Re: [Freesurfer] mri_synthmorph regularisation

External Email - Use Caution Hi Malte Thanks. The Singularity version worked well! Simon From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Hoffmann, Malte,PhD Sent: 21 October 2024 6:38 PM To: freesurfer@nmr.mgh.harvard.edu Subject

[Freesurfer] mri_synthmorph regularisation

External Email - Use Caution Dear all I tried to use change the regularisation parameter of mri_synthmorph using -s option in Freesurfer 7.4.1 but this option does not seem implemented. Is there a way to reduce the amount of regularisation? Thanks for your help, Simon

[Freesurfer] Freesurfer v. 7.3.2 careg error

and then it completed without error. Maybe this is intentional and there is another recommended way to do this multistage pipeline. Thanks, Simon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman

[Freesurfer] VM file password

External Email - Use Caution Dear Mailinglist, I would like to request the password for the vmware gz file. I was referred to this mailing list. Could you send me the password? I already have a license file. Best regards, Simon Kern -- [1570451663583] Simon Kern MSc

[Freesurfer] Question about freesurfer default settings.

othed?" I have tried to look through the archives and freesurfer papers but dont see anything that directly addresses these aspects, and some help would be appreciated. Thank you! Katrina -- Katrina Simon ___ Freesurfer mailing list

[Freesurfer] unziping problems

in it. Is there something I am missing ? If so, please enlight me. Have a good day Dr Simon TAIB Centre Régional Psychotraumatisme Occitanie - CHU de Purpan INSERM U1214 ToNIC - Université Toulouse 3 Ce message et les éventuelles pièces jointes sont confidentie

[Freesurfer] SAMSEG seg output contains holes

Simon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] aparc regions misclassified

External Email - Use Caution Hi Bruce, It's freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c I uploaded it I think. Thanks, Simon -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Bruce Fischl Sent: 11 December 2018 16:

Re: [Freesurfer] QA_tools do not find v.mgz

External Email - Use Caution Ah, all the ones with v.mgz used the bigventricles option… Must be something to do with that. Simon From: Simon Jones Sent: 13 November 2018 21:35 To: freesurfer@nmr.mgh.harvard.edu Subject: QA_tools do not find v.mgz I have run some

[Freesurfer] QA_tools do not find v.mgz

pages. I don’t think I have been aware of this file previously. Why are many subjects missing this file and should I worry about it. Thanks for your help, Simon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] paradigm file for functional block design

in advance! Sincerely, Simon Desch Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c _ Simon Desch Department of Cognitive and Clinical Neuroscience Central Institute of Mental Health Square J5, 68159 Mannheim Germany Phone

[Freesurfer] structure of project directory for longitudinal functional analysis

esurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c _____ Simon Desch Department of Cognitive and Clinical Neuroscience Central Institute of Mental Health Square J5, 68159 Mannheim Germany Phone: +49 (0

Re: [Freesurfer] Question regarding exporting subcortical segmentation to

Hi Bruce Thanks, mri_binarize works great! Best, Joe Dr. Dipl.-Psych. Joe Simon Universitätsklinikum Heidelberg Klinik für Allgemeine Innere Medizin und Psychosomatik Im Neuenheimer Feld 410 69120 Tel.: ++49(0)6221-56-38667

[Freesurfer] Question regarding exporting subcortical segmentation to .nii ROIs for further analysis in SPM

subcortical structure. What would be the easiest way to do this? Any help is appreciated. Thanks a lot! Best regards, Joe Dr. Dipl.-Psych. Joe Simon Universitätsklinikum Heidelberg Klinik für Allgemeine Innere Medizin und

Re: [Freesurfer] TRACULA -path issue

-prior by itself and I still had an error. Any thoughts would be appreciated, otherwise I am trying to run it again with more memory allocation and will see how it goes. Best Katrina On Jun 8, 2017, at 10:07 AM, Simon, Katrina R mailto:katsi...@sas.upenn.edu>> wrote: Hi Anastasia-

Re: [Freesurfer] TRACULA -path issue

Hi Anastasia- it is attached- one note is that it is actually a .txt file but i just copied and pasted it into an RTF from our group’s cluster for this purpose. On Jun 7, 2017, at 4:43 PM, Simon, Katrina R mailto:katsi...@sas.upenn.edu>> wrote: Hi Anastasia, when running -prior, I am g

Re: [Freesurfer] TRACULA -path issue

t, a.y From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Simon, Katrina R [katsi...@sas.upenn.edu<mailto:katsi...@sas.upenn.edu>]

[Freesurfer] TRACULA -path issue

same issue for each one. Any help would be appreciated. Thanks, Katrina Katrina Simon Research Specialist- Mackey Lab University of Pennsylvania Department of Psychology katsi...@sas.upenn.edu<mailto:katsi...@sas.upenn.edu> (215) 57

[Freesurfer] Question regarding errors with TRACULA pre-processing

Hi, I keep trying to run TRACULA and getting the following errors: ERROR: run list is longer than subject list and : Command not found. : Command not found. : Command not found. Badly placed (. **My configuration file is below: *** # FreeSurfer SUBJECTS_DIR # T1 images and FreeSurfer segmen

[Freesurfer] nu_correct error (FS 6 beta)

rmination status=768) ERROR: nu_correct The directory exists, and there are several other files written here ("nu0.mnc", "nu1_corr.mnc", "nu1_mask.mnc", "nu1_residue.mnc" and "nu1_temp.mnc") so it doesn't appear to be having an issue with wr

[Freesurfer] Tracula stats COR-.info does not exist

ng to an image in the cvs_avg35 directory and the stats seem to complete without error. Is that the right thing to do? Thanks for your help, Simon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvar

Re: [Freesurfer] Sulcal depth units (Simon Vandekar)

still unclear on what the units are. They are too small to be millimeters. Given other published measurements of sulcal depth I think they might be in centimeters, but can you confirm? Thanks again, Simon >Hi Simon > >I just took a look at the code and I believe that we make it 0 median

Re: [Freesurfer] Sulcal depth units

Hi Bruce, I think that unnormalized sulcal depth would be useful. However, I am also curious what the units are in the standard output, because they appear to not be z-score standardized in each hemisphere. Thanks again, Simon >H I Simon >Do you need the unnormalized sulc? It would be

Re: [Freesurfer] Sulcal depth units

0% 25% 50% 75% 100% -1.72503 -0.42128 -0.03963 0.40072 1.80980 Thanks again, Simon Hi Simon they are originally mm, but I believe we z-score normalize them so that the sulc file is 0 mean and unit variance. cheers Bruce On Wed, 21 Oct 2015, Simon Vandekar wrote:

[Freesurfer] Sulcal depth units

I am still unsure of the exact units of sulcal depth. Are the units for sulcal depth in mm or are they in arbitrary units? Thanks in advance, Simon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/

[Freesurfer] Tracula stats COR-.info does not exist

using tracula.update.centos4_x86_64.5.3.2014_05_26 in freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0. I performed all tracula processing steps before stats without the tracula.update.centos4_x86_64.5.3.2014_05_26, and then added the update to perform the stat step. Thanks for your help, Simon lh.cst_AS.avg33_cvs_fl

[Freesurfer] Custom parcellation for HCP data

hemisphere to create the random parcellation volume. 9. Overlay the random parcellation volume on the template volume. See attached screenshot.jpeg showing the misalignment between the random parcellation volume and the template volume. Kind regards, Simon Baker Brain & Mental Health Labora

Re: [Freesurfer] Surface based smoothing

Hello all, I am trying to determine the neighbors and weights used in the smoothing implemented in the surface based smooth used by freesurfer (e.g. as called by mris_preproc). Can anyone point me to the code that performs the surface based smoothing in freesurfer? Thanks in advance, Simon

[Freesurfer] PhD position: Neuroimaging (MRI) in Epilepsy, University of Liverpool

Nov 2013 17:00:00 GMT A PhD Studentship is available in the Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine at the University of Liverpool, supervised jointly between Dr. Simon Keller and Professor Tony Marson. This is an exciting project that invo

[Freesurfer] entorhinal ex vivo > stats 2 table?

le or aparcstats2table? mris_anatomical_stats obviously gets the values out for individuals - but with a sample at n>200 I'd obviously rather batch this. Thanks in advance, Simon. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mg

Re: [Freesurfer] Using SPM transformation matrices as initial guess in talairach_avi

the larger flip angle FLASH. I will follow your both suggestions, i.e. try to process the FLASH and also the pre-realinged R1 maps in case freesurfer registration step fails. Cheers Simon Von: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Gesendet: Donnerstag

Re: [Freesurfer] Using SPM transformation matrices as initial guess in talairach_avi

mations). As my doctorate fellow sees himself manually segmenting all the subcortical structurs any help would be greatly appreciated -:) Thanks, Simon Baudrexel Brain Imaging Center Goethe University Frankfurt Von: Snyder, Avi [a...@npg.wustl.edu] Gesendet:

Re: [Freesurfer] Using SPM transformation matrices as initial guess in talairach_avi

n the other hand works pretty well on both T1 and FLASH images (probably because of using header origin information - which was set to the anterior commissure- as first guess in the registration). Thanks Simon Von: Bruce Fischl [fis...@nmr.mgh.harvar

[Freesurfer] Using SPM transformation matrices as initial guess in talairach_avi

so did not improve the results (I think a template made from skull-stripped images has to be used in that case) Any help would be much appreciated Regards, Simon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.e

[Freesurfer] best orientation of t1 images for recon-all

sufficient to change only the header information? Is it advisable to reorient the anatomical images manually to AC-PC before running recon-all? Thanks in advance for your help, Simon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] extract aparc.anot area

desired areas from the “aparc.annot.a2005s” files and how to modify them manually? Thanks Grégory SIMON ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Re: Freesurfer Digest, Vol 47, Issue 2

Any tips regarding how to do the visual inspection, ie what to look at, and what to look for? simon On 2 Jan 2008, at 11:05PM, Bruce Fischl wrote: your concern isn't misplaced. We *always* visually inspect every dataset. It's just that things work so frequently now that we don&#

[Freesurfer] Re: Freesurfer Digest, Vol 47, Issue 2

some independent checking, are there a couple of simple things (later reconstructions) that can be checked that indicate whether all is fine, or whether it is necessary to go back and check systematically each of the various stages documented on the wiki pages? simon Date: Wed, 2 Jan 2008

Re: [Freesurfer] using BET prior to recon-all?

l before starting to dig deep into other things? simon On 14 Dec 2007, at 09:40, Martin Kavec wrote: In my experience, the FreeSurfer's brain extraction works better than the BET. Although, now with an option of iterative BET in the latest FSL, the outcomes are much better than before.

[Freesurfer] using BET prior to recon-all?

pped brain: mri_watershed -brain_atlas /Applications/freesurfer/average/ RB_all_withskull_2007-08-08.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Does this suggest that I either should not try the BET trick or that if I do that I should make some modifications to the recon-all script

[Freesurfer] convert xfm to dat?

Hello I am using fsfast to perform a retinotopy analysis. The initial stages are working well, however when I come to register my low-resolution functional scans to my high-resolution anatomical data using spmregister-sess I get a poor regestration which is very time-consuming to correct wit