -59.1 54.7 165 superiorparietal 9 -2.5570 106020 75.96 -22.8 -8.6 47.9 200 precentral 10 -2.5070 88002 66.59 -17.6 -31.2 37.8 198 posteriorcingulate 11 -2.4736 113974 181.87 -52.7 -10.3 -26.6 236 middletemporal 12 -2.4496 118370 142.88 -43.6 -18.0 -25.5 289 inferiortemporal 13 -2.3087 111885 55.43 -46.6 -36.2 -3.9 165 bankssts 14 -2.2179 153596 36.91 -11.3 3.4 42.0 103 superiorfrontal 15 -2.1861 145681 95.36 -11.3 60.1 19.1 147 superiorfrontal 16 -2.1733 29252 59.92 -42.6 37.5 -4.4 92 parstriangularis 17 -2.1689 155583 34.83 -45.3 -14.7 -11.2 87 superiortemporal 18 -2.1636 22443 27.76 -41.6 -79.0 -3.1 43 lateraloccipital 19 -2.1592 139736 21.75 -47.5 -25.1 37.0 61 postcentral 20 -2.0221 19174 4.10 -34.2 33.8 29.2 6 rostralmiddlefrontal From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, August 21, 2012 4:55 PM Subject: Re: [Freesurfer] Convert QDEC clusters on the MNI_152_T1 space You can use mri_label2vol and $FREESURFER_HOME/average/mni152.register.dat doug On 08/21/2012 11:06 AM, Antonella Kis wrote: Dear All, Is possible to overlap my QDEC clusters onto MNI_152_T1 _1mm_brain template? Thank you. Antonella ___ 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.___ 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] 3rd level surface analysis of fMRI data
Hi,I’m a Freesurfer novice, and am confused about how to run a 3rd level cross-subject analysis on the surface using as input cross-run .gfeats from 10 subjects generated from a 2nd level analysis of fMRI data in FSL.Following the directions posted at http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslGroupFeat, I have sampled the .gfeat copes and varcopes into standard surface space, using mris_preproc.I would then go on to perform a 3rd level surface based analysis as the instructions suggest, using:mri_glmfit --y xrun/lh.cope1.mgh --yffxvar xrun/lh.varcope1.mgh --ffxdof 163 --osgm --glmdir xrun/lh.osgm.ffx --surf fsaverage lh --label $SUBJECTS_DIR/fsaverage/label/lh.cortex.labelHowever, I want to use a random effects rather than fixed effects analysis. How do I do this? I tried --yrfxvar as opposed to --yffxvar but it didn’t work. And if I’m going to display the map resulting from this analysi! s, do I need to correct for multiple comparisons?Many thanks in advance,Susan McLaughlinDoctoral CandidateSPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex)Dept. of Speech and Hearing SciencesUniversity of Washington ___ 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.
