[Freesurfer] VBM
Hello Experts, Can we do VBM in MNI template using the outputs from recon all? Which file should I be using? And how do I smooth the volumes? Thank you for the tips! -- Shane S ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_concat pet images into 1 template image
Hi Doug, There is a bit of movement across the 3 acquisitions. How may I align everything together before running mri_concat? 1. Run bbregister or mri_coreg to register 1 acquisition to T1 2. Use the reg file to move the remaining 2 acquisitions ? Is there a quicker way? Thank you. -- Shane Schofield On 9 March 2017 at 17:01:28, Douglas N Greve (gr...@nmr.mgh.harvard.edu) wrote: If the 3 volumes are in register (ie, no motion between them), then I would just run the mri_concat command to create a single volume which is the average of the 3, then proceed as described. On 03/09/2017 11:58 AM, Shane S wrote: > Hi Doug, > > I want to derive a single averaged PET volume from the three > reconstructed 5 min acquisitions, expressed in detected counts. Then > we will divide the counts based on the cerebellum. Following that, I > want to use PetSurfer for partial volume correction and GLM > comparisons. May I upload the 3 images per subject? > > Thank you. > > -- > Shane S > > On 9 March 2017 at 16:18:33, Douglas N Greve > (gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>) wrote: > >> How are you planning on analyzing the different time points? >> >> >> On 03/08/2017 05:33 PM, Shane S wrote: >> > Dear Doug, >> > >> > My PET data is 3 x 5 minute acquisitions. Each subject has >> > subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz and I am >> > supposed to align and average them. >> > >> > Please advise. >> > >> > Thanks! >> > >> > -- >> > Shane Schofield >> > >> > On 8 March 2017 at 22:31:06, Douglas Greve (gr...@nmr.mgh.harvard.edu >> > <mailto:gr...@nmr.mgh.harvard.edu>) wrote: >> > >> >> No, the template is a within subject template used for registration. >> >> If your pet data only has one frame (eg, FDG SUV), then you don't >> >> need to run mri_convert or mri_concat, just use your pet image as the >> >> template >> >> >> >> >> >> On 3/8/17 11:11 AM, Shane S wrote: >> >>> Hello Freesurfer, >> >>> >> >>> I have 3 PET images per individual. I am learning PetSurfer based on >> >>> the Greve et al., 2014 paper. >> >>> >> >>> On the PetSurfer link, there are 2 methods. >> >>> >> >>> mri_convert pet.nii.gz —frame frameno template.nii.gz >> >>> or >> >>> mri_concat pet.nii.gz --mean —0 template.nii.gz >> >>> >> >>> What are the differences? My files are listed as >> >>> subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz >> >>> >> >>> Is "mri_concat subject123_a.nii.gz, subject123_b.nii.gz, >> >>> subject123_c.nii.gz —mean —o template.nii.gz” correct? >> >>> >> >>> Thank you for helping. >> >>> >> >>> Best Wishes, >> >>> >> >>> S >> >>> -- >> >>> Shane Schofield >> >>> >> >>> >> >>> ___ >> >>> 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] Bits of dura being captured as GM ..
Hi Freesurfer Users, I am checking my data and there are many scans with a bit of dura being captured as GM. I have attached some screenshots below. This happens in more than 50% of my subjects. I am removing them manually them using Freeview, then running the autorecon-pial. But this will take a lot of time on 200+ subjects.. Does anyone have any tips to deal with these little inclusions? Thanks =) Best Wishes, Shane___ 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] How to segment subnuclei of thalamus?
Hello Experts, I am interested to do a segmentation of the thalamus subnuclei based on T1 data. Is there any atlas that I could use for this? Best Wishes, S ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_concat pet images into 1 template image
Thank you very much!! -- Shane S On 9 March 2017 at 17:01:28, Douglas N Greve (gr...@nmr.mgh.harvard.edu) wrote: If the 3 volumes are in register (ie, no motion between them), then I would just run the mri_concat command to create a single volume which is the average of the 3, then proceed as described. On 03/09/2017 11:58 AM, Shane S wrote: > Hi Doug, > > I want to derive a single averaged PET volume from the three > reconstructed 5 min acquisitions, expressed in detected counts. Then > we will divide the counts based on the cerebellum. Following that, I > want to use PetSurfer for partial volume correction and GLM > comparisons. May I upload the 3 images per subject? > > Thank you. > > -- > Shane S > > On 9 March 2017 at 16:18:33, Douglas N Greve > (gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>) wrote: > >> How are you planning on analyzing the different time points? >> >> >> On 03/08/2017 05:33 PM, Shane S wrote: >> > Dear Doug, >> > >> > My PET data is 3 x 5 minute acquisitions. Each subject has >> > subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz and I am >> > supposed to align and average them. >> > >> > Please advise. >> > >> > Thanks! >> > >> > -- >> > Shane Schofield >> > >> > On 8 March 2017 at 22:31:06, Douglas Greve (gr...@nmr.mgh.harvard.edu >> > <mailto:gr...@nmr.mgh.harvard.edu>) wrote: >> > >> >> No, the template is a within subject template used for registration. >> >> If your pet data only has one frame (eg, FDG SUV), then you don't >> >> need to run mri_convert or mri_concat, just use your pet image as the >> >> template >> >> >> >> >> >> On 3/8/17 11:11 AM, Shane S wrote: >> >>> Hello Freesurfer, >> >>> >> >>> I have 3 PET images per individual. I am learning PetSurfer based on >> >>> the Greve et al., 2014 paper. >> >>> >> >>> On the PetSurfer link, there are 2 methods. >> >>> >> >>> mri_convert pet.nii.gz —frame frameno template.nii.gz >> >>> or >> >>> mri_concat pet.nii.gz --mean —0 template.nii.gz >> >>> >> >>> What are the differences? My files are listed as >> >>> subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz >> >>> >> >>> Is "mri_concat subject123_a.nii.gz, subject123_b.nii.gz, >> >>> subject123_c.nii.gz —mean —o template.nii.gz” correct? >> >>> >> >>> Thank you for helping. >> >>> >> >>> Best Wishes, >> >>> >> >>> S >> >>> -- >> >>> Shane Schofield >> >>> >> >>> >> >>> ___ >> >>> 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 >> >> -- >> 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
Re: [Freesurfer] mri_concat pet images into 1 template image
Hi Doug, I want to derive a single averaged PET volume from the three reconstructed 5 min acquisitions, expressed in detected counts. Then we will divide the counts based on the cerebellum. Following that, I want to use PetSurfer for partial volume correction and GLM comparisons. May I upload the 3 images per subject? Thank you. -- Shane S On 9 March 2017 at 16:18:33, Douglas N Greve (gr...@nmr.mgh.harvard.edu) wrote: How are you planning on analyzing the different time points? On 03/08/2017 05:33 PM, Shane S wrote: > Dear Doug, > > My PET data is 3 x 5 minute acquisitions. Each subject has > subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz and I am > supposed to align and average them. > > Please advise. > > Thanks! > > -- > Shane Schofield > > On 8 March 2017 at 22:31:06, Douglas Greve (gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>) wrote: > >> No, the template is a within subject template used for registration. >> If your pet data only has one frame (eg, FDG SUV), then you don't >> need to run mri_convert or mri_concat, just use your pet image as the >> template >> >> >> On 3/8/17 11:11 AM, Shane S wrote: >>> Hello Freesurfer, >>> >>> I have 3 PET images per individual. I am learning PetSurfer based on >>> the Greve et al., 2014 paper. >>> >>> On the PetSurfer link, there are 2 methods. >>> >>> mri_convert pet.nii.gz —frame frameno template.nii.gz >>> or >>> mri_concat pet.nii.gz --mean —0 template.nii.gz >>> >>> What are the differences? My files are listed as >>> subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz >>> >>> Is "mri_concat subject123_a.nii.gz, subject123_b.nii.gz, >>> subject123_c.nii.gz —mean —o template.nii.gz” correct? >>> >>> Thank you for helping. >>> >>> Best Wishes, >>> >>> S >>> -- >>> Shane Schofield >>> >>> >>> ___ >>> 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 -- 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 ___ 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_concat pet images into 1 template image
Dear Doug, My PET data is 3 x 5 minute acquisitions. Each subject has subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz and I am supposed to align and average them. Please advise. Thanks! -- Shane Schofield On 8 March 2017 at 22:31:06, Douglas Greve (gr...@nmr.mgh.harvard.edu) wrote: No, the template is a within subject template used for registration. If your pet data only has one frame (eg, FDG SUV), then you don't need to run mri_convert or mri_concat, just use your pet image as the template On 3/8/17 11:11 AM, Shane S wrote: Hello Freesurfer, I have 3 PET images per individual. I am learning PetSurfer based on the Greve et al., 2014 paper. On the PetSurfer link, there are 2 methods. mri_convert pet.nii.gz —frame frameno template.nii.gz or mri_concat pet.nii.gz --mean —0 template.nii.gz What are the differences? My files are listed as subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz Is "mri_concat subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz —mean —o template.nii.gz” correct? Thank you for helping. Best Wishes, S -- Shane Schofield ___ 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] mri_concat pet images into 1 template image
Hello Freesurfer, I have 3 PET images per individual. I am learning PetSurfer based on the Greve et al., 2014 paper. On the PetSurfer link, there are 2 methods. mri_convert pet.nii.gz —frame frameno template.nii.gz or mri_concat pet.nii.gz --mean —0 template.nii.gz What are the differences? My files are listed as subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz Is "mri_concat subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz —mean —o template.nii.gz” correct? Thank you for helping. Best Wishes, S -- Shane Schofield___ 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] chose between 5.3 and 6.0
Hi Bruce, Where may I find more information about the differences in recon-all or subcortical segmentations (aseg) between 5.3 and 6.0? Is the 6.0 pipeline still based on this paper? Fischl, B., Salat, D. H., Busa, E., Albert, M., Dieterich, M., Haselgrove, C., … Dale, A. M. (2002). Whole brain segmentation: automated labeling of neuroanatomical structures in the human brain. Neuron, 33(3), 341–355. If not, could you please shed some light on the improvements in 6.0? Thanks a lot. S -- Shane Schofield On 27 February 2017 at 23:40:12, Bruce Fischl (fis...@nmr.mgh.harvard.edu) wrote: Hi weiwei if the aseg looks good you don't have to worry about how the subcortical structures look in the brainmask - it's irrelevant. Not sure about the pial surfaces - we find the surfaces in 6.0 more accurate than 5.3, but maybe not for your specific sequence? It's hard to say cheers Bruce On Mon, 27 Feb 2017, ? ? wrote: > dear FS community: > now i have more than 200 subjects which already finished recon-all with > 5.3, > since 6.0 released, i wonder should i re-run them with 6.0 as lots of changes > like > different surf-map and registration. i ran a bit of them as test and i found > the pial > problems were more than 5.3, and it seems some subcortical structures were > vanished > in the brainmask.mgz, though the aseg.mgz looked good. > i wanna ask is my problem serious or it is usual with 6.0, and which > version you > think is better for cortical volume and surface thickness reserch? > best regards > > weiwei > west china hospital > > _ > > weiqi77...@live.com > >___ 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] editing topological defect
Hi Antonin, Thanks a lot. Those links are very helpful for me! Cheers, S -- Shane Schofield On 26 February 2017 at 12:51:23, Antonin Skoch (a...@ikem.cz) wrote: Dear Shane, the "topological defect" in FreeSurfer jargon means that the estimated surface contains errors like "holes" or "handles". See PPT from FreeSurfer course http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.failure_modes.ppt or https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData XL (=extra large?) defect often means large error in previous steps of recon-all, usually skullstrip or white matte segmentation. In some cases the error is automatically corrected, but not always. To see, what is happening, I would suggest to inspect brainmask.mgz or wm.mgz and correct errors. You can also find more information on the forum, there are quite large amount of posts related to topological defects. For example: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg30763.html Antonin Skoch Hi Freesurfer Team, I am running recon-all on Freesurfer version 6. A few of my subjects have “XL defect detected …” and their recon-all have been running for more than 20 hours. I hope this is not a silly question, but will this XL defect be corrected eventually…? Another question, what are “defects”? Is there anything I could do to the raw T1 before recon-all? Thanks! Shane ___ 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] XL defect detected
Thanks Doug, I will give it try and update you on it. S -- Shane Schofield On 26 February 2017 at 22:35:52, Douglas Greve (gr...@nmr.mgh.harvard.edu) wrote: Probably not. Probably you the cerebellum is still attached. You should check the wm.mgz volume. On 2/24/17 11:21 AM, Shane Schofield wrote: Hi Freesurfer Team, I am running recon-all on Freesurfer version 6. A few of my subjects have “XL defect detected …” and their recon-all have been running for more than 20 hours. I hope this is not a silly question, but will this XL defect be corrected eventually…? Another question, what are “defects”? Is there anything I could do to the raw T1 before recon-all? Thanks! Shane -- Shane Schofield ___ 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.
Re: [Freesurfer] Overestimation of volume in Hippocampus
Hi Michel Hu, Yes, that’s too large for MCI or even controls for that matter I think. Have you checked the aseg.mgz? I generally find that the hippocampus is well segmented, even in patients with a lot of atrophy. Are you taking the measurements with the asegstats2table? Sincerely, -- Shane S On 27 February 2017 at 10:12:09, Michel Hu (a...@live.nl) wrote: Dear Shane, I apologize for not being clear. The reported value is of only one half of the hippocampus. I have only run 4 subjects of the 75 however they all have a reported value of between 6000 to 1 mm^3 summed together for the hippocampus. Sincerely, Michel Hu Van: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> namens Shane S <shane.schofi...@yahoo.com> Verzonden: maandag 27 februari 2017 11:00 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] Overestimation of volume in Hippocampus Hi Michel Hu, Is that a summed value of left and right hippocampus? That seems normal to me since averaged total hippocamppal volumes for MCI have been typically reported at around 2500-3500mm3. Thanks, -- Shane S On 27 February 2017 at 09:44:27, Michel Hu (a...@live.nl) wrote: Dear Freesurfer experts, I have run several subjects through the recon-all pipeline including the hippocampal segmentation with freesurfer 6.0 on Ubuntu 16.04. However when looking at the text file with the volumes it seems that all the numbers are bigger than normal as all my subjects have MCI and freesurfer reports them having all over 5000 mm^3. I was wondering if the problem could lie somewhere in the recon-all process? Thank you for your time Sincerely, Michel Hu ___ 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 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] Overestimation of volume in Hippocampus
Hi Michel Hu, Is that a summed value of left and right hippocampus? That seems normal to me since averaged total hippocamppal volumes for MCI have been typically reported at around 2500-3500mm3. Thanks, -- Shane S On 27 February 2017 at 09:44:27, Michel Hu (a...@live.nl) wrote: Dear Freesurfer experts, I have run several subjects through the recon-all pipeline including the hippocampal segmentation with freesurfer 6.0 on Ubuntu 16.04. However when looking at the text file with the volumes it seems that all the numbers are bigger than normal as all my subjects have MCI and freesurfer reports them having all over 5000 mm^3. I was wondering if the problem could lie somewhere in the recon-all process? Thank you for your time Sincerely, Michel Hu ___ 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.
