Re: [Freesurfer] excluding labels
Hi,I would like to exclude areas which were incorrectly segmented and could not be corrected after editing and re-running recon-all from the cortical thickness measure. Thank you again.Best,ruthiOn 09 Oct 2014, at 19:57, Douglas Grevewrote: What analysis? On 10/9/14 11:35 AM, Adam, Ruth wrote: Hi all, Would be great is someone can tell me how to exclude user-defined labels from the analysis. As far as I understand after creating all labels, mris_label2annot with a custom colortable should be used. -Is this correct or is there a more efficient way to exclude labels form analysis? -How can the new annotation file be incorporated with old annotation files to mark what should be excluded/included in the analysis? -Can a similar operation be done directly for labels created in Tkmedit and volumes? Thank you very much in advance! Best, ruthi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe information in this e-mail is intended only for the person to whom it isaddressed. If you believe this e-mail was sent to you in error and the e-mailcontains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in errorbut does not contain patient information, please contact the sender and properlydispose 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] rawfunc2surf-sess with a limited set of surface files
No, use fmc.sm2.F99.lh.iter05 On 10/10/14 1:55 AM, Reza Rajimehr wrote: > Thanks Doug! I got it to work. The outputs are like > fmc.sm2.F99.lh.iter05.nii.gz > > Should I still specify stem as fmc.iter05 in mkanalysis-sess? > > Reza > > > Try added something like "-expkey iter05". When you make the analysis > you will have to spec "-stem fmc.iter05" > doug > > > > On 10/09/2014 12:12 AM, Reza Rajimehr wrote: >> 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 > > ___ 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
We re-ran that subject and it seemed to fix the problem, thanks! We will test it out on the other subjects with the same issue and see how that goes, but it looks like everything is good. Thanks again! -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Varjabedian, Ani Sent: Thursday, October 09, 2014 10:02 AM To: Freesurfer support list Subject: Re: [Freesurfer] WM & Pial Segmentation Errors Hi Michael, I took a look at your data and it seems that you paired a T2 image with a T1 image when you submitted to recon all. Recon-all will try to average these together, and since they have such different contrasts, you will end up with a poor template for surfaces later on. Try running recon-all again without the T2 and see if that helps. -Ani On Wed, 2014-10-08 at 17:21 +, Smith, Michael wrote: > 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" 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" 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" > 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 ___ 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
glad to hear it Bruce On Fri, 10 Oct 2014, Smith, Michael wrote: We re-ran that subject and it seemed to fix the problem, thanks! We will test it out on the other subjects with the same issue and see how that goes, but it looks like everything is good. Thanks again! -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Varjabedian, Ani Sent: Thursday, October 09, 2014 10:02 AM To: Freesurfer support list Subject: Re: [Freesurfer] WM & Pial Segmentation Errors Hi Michael, I took a look at your data and it seems that you paired a T2 image with a T1 image when you submitted to recon all. Recon-all will try to average these together, and since they have such different contrasts, you will end up with a poor template for surfaces later on. Try running recon-all again without the T2 and see if that helps. -Ani On Wed, 2014-10-08 at 17:21 +, Smith, Michael wrote: 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" 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" 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" 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 ___ 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 ___ 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] Image normalization and pial/wm error
Hi Sneha it looks like it is grabbing a bunch of dura. Do you happen to have a hires T2 or flair image? If so, you can use that in recon-all postprocessing to remove the dura. If not you can try using the graph cuts skull stripping to get rid of some of it. I can't tell the accuracy of the surfaces in other locations in the images. Other than dura is it reasonably acurate? cheers Bruce On Fri, 10 Oct 2014, Sneha Pandya wrote: > Dear all, > > I am running recon-all on few SPGR T1s and few MPRAGE T1s. However most of > my dataset, may it be SPGR or MPRAGE has some artifacts and poor wm/gm > contrast. Have attached a screen shot of bad pial and wm error (going beyond > dura). Even gcut did not do a good job of cutting of all the dura, and I had > to manually edit voxels in all the slices. I feel even after that if I run > recon-all, it will not give me any reliable cortical thickness measures. > > Can anyone please suggest me if I should still manually edit all other > subjects for all the slices throughout the volume or exclude them from > analysis? > > PS: attached image FOV is 260 and I used -cw256 flag to restrict FOV to 256. > For other images FOV is within 256, but still there is lot of dura in the > brainmask. > > Thanks, > Sneha > > > ___ 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] Image normalization and pial/wm error
Hi Bruce, Yes, there is a lot of dura. Unfortunately we do not have either flair or T2 as a reference to remove dura. I tried running gcut to cut off dura, it still won't help and I still had to manually edit whole volume to get rid of it. If it helps I can send you orig.mgz, nu.mgz and brainmask.mgz post graph cut to look at. However for other structures it is difficult to tell about the accuracy because I feel contrast is a little poor. Sequence of this subject is spgr with voxel size of 1.01mm*1.35mm*1.5mm(sl. thk), with 26FOV. I even used cw256 flag to restrict the field of view. So not really sure why is segmentation so poor. Other subjects in this dataset has between 20 to 25FOV, and varying voxel size from 0.93*1.25*1.5 to 1*1*2. Thanks, Sneha ___ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Friday, October 10, 2014 1:58 PM To: Freesurfer support list Subject: Re: [Freesurfer] Image normalization and pial/wm error Hi Sneha it looks like it is grabbing a bunch of dura. Do you happen to have a hires T2 or flair image? If so, you can use that in recon-all postprocessing to remove the dura. If not you can try using the graph cuts skull stripping to get rid of some of it. I can't tell the accuracy of the surfaces in other locations in the images. Other than dura is it reasonably acurate? cheers Bruce On Fri, 10 Oct 2014, Sneha Pandya wrote: > Dear all, > > I am running recon-all on few SPGR T1s and few MPRAGE T1s. However most of > my dataset, may it be SPGR or MPRAGE has some artifacts and poor wm/gm > contrast. Have attached a screen shot of bad pial and wm error (going beyond > dura). Even gcut did not do a good job of cutting of all the dura, and I had > to manually edit voxels in all the slices. I feel even after that if I run > recon-all, it will not give me any reliable cortical thickness measures. > > Can anyone please suggest me if I should still manually edit all other > subjects for all the slices throughout the volume or exclude them from > analysis? > > PS: attached image FOV is 260 and I used -cw256 flag to restrict FOV to 256. > For other images FOV is within 256, but still there is lot of dura in the > brainmask. > > Thanks, > Sneha > > > ___ 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] Image normalization and pial/wm error
Hi Sneha then I think manually editing is your best bet (sorry) Bruce On Fri, 10 Oct 2014, Sneha Pandya wrote: > Hi Bruce, > > Yes, there is a lot of dura. Unfortunately we do not have either flair or > T2 as a reference to remove dura. I tried running gcut to cut off dura, > it still won't help and I still had to manually edit whole volume to get > rid of it. If it helps I can send you orig.mgz, nu.mgz and brainmask.mgz > post graph cut to look at. However for other structures it is difficult > to tell about the accuracy because I feel contrast is a little poor. > Sequence of this subject is spgr with voxel size of > 1.01mm*1.35mm*1.5mm(sl. thk), with 26FOV. I even used cw256 flag to > restrict the field of view. So not really sure why is segmentation so > poor. > > Other subjects in this dataset has between 20 to 25FOV, and varying voxel > size from 0.93*1.25*1.5 to 1*1*2. > > Thanks, > Sneha > ___ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Friday, October 10, 2014 1:58 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Image normalization and pial/wm error > > Hi Sneha > > it looks like it is grabbing a bunch of dura. Do you happen to have a > hires T2 or flair image? If so, you can use that in recon-all > postprocessing to remove the dura. If not you can try using the graph > cuts skull stripping to get rid of some of it. I can't tell the accuracy > of the surfaces in other locations in the images. Other than dura is it > reasonably acurate? > cheers > Bruce > > On Fri, 10 Oct 2014, Sneha Pandya wrote: > >> Dear all, >> >> I am running recon-all on few SPGR T1s and few MPRAGE T1s. However most of >> my dataset, may it be SPGR or MPRAGE has some artifacts and poor wm/gm >> contrast. Have attached a screen shot of bad pial and wm error (going beyond >> dura). Even gcut did not do a good job of cutting of all the dura, and I had >> to manually edit voxels in all the slices. I feel even after that if I run >> recon-all, it will not give me any reliable cortical thickness measures. >> >> Can anyone please suggest me if I should still manually edit all other >> subjects for all the slices throughout the volume or exclude them from >> analysis? >> >> PS: attached image FOV is 260 and I used -cw256 flag to restrict FOV to 256. >> For other images FOV is within 256, but still there is lot of dura in the >> brainmask. >> >> Thanks, >> Sneha >> >> >> > ___ > 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 > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Image normalization and pial/wm error
Thanks again, yes that's what it looks like, but I just have one concern, if I have to manually edit dura and wm in all the slices and in most of the subjects, will it still give me reliable cortical thickness measure? Thanks, Sneha From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Friday, October 10, 2014 2:30 PM To: Freesurfer support list Subject: Re: [Freesurfer] Image normalization and pial/wm error Hi Sneha then I think manually editing is your best bet (sorry) Bruce On Fri, 10 Oct 2014, Sneha Pandya wrote: > Hi Bruce, > > Yes, there is a lot of dura. Unfortunately we do not have either flair or > T2 as a reference to remove dura. I tried running gcut to cut off dura, > it still won't help and I still had to manually edit whole volume to get > rid of it. If it helps I can send you orig.mgz, nu.mgz and brainmask.mgz > post graph cut to look at. However for other structures it is difficult > to tell about the accuracy because I feel contrast is a little poor. > Sequence of this subject is spgr with voxel size of > 1.01mm*1.35mm*1.5mm(sl. thk), with 26FOV. I even used cw256 flag to > restrict the field of view. So not really sure why is segmentation so > poor. > > Other subjects in this dataset has between 20 to 25FOV, and varying voxel > size from 0.93*1.25*1.5 to 1*1*2. > > Thanks, > Sneha > ___ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Friday, October 10, 2014 1:58 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Image normalization and pial/wm error > > Hi Sneha > > it looks like it is grabbing a bunch of dura. Do you happen to have a > hires T2 or flair image? If so, you can use that in recon-all > postprocessing to remove the dura. If not you can try using the graph > cuts skull stripping to get rid of some of it. I can't tell the accuracy > of the surfaces in other locations in the images. Other than dura is it > reasonably acurate? > cheers > Bruce > > On Fri, 10 Oct 2014, Sneha Pandya wrote: > >> Dear all, >> >> I am running recon-all on few SPGR T1s and few MPRAGE T1s. However most of >> my dataset, may it be SPGR or MPRAGE has some artifacts and poor wm/gm >> contrast. Have attached a screen shot of bad pial and wm error (going beyond >> dura). Even gcut did not do a good job of cutting of all the dura, and I had >> to manually edit voxels in all the slices. I feel even after that if I run >> recon-all, it will not give me any reliable cortical thickness measures. >> >> Can anyone please suggest me if I should still manually edit all other >> subjects for all the slices throughout the volume or exclude them from >> analysis? >> >> PS: attached image FOV is 260 and I used -cw256 flag to restrict FOV to 256. >> For other images FOV is within 256, but still there is lot of dura in the >> brainmask. >> >> Thanks, >> Sneha >> >> >> > ___ > 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 > > > ___ 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
Re: [Freesurfer] Image normalization and pial/wm error
I don't really know, sorry. You could to an inter- and intra-rater test by editing some of the images twice On Fri, 10 Oct 2014, Sneha Pandya wrote: > Thanks again, yes that's what it looks like, but I just have one concern, if > I have to manually edit dura and wm in all the slices and in most of the > subjects, will it still give me reliable cortical thickness measure? > > Thanks, > Sneha > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Friday, October 10, 2014 2:30 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Image normalization and pial/wm error > > Hi Sneha > > then I think manually editing is your best bet (sorry) > Bruce > > > On Fri, 10 Oct 2014, Sneha Pandya wrote: > >> Hi Bruce, >> >> Yes, there is a lot of dura. Unfortunately we do not have either flair or >> T2 as a reference to remove dura. I tried running gcut to cut off dura, >> it still won't help and I still had to manually edit whole volume to get >> rid of it. If it helps I can send you orig.mgz, nu.mgz and brainmask.mgz >> post graph cut to look at. However for other structures it is difficult >> to tell about the accuracy because I feel contrast is a little poor. >> Sequence of this subject is spgr with voxel size of >> 1.01mm*1.35mm*1.5mm(sl. thk), with 26FOV. I even used cw256 flag to >> restrict the field of view. So not really sure why is segmentation so >> poor. >> >> Other subjects in this dataset has between 20 to 25FOV, and varying voxel >> size from 0.93*1.25*1.5 to 1*1*2. >> >> Thanks, >> Sneha >> ___ >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >> [fis...@nmr.mgh.harvard.edu] >> Sent: Friday, October 10, 2014 1:58 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] Image normalization and pial/wm error >> >> Hi Sneha >> >> it looks like it is grabbing a bunch of dura. Do you happen to have a >> hires T2 or flair image? If so, you can use that in recon-all >> postprocessing to remove the dura. If not you can try using the graph >> cuts skull stripping to get rid of some of it. I can't tell the accuracy >> of the surfaces in other locations in the images. Other than dura is it >> reasonably acurate? >> cheers >> Bruce >> >> On Fri, 10 Oct 2014, Sneha Pandya wrote: >> >>> Dear all, >>> >>> I am running recon-all on few SPGR T1s and few MPRAGE T1s. However most of >>> my dataset, may it be SPGR or MPRAGE has some artifacts and poor wm/gm >>> contrast. Have attached a screen shot of bad pial and wm error (going beyond >>> dura). Even gcut did not do a good job of cutting of all the dura, and I had >>> to manually edit voxels in all the slices. I feel even after that if I run >>> recon-all, it will not give me any reliable cortical thickness measures. >>> >>> Can anyone please suggest me if I should still manually edit all other >>> subjects for all the slices throughout the volume or exclude them from >>> analysis? >>> >>> PS: attached image FOV is 260 and I used -cw256 flag to restrict FOV to 256. >>> For other images FOV is within 256, but still there is lot of dura in the >>> brainmask. >>> >>> Thanks, >>> Sneha >>> >>> >>> >> ___ >> 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 >> >> >> > ___ > 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 > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] cortical surface area measurement and vertex-wise analysis
Dear Freesurfers, I recently heard that there are several disadvantages to using a measure of cortical surface area in Freesurfer, specifically due to conducting a vertex-wise analysis. Can someone help me understand why a measure of surface area using this approach might be flawed? Thanks! ___ 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 surface area measurement and vertex-wise analysis
Hi Emma, I might not be the only one who is unsure what you mean by a vertex-wise cortical surface area measure. Do you mean something like what is illustrated in figures 2 and 3 here: http://www.pnas.org/content/107/29/13135.figures-only … which is similar, but not identical to the local gyrification index? If so, would you use this measure on surfaces before or after registration to a target atlas? Donna On Oct 10, 2014, at 4:19 PM, Emma Thompson wrote: > Dear Freesurfers, > I recently heard that there are several disadvantages to using a measure of > cortical surface area in Freesurfer, specifically due to conducting a > vertex-wise analysis. Can someone help me understand why a measure of surface > area using this approach might be flawed? Thanks! ___ 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.