Re: [Freesurfer] Question about FreeSurfer
Hi, I am graduate student at the University of Michigan and I am performing research on deep brain stimulation. I want to warp an anatomical brain atlas to individual patient MRIs to get the patient specific brain models out of it. I chose FreeSurfer to do this and I have installed it on my computer. I realized that it takes 10-20 hrs to reconstruct the image. I wanted to ask if that is the time for one image? or the whole series of images? I also wanted to ask if there is a step by step tutorial on how to do this. Thank you > > Dorsa Ghaffari > ___ 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 about FreeSurfer
Hi, I need patient specific brain models created by warping atlases to individual MRIs. I want the model to include the Subthalamic Nucleus, Gpi, Thalamus and their surrounding organs. (Cortical segmentation is not necessary). When I use the" recon all "command on one MRI image, I get the error "cannot find mri.dcm". I have copied the MRI in Freesurfer Home directory. I really appreciate it if you can help me with that. Thank you Dorsa Ghaffari On Mon, Jun 27, 2016 at 3:13 PM, Bruce Fischl wrote: > Hi Dorsa > > what specific models do you need? The 10-20 hours is to process the data > from a single subject at a single timepoint. If you check out our wiki > (http://surfer.nmr.mgh.harvard.edu/fswiki) there are lots of tutorials and > sample datasets and such > > cheers > Bruce > > On Mon, 27 Jun 2016, Dorsa Haji > Ghaffari wrote: > > > Hi, > > I am graduate student at the University of Michigan and I am performing > > research on deep brain stimulation. I want to warp an anatomical brain > atlas > > to individual patient MRIs to get the patient specific brain models out > of > > it. I chose FreeSurfer to do this and I have installed it on my > computer. I > > realized that it takes 10-20 hrs to reconstruct the image. I wanted to > ask > > if that is the time for one image? or the whole series of images? > > I also wanted to ask if there is a step by step tutorial on how to do > this. > > > > Thank you > > > > Dorsa Ghaffari > > > > > > > > > ___ > 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] Question about FreeSurfer
Hi, I am a little confused about how should I save my files to execute recon-all on them. I have 240 slices of dicom format and I put them in a folder in my subjects_dir. but I get errors when using recon-all on the folder containing the MRIs. Can you help me with that? I really appreciate your help Thank you Dorsa On Mon, Jun 27, 2016 at 3:13 PM, Bruce Fischl wrote: > Hi Dorsa > > what specific models do you need? The 10-20 hours is to process the data > from a single subject at a single timepoint. If you check out our wiki > (http://surfer.nmr.mgh.harvard.edu/fswiki) there are lots of tutorials and > sample datasets and such > > cheers > Bruce > > On Mon, 27 Jun 2016, Dorsa Haji > Ghaffari wrote: > > > Hi, > > I am graduate student at the University of Michigan and I am performing > > research on deep brain stimulation. I want to warp an anatomical brain > atlas > > to individual patient MRIs to get the patient specific brain models out > of > > it. I chose FreeSurfer to do this and I have installed it on my > computer. I > > realized that it takes 10-20 hrs to reconstruct the image. I wanted to > ask > > if that is the time for one image? or the whole series of images? > > I also wanted to ask if there is a step by step tutorial on how to do > this. > > > > Thank you > > > > Dorsa Ghaffari > > > > > > > > > ___ > 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] Question about FreeSurfer
Thank you! When I recon-all my files, I get the following error: files are not found to be different and cannot be sorted Do you have any suggestions? Thank you Dorsa On Tue, Jun 28, 2016 at 12:57 PM, Bruce Fischl wrote: > just give recon-all a single slice from the series with -i name>. It will figure out > > the rest of them > > On Tue, 28 Jun 2016, Dorsa Haji Ghaffari wrote: > > > Hi, > > I am a little confused about how should I save my files to execute > recon-all on > > them. I have 240 slices of dicom format and I put them in a folder in my > > subjects_dir. but I get errors when using recon-all on the folder > containing the > > MRIs. Can you help me with that? I really appreciate your help > > > > Thank you > > > > Dorsa > > > > On Mon, Jun 27, 2016 at 3:13 PM, Bruce Fischl < > fis...@nmr.mgh.harvard.edu> wrote: > > Hi Dorsa > > > > what specific models do you need? The 10-20 hours is to process the > > data > > from a single subject at a single timepoint. If you check out our > > wiki > > (http://surfer.nmr.mgh.harvard.edu/fswiki) there are lots of > > tutorials and > > sample datasets and such > > > > cheers > > Bruce > > > > On Mon, 27 Jun 2016, Dorsa Haji > > Ghaffari wrote: > > > > > Hi, > > > I am graduate student at the University of Michigan and I am > > performing > > > research on deep brain stimulation. I want to warp an anatomical > > brain atlas > > > to individual patient MRIs to get the patient specific brain > models > > out of > > > it. I chose FreeSurfer to do this and I have installed it on my > > computer. I > > > realized that it takes 10-20 hrs to reconstruct the image. I > wanted > > to ask > > > if that is the time for one image? or the whole series of images? > > > I also wanted to ask if there is a step by step tutorial on how > to > > do this. > > > > > > Thank you > > > > > > Dorsa Ghaffari > > > > > > > > > > > > > > ___ > > 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.
[Freesurfer] question about exporting volumes
Hi, I was able to segment the MRI successfully, now I am trying to isolate the thalamus and export it out of FS as a volume. Is there a way to do that in FS? Thank you Dorsa ___ 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] Question about Thalamus segmentation
Hi, I am trying to segment the thalamus into its nuclei such as VLA , VLP and VIM. I see those labels available in the atlas but I do not get any of them in my segmentation. Does anyone have any idea how to do that? Thank you Dorsa ___ 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 about exporting volumes
Thank you. I want to view the thalamus as a volume in freesurfer. Do you know how to do that? also by exporting I mean exporting it as a volume and then import it into COMSOL as a geometry. Thank you for your help! Dorsa On Wed, Jul 6, 2016 at 7:50 PM, Douglas N Greve wrote: > what do you mean isolate? what do you mean export? You can create a > binary mask in nifti format with mri_binarize --i aseg.mgz --match 10 49 > --o thalamus.mask.nii.gz > > > On 07/06/2016 04:46 PM, Dorsa Haji Ghaffari wrote: > > > > > > > > Hi, > > > > I was able to segment the MRI successfully, now I am trying to isolate > > the thalamus and export it out of FS as a volume. Is there a way to do > > that in FS? > > > > Thank you > > > > Dorsa > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer 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] Refining subcortical structures
Hi, I want to refine the surface of my segmented subcortical structures such as thalamus. I know -fix is used for refining the cortex surface, but is there any function that refines the subcortical structures? Thank you Dorsa ___ 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] question about voxel size
Hi, I have a T1 weighted MRI which I want to segment using Freesurfer. The voxel sizes are 0.48*0.48*0.48. I read that the ideal voxel size for freesurfer is 1mm^3. Is there any manual adjustments that I can make to get good results with my 0.48 voxel size images? Thank you Dorsa Ghaffari ___ 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 about voxel size
Hi Bruce, The original 3TS images have 1mm^3 resolution, but we resample and co-register them to our CT scans and the resulting image has a higher resolution. My problem now is that the volume of the left thalamus segmented out by Freesurfer is half of the volume of the thalamus traced manually by one of my labmates. Do you have any guesses on why is this happening? Thank you Dorsa On Tue, Jul 19, 2016 at 1:49 PM, Bruce Fischl wrote: > Hi Dorsa > > are they really that highres? Sometimes people do zero-padding and Fourier > interpolation on the scanner. 1/2mm cubic is pushing the resolution and if > they are really that high res they will be either very noisy or very long > scans (or both) > > cheers > Bruce > > > On Tue, 19 Jul 2016, Dorsa Haji Ghaffari wrote: > > Hi, >> I have a T1 weighted MRI which I want to segment using Freesurfer. The >> voxel sizes are 0.48*0.48*0.48. I read that the ideal voxel size for >> freesurfer is >> 1mm^3. Is there any manual adjustments that I can make to get good >> results with my 0.48 voxel size images? >> >> Thank you >> >> Dorsa Ghaffari >> >> > ___ > 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: question about voxel size
Hi Bruce, that is a 3TS T1 weighted image and is taken after the patients have taken the contrast medium. I have played with the intensities in Analyze and this is the best I could get. Do you have any suggestions for getting better contrast? Thank you Dorsa On Tue, Jul 19, 2016 at 4:29 PM, Bruce Fischl wrote: > also, please post to the list so that others can answer! > thanks > Bruce > On Tue, 19 Jul 2016, Dorsa Haji Ghaffari wrote: > > Here it is. Also can you explain why the algorithm works best with 1mm^3 >> voxel size? >> >> Thank you! >> >> >> >> >> >> >> > > 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: question about voxel size
Yes it is taken at 3T. I have asked our team to provide these information about the MRIs and will let you know when I hear back. I also wanted to ask if you know a good way to refine the thalamus and fill out the missing parts within the volume? Thank you Dorsa On Tue, Jul 19, 2016 at 5:10 PM, Bruce Fischl wrote: > what is a "3TS" image? Do you mean it was acquired at 3T? What sequence > and what parameters (TE/TR/TI/TD/flip angle)? > > cheers > Bruce > On Tue, 19 Jul 2016, Dorsa > Haji Ghaffari wrote: > > > Hi Bruce, > > that is a 3TS T1 weighted image and is taken after the patients have > taken > > the contrast medium. I have played with the intensities in Analyze and > this > > is the best I could get. Do you have any suggestions for getting better > > contrast? > > > > Thank you > > > > Dorsa > > > > On Tue, Jul 19, 2016 at 4:29 PM, Bruce Fischl < > fis...@nmr.mgh.harvard.edu> > > wrote: > > also, please post to the list so that others can answer! > > thanks > > Bruce > > On Tue, 19 Jul 2016, Dorsa Haji Ghaffari wrote: > > > > Here it is. Also can you explain why the algorithm > > works best with 1mm^3 > > voxel size? > > > > Thank you! > > > > > > > > > > > > > > > > > > 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] Fwd: question about voxel size
I mean the holes in the thalamus and also some parts that are labeled as thalamus but not attached to the rest of thalamus volume. On Wed, Jul 20, 2016 at 10:49 AM, Bruce Fischl wrote: > what missing parts do you mean? The segmentation seemed pretty reasonable, > but the contrast wasn't good enough to say how accurate it was in some > places > > On Wed, 20 Jul 2016, Dorsa Haji Ghaffari wrote: > > Yes it is taken at 3T. I have asked our team to provide these information >> about the >> MRIs and will let you know when I hear back. I also wanted to ask if you >> know a >> good way to refine the thalamus and fill out the missing parts within the >> volume? >> Thank you >> Dorsa >> >> On Tue, Jul 19, 2016 at 5:10 PM, Bruce Fischl >> wrote: >> what is a "3TS" image? Do you mean it was acquired at 3T? What >> sequence >> and what parameters (TE/TR/TI/TD/flip angle)? >> >> cheers >> Bruce >> On Tue, 19 Jul 2016, Dorsa >> Haji Ghaffari wrote: >> >> > Hi Bruce, >> > that is a 3TS T1 weighted image and is taken after the patients >> have >> taken >> > the contrast medium. I have played with the intensities in Analyze >> and this >> > is the best I could get. Do you have any suggestions for getting >> better >> > contrast? >> > >> > Thank you >> > >> > Dorsa >> > >> > On Tue, Jul 19, 2016 at 4:29 PM, Bruce Fischl >> >> > wrote: >> > also, please post to the list so that others can answer! >> > thanks >> > Bruce >> > On Tue, 19 Jul 2016, Dorsa Haji Ghaffari wrote: >> > >> > Here it is. Also can you explain why the algorithm >> > works best with 1mm^3 >> > voxel size? >> > >> > Thank you! >> > >> > >> > >> > >> > >> > >> > >> > >> > 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. > > ___ 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] question about image size
Hi, I have segmented 288 slices of 512x512 dicom MRIs but when I create a mask of the left thalamus I get 256 slices of 256x256 images. Is there any way to get the same number of slices with the same size as I had before? Thank you Dorsa ___ 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 about image size
Thank you I'll try that. On Thursday, July 21, 2016, Bruce Fischl wrote: > try using the -rl switch in mri_convert. It will "reslice > like" the you give. Give it the 512 volume as > > cheers > Bruce > On Thu, > 21 Jul 2016, Dorsa Haji Ghaffari wrote: > > > Hi, > > I have segmented 288 slices of 512x512 dicom MRIs but when I create a > mask of the > > left thalamus I get 256 slices of 256x256 images. Is there any way to > get the same > > number of slices with the same size as I had before? > > > > Thank you > > > > Dorsa > > > > > ___ > 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] question about reslicing
Hi, Yes my original data has 1x1x1mm voxel dimension but I prefer to work with the upsampled data. I am satisfied with the results I get from Freesurfer and the results actually look better than the results I get with the 1mm data, the only problem I have is that the thalamus mask does not keep the original dimensions in both cases. It is 256x256x256 ,so in terms of the thalamus position I do not know if it is at the right place. I will need to combine the STN that I have traced out in Analyze with the thalamus, thats why I need to make sure everything are in the correct position with respect to others. Thank you Dorsa On Tue, Jul 26, 2016 at 1:58 PM, Bruce Fischl wrote: > sorry, I'm confused about what you are trying to do. Can you start from > the beginning and explain? If the data you have is 1mm but upsampled by the > scanner there is really nothing to be gained by processing the upsampled > data and it will waste lots of time > > > cheers > Bruce > > On Mon, 25 Jul 2016, Dorsa Haji Ghaffari wrote: > > Yes I created it using the higher resolution and I think it looks fine. I >> attached the aseg.mgz. Is there any way to create the thalamus mask with >> the >> original properties ( same as the original mri) at the first place? I need >> to make sure the size and position of the thalamus corresponds to the >> original mri. >> >> Thank you! >> >> Dorsa >> >> On Mon, Jul 25, 2016 at 3:29 PM, Bruce Fischl > > >> wrote: >> Hi Dorsa >> >> did you create the aseg.mgz from 1mm data (using the standard >> "conform" process), or higher res? The file you sent is higher: >> >> mri_info resliceduncoregtahalmus.nii.gz >> Volume information for resliceduncoregtahalmus.nii.gz >> type: nii >> dimensions: 512 x 512 x 288 >> voxel sizes: 0.488281, 0.488281, 0.625000 >> type: SHORT (4) >> fov: 250.000 >> dof: 0 >> xstart: -125.0, xend: 125.0 >> ystart: -125.0, yend: 125.0 >> zstart: -90.0, zend: 90.0 >> TR: 8.06 msec, TE: 0.00 msec, TI: 0.00 msec, flip >> angle: 0.00 degrees >> nframes: 1 >> PhEncDir: UNKNOWN >> FieldStrength: 0.00 >> ras xform present >> >> >> it also has strange values in it (-32K and 32K, so probably >> things that can't be represented as a short). Does your aseg.mgz >> look right? >> >> cheers >> Bruce >> >> >> On Mon, 25 Jul 2016, Dorsa Haji Ghaffari wrote: >> >> Hi, This is the command line for reslicing: >> mri_convert -rl aseg.mgz thalamus.nii >> resliceduncoregtahalmus.nii >> >> thalamus.nii is the thalamus mask obtained by using >> the following command: >> mri_binarize --i aseg.mgz --match 10 --o >> thalamus.mask.nii.gz >> >> and I have attached the out put. >> >> Thank you! >> >> On Mon, Jul 25, 2016 at 12:41 PM, Bruce Fischl >> >> wrote: >> Hi Dorsa >> >> you need to give us more details. What was >> your reslicing >> command line? And the screen output? >> >> Bruce >> On Mon, 25 Jul 2016, Dorsa Haji Ghaffari >> wrote: >> >> >> Hi, >> >> I re-sliced my left thalamus so that the >> size and >> number of slices correspond with the >> original MRI, >> but when I open it in freeview, it shows >> an extra >> part( >> like a cube) on the bottom of the image >> ( I have >> attached the mask). do you have any >> idea how to >> solve that? >> Also how can I make sure that the >> position and size >> of the thalamus makes sense since the >> thalamus mask >> has a different slice size and number >> than the >> original mri? >> >> Thank you >>
[Freesurfer] question about mask coordinates
Hi all, I have done segmentation with Freesurfer but when I create a mask for the left thalamus and import it to CAD software it doesn't seem to be at the right coordinates. This may be due to the change in the mask volume(256x256x256) from the original MRI volume(512x512x288). I did re-slice the mask to get the original volume but it gives me an additional piece of cube at the bottom of the image. Does anyone know how to get the authentic coordinates for the mask? Thank you Dorsa ___ 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] question about thalamus
Hi, I have done the sub-cortical segmentation in Freesurfer and have extracted the left thalamus, when I put it on top of the original MRI, it seems like it is getting out of the border of thalamus, also it is not smooth. I wanted to ask if anyone knows how to limit the computation only to thalamus, and also make it trace the thalamus more accurately? Thank you Dorsa ___ 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 about thalamus
So what I understand is that we can do the segmentation using the whole brain MRI and then use the higher contrast MRI to refine the thalamus segmentation? if so, can you explain more about it? Thank you Dorsa On Thu, Oct 20, 2016 at 12:20 PM, Bruce Fischl wrote: > no, you need full brain coverage in at least one, but we do have some > prototype tools that use a smaller FOV image after a recon to segment > specific structures (including at least a bit of work on the STN). > > As I said though, depending on the details of the 40 slice image I would > be cautious about using it as a gold-standard to interpret the T1. I would > need more information to say for sure > > > > On Thu, 20 Oct 2016, Dorsa Haji Ghaffari wrote: > > So basically we have two types of images. One has a better contrast for >> seeing the STN to that we can target it for deep brain >> stimulation, but that one is only 40 slices and is not the whole brain. >> We have another set of images which is complete but does >> not have a good contrast for showing the sub-cortical structures. I have >> attached a sample of each one. I have also attached my >> subject. Does Freesurfer work with only 40 slices? >> >> On Thu, Oct 20, 2016 at 9:51 AM, Bruce Fischl >> wrote: >> Hi Dorsa >> >> if you upload your subject I'll take a look. What is a 3TC image? I >> don't know what contrast the image you sent is >> but I would be cautious about only using it to assess the accuracy >> of the T1 segmentation >> >> cheers >> Bruce >> >> On Wed, 19 Oct 2016, Dorsa Haji Ghaffari wrote: >> >> I have attached a screenshot of one of the slices. from what >> I see it is going a little far in the >> medial and lateral parts. I am using a 3TC image taken by >> Philips device. Is there any way to limit the >> region of interest before running the recon-all to only >> segment the thalamus and may give better >> results? >> Thank you >> >> Dorsa >> >> On Wed, Oct 19, 2016 at 5:21 PM, Bruce Fischl < >> fis...@nmr.mgh.harvard.edu> wrote: >> Hi Dorsa >> >> why do you think it is going out too far? What >> intensity volume are you >> overlaying it on? Many segmentations miss the lateral >> parts of the >> thalamus since they have so much myelin in them >> >> cheers >> Bruce >> On Wed, 19 Oct 2016, Dorsa >> Haji Ghaffari wrote: >> >> > Hi, >> > I have done the sub-cortical segmentation in >> Freesurfer and have extracted the left >> thalamus, when I put >> > it on top of the original MRI, it seems like it is >> getting out of the border of thalamus, >> also it is not >> > smooth. I wanted to ask if anyone knows how to limit >> the computation only to thalamus, and >> also make it >> > trace the thalamus more accurately? >> > >> > Thank you >> > >> > Dorsa >> > >> > >> ___ >> 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-
[Freesurfer] Fwd: question about thalamus
So what I understand is that we can do the segmentation using the whole brain MRI and then use the higher contrast MRI to refine the thalamus segmentation? if so, can you explain more about it? Thank you Dorsa On Thu, Oct 20, 2016 at 12:20 PM, Bruce Fischl wrote: > no, you need full brain coverage in at least one, but we do have some > prototype tools that use a smaller FOV image after a recon to segment > specific structures (including at least a bit of work on the STN). > > As I said though, depending on the details of the 40 slice image I would > be cautious about using it as a gold-standard to interpret the T1. I would > need more information to say for sure > > > > On Thu, 20 Oct 2016, Dorsa Haji Ghaffari wrote: > > So basically we have two types of images. One has a better contrast for >> seeing the STN to that we can target it for deep brain >> stimulation, but that one is only 40 slices and is not the whole brain. >> We have another set of images which is complete but does >> not have a good contrast for showing the sub-cortical structures. I have >> attached a sample of each one. I have also attached my >> subject. Does Freesurfer work with only 40 slices? >> >> On Thu, Oct 20, 2016 at 9:51 AM, Bruce Fischl >> wrote: >> Hi Dorsa >> >> if you upload your subject I'll take a look. What is a 3TC image? I >> don't know what contrast the image you sent is >> but I would be cautious about only using it to assess the accuracy >> of the T1 segmentation >> >> cheers >> Bruce >> >> On Wed, 19 Oct 2016, Dorsa Haji Ghaffari wrote: >> >> I have attached a screenshot of one of the slices. from what >> I see it is going a little far in the >> medial and lateral parts. I am using a 3TC image taken by >> Philips device. Is there any way to limit the >> region of interest before running the recon-all to only >> segment the thalamus and may give better >> results? >> Thank you >> >> Dorsa >> >> On Wed, Oct 19, 2016 at 5:21 PM, Bruce Fischl < >> fis...@nmr.mgh.harvard.edu> wrote: >> Hi Dorsa >> >> why do you think it is going out too far? What >> intensity volume are you >> overlaying it on? Many segmentations miss the lateral >> parts of the >> thalamus since they have so much myelin in them >> >> cheers >> Bruce >> On Wed, 19 Oct 2016, Dorsa >> Haji Ghaffari wrote: >> >> > Hi, >> > I have done the sub-cortical segmentation in >> Freesurfer and have extracted the left >> thalamus, when I put >> > it on top of the original MRI, it seems like it is >> getting out of the border of thalamus, >> also it is not >> > smooth. I wanted to ask if anyone knows how to limit >> the computation only to thalamus, and >> also make it >> > trace the thalamus more accurately? >> > >> > Thank you >> > >> > Dorsa >> > >> > >> ___ >> 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-
