Re: [Freesurfer] Hippocampal segmentation on two sets of MRI with different resolution

Hi Jacob, 0.9 vs 1mm shouldn’t change much. If you want to use the T2, then definitely provide it as “additional volume” eg with segmentHA_T2.sh Cheers, /Eugenio -- Juan Eugenio Iglesias http://www.jeiglesias.com From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Jacob Bunyamin Date: T

Re: [Freesurfer] Error in SegmentSubfieldsT1Longitudinal (line 2148)

Dear Annchen, Do you get this error with a more recent stable version, e.g., 7.4.1? Cheers, /Eugenio -- Juan Eugenio Iglesias http://www.jeiglesias.com From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Annchen Knodt Date: Tuesday, September 3, 2024 at 1:57 PM To: freesurfer@nmr.mgh.h

Re: [Freesurfer] Question on hippocampus segmentation algorithm

Dear Alice: 1. Can you please send another capture without the mask, or with the option “show label boundaries only” activated? It’s hard to tell, without seeing what’s behind 😊 2. You can read the paper for free here: https://www.sciencedirect.com/science/article/pii/S1053811915003420 Ch

Re: [Freesurfer] Comparison of "segment_subregions" and "recon-all"

Dear Yongoo These are different modules with different atlases; rather than worrying about absolute differences, I would worry if the correlation was low. Cheers, /Eugenio -- Juan Eugenio Iglesias http://www.jeiglesias.com From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Yoonho Hwang

Re: [Freesurfer] Is ICV needed as a covariate if matched between groups

It’s always a good idea to divide the volumes by ICV (or add ICV as a regressor). This is very unlikely, but what if your controls happened to have smaller heads than your patients? For peace of mind, I’d correct by ICV. Cheers, /Eugenio -- Juan Eugenio Iglesias http://www.jeiglesias.com From:

Re: [Freesurfer] Can find "mri_WMHsynthseg" command in freesurfer 7.4.1

Dear Naveen, WMH-SynthSeg is currently only available in the development version of FreeSurfer. I have updated the wiki with this information. Apologies for the inconvenience. /E -- Juan Eugenio Iglesias http://www.jeiglesias.com From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Byripud

Re: [Freesurfer] recon-all clinical : usage with contrast-enhanced T1-weighted images?

Dear Barbara, you could in principle use recon-all-clinical for the enhanced T1 but the surface reconstruction would probably fail. Instead, I’d probably run SynthSR to synthesize 1mm T1 intensities while inpainting abnormalities and then run the standard recon-all. Cheers, /Eugenio -- Juan Euge

[Freesurfer] Bug in mri_convert reslice-like with 4D images

Dear FS experts, We get a segfault when I try to resample images with the command: mri_convert input.mgz output.mgz -rl reference.mgz when reference.mgz has multiple frames (e.g., a RGB volume). Any idea of why this is happening? Cheers, /Eugenio (&Stefano & Pranav) ___

Re: [Freesurfer] Easyreg > cortical parcels missing after SynthSeg with --parc option ?

advancing my research, and I wish to express my sincere appreciation for your assistance. Warm regards, Edward From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Iglesias Gonzalez, Juan E. Sent: Saturday, April 6, 2024 3:39 AM To: Freesurfer support list Subject: Re: [Freesurfer] Easyr

Re: [Freesurfer] Recon-All Clinical Stream: Image Output Observations in Creating ENIGMA QC Images

Dear Sam, The native images live in one space (typically anisotropic), whereas the recon-all-clinical files always live in their own 1x1x1mm isotropic grid (which is the whole point!). I am not familiar with the Enigma QC procedure but I wouldn’t be surprised if it’s not compatible with these va

Re: [Freesurfer] Easyreg > cortical parcels missing after SynthSeg with --parc option ?

ing this objective. Thanks in advance! Best regards, Edward Sent from my iPad > On Apr 5, 2024, at 9:57 AM, Hoffmann, Malte,PhD > wrote: > > What are you trying to achieve? > > ____ > From: Iglesias Gonzalez, Juan E. > Sent: Thursda

Re: [Freesurfer] Easyreg > cortical parcels missing after SynthSeg with --parc option ?

h.harvard.edu On Behalf Of Iglesias Gonzalez, Juan E. Sent: Wednesday, April 3, 2024 4:16 AM To: Freesurfer support list Subject: Re: [Freesurfer] Easyreg > cortical parcels missing after SynthSeg with --parc option ? Ha! I understand that sharing the images may be tricky, but do you think

Re: [Freesurfer] Easyreg > cortical parcels missing after SynthSeg with --parc option ?

esurfer/python/lib/python3.8/site-packages/numpy/linalg/linalg.py", line 89, in _raise_linalgerror_singular raise LinAlgError("Singular matrix") numpy.linalg.LinAlgError: Singular matrix From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Iglesias Gonzalez, Juan E. Sent: Monday, April 1,

Re: [Freesurfer] Easyreg > cortical parcels missing after SynthSeg with --parc option ?

Dear Edward, Try deleting: /home/chang/GBM_Data/T1_template/Template_MNI_Normal122_sc_age19-40_tirq_1.0mm_T1_scalp_trip_synthseg.nii and /home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only_synthseg/042/pre_042__synthseg.nii.gz And then run the same command. Easy_reg will create the

Re: [Freesurfer] Too large volumes thalamus segmentation in version 7.2

Dear Katharina, First of all, and to avoid any confusion, the bug only affected the script to gather the volumes from different subjects (“quantifyThalamicNuclei.sh”), and not the segmentations themselves. Would you mind sharing some images, showing how/where the LGN is oversegmented, please? It

[Freesurfer] Problem with mris_remiesh in recon-all

Dear experts, My collaborator Martina Bocchetta is encountering a weird problem with recon-all, specifically with mris_remesh after the topology correction (see below). Any insight? Thanks in advance, /Eugenio mris_remesh --remesh --iters 3 --input /path/to/subject/surf/rh.orig.premesh --outpu

Re: [Freesurfer] Choice of ICV estimation

I’m not taking sides on this one, but I’ll nevertheless pinpoint that you can also get a sbTIV using SynthSeg, hehe. Looking forward to reading people’s opinions on this one! -- Juan Eugenio Iglesias http://www.jeiglesias.com From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Jackson Le

Re: [Freesurfer] longitudinal hippocampal segmentation error in Mac OS Sonoma + Freesurfer 7.2.0

Dear Joao, I’ll defer to our software specialists, but another option may be trying the Python version: https://surfer.nmr.mgh.harvard.edu/fswiki/SubregionSegmentation Cheers, /E -- Juan Eugenio Iglesias http://www.jeiglesias.com From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of João

Re: [Freesurfer] MRIread and RAS orientation

I’m pretty sure that the Matlab code does not reorient. Cheers, Eugenio -- Juan Eugenio Iglesias http://www.jeiglesias.com From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Huang, Yujing Date: Tuesday, January 23, 2024 at 08:49 To: Freesurfer support list Subject: Re: [Freesurfer] MR

Re: [Freesurfer] EasyReg question

I would totally give it a try! It runs pretty fast and gives you a segmentation along the way. Cheers, /E -- Juan Eugenio Iglesias http://www.jeiglesias.com From: Èlia Pedregosa Date: Monday, January 22, 2024 at 8:07 AM To: Iglesias Gonzalez, Juan E. , freesurfer@nmr.mgh.harvard.edu Cc

Re: [Freesurfer] recon-all vs. recon-all-clinical: missing ROIs

Dear Francesca, Our method cannot reliably segment these thin/faint structures from clinical scans of arbitrary resolution and contrast, which is why they don’t get segmented. If you want to segment the choroid plexus, you could take then intensities under the ventricles and split them into cere

Re: [Freesurfer] SynthSR for T2-weighted images

Dear Hengameh, Synthesis of T2 and FLAIR images is on the to-do list, and should happen in the next couple of months 😉 Cheers, /Eugenio -- Juan Eugenio Iglesias http://www.jeiglesias.com From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of hmarz...@student.ubc.ca Date: Thursday, January

Re: [Freesurfer] Brainstem segmentation without pre-processing

Dear Ali, Making a SynthSeg version of the tool is on the to-do list but has not happened yet. For now, you need to run recon-all. The good news is that you get a ton of additional useful information on the brains! Kind regards, /Eugenio -- Juan Eugenio Iglesias http://www.jeiglesias.com From:

Re: [Freesurfer] SUBJECTS_DIR writing permissions to run hippocampal/amygdala subfields

FREESURFER_HOME too? Best, Eva Van: freesurfer-boun...@nmr.mgh.harvard.edu Namens Iglesias Gonzalez, Juan E. Verzonden: vrijdag 22 december 2023 15:28 Aan: Freesurfer support list CC: Brouwer, I. (Iman) ; Gool, J.K. (Jari) Onderwerp: Re: [Freesurfer] SUBJECTS_DIR writing permissions to run hippocampal

Re: [Freesurfer] SUBJECTS_DIR writing permissions to run hippocampal/amygdala subfields

Dear Eva, The subfield temporary directory is under SUBJECTS_DIR, not FREESURFER_HOME. So you only need SUBJECTS_DIR to be local. Cheers, /Eugenio -- Juan Eugenio Iglesias http://www.jeiglesias.com From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Heese, E. van (Eva) Date: Friday, De

Re: [Freesurfer] Killed procees during running WMH-SynthSeg

Dear Chuyue, It’s very posible that you ran out of RAM. I think you need about 32GB to run this module. Do you think that could be the problem? Cheers, /Eugenio -- Juan Eugenio Iglesias http://www.jeiglesias.com From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 赵楚越 Date: Thursday, De

Re: [Freesurfer] Unable to add FGATIR during thalamic segmentation

Dear Amrita, Please insert your subject directory between your subject name(sub-19253779) and your FGATIR scan (sub-19253779/mri/FGATIR.nii.gz). If you running your code from the subjects directory, which seems to be the case, it would simply be: segmentThalamicNuclei.sh sub-19253779 . sub-19253

Re: [Freesurfer] Segmentation of hippocampal subfields and nuclei of the amygdala

Dear Joshua, This is a bit of an empirical question. I’d totally run both on a few subjects and compare the results. If you do so: I would selfishly/greatly appreciate it if you shared your impressions with me :-) Cheers, /Eugenio -- Juan Eugenio Iglesias http://www.jeiglesias.com From: freesur

Re: [Freesurfer] Recon all clinical with multiple input scans

Dear Pauline, Thanks for the interest in our new pipeline! You can only run one scan at the time (but that scan may be of any resolution / contrast). Cheers, /E -- Juan Eugenio Iglesias http://www.jeiglesias.com From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Lieshout, P.B. van (Pau

Re: [Freesurfer] extracting measurements from segment_subregions

Dear Victor, Thanks for letting us know. We’ll look into this ASAP. Cheers, /E -- Juan Eugenio Iglesias http://www.jeiglesias.com From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Zeng, Victor (BIDMC - Keshavan - Psychiatry) Date: Wednesday, November 8, 2023 at 00:37 To: freesurfer@n

Re: [Freesurfer] Using Synthseg segmentations to fix recon-all outputs

I’ll defer to the software engineers for the first issue! For the second: does it work if you copy norm.mgz into orig/001.mgz? :-D -- Juan Eugenio Iglesias http://www.jeiglesias.com From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Maya Yablonski Date: Tuesday, October 31, 2023 at 1:

Re: [Freesurfer] Using Synthseg segmentations to fix recon-all outputs

Dear Maya, You can use then -synthseg flag with recon-all to use SynthSeg instead of the standard algorithm 😉 For fmriprep: which is the offending volume? There are very minor differences with the standard recon-all output. Cheers, /E -- Juan Eugenio Iglesias http://www.jeiglesias.com From: fre

Re: [Freesurfer] SynthSEG continued developments

Dear Dawn, Integrating the hippocampal subfields into SynthSeg in on the to-do list, but it’s tricky due to differences in resolution. In terms of robustness, we are making progress – but I like your suggestion of adding defacing to the list of “artifacts”! We’ll take it into consideration 😊 Che

Re: [Freesurfer] HBT/FS60/CA segmentation

Hi Jasmine, This is tricky because the “absorption” happens at the discrete segmentation level (rather than using the soft probabilities). At that point, you’re probably better off counting voxels and multiplying by their volume. Doug: is there a way to do this with FreeSurfer programs, as oppose

Re: [Freesurfer] SynthSeg volume labels

JgDuCjLKOCEBQpCSEDa4xKQ/https%3A%2F%2Fscholar.harvard.edu%2Floggia> From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Juan E. Sent: Tuesday, October 3, 2023 8:52 PM To: Freesurfer support list Subject: Re: [Freesurfer] SynthSeg volume

Re: [Freesurfer] segmentThalamicNuclei.sh and Matlab Runtime

External Email - Use Caution Dera Lauren, I am a bit confused: is /Applications/freesurfer/7.3.2/MCRv97 pointing to /Applications/MATLAB/MATLAB_Runtime/R2019b/MCRv97? Cheers, /Eugenio -- Juan Eugenio Iglesias http://secure-web.cisco.com/1X-6jqhKciXd6EPCb1LpoJ_D-PycfnYplnrld0ymBS

Re: [Freesurfer] SynthSeg volume labels

External Email - Use Caution Thanks, this is super weird. When did you download this dev version? Also: would it be possible to share the CSV file, please? Cheers, /Eugenio -- Juan Eugenio Iglesias http://secure-web.cisco.com/17R5U4dEBJCcdG3QUUTbhXq98ahPm8wK3gHT_Kp2MyRltQVDu9UikD

Re: [Freesurfer] mri_easyreg error: Killed

External Email - Use Caution Dear Kaibo, How much RAM does your machine have? Cheers, /Eugenio -- Juan Eugenio Iglesias http://secure-web.cisco.com/1f4DYOHf8Rr4YRZ9OT7geQMSYd2V5bpiQti0xpXTDLLzxMI7NosKCSWMzsvo08dZ8aEYauyNz8JGo2myKBy3e4PsLDLFEJCB0iaw8i3ezyCW698CCDeAg98tINFdWmSLWzhSE

Re: [Freesurfer] Recon-all-clinical error: Illegal instruction Error in SynthSeg

External Email - Use Caution Dear Julian, I believe this is a problem with SynthSeg not being compatible with the new microprocessor in MAC computers. Our software engineers are looking into solutions to this. Sorry for the inconvenience, Eugenio -- Juan Eugenio Iglesias http://

Re: [Freesurfer] FreeSurfer hippo-amygala module

External Email - Use Caution Thanks for the interest in our work, Anton! We don’t have a template in MNI space, sorry (it’s on the to-do list, but buried among many other items). But you can always segment the template with the atlas 😃 Cheers, /Eugenio -- Juan Eugenio Iglesias h

Re: [Freesurfer] Converting hyperfine MRI to nifti

External Email - Use Caution Dear Fatima, You can use dcm2niix to convert Hyperfine to Nifti, and then use our FreeSurfer tools directly on those (mri_synthsr, etc). Kind regards, Eugenio -- Juan Eugenio Iglesias http://secure-web.cisco.com/1biIzD2_G4nFSdmA5Ydn6CcUOvXhaPhM2Ck-Z0o

Re: [Freesurfer] Import Matlab SynthSeg labels to FS

External Email - Use Caution Dear Haley, The Matlab version of SynthSeg writes nifty files. You could run the FreeSurfer command to convert to mgz (and rename to aseg, along the way): mri_convert synthseg.nii.gz aseg.mgz Now: I don’t know if it’s possible to simply replace FreeS

Re: [Freesurfer] Easyreg > cortical parcels missing after SynthSeg with --parc option ?

/1DRP30tSXMppp0KyzN8sBiVb_rbxRjFPmjNRpJ3ep6UGsmPgdFdL1PHpTB2HiZikT7mhDnrOSuMMNSyfWBC9ExkKF0npewjTGTJgEMsFLawYntgwWgMNuZX9F5v8wQsflOvhLxItA2W7jYwGI8Cq2vXFN4aiKieIWckGqFLsw8C0LJXSmsoAoKcQtCUEb549gkPIJD-OI9wJ_b9xR4nL2-29eow6o6Uz_ZrSOtwJGbb8aoGTToKo_15rmCrhx2wKl/http%3A%2F%2Fwww.jeiglesias.com From: Eric BARDINET Date: Thursday, August 24, 2023 at 11:53 AM To: Iglesias Gonzalez, Juan E. , Freesurfer support list Subject: Re: [Freesurfer] Easyreg

Re: [Freesurfer] Easyreg > cortical parcels missing after SynthSeg with --parc option ?

-Hjz58DwOlAqvsv0QtYWZbj0obWyvYKUSBsYkOBbSGZCgVjrd6KvPVp4G9dmPqfdWQRoGAmacG4ezf1nh2KJjy9DHaSDROF3vvRKeZUeRV-MA/http%3A%2F%2Fwww.jeiglesias.com From: Eric BARDINET Date: Wednesday, August 23, 2023 at 9:32 AM To: Iglesias Gonzalez, Juan E. , Freesurfer support list Subject: Re: [Freesurfer] Easyreg > cortical parcels missing after SynthSeg w

Re: [Freesurfer] Easyreg > cortical parcels missing after SynthSeg with --parc option ?

External Email - Use Caution Dear Eric, Thanks for the interest in our tool! Can you please send us the exact command line that you used, and the full output of mri_easyreg? Cheers, /Eugenio -- Juan Eugenio Iglesias http://secure-web.cisco.com/1U33kJUEZ__sfspXazQKQX0hyZheFOuaPY4

Re: [Freesurfer] Questions for the estimated brain volume based on new version of FreeSurfer

External Email - Use Caution Sorry for the slow response. 1.1: the results are bound to be different (since they are different methods) but they should be very highly correlated. For the eTIV, please take a look at Figure 4 of https://secure-web.cisco.com/1pF9TRM2P6hqsAScfzof5e0

Re: [Freesurfer] some thalamic subregions are not shown in image of ThalamicNuclei.v13.T1.mgz

External Email - Use Caution Dear zlseu, We currently do not have an “official” release of the probabilistic atlas in a reference space. It is try that some of the smallest nuclei may not appear in the hard (discrete) segmentation, but you can always use the option to write down

Re: [Freesurfer] Hippo subfields long

External Email - Use Caution Dear Andrei, The script requires that you’ve run the main FreeSurfer longitudinal pipeline (see Longitudinal Processing in the wiki). Don’t worry about the files, they have different names and can coexist without issues 😉 Cheers, /E -- Juan Eugenio

Re: [Freesurfer] recon-all-clinical

External Email - Use Caution Uuummm I don’t think this would work, as a lot of our intermediate files (eg norm.mgz) are not comparable to their counterparts in the standard recon-all stream. Sorry! -- Juan Eugenio Iglesias http://secure-web.cisco.com/1R9UOepVdGkzRhS_JbSZ7bkBYP0O

Re: [Freesurfer] Error running hippocampus subfields and amygdala nuclei segmentation pipeline

External Email - Use Caution I’ll defer to our software engineering experts, but in the meantime, you could maybe try the Python version? https://secure-web.cisco.com/1Cv_49AxchVd_2vIYynJ4qP6kfmnE5Dy5Tw3AuuGeUNzzOEqT7zCC8a1jFBudPBWmbpay8jscwU4QvGJDaMi2Cexs8SJBYFvrJeX-LR2OR0B-B8vsf

Re: [Freesurfer] EasyReg Troubleshoot - Killed

External Email - Use Caution Dear Nadia, It seems like many centroids are missing. Did you visually check the segmentations of the reference and floating image, e.g., with Freeview? Do they look good? Cheers, /Eugenio -- Juan Eugenio Iglesias http://secure-web.cisco.com/1b2Y7tMk

Re: [Freesurfer] EasyReg for group-average template?

External Email - Use Caution Dear Amir, We don’t have a script to make templates, but I don’t think it’d be too hard to do it yourself. You can start from eg MNI (not a problem to start from an existing atlas since your first iterations will be linear anyway), and use the usual

Re: [Freesurfer] Hippocampal/amygdala subfields hemisphere error

External Email - Use Caution Dear Chris, This is a pretty weird one! Question: what files are there in the temporary directory subjectDir/subjectBase/tmp/hippoSF_T1_long.v22_left/ ? Cheers, /E -- Juan Eugenio Iglesias http://secure-web.cisco.com/1FmaPIPrt8VADXFs3ezSt_rWHcBh_tWsK4

Re: [Freesurfer] ERROR: flag i unrecognized

External Email - Use Caution I am with Yujing; if you copy-pasted the command from somewhere, can you please make sure that what you have in front of the ‘s’, ‘i’, and ‘all’ are all dashes? They look different in the capture… -- Juan Eugenio Iglesias http://secure-web.cisco.com/

Re: [Freesurfer] How to extract hippocampus from nu.mgz using lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz

Dear Minh, Maybe user mri_binarize on lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz to create a mask, and then use mri_mask to extract the hippocampus? Cheers, /E -- Juan Eugenio Iglesias http://www.jeiglesias.com From: on behalf of Hoang Gia Minh Reply-To: Freesurfer support list Date: Tuesday,

Re: [Freesurfer] Hippocampal subregions - FreeSurfer segmentation

Dear Emily, These boundaries are mostly geometric and based on the atlas. For the atlas building: * the head/body boundary was place at the level of the uncal apex. * For the body/tail boundary, I’ll defer to Jean Augustinack (CCed) Cheers, /Eugenio -- Juan Eugenio Iglesias http://www.jei

Re: [Freesurfer] mri_synthsr with CT images

day, March 17, 2023 at 16:49 To: "Iglesias Gonzalez, Juan E." Cc: "freesurfer@nmr.mgh.harvard.edu" Subject: mri_synthsr with CT images External Email - Use Caution Dear Juan: I tested mri_synthsr using three different CT images with the threshold (80 value) that you tol

Re: [Freesurfer] CT and mri_synthsr

It totally looks like it. How much RAM do you have on the machine you’re using? Cheers, Eugenio -- Juan Eugenio Iglesias http://www.jeiglesias.com From: "Fischl, Bruce R.,PHD" Date: Thursday, March 16, 2023 at 14:04 To: Freesurfer support list , "Iglesias Gonzalez, Juan E

Re: [Freesurfer] Question on EasyReg forward field

Correct! Switching the orders of the inputs will switch the assignment of the fwd and bak fields, which will otherwise be the same in both cases. Cheers, /Eugenio -- Juan Eugenio Iglesias http://www.jeiglesias.com From: on behalf of Codrin Mironiuc Reply-To: Freesurfer support list Date: Thu

Re: [Freesurfer] Question on easy reg

Hi again, Codrin. mri_easyreg currently does not support part to whole registration, unless that part covers most of the brain. Cheers, /Eugenio -- Juan Eugenio Iglesias http://www.jeiglesias.com From: on behalf of Codrin Mironiuc Reply-To: Freesurfer support list Date: Thursday, March 16

Re: [Freesurfer] Question on EasyReg package syntax

Dear Codrin, There was a bug incode, that caused mri_easyreg (and mri_synthseg, and mri_synthsr) to crash if absolute paths were not used. This is now fixed in the the development version. Cheers, /Eugenio -- Juan Eugenio Iglesias http://www.jeiglesias.com From: on behalf of Codrin Mironiuc

Re: [Freesurfer] EasyReg usage

Dear Fidel, This is really weird… that’s essentially the last step. I you eg didn’t have writing permissions, you’d get an error. Would it be possible to share the data, so I can try to reproduce the issue on my end? Cheers, /Eugenio -- Juan Eugenio Iglesias http://www.jeiglesias.com From: on

Re: [Freesurfer] Hypothalamus segmentation using hypothalamic subunits vs ScLimbic

Dear Asmin, The discrepancies arise from differences in anatomical protocols. You can look at the definitions in the corresponding papers and keep the one that adapts better to your needs. The results should be fairly highly correlated. Kind regards, Eugenio -- Juan Eugenio Iglesias http://www.j

Re: [Freesurfer] SynthSeg with CT images.

: Wednesday, March 8, 2023 at 13:56 To: Benjamin Billot Cc: "Iglesias Gonzalez, Juan E." , "freesurfer@nmr.mgh.harvard.edu" Subject: Re: SynthSeg with CT images. External Email - Use Caution Hi Benjamin: I tested with the clipping, and it works ok with a CT image. Since

Re: [Freesurfer] SynthSeg with CT images.

http://www.jeiglesias.com From: Gonzalo Rojas Costa Date: Wednesday, March 8, 2023 at 12:04 To: "freesurfer@nmr.mgh.harvard.edu" Cc: "Iglesias Gonzalez, Juan E." Subject: SynthSeg with CT images. External Email - Use Caution Hi: I tried SynthSeg using CT images

Re: [Freesurfer] mri_easyreg tool

Sorry for the late response, I went on vacation the very same day you posted your question. The floating image is the one you want to deform, and the reference image is the one you use as target for the registration /deformation. In other words: the deformed floating image should overlap with t

Re: [Freesurfer] segmenThalamicNuclei.sh exited with ERRORS

Thanks for the interest in our software! Could you please try running this command from the terminal? sudo apt-get install libncurses5 Cheers, /Eugenio -- Juan Eugenio Iglesias http://www.jeiglesias.com From: on behalf of behçet ayyıldız Reply-To: Freesurfer support list Date: Wednesday, Febru

Re: [Freesurfer] Skull stripping with external brainmask

Dear Narlon, I believe you can add -xmask [mask_volume_file] to your recon-all command. To generate such external mask, maybe you could use mri_synthseg with the --robust flag and binarize the output? Cheers, /Eugenio -- Juan Eugenio Iglesias http://www.jeiglesias.com From: on behalf of "Boa So

Re: [Freesurfer] Problem with quantifyHAsubregions.sh

: "Iglesias Gonzalez, Juan E." , "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] Problem with quantifyHAsubregions.sh External Email - Use Caution Dear Eugenio, Thank you for your kindly reply. Actually, I tried both options and neither worked. When I renamed

Re: [Freesurfer] Problem with quantifyHAsubregions.sh

Dear Georgina, Can you please send me the list of files (a screenshot is also fine) inside the mri directory of any of your subjects, please? Cheers, /Eugenio -- Juan Eugenio Iglesias http://www.jeiglesias.com From: on behalf of Georgina Angelopoulou Reply-To: Freesurfer support list Date:

Re: [Freesurfer] Hippocampal/Amygdala subfield segmentation error - Anterior Amygdala Area missing in FreeView

Thanks for the interest in our tool, Sarah! With the smallest nuclei, it is possible that nucleus X has non-zero probability for a bunch of voxels, but does not win any of those voxels (i.e., there’s another label with larger probability). If that happens, the volume will be non-zero (as you hav

Re: [Freesurfer] Any differences by Freesurfer version for hippocampal subfields and nuclei of the amygdala ?

Dear Anna, There’s 3 factors affecting the results: 1. Atlas: we haven’t changed that in ages. 2. Optimization in segmentation code: there’s tiny differences in there but as long as you’ve used the same version for every case, you should be good. 3. Version of FS used to process the subject. Thi

Re: [Freesurfer] Thalamic segmentation error

Dear Alan, How did you install the runtime? Did you follow the instructions in the wiki? Cheers, /Eugenio Juan Eugenio Iglesias www.jeiglesias.com On Oct 18, 2022, at 2:37 PM, Alan Francis mailto:alandarkene...@gmail.com>> wrote: External Email - Use Caution

Re: [Freesurfer] Thalamic nucleus segmentation 3D export

t; mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Iglesias Gonzalez, Juan E.,PHD mailto:jiglesiasgonza...@mgh.harvard.edu>> Sent: Saturday, September 24, 2022 8:09 PM To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Thalamic n

Re: [Freesurfer] SynthSR

Dear AJ, Thanks for the interest in our tool. Answers inline Can SynthSR be used on MRI scans of subjects with T2 lesions, such as MS? Yes! If yes, is their a way to save the masks of lesions that were Inpainted or their volume? Nope, sorry. For the output files, what are their image parameters

Re: [Freesurfer] Thalamic nucleus segmentation 3D export

Dear Angelique I’m not a 3DSlicer expert but you can extract the regions with mri_extract_region, turn them into stl meshes with mri_mc, and possibly smooth them a bit with mris_smooth Cheers, /E Juan Eugenio Iglesias http://www.jeiglesias.com On Sep 24, 2022, at 16:15, Paulk, Angelique C.,PHD

Re: [Freesurfer] Help - segmentHA_T1_long.sh "list of time points not found"

Dear Kimi, When you process the scans longitudinally with FreeSurfer, the file base-tps should be created in the subject directory of the template. Isn’t this the case? Cheers, /Eugenio Juan Eugenio Iglesias http://www.jeiglesias.com On 19 Sep 2022, at 01:02, Raikkonen Kimi mailto:akdaus

Re: [Freesurfer] transform amygdala mask from FS to native space

mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Iglesias Gonzalez, Juan E. mailto:jiglesiasgonza...@mgh.harvard.edu>> Sent: 16 August 2022 08:29 To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] transform amygdala mask from FS to native spac

Re: [Freesurfer] transform amygdala mask from FS to native space

is why I was confused and at a loss as to what else I could to do. Any suggestions? Thanks, Elizabeth From: mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of "Iglesias Gonzalez, Juan E." mailto:jiglesiasgonza...@mgh.harvard.edu>> Reply to: Freesurfer sup

Re: [Freesurfer] transform amygdala mask from FS to native space

Dear Elizabeth, You command looks good to me. Did you visualize lh_Amyg_native.mgz with colormap=lookup table? Cheers, /Eugenio Juan Eugenio Iglesias http://www.jeiglesias.com On Aug 14, 2022, at 18:58, Elizabeth Haris mailto:e.ha...@unsw.edu.au>> wrote: External Email - Use Caution H

Re: [Freesurfer] Thalamus Parcellation - HCP data

Dear Asa, Rather than resampling to 2mm and then applying a linear transform, I would first transform and then resample. Cheers, Juan Eugenio Iglesias www.jeiglesias.com On Aug 9, 2022, at 3:32 PM, Asa Borzabadi Farahani mailto:asa.borzabadifarah...@mail.mcgill.ca>

[Freesurfer] Postdoc position available at FS team (NIH BRAIN Initiative project)

Dear all, Prof. Fischl and I are looking for a postdoc to work on a multi-site, international project (18 institutions, 3 continents) sponsored by the NIH BRAIN Initiative. Details on the project, position, and application here: https://scholar.harvard.edu/iglesias/jobs Cheers, Juan Eugenio I

Re: [Freesurfer] Problem with hypothalamus subunits?

an Lab -- From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Iglesias Gonzalez, Juan E. mailto:jiglesiasgonza...@mgh.harvard.edu>> Sent: Thursday, July 28, 2022 11:28 AM To:

Re: [Freesurfer] Subregion Segmentation of thalamus for TRACULA

Dear Makenna (and rest of users) Thanks for spotting this bug, and for bearing with us while we transition to the new, Matlab-free code. Renaming should be fine for now but we’ll certainly fix this on our end ASAP. Kind regards, Juan Eugenio Iglesias http://www.jeiglesias.com On Jul 28, 2022,

Re: [Freesurfer] Problem with hypothalamus subunits?

Thanks for reporting this bug, Victor. I just fixed it. The fix will be propagated to the development version in the next couple of days but, if you want, you can keep using the version you’ve got by adding the flag --crop 1000 (where 1000 is a number bigger than your image size in any dimensio

Re: [Freesurfer] questions about ThalamicNuclei.sh, segmentHA_T1.sh, segmentBS.sh

Dear Wenjun, It’s perfectly fine. Just make sure to report the versions you used if you use the outputs to publish anything ;-) Cheers, Juan Eugenio Iglesias http://www.jeiglesias.com On 18 May 2022, at 23:42, Wenjun Huang mailto:wh2...@nyu.edu>> wrote: External Email - Use Caut

Re: [Freesurfer] Probabilistic atlas of human thalamic nuclei

Dear Asa, Thank you very much for the interest in our thalamic atlas. The atlas is defined as a tetrahedral mesh (not voxels) in its own average space. So there is no probabilistic map in MNI space. You could try segmenting your MNI template with FreeSurfer + the thalamic module and use that. B

Re: [Freesurfer] whole brain volume measures from SynthSeg+ ??

Dear Jason, Thank you very much for the interest in our tools. We understand that intracranial volume (ICV) is a crucial covariate in volumetric analysis and are working on incorporating it into SynthSeg (and SynthSeg+). The good news is that we have a prototype pretty much ready and it should

Re: [Freesurfer] [IMPORTANT MESSAGE] Subfields & MCR problems solved

? 2- Is the development version, or a beta version, already available for download? Best regards, Andrei Bieger PhD Candidate in Biochemistry UFRGS - Porto Alegre, Brazil Em sex., 8 de abr. de 2022 às 12:43, Iglesias Gonzalez, Juan E. mailto:jiglesiasgonza...@mgh.harvard.edu>> escreveu: PS: t

Re: [Freesurfer] [IMPORTANT MESSAGE] Subfields & MCR problems solved

n in FreeSurfer 7.1 version? Thank you for reporting this issue. with kind regards, -- Otília C.d'Almeida A 2022-04-08 16:42, Iglesias Gonzalez, Juan E. escreveu: PS: these changes have happened in the development version, and will be incorporated into the next release. Juan Eugenio

Re: [Freesurfer] [IMPORTANT MESSAGE] Subfields & MCR problems solved

PS: these changes have happened in the development version, and will be incorporated into the next release. Juan Eugenio Iglesias http://www.jeiglesias.com On Apr 8, 2022, at 11:25, Iglesias Gonzalez, Juan E. mailto:jiglesiasgonza...@mgh.harvard.edu>> wrote: Dear all, We have recently

[Freesurfer] [IMPORTANT MESSAGE] Subfields & MCR problems solved

Dear all, We have recently fixed two problems in the subfield modules using the Matlab runtime: 1. We have moved on from MatlabR2014b to MatlabR2019b, which enables users to run the code in more modern versions of Mac OS. 2. A bug in the the longitudinal hippocampal subfield (& amygdala) segme

Re: [Freesurfer] MCRv84 issue on Freesurfer 7.2.0 on MacOS Monterey 12.2

- Dementia Research Centre Lee Kong Chian School of Medicine Nanyang Technological University, Singapore From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Iglesias Gonzalez, Ju

Re: [Freesurfer] MCRv84 issue on Freesurfer 7.2.0 on MacOS Monterey 12.2

Dear Ashwati, What are the current contents of /Applications/freesurfer/7.2.0/MCRv84/? It should be something like this: MCR_license.txt bin extern java polyspace runtime sys VersionInfo.xml derived help mcr remote settings toolbox appdata etc interprocess patents.txt resources src trademarks.tx

Re: [Freesurfer] mri_segment_hypothalamic_subunits error: Illegal instruction 4

Dear Alice, Can you please send us your full command line and output? Cheers, /E Juan Eugenio Iglesias http://www.jeiglesias.com On Mar 23, 2022, at 10:41, Alice Tao mailto:ajt4...@med.cornell.edu>> wrote: External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to

Re: [Freesurfer] hypothalamic nuclei question

Dear Niels, Would it be possible to share T1w_acpc_dc_restore_1mm.nii.gz with us so we can try on our end? Cheers, Eugenio Juan Eugenio Iglesias http://www.jeiglesias.com On 9 Mar 2022, at 09:16, Niels Janssen mailto:njans...@ull.edu.es>> wrote: External Email - Use Caution I

Re: [Freesurfer] Hippocampal segmentation - data processed in different fs version

Yes! As long as you explain it clearly in whatever paper you may write with the results ;-) Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com On Jan 10, 2022, at 23:28, Katarina Vulić mailto:vulic.katari...@gmail.com>> wrote:

Re: [Freesurfer] Hippocampal subfield data

gh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Iglesias Gonzalez, Juan E. mailto:jiglesiasgonza...@mgh.harvard.edu>> Sent: Friday, December 10, 2021 11:22 AM To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] H

Re: [Freesurfer] Hippocampal subfield data

Dear Lisa, Is it possible that you’re running out of RAM memory? How much RAM do you have available? Cheers, Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com On Dec 10, 2021, at 14:19, Taylor, Lisa mailto:ltayl...@hs.uci.edu>> w

Re: [Freesurfer] Hippocampal Subfield data not populating

Dear Lisa, It’s difficult to tell without seeing the logs, but it seems like you ran out of RAM memory? Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com On Dec 8, 2021, at 15:57, Taylor, Lisa mailto:ltayl...@hs.uci.edu

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