[Freesurfer] T1 maps longitudinal data

? Many thanks AJ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e

[Freesurfer] Cerebellum segmentation pipeline

External Email - Use Caution Hi, Is there a specific pipeline for segmenting the cerebellum, cortical gray and deep nuclei? Like the one for hippocampus and thalamus? Best ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] SynthSR

, AJ ___ 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

Re: [Freesurfer] SynthSR

External Email - Use Caution These are the same ROIs, just labeled differently by me late at night. They are all normalized by the ICV. Just didn't add the N next to the ROI in a different row. Good point. I am not correcting for gradient distortions. Will do. Many thanks AJ

Re: [Freesurfer] SynthSR

t. my best, AJ Scanners used for controls and test subjects: Achieva_TFE_R1 Achieva_TFE_R2 Ingenia_R1 Ingenia_R2 GE_SPGR_1529_R1 GE_SPGR_1529_R2 GE_SPGR_R1 GE_SPGR_R2 Phillip_Achieva_R1 Achieva_R2 GE_R1 GE_R2 On Sun, Nov 28, 2021, 20:41 Douglas N. Greve wrote: > Also samseg, see > ht

Re: [Freesurfer] SynthSeg

External Email - Use Caution Many thanks. Best AJ On Sat, Nov 27, 2021, 20:04 Fischl, Bruce wrote: > Sorry, what is the “sb” in sbTIV? I’m sure you can use it from samseg, or > just use samseg for the segmentation as well if you want, since it is > agnostic with respe

[Freesurfer] SynthSeg

External Email - Use Caution Hi Thank you for your help. I ran SynthSeg successfully. How do you derive sbTIV value ? Could one use sbTIV from SAMSEG? Many thanks AJ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] SynthSR

External Email - Use Caution Hi, Could synthetic MRIs generated by the SynthSR script be potentially used to harmonize T1w weighted images acquired on different scanners? Then used harmonized images for volumetric analyses? Many thanks AJ

Re: [Freesurfer] Hypothalamic segmentation

External Email - Use Caution Many thanks. My best. AJ On Sun, Oct 17, 2021, 09:09 Iglesias Gonzalez, Juan E. < jiglesiasgonza...@mgh.harvard.edu> wrote: > Dear AJ, > > Both sbTIV and eTIV are trying to model the same thing, but sbTIV seems to > be a slightly be

[Freesurfer] Hypothalamic segmentation

External Email - Use Caution Hi, How does one normalize the data output from hypo_seg for the head size, with sbTIV or eTIV, which are a bit different from each other. Many thanks AJ ___ Freesurfer mailing list Freesurfer

Re: [Freesurfer] SAMstats2table option

External Email - Use Caution Many thanks. My best On Mon, Aug 2, 2021, 10:13 Douglas N. Greve wrote: > You should be able to use asegstats2table specifying the samseg inputs > with --inputs samseg1/seg.stats samseg2/seg.stats samseg3/seg.stats ... > > On 7/26/2021

[Freesurfer] Samseg.stats file to table

of files in the samsegOutput/stats versus the aseg.stats file? Thank you. AJ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] SAMstats2table option

of files in the samsegOutput/stats versus the aseg.stats file? Thank you. AJ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Intensity equalization

External Email - Use Caution Great. Many thanks for your suggestions. My best Aj On Wed, Jul 21, 2021, 12:31 Fischl, Bruce wrote: > There isn’t really anything available for the latter approach. I would > suggest the former and potentially including site as a nuisance va

Re: [Freesurfer] Intensity equalization

an additional program, if you would suggest one? Many thanks AJ On Wed, Jul 21, 2021, 09:40 Fischl, Bruce wrote: > Hi AJ > > > > No, not easily. Maybe you can tell us your overall goal to see if we can > help? > > > > Cheers > Bruce > > > > *

[Freesurfer] Intensity equalization

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Re: [Freesurfer] sbTIV versus eTIV

mentation and counts voxels > within skull. The eTIV is computed from the talairach registration, which > is going to be inherently more variable (eg, more or less neck will affect > it). > > On 7/20/2021 3:24 PM, AJ wrote: > > External Email - Use Caution > Hi, > I am

[Freesurfer] sbTIV versus eTIV

why? Normalizing ROIs with sbTIV improves these differences even more. Thanks for your help. AJ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] interscan variability

way to harmonize between GE and PH values? Many thanks, AJ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Interscanner variability

External Email - Use Caution Thank you for your response. Yes, the key question is to adjust for interscan variability through either histogram matching or ComBat before or after longitudinal run. Will await to see what the longitudinal freesufer experts think. My best AJ

[Freesurfer] Interscanner variability

crossectionally each time point separately and normalize these time points with eTIV? Many thanks AJ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Longitudinal processing

External Email - Use Caution Many thanks. Best regards On Thu, Jun 24, 2021, 10:07 Douglas N. Greve wrote: > If you are going to compare the volume across subject, then it does need > to be corrected with eTIV > > On 6/15/2021 8:06 AM, AJ wrote: > > Ex

[Freesurfer] Longitudinal processing

thanks for your input. Sincerely, AJ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Long_stats_slopes

External Email - Use Caution Hi, Is there any way to run long_stats_slopes on the aseg.stats file on the total thalamic structure instead of separately as right and left. Many thanks. AJ ___ Freesurfer mailing list Freesurfer

[Freesurfer] Combined right and left analysis

External Email - Use Caution Hi, I am trying to do long_stats_slopes on the aseg.stats file. Is there any way I could examine percent change as total thalamic or total corpus callosum instead of separately as right and left structures or various parts of CC? Thanks, AJ

Re: [Freesurfer] T2 lesion editing

External Email - Use Caution Many thanks. This really helps. My best AJ On Mon, Apr 26, 2021, 02:21 Stefano Cerri wrote: > Hi AJ, > > > Did you already use the *--lesion-mask-pattern *flag for the T2 contrast > (Cf. > https://secure-web.cisco.com/1

Re: [Freesurfer] T2 lesion editing

External Email - Use Caution Many thanks. Best. AJ On Sun, Apr 25, 2021, 21:45 Douglas N. Greve wrote: > > > On 4/24/2021 5:56 PM, AJ wrote: > > External Email - Use Caution > Hi, > Once SAMSEG has finished segmenting T2 lesions, other th

[Freesurfer] T2 lesion editing

External Email - Use Caution Hi, Once SAMSEG has finished segmenting T2 lesions, other than trying different --threshold flags, any way to manually modify them? Can --eTIV be added to SAMSEG? In Samseg, can brainstem be segmented into parts, such as medulla, pons, mid brain like

Re: [Freesurfer] error installing tensorflow

External Email - Use Caution Thank you for your help. I think I'm getting closer to installing tensor flow. 1-as you suggested: installed .NET (myenv) MacBook-Pro-4:~ AJ$ dotnet --info .NET SDK (reflecting any global.json): Version: 5.0.202 Commit:db7cc87d51 Runtime

Re: [Freesurfer] error installing tensorflow

External Email - Use Caution sorry, but I get the same error after conda create -n myenv python=3.6 conda activate myenv (myenv) MacBook-Pro-4:~ AJ$ fspython -m pip install tensorflow==1.13.1 Collecting tensorflow==1.13.1 Using cached https://secure-web.cisco.com

Re: [Freesurfer] error installing tensorflow

External Email - Use Caution thank you so much. I just installed conda. (base) MacBook-Pro-4:~ AJ$ conda -V conda 4.9.2 Is myenv /Aplications/freesurfer/7.1.0 thank you. aj On Fri, Apr 16, 2021 at 10:22 PM Vishnu S wrote: > External Email - Use Caution > > 1.

Re: [Freesurfer] error installing tensorflow

External Email - Use Caution sorry for being non-tech, but how do I exactly do creating a conda venv with Python 3.6. many thanks aj On Fri, Apr 16, 2021 at 9:56 PM Vishnu S wrote: > External Email - Use Caution > > Hi AJ, > > So tensorflow 1.13.0 is loo

Re: [Freesurfer] error installing tensorflow

External Email - Use Caution Thank you so much for your help. Here's the error: MacBook-Pro-4:~ AJ$ fspython -m pip install tensorflow==1.15 Collecting tensorflow==1.15 Using cached https://secure-web.cisco.com/1ZvNOAlnI2lRZHzC8bF1ZCoyoP8DTiHNr8j1wTUnCTH_6rls1cn1Sa

Re: [Freesurfer] error installing tensorflow

External Email - Use Caution Hi, I have python both versions of python installed: MacBook-Pro-4:~ AJ$ python3 --version Python 3.9.4 MacBook-Pro-4:~ AJ$ python --version Python 2.7.10 when installing fspython -m pip install tensorflow==1.13.1, I get the error: dyld: Symbol

[Freesurfer] error installing tensorflow

External Email - Use Caution Hi, I am having trouble installing: fspython -m pip install tensorflow==1.13.1 Not sure what the issue is. Any help would be greatly appreciated. best AJ Error message while installing: dyld: lazy symbol binding failed: Symbol not found: _utimensat