[Freesurfer] Running recon-all on external hard-disk?
Hello, I am new to image analysis and I have a basic question: is it recommended to run recon-all on external hard-disks (USB3.0) to save space on my laptop? Will there be any issues with regards to the performance of recon-all? I have just finished a recon-all on 1 subject and it took me 10 hours. System spec is Mac Book Pro 13” 2016 model: 2 ghz Intel core i5. 8GB ram. Thank you. 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.
Re: [Freesurfer] Running recon-all on external hard-disk?
Hi Z K, Thanks. I had thought that the recon-all speed will run much slower on the external HD but 10 hours seems to be the average recon-all time so I am pleasantly surprised. 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] mri_glmfit-sim
Hi, I have 3 beginner questions about the use of mri_glmfit-sim 1. Under what type of circumstances should I run mri_glmfit-sim with permutation simulations? 2. The voxel threshold of 0.01 (cache 2) is used a lot. Is this too lenient in cortical thickness comparisons? 3. About the sign of the test (abs, neg, pos): is a one-tailed sign justified if I have an hypothesis? If the uncorrected (mri_glmfit) test shows a significant difference in one direction but not the other, am I justified to use pos/neg (instead of abs) in the mri_glmfit-sim stage and explicitly state that in the manuscript? Thanks. Hope to learn more. Have a good week. Cheers, 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] LGI data for each region?
Hi Freesurfer, How can I get the LGI measurements for each brain region in Desikan atlas? Instead of getting thickness with aparcstats2table, I want the gyrification instead. Thank you. Cheers, Shane -- 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] Mindboggle official software release and publication!
Hello, Thanks. Seems very interesting! Is there any way to run this on Mac? Cheers -- 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.
[Freesurfer] XL defect detected
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 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] bbregister vs spmregister vs mri_coreg
Dear Doug, If I want to create a new volume that is registered to the MNIspace (using mni1525reg), can I mask out other voxels that are not part of the mni template brain? It is a PET volume (already in individual space using bbregister) that has noisy signals in non-brain regions. Thank you. S On 25 February 2017 at 22:33:35, Antonin Skoch (a...@ikem.cz) wrote: Dear Doug, I was wondering, why do you prefer mni152reg to mri_coreg for gregistration to MNI? According to help, mri_coreg is also able to do 12 DOF registration. Antonin mri_coreg is the FS implementation of spm_coreg (spmregister) both of which use normalized mutual info. bbregister uses the BBR cost function and is preferred for all MRI. For registration to MNI space, we usually use mni152reg (a wrapper around fsl's flirt) On 2/25/17 8:49 AM, John Anderson wrote: Dear Freesurfer experts, I see that the tool "mri_coreg" has been implemented recently in Free Surfer 6 and I really wanted to know what are the differences between the registration tools "bbregister", " spmregister" and "mri_coreg"! Kindly: 1. Are these tools similar? if not what are the differences ? 2. Is there any preference of using a tool over the others for specific type of data. For example: A. If I want to register FA map to T1 image which tool ismore robust? B. if I want to register FA map to MNI space which tool is more robust? I highly appreciate your input on this! John ___ 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] Filling in missing ventricles in WM
Hi Bruce, Thanks! The -bigventricles flag worked like a charm! But I have now run into other cases with fuzzy data and thin cortex that are not captured, such as the picture below: Any tips on filing them out? Thank you. On Sunday, April 23, 2017 3:41 PM, Bruce Fischl wrote: yes, that is correct. An alternative would be editing the aseg directly. Editing the wm will help the surfaces but not correct the aseg. But as Antonin suggests, try running with -bigventricles and see if that fixes your problems cheers Bruce On Sun, 23 Apr 2017, Shane Schofield wrote: > Thank you. I will try that. Do I run that command after editing the wm.mgz > to fill in the ventricles? I noticed that the voxels (value = 255) are still > 255 in the new WM.mgz after autorecon2-wm. Is this correct? > > > On Sunday, April 23, 2017 1:33 PM, Antonin Skoch wrote: > > > Dear Shane, > > I would suggest to run: > > recon-all -bigventricles -s subject -autorecon2 -autorecon3 (-T2pial or > -FLAIRpial if you have 3D T2 or 3D FLAIR). This should help to correct aseg > in case of such large ventricles. > > Antonin Skoch > > > From: Shane Schofield > To: Freesurfer Support List , Antonin Skoch > > Sent: 4/22/2017 11:30 PM > Subject: Filling in missing ventricles in WM > > Hi Freesurfer Experts and Antonin, > > About an earlier question on XL Defects > > I have used your suggestions to check the orig.nofix surfaces and I > think the skull and missing ventricle voxels are causing the problem. > Picture pasted. > > Inline image > I have removed the WM voxels in the skull, filled in the ventricles > by adding WM voxels (brush value = 255 ), and ran the command > recon-all -s subject -autorecon2-wm -autorecon3 > Recon-all was completed successfully and the surfaces look good. > However, the aseg volume in the lateral ventricles are still wrong. > Inline image > At the crosshair, the WM value is 255 and the ASEG value is 0. Should > I be editing the aseg now? Or should I be doing something else to the > wm.mgz? > Appreciate your tips! > 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 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 get SUVR images with cerebellar GM reference?
Hello PetSurfer and Freesurfer Developers, I am using PetSurfer to obtain PVC SUVR images . I have already used mri_concat to derive the mean images over three acquisitions (template image). After gtmseg amd mri_coreg, I want to get the SUVR map with whole cerebellum as the reference (instead of the pons). How could this be done? What can I modify in mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --psf FWHM --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx .01 --o gtmpvc.output to achieve this goal? Thank you. ___ 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] How to get SUVR images with cerebellar GM reference?
Hi Doug, Great, thanks for the speedy help. If I use --save-input, will I be using the input.rescaled.nii.gz as the partial volumed corrected SUVR maps for surface-based comparisons with mri_glmfit ? On Friday, April 28, 2017 11:06 PM, Douglas N Greve wrote: add --rescale 7 8 46 47 these are the ids for left and right cblum wm and gm On 04/28/2017 06:13 AM, Shane Schofield wrote: > Hello PetSurfer and Freesurfer Developers, > > I am using PetSurfer to obtain PVC SUVR images . I have already used > mri_concat to derive the mean images over three acquisitions (template > image). > > Inline image > > After gtmseg amd mri_coreg, I want to get the SUVR map with whole > cerebellum as the reference (instead of the pons). How could this be > done? What can I modify in mri_gtmpvc --i pet.nii.gz --reg > template.reg.lta --psf FWHM --seg gtmseg.mgz > --default-seg-merge --auto-mask PSF .01 --mgx .01 --o gtmpvc.output > to achieve this goal? > > Thank you. > > > > ___ > 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] mri_convert : pix vs no pix ?
Dear Doug,I am trying to flip some PET images so that they are in the same orientation as the T1.I came across this post http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg29281.htmlCan you explain what what it means to change the pixel data? Should I use pix or without pix? For context I am working with PET data (in img/hdr formats) that seemed to have been flipped L/R somehow. Thank you. ___ 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_convert : pix vs no pix ?
Sorry, I don't quite understand yet.. Would the header be important as I am not using img / hdr ? Under what sort of circumstances would pix be favourable? I am using .nii after executing mri_convert to go from img/hdr to nii. I note that pix is used in other older threads too. On Tuesday, May 9, 2017 5:58 PM, Douglas N Greve wrote: When the pixel data are flipped, you are actually changing the way that the data are stored on disk (while keeping the direction info in the header constant). On 05/09/2017 12:52 PM, Shane Schofield wrote: > Dear Doug, > I am trying to flip some PET images so that they are in the same > orientation as the T1. > I came across this post > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg29281.html > Can you explain what what it means to change the pixel data? Should I > use pix or without pix? For context I am working with PET data (in > img/hdr formats) that seemed to have been flipped L/R somehow. > Thank you. > > > > > ___ > 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] How to capture missing grey matter after recon-all
Hi Freesurfer Experts, Does anyone know how to deal with situations where the part of the brain is not being captured in aseg.mgz or in the surfaces? I have attached some screenshots. I have tried adding control points but it is not working. Thanks for helping. Best,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] Mean diffusivity on cortex?
Hi DTI Experts, Is it sensible to do comparisons of MD on the cortex surface like a normal cortical thickness comparisons between group? If the answer is yes, are there recommended on smoothing ? DT_RECON has been completed in Freesurfer. Thank you. ___ 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] Mean diffusivity on cortex?
Thanks Dr Yendiki. I am more interested to compare MD in grey matter regions by putting the MD on the surface, and then do a glmfit type of comparisons. Is that OK? Would you recommend me to smooth the data after spatial normalisation? I have also used the mri_cvs_register as described on the tutorial. On Friday, August 11, 2017, 7:03:49 AM GMT+1, Shane Schofield wrote: Hi DTI Experts, Is it sensible to do comparisons of MD on the cortex surface like a normal cortical thickness comparisons between group? If the answer is yes, are there recommended on smoothing ? DT_RECON has been completed in Freesurfer. Thank you. ___ 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] Mean diffusivity on cortex?
Hi Dr Yendiki, I am studying a group of people with APOE4 and I want to see
whether cortical MD increases can be detected relative to non-carriers, and if
so, is the effect size bigger than changes in cortical thickness.
On Friday, August 11, 2017, 11:19:32 AM GMT+1, Yendiki, Anastasia
wrote:
#yiv9314780658 P {margin-top:0;margin-bottom:0;}What effect are you trying to
measure with MD on the cortex?
From: Shane Schofield [shane.schofi...@yahoo.com]
Sent: Friday, August 11, 2017 3:12 AM
To: Freesurfer Support List; Yendiki, Anastasia
Subject: Re: Mean diffusivity on cortex?
Thanks Dr Yendiki.
I am more interested to compare MD in grey matter regions by putting the MD on
the surface, and then do a glmfit type of comparisons. Is that OK? Would you
recommend me to smooth the data after spatial normalisation? I have also used
the mri_cvs_register as described on the tutorial.
On Friday, August 11, 2017, 7:03:49 AM GMT+1, Shane Schofield
wrote:
Hi DTI Experts,
Is it sensible to do comparisons of MD on the cortex surface like a normal
cortical thickness comparisons between group? If the answer is yes, are there
recommended on smoothing ?
DT_RECON has been completed in Freesurfer.
Thank you.
___
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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.
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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
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Re: [Freesurfer] Mean diffusivity on cortex?
Appreciate it Dr Bruce. Do you have guidelines for smoothing MD? Dr Yendiki, I am trying to investigate whether cortical MD can be a marker of neurodegeneration. The idea is that during the early stages of a disease, cellular microstructure may breakdown before cortical thinning occurs. This results in "less" barriers against diffusion resulting in an increase of MD. On Friday, August 11, 2017, 5:49:40 PM GMT+1, Bruce Fischl wrote: Hi Shane you probably don't need cvs as it is more to extend the surface-based registration to the entire volume. Here you just need the surface-based registration I believe. Use mri_vol2surf to sample the FA onto the surface. After that it is identical to a thickness study cheers Bruce On Fri, 11 Aug 2017, Shane Schofield wrote: > Thanks Dr Yendiki. > > I am more interested to compare MD in grey matter regions by putting the MD > on the surface, and then do a glmfit type of comparisons. Is that OK? Would > you recommend me > to smooth the data after spatial normalisation? I have also used the > mri_cvs_register as described on the tutorial. > > > On Friday, August 11, 2017, 7:03:49 AM GMT+1, Shane Schofield > wrote: > > > Hi DTI Experts, > > Is it sensible to do comparisons of MD on the cortex surface like a normal > cortical thickness comparisons between group? If the answer is yes, are there > recommended on > smoothing ? > > DT_RECON has been completed in Freesurfer. > > Thank you. > > >___ 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] Mean diffusivity on cortex?
Thank you both. How can I deal with partial volume in this case? Would it be possible to use the partial volume tool for PET on my MD volumes? Sorry if it is a silly idea. Best Wishes,Shane On Friday, August 11, 2017, 6:19:45 PM GMT+1, Yendiki, Anastasia wrote: Agreed, especially so with MD. Keep in mind that you¹re upsampling MD from a lower-res (diffusion) space to a higher-res (T1) space, so it should be smooth already, relatively to measure derived from the T1. And MD varies pretty smoothly (it¹s a mean of 3 things, after all). On 8/11/17, 1:11 PM, "Bruce Fischl" wrote: >Hi Shane > >not really - it totally depends on the size of the effect you are looking >for. I would be *very* careful about partial volume effects though > >cheers >Bruce >On Fri, >11 Aug 2017, Shane Schofield wrote: > >> Appreciate it Dr Bruce. Do you have guidelines for smoothing MD? >> >> Dr Yendiki, I am trying to investigate whether cortical MD can be a >>marker >> of neurodegeneration. The idea is that during the early stages of a >>disease, >> cellular microstructure may breakdown before cortical thinning occurs. >>This >> results in "less" barriers against diffusion resulting in an increase of >> MD. >> >> >> On Friday, August 11, 2017, 5:49:40 PM GMT+1, Bruce Fischl >> wrote: >> >> >> Hi Shane >> >> you probably don't need cvs as it is more to extend the surface-based >> registration to the entire volume. Here you just need the surface-based >> registration I believe. Use mri_vol2surf to sample the FA onto the >>surface. >> After that it is identical to a thickness study >> >> cheers >> Bruce >> >> >> >> On Fri, 11 Aug 2017, Shane Schofield >> wrote: >> >> > Thanks Dr Yendiki. >> > >> > I am more interested to compare MD in grey matter regions by putting >>the >> MD on the surface, and then do a glmfit type of comparisons. Is that OK? >> Would you recommend me >> > to smooth the data after spatial normalisation? I have also used the >> mri_cvs_register as described on the tutorial. >> > >> > >> > On Friday, August 11, 2017, 7:03:49 AM GMT+1, Shane Schofield >> wrote: >> > >> > >> > Hi DTI Experts, >> > >> > Is it sensible to do comparisons of MD on the cortex surface like a >>normal >> cortical thickness comparisons between group? If the answer is yes, are >> there recommended on >> > smoothing ? >> > >> > DT_RECON has been completed in Freesurfer. >> > >> > Thank you. >> > >> > >> > >> ___ >> 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] Mean diffusivity on cortex?
Hi Dr Greve, Thank you very much! I will use the MGX CTX volume for the surface sampling. Best Wishes,Shane. On Monday, August 14, 2017, 4:36:28 PM GMT+1, Douglas N Greve wrote: The mri_gtmpvc command will remove volume fraction effects. Look at the PETsurfer page. Run it with --psf 0 and use the muller-gartner output. The output will only be valid for gray matter On 08/12/2017 10:55 AM, Bruce Fischl wrote: > Hi Shane > > we do have some tools to deal with it like > mri_compute_volume_fractions and mri_compute_volume_intensities, or > maybe Doug's PET stuff. At the very least you should probably regress > thickness out. > > cheers > Bruce > > On Sat, 12 Aug 2017, Shane Schofield wrote: > >> Thank you both. >> >> How can I deal with partial volume in this case? Would it be possible >> to use >> the partial volume tool for PET on my MD volumes? Sorry if it is a silly >> idea. >> >> Best Wishes, >> Shane >> >> >> On Friday, August 11, 2017, 6:19:45 PM GMT+1, Yendiki, Anastasia >> wrote: >> >> >> Agreed, especially so with MD. Keep in mind that you¹re upsampling MD >> from >> a lower-res (diffusion) space to a higher-res (T1) space, so it >> should be >> smooth already, relatively to measure derived from the T1. And MD varies >> pretty smoothly (it¹s a mean of 3 things, after all). >> >> On 8/11/17, 1:11 PM, "Bruce Fischl" wrote: >> >> >Hi Shane >> > >> >not really - it totally depends on the size of the effect you are >> looking >> >for. I would be *very* careful about partial volume effects though >> > >> >cheers >> >Bruce >> >On Fri, >> >11 Aug 2017, Shane Schofield wrote: >> > >> >> Appreciate it Dr Bruce. Do you have guidelines for smoothing MD? >> >> >> >> Dr Yendiki, I am trying to investigate whether cortical MD can be a >> >>marker >> >> of neurodegeneration. The idea is that during the early stages of a >> >>disease, >> >> cellular microstructure may breakdown before cortical thinning >> occurs. >> >>This >> >> results in "less" barriers against diffusion resulting in an >> increase of >> >> MD. >> >> >> >> >> >> On Friday, August 11, 2017, 5:49:40 PM GMT+1, Bruce Fischl >> >> wrote: >> >> >> >> >> >> Hi Shane >> >> >> >> you probably don't need cvs as it is more to extend the surface-based >> >> registration to the entire volume. Here you just need the >> surface-based >> >> registration I believe. Use mri_vol2surf to sample the FA onto the >> >>surface. >> >> After that it is identical to a thickness study >> >> >> >> cheers >> >> Bruce >> >> >> >> >> >> >> >> On Fri, 11 Aug 2017, Shane Schofield >> >> wrote: >> >> >> >> > Thanks Dr Yendiki. >> >> > >> >> > I am more interested to compare MD in grey matter regions by >> putting >> >>the >> >> MD on the surface, and then do a glmfit type of comparisons. Is >> that OK? >> >> Would you recommend me >> >> > to smooth the data after spatial normalisation? I have also used >> the >> >> mri_cvs_register as described on the tutorial. >> >> > >> >> > >> >> > On Friday, August 11, 2017, 7:03:49 AM GMT+1, Shane Schofield >> >> wrote: >> >> > >> >> > >> >> > Hi DTI Experts, >> >> > >> >> > Is it sensible to do comparisons of MD on the cortex surface like a >> >>normal >> >> cortical thickness comparisons between group? If the answer is >> yes, are >> >> there recommended on >> >> > smoothing ? >> >> > >> >> > DT_RECON has been completed in Freesurfer. >> >> > >> >> > Thank you. >> >> > >> >> > >> >> > >> >> ___ >> >> 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 be
Re: [Freesurfer] Mean diffusivity on cortex?
Hi Dr Greve, Are the settings correct to do partial volume correction of my MD images? mri_gtmpvc --i subject/dtrecon/adc.nii.gz --reg subject/dtrecon/register.lta --psf 0 --seg subject/mri/gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx 0.25 --o subject/dtrecon/adc.pvc.mgz --no-rescale Thank you! On Monday, August 14, 2017, 4:36:28 PM GMT+1, Douglas N Greve wrote: The mri_gtmpvc command will remove volume fraction effects. Look at the PETsurfer page. Run it with --psf 0 and use the muller-gartner output. The output will only be valid for gray matter On 08/12/2017 10:55 AM, Bruce Fischl wrote: > Hi Shane > > we do have some tools to deal with it like > mri_compute_volume_fractions and mri_compute_volume_intensities, or > maybe Doug's PET stuff. At the very least you should probably regress > thickness out. > > cheers > Bruce > > On Sat, 12 Aug 2017, Shane Schofield wrote: > >> Thank you both. >> >> How can I deal with partial volume in this case? Would it be possible >> to use >> the partial volume tool for PET on my MD volumes? Sorry if it is a silly >> idea. >> >> Best Wishes, >> Shane >> >> >> On Friday, August 11, 2017, 6:19:45 PM GMT+1, Yendiki, Anastasia >> wrote: >> >> >> Agreed, especially so with MD. Keep in mind that you¹re upsampling MD >> from >> a lower-res (diffusion) space to a higher-res (T1) space, so it >> should be >> smooth already, relatively to measure derived from the T1. And MD varies >> pretty smoothly (it¹s a mean of 3 things, after all). >> >> On 8/11/17, 1:11 PM, "Bruce Fischl" wrote: >> >> >Hi Shane >> > >> >not really - it totally depends on the size of the effect you are >> looking >> >for. I would be *very* careful about partial volume effects though >> > >> >cheers >> >Bruce >> >On Fri, >> >11 Aug 2017, Shane Schofield wrote: >> > >> >> Appreciate it Dr Bruce. Do you have guidelines for smoothing MD? >> >> >> >> Dr Yendiki, I am trying to investigate whether cortical MD can be a >> >>marker >> >> of neurodegeneration. The idea is that during the early stages of a >> >>disease, >> >> cellular microstructure may breakdown before cortical thinning >> occurs. >> >>This >> >> results in "less" barriers against diffusion resulting in an >> increase of >> >> MD. >> >> >> >> >> >> On Friday, August 11, 2017, 5:49:40 PM GMT+1, Bruce Fischl >> >> wrote: >> >> >> >> >> >> Hi Shane >> >> >> >> you probably don't need cvs as it is more to extend the surface-based >> >> registration to the entire volume. Here you just need the >> surface-based >> >> registration I believe. Use mri_vol2surf to sample the FA onto the >> >>surface. >> >> After that it is identical to a thickness study >> >> >> >> cheers >> >> Bruce >> >> >> >> >> >> >> >> On Fri, 11 Aug 2017, Shane Schofield >> >> wrote: >> >> >> >> > Thanks Dr Yendiki. >> >> > >> >> > I am more interested to compare MD in grey matter regions by >> putting >> >>the >> >> MD on the surface, and then do a glmfit type of comparisons. Is >> that OK? >> >> Would you recommend me >> >> > to smooth the data after spatial normalisation? I have also used >> the >> >> mri_cvs_register as described on the tutorial. >> >> > >> >> > >> >> > On Friday, August 11, 2017, 7:03:49 AM GMT+1, Shane Schofield >> >> wrote: >> >> > >> >> > >> >> > Hi DTI Experts, >> >> > >> >> > Is it sensible to do comparisons of MD on the cortex surface like a >> >>normal >> >> cortical thickness comparisons between group? If the answer is >> yes, are >> >> there recommended on >> >> > smoothing ? >> >> > >> >> > DT_RECON has been completed in Freesurfer. >> >> > >> >> > Thank you. >> >> > >> >> > >> >> > >> >> ___ >> >> Freesurfer mailing list >> >> Freesurfer@nmr.mgh.harvard.edu >> >> https://mail.nmr.mgh.harvard.edu/mailman/listin
Re: [Freesurfer] Mean diffusivity on cortex?
Hello Dr Greve, I have ran the command and got the data from the gtm.stats.dat. However, all the values are 0.001 - 0.003. Can I scale it up or show the data with more precision? Thank you. On Monday, August 14, 2017, 9:31:38 PM GMT+1, Douglas N Greve wrote: You will need to run gtmseg --s subject (takes an hour or so), then add --seg gtmseg.mgz to the cmd line On 08/14/2017 04:12 PM, Shane Schofield wrote: > Hi Dr Greve, > > Are the settings correct to do partial volume correction of my MD images? > > mri_gtmpvc --i subject/dtrecon/adc.nii.gz --reg > subject/dtrecon/register.lta --psf 0 --seg subject/mri/gtmseg.mgz > --default-seg-merge --auto-mask PSF .01 --mgx 0.25 --o > subject/dtrecon/adc.pvc.mgz --no-rescale > > Thank you! > > > > On Monday, August 14, 2017, 4:36:28 PM GMT+1, Douglas N Greve > wrote: > > > The mri_gtmpvc command will remove volume fraction effects. Look at the > PETsurfer page. Run it with --psf 0 and use the muller-gartner output. > The output will only be valid for gray matter > > > On 08/12/2017 10:55 AM, Bruce Fischl wrote: > > Hi Shane > > > > we do have some tools to deal with it like > > mri_compute_volume_fractions and mri_compute_volume_intensities, or > > maybe Doug's PET stuff. At the very least you should probably regress > > thickness out. > > > > cheers > > Bruce > > > > On Sat, 12 Aug 2017, Shane Schofield wrote: > > > >> Thank you both. > >> > >> How can I deal with partial volume in this case? Would it be possible > >> to use > >> the partial volume tool for PET on my MD volumes? Sorry if it is a > silly > >> idea. > >> > >> Best Wishes, > >> Shane > >> > >> > >> On Friday, August 11, 2017, 6:19:45 PM GMT+1, Yendiki, Anastasia > >> mailto:ayend...@mgh.harvard.edu>> wrote: > >> > >> > >> Agreed, especially so with MD. Keep in mind that you¹re upsampling MD > >> from > >> a lower-res (diffusion) space to a higher-res (T1) space, so it > >> should be > >> smooth already, relatively to measure derived from the T1. And MD > varies > >> pretty smoothly (it¹s a mean of 3 things, after all). > >> > >> On 8/11/17, 1:11 PM, "Bruce Fischl" <mailto:fis...@nmr.mgh.harvard.edu>> wrote: > >> > >> >Hi Shane > >> > > >> >not really - it totally depends on the size of the effect you are > >> looking > >> >for. I would be *very* careful about partial volume effects though > >> > > >> >cheers > >> >Bruce > >> >On Fri, > >> >11 Aug 2017, Shane Schofield wrote: > >> > > >> >> Appreciate it Dr Bruce. Do you have guidelines for smoothing MD? > >> >> > >> >> Dr Yendiki, I am trying to investigate whether cortical MD can be a > >> >>marker > >> >> of neurodegeneration. The idea is that during the early stages of a > >> >>disease, > >> >> cellular microstructure may breakdown before cortical thinning > >> occurs. > >> >>This > >> >> results in "less" barriers against diffusion resulting in an > >> increase of > >> >> MD. > >> >> > >> >> > >> >> On Friday, August 11, 2017, 5:49:40 PM GMT+1, Bruce Fischl > >> >> mailto:fis...@nmr.mgh.harvard.edu>> > wrote: > >> >> > >> >> > >> >> Hi Shane > >> >> > >> >> you probably don't need cvs as it is more to extend the > surface-based > >> >> registration to the entire volume. Here you just need the > >> surface-based > >> >> registration I believe. Use mri_vol2surf to sample the FA onto the > >> >>surface. > >> >> After that it is identical to a thickness study > >> >> > >> >> cheers > >> >> Bruce > >> >> > >> >> > >> >> > >> >> On Fri, 11 Aug 2017, Shane Schofield > >> >> wrote: > >> >> > >> >> > Thanks Dr Yendiki. > >> >> > > >> >> > I am more interested to compare MD in grey matter regions by > >> putting > >> >>the > >> >> MD on the surface, and then do a glmfit type of comparisons. Is > >> that OK? > >> >> Would you recommend me > >> >> > to smooth the data af
Re: [Freesurfer] Mean diffusivity on cortex?
Hi Dr Greve, On a similar note, can I use the Petsurfer on PET data that have already been averaged into a single frame 3D volume instead of 4D? Example, SUVR and BPND data. Thanks for your help again. On Tuesday, August 15, 2017, 9:09:33 AM GMT+1, Shane Schofield wrote: Hello Dr Greve, I have ran the command and got the data from the gtm.stats.dat. However, all the values are 0.001 - 0.003. Can I scale it up or show the data with more precision? Thank you. On Monday, August 14, 2017, 9:31:38 PM GMT+1, Douglas N Greve wrote: You will need to run gtmseg --s subject (takes an hour or so), then add --seg gtmseg.mgz to the cmd line On 08/14/2017 04:12 PM, Shane Schofield wrote: > Hi Dr Greve, > > Are the settings correct to do partial volume correction of my MD images? > > mri_gtmpvc --i subject/dtrecon/adc.nii.gz --reg > subject/dtrecon/register.lta --psf 0 --seg subject/mri/gtmseg.mgz > --default-seg-merge --auto-mask PSF .01 --mgx 0.25 --o > subject/dtrecon/adc.pvc.mgz --no-rescale > > Thank you! > > > > On Monday, August 14, 2017, 4:36:28 PM GMT+1, Douglas N Greve > wrote: > > > The mri_gtmpvc command will remove volume fraction effects. Look at the > PETsurfer page. Run it with --psf 0 and use the muller-gartner output. > The output will only be valid for gray matter > > > On 08/12/2017 10:55 AM, Bruce Fischl wrote: > > Hi Shane > > > > we do have some tools to deal with it like > > mri_compute_volume_fractions and mri_compute_volume_intensities, or > > maybe Doug's PET stuff. At the very least you should probably regress > > thickness out. > > > > cheers > > Bruce > > > > On Sat, 12 Aug 2017, Shane Schofield wrote: > > > >> Thank you both. > >> > >> How can I deal with partial volume in this case? Would it be possible > >> to use > >> the partial volume tool for PET on my MD volumes? Sorry if it is a > silly > >> idea. > >> > >> Best Wishes, > >> Shane > >> > >> > >> On Friday, August 11, 2017, 6:19:45 PM GMT+1, Yendiki, Anastasia > >> mailto:ayend...@mgh.harvard.edu>> wrote: > >> > >> > >> Agreed, especially so with MD. Keep in mind that you¹re upsampling MD > >> from > >> a lower-res (diffusion) space to a higher-res (T1) space, so it > >> should be > >> smooth already, relatively to measure derived from the T1. And MD > varies > >> pretty smoothly (it¹s a mean of 3 things, after all). > >> > >> On 8/11/17, 1:11 PM, "Bruce Fischl" <mailto:fis...@nmr.mgh.harvard.edu>> wrote: > >> > >> >Hi Shane > >> > > >> >not really - it totally depends on the size of the effect you are > >> looking > >> >for. I would be *very* careful about partial volume effects though > >> > > >> >cheers > >> >Bruce > >> >On Fri, > >> >11 Aug 2017, Shane Schofield wrote: > >> > > >> >> Appreciate it Dr Bruce. Do you have guidelines for smoothing MD? > >> >> > >> >> Dr Yendiki, I am trying to investigate whether cortical MD can be a > >> >>marker > >> >> of neurodegeneration. The idea is that during the early stages of a > >> >>disease, > >> >> cellular microstructure may breakdown before cortical thinning > >> occurs. > >> >>This > >> >> results in "less" barriers against diffusion resulting in an > >> increase of > >> >> MD. > >> >> > >> >> > >> >> On Friday, August 11, 2017, 5:49:40 PM GMT+1, Bruce Fischl > >> >> mailto:fis...@nmr.mgh.harvard.edu>> > wrote: > >> >> > >> >> > >> >> Hi Shane > >> >> > >> >> you probably don't need cvs as it is more to extend the > surface-based > >> >> registration to the entire volume. Here you just need the > >> surface-based > >> >> registration I believe. Use mri_vol2surf to sample the FA onto the > >> >>surface. > >> >> After that it is identical to a thickness study > >> >> > >> >> cheers > >> >> Bruce > >> >> > >> >> > >> >> > >> >> On Fri, 11 Aug 2017, Shane Schofield > >> >> wrote: > >> >> > >> >> > Thanks Dr Yendiki. > >> >> > > >> >> > I am more interested to c
Re: [Freesurfer] Mean diffusivity on cortex?
Okay I understand. So I ideally would like to do the PetSurfer before actually working on the BPND but I already got them in the BPND format as well as the raw dynamic images. I tried to obtain the BPND data out from PetSurfer myself, but then I realise I don't any time.dat with me.mri_glmfit --y km.hb.tac.nii.gz --mrtm1 km.ref.tac.dat time.dat --o mrtm1 --no-est-fwhm --nii.gzIs there a way to extract the time.dat in the DICOM? Can you show me an example of what it is the correct time.dat so I can ask my colleagues if they have it somewhere? Thanks a lot!! On Wednesday, August 16, 2017, 10:46:09 PM GMT+1, Douglas N Greve wrote: SUVR you can. BP is a little trickier because BP estimation is a nonlinear operation that can be biased by noise. Probably it comes out similarly. On 08/16/2017 02:50 PM, Shane Schofield wrote: > Hi Dr Greve, > > On a similar note, can I use the Petsurfer on PET data that have > already been averaged into a single frame 3D volume instead of 4D? > Example, SUVR and BPND data. > > Thanks for your help again. > > > On Tuesday, August 15, 2017, 9:09:33 AM GMT+1, Shane Schofield > wrote: > > > Hello Dr Greve, > > I have ran the command and got the data from the gtm.stats.dat. > However, all the values are 0.001 - 0.003. Can I scale it up or show > the data with more precision? > > Thank you. > > > On Monday, August 14, 2017, 9:31:38 PM GMT+1, Douglas N Greve > wrote: > > > You will need to run gtmseg --s subject (takes an hour or so), then add > --seg gtmseg.mgz to the cmd line > > > On 08/14/2017 04:12 PM, Shane Schofield wrote: > > Hi Dr Greve, > > > > Are the settings correct to do partial volume correction of my MD > images? > > > > mri_gtmpvc --i subject/dtrecon/adc.nii.gz --reg > > subject/dtrecon/register.lta --psf 0 --seg subject/mri/gtmseg.mgz > > --default-seg-merge --auto-mask PSF .01 --mgx 0.25 --o > > subject/dtrecon/adc.pvc.mgz --no-rescale > > > > Thank you! > > > > > > > > On Monday, August 14, 2017, 4:36:28 PM GMT+1, Douglas N Greve > > mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > > > The mri_gtmpvc command will remove volume fraction effects. Look at the > > PETsurfer page. Run it with --psf 0 and use the muller-gartner output. > > The output will only be valid for gray matter > > > > > > On 08/12/2017 10:55 AM, Bruce Fischl wrote: > > > Hi Shane > > > > > > we do have some tools to deal with it like > > > mri_compute_volume_fractions and mri_compute_volume_intensities, or > > > maybe Doug's PET stuff. At the very least you should probably regress > > > thickness out. > > > > > > cheers > > > Bruce > > > > > > On Sat, 12 Aug 2017, Shane Schofield wrote: > > > > > >> Thank you both. > > >> > > >> How can I deal with partial volume in this case? Would it be possible > > >> to use > > >> the partial volume tool for PET on my MD volumes? Sorry if it is a > > silly > > >> idea. > > >> > > >> Best Wishes, > > >> Shane > > >> > > >> > > >> On Friday, August 11, 2017, 6:19:45 PM GMT+1, Yendiki, Anastasia > > >> mailto:ayend...@mgh.harvard.edu> > <mailto:ayend...@mgh.harvard.edu <mailto:ayend...@mgh.harvard.edu>>> > wrote: > > >> > > >> > > >> Agreed, especially so with MD. Keep in mind that you¹re upsampling MD > > >> from > > >> a lower-res (diffusion) space to a higher-res (T1) space, so it > > >> should be > > >> smooth already, relatively to measure derived from the T1. And MD > > varies > > >> pretty smoothly (it¹s a mean of 3 things, after all). > > >> > > >> On 8/11/17, 1:11 PM, "Bruce Fischl" <mailto:fis...@nmr.mgh.harvard.edu> > > <mailto:fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu>>> wrote: > > >> > > >> >Hi Shane > > >> > > > >> >not really - it totally depends on the size of the effect you are > > >> looking > > >> >for. I would be *very* careful about partial volume effects though > > >> > > > >> >cheers > > >> >Bruce > > >> >On Fri, > > >> >11 Aug 2017, Shane Schofield wrote: > > >> > > > >> >> Appreciate it Dr Bruce. Do you have guidelines for smoothing MD? > > >> >> > > >> >> Dr Yendik
[Freesurfer] Question about mg and mgx
Hi Freesurfer, I have two question about the different partial volume correction options. Basically how is the --mg method different from the --mgx? I cannot seem to find papers that have compared these methods. Any opinions on this? Does this have any effect on the region of interest GTM results? Cheers and have a great day,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] Help with Reviewer Comment
External Email - Use Caution Hi Freesurfer A reviewer asked whether there are concerns about whether Freesurfer may obtain accurate cortical thickness data in people with developmental conditions - the main focus in my study. I did a search and could not find any validation studies in these cohorts. Any idea? Thanks a lot. Regards,Shane___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] PetSurfer
External Email - Use Caution Hello PetSurfer Developers On the tutorial page, I do not understand this part: --km-hb 11 12 13 50 51 52 specifies the ROIs to use as the high-binding region if using MRTM2. This creates km.hb.tac.nii.gz with the value for the high-binding region for each time point. What exactly is a high-binding region and how do these inputs affect the rest of the estimation? If I do not know what the high binding regions for a tracer are, may I leave this blank? Thank you.___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] PetSurfer
External Email - Use Caution Hi Doug, thanks for the explanation. My question is more related to how we might go about knowing what are the high binding regions for any tracer? If I am going to do an FDG-PET study, will the HB region parameters be different from a [11C]-PK11195 study for example? And secondly, might be these be different across subjects? Thanks for your help. Previous email :You should read up on the MRTM2. Basically, when you run MRTM1, it computes a separate k2 for each voxel eventhough the k2 should be the same across the entire brain (since it actually refers to the reference region). With MRTM2, you estimate the single k2 value from high binding regions. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Petsurfer: Motion Correction
External Email - Use Caution Hi Freesurfer Team, How may I align 5 volumes of my PET data ( 5 min acquisitions each) to a mean image for motion correction across the acquisition? I can use mri_concat to get the the mean image, but I am not sure how to do the realignment after that. Thank you. Best Wishes,Shane___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Petsurfer: Motion Correction
External Email - Use Caution Thanks, Doug. I think the command is MCFLIRT. https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/MCFLIRT Best Wishes,Shane On Friday, May 3, 2019, 6:18:54 PM GMT+1, Shane Schofield wrote: Hi Freesurfer Team, How may I align 5 volumes of my PET data ( 5 min acquisitions each) to a mean image for motion correction across the acquisition? I can use mri_concat to get the the mean image, but I am not sure how to do the realignment after that. Thank you. Best Wishes,Shane ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Longitudinal MRI but different scanner
Hi Freesurfer Team, I try to calculate a within-subject decrease in cortical thickness over 2 years, but the MRI scanner was changed during the project. Is it still possible to do that using the longitudinal stream in Freesurfer? 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] Outlier voxels after partial volume correction using Petsurfer
External Email - Use Caution Hello Petsurfers! A few of my subjects ended up with vertices that had outlier PET values after I followed the PetSurfer steps. Most of the binding potentials are in the range of 0 - 3. Looking at the histogram though there are a couple of vertices with values around -30. First of all how can I deal with this? Can these voxels be excluded from the data, and how? Secondly, does this mean that there is something not right with my parameters for mri_gtmpvc? Cheers,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.
Re: [Freesurfer] Outlier voxels after partial volume correction using Petsurfer
External Email - Use Caution Hi Doug, it is kinetic modelling, not uptake. Thank you. On Monday, August 13, 2018, 10:36:13 AM GMT+1, Shane Schofield wrote: Hello Petsurfers! A few of my subjects ended up with vertices that had outlier PET values after I followed the PetSurfer steps. Most of the binding potentials are in the range of 0 - 3. Looking at the histogram though there are a couple of vertices with values around -30. First of all how can I deal with this? Can these voxels be excluded from the data, and how? Secondly, does this mean that there is something not right with my parameters for mri_gtmpvc? Cheers,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] vol2subfield: which file to use?
External Email - Use Caution Hi Freesurfer Tema, I am trying to use vol2subfield to extract DTI measurements like FA and MD. For this purpose, should I be using the rh.hippoAmygLabels-T1.v21.CA.FSvoxelSpace.mgz or rh.hippoAmygLabels-T1.v21.CA.mgz ? Thank you!___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] bbregister on DWI volumes using DOF 12 for epi distortions ?
External Email - Use Caution Hi Freesurfer Experts, I am trying to obtain coregister diffusion data b0 with T1. One problem is that I do not have any means to correct for EPI distortions. Because of this, I am experimenting with DOF = 9 and DOF = 12. The mincost for 12 was consistently the lowest compared to 6 and 9 across my datasets [DOF 6 = 0.23, DOF 9 = 0.22, DOF 12 = 0.19]. However, it is hard to tell that DOF 12 is the best just by looking at the coregistered B0s overlaid on the brainmask. Would it be fine to proceed with the DOF 12 option? Thank you. Best Wishes,Shane___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Subject with extremely large ventricles
External Email - Use Caution Hi Freesurfer Experts, Is there anything that could be done to improve the surface definitions for this particular subject (attached)? The pial and white matter boundaries in the cortex are generally accurate though. Thank you. Best Wishes,Shane___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Mri_segstats for PET data: Reviewer question
External Email - Use Caution Hi Freesurfer Team, I have used mri_segstats to get ythe mean PET uptake across all the parcellations in the WMPARC space. These values were calculated in the native PET space (following the DTI tutorial). A reviewer asked what is the grey matter probability of the ROI and I am not sure how to address this. Any help is kindly appreciated. Thanks. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] PETSURFER for AV1451
External Email - Use Caution Hi PETSURFERs, A quick question to the group: Does any one have experience using PETSURFER on dynamic AV1451 scans? How can I know whether the MRTM1 or MRTM2 using midbrains (due to off target AV1451 binding) is suitable for my data? Thank you! Best Wishes,Shane ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
