Re: [Freesurfer] Reposting TRACULA trac-all -prep finishes with errors

Hi Bryna - I see that the error occurs in the corticospinal tract. Any change the top or bottom of the brain is truncated in this subject's scan? Anastasia. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Goeckner, Bryna Sent: Thursday, March 17, 202

Re: [Freesurfer] Trac-all -prep -c error

Hi Elizabeth - This was a tricky one. My guess is that there's an error in what comes right after the mri_binarize command, but the error doesn't get written into the log file and is only shown on your terminal (I'm going to fix the error logging aspect of this). If my guess is right, the error

Re: [Freesurfer] Tracula 6.0 or 7.2 - sub in alternative metric maps

abase Specialist Medical University of South Carolina Department of Neurology Center for Biomedical Imaging 135 Cannon St. CS101 Charleston, SC 29425 From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia

[Freesurfer] Advanced fMRI Applications Postdoctoral Fellow Position at Carle Health

Passing along this opening at the Carle Illinois Advanced Imaging Center on behalf of Dr. Sheeba Arnold Anteraper: https://www.ismrm.org/jobs/j07799.pdf Anastasia. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard

Re: [Freesurfer] Tracula 6.0 or 7.2 - sub in alternative metric maps

Of Yendiki, Anastasia Sent: Thursday, March 17, 2022 3:50 PM To: Freesurfer support list Subject: Re: [Freesurfer] Tracula 6.0 or 7.2 - sub in alternative metric maps CAUTION: External Hi Kayti - About the orientation, you can put your other maps in the same orientation by running the

Re: [Freesurfer] bedpostx error inside trac-all

Hi Amy - This will have the same effect as running it locally. All the the *_mgh version does is submit each slice as a separate job on a certain type of cluster. If you run trac-all with --jobs , it will save a text file with the commands that would've been submitted as jobs, instead of actual

Re: [Freesurfer] bedpostx error inside trac-all

trac_all_bed_call above with something like: bedpost -n $nstick -model 1 /path/to/subjects/dmri/directory Would that work? Sorry if I am misunderstanding. Thanks so much for your help! Thanks, Amy From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Yendiki, Anastasia Sent: W

Re: [Freesurfer] meanings of trac-all outputs

Hi Qi - nodif_brain_mask is just a symbolic link to the brain mask that's used by bedpostx. By default, that's the mask created from the anatomical segmentation and mapped to DWI space (aparc+aseg_mask) and not the one created from the DWIs with bet (lowb_brain_mask). You could change that behav

Re: [Freesurfer] TRACULA question

Hi Gonzalo - The input to TRACULA can be any file that can be converted to nifti by mri_convert. See: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula#line-156 Anastasia. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Gonzalo Rojas Costa

Re: [Freesurfer] "B0 distortion correction with reverse-polarity DWIs"

Hi Gonzalo - The different options for correction are also described in the tutorial: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula#line-234 Anastasia. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Gonzalo Rojas Costa Sent: Thursday,

Re: [Freesurfer] An estimated date for FreeSurfer 7.3 release

Hi King-Wai - I maintain that list of TRACULA features that are in the dev version now and therefore will definitely be included in 7.3, but that doesn't necessarily mean that 7.3 is imminent. I'd use the 7.2 version for now, or the dev version if you're specifically interested in what's on that

Re: [Freesurfer] TRACULA -bedp parallel processing

You run them in that order. First the pre, then the parallel, then the post. You can queue them that way, so that the parallel jobs wait for the pre to finish, and the post waits for all the parallel jobs to finish. From: freesurfer-boun...@nmr.mgh.harvard.edu o

Re: [Freesurfer] TRACULA -bedp parallel processing

What kind of cluster are you running the parallel processes on? From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Salar Dini, Elaheh Sent: Friday, June 3, 2022 7:44 PM To: Freesurfer support list Subject: Re: [Freesurfer] TRACULA -bedp parallel process

Re: [Freesurfer] TRACULA -bedp parallel processing

Hi Ela - Which version of FSL are you using? Anastasia. From: Salar Dini, Elaheh Sent: Monday, June 6, 2022 5:26 PM To: Yendiki, Anastasia ; Freesurfer support list Subject: Re: TRACULA -bedp parallel processing External Email - Use Caution Thanks

Re: [Freesurfer] TRACULA -bedp parallel processing

What if you create the directory (that shows up in the "not a directory" error)? From: Salar Dini, Elaheh Sent: Tuesday, June 7, 2022 11:46 AM To: Yendiki, Anastasia ; Freesurfer support list Subject: Re: TRACULA -bedp parallel processing

Re: [Freesurfer] traculina errors in -prep process

Hi Emmanuel - the infant version is under construction at the moment, which is why it is not documented on the website. Best, Anastasia. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Emmanuel Rodríguez Silva Sent: Monday, June 6, 2022 12:28 PM To:

Re: [Freesurfer] Trac-all error assistance

Hi Emmanuel - Not sure if you saw my earlier response, but the infant stream is under construction and not currently supported. Anastasia. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Emmanuel Rodríguez Silva Sent: Monday, June 13, 2022 12:39 PM T

Re: [Freesurfer] TRACULA -bedp parallel processing

Unfortunately it's not something we've been able to replicate here ? From: Salar Dini, Elaheh Sent: Tuesday, June 14, 2022 8:53 PM To: Yendiki, Anastasia ; Freesurfer support list Subject: Re: TRACULA -bedp parallel processing External E

Re: [Freesurfer] about the error on running TRACULA using tutorial data

Hi Xin - Please see the note in the blue box at the top of the tutorial pages. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula Anastasia. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Xin Qi Sent: Tuesday, June 14, 2022 11:54 AM To: Fre

Re: [Freesurfer] about the error on running TRACULA using tutorial data

The tutorial data are obsolete, from old versions of TRACULA (FreeSurfer versions 7.1 or older). From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Xin Qi Sent: Friday, June 17, 2022 5:46 AM To: Freesurfer support list Subject: Re: [Freesurfer] about th

Re: [Freesurfer] trac-all -prep -c ERROR

Any chance that part of the left CST is truncated in this one subject? E.g., if the top part of the brain was outside the field of view? Anastasia. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Salar Dini, Elaheh Sent: Wednesday, June 29, 2022 11:3

Re: [Freesurfer] trac-all -prep -c ERROR

gle.com%2Ffile%2Fd%2F1twW57_d5f1G32GtcxYp-A2u2OsnQF3kF%2Fview%3Fusp%3Dsharing> Moreover, it is worth mentioning that this specific subject had profound global atrophy with diagnosis of Alzheimer's. As always, I appreciate your time and help. Kind regards, Ela Yendiki, Anastasia<

Re: [Freesurfer] trac-all -prep -c ERROR

XhwXhBNxFn7nI-I74hjqFmpZsF8mA4qlZouKMphk5t0qqcAKNcUjlISrWw3lxT_thARtkXppnJtpXaAU_6HUa3jcMs4Rjb4q7eJYv4jInujKXvt-OTVCGaGH7L5CAzEi3vhLtLwE1xKy4Hn046eARCCbdUuFPK4RiHKeapu1gceaxc/https%3A%2F%2Fdrive.google.com%2Fdrive%2Ffolders%2F1pkss2G7AYmlrCWYPVItnctl4W7H_OV7W%3Fusp%3Dsharing> Thank you, Ela Yendiki, Anastasia<https://secure-web.cis

[Freesurfer] Call for applications: LINC fellows program 2024-25

Dear FreeSurfers - Our BRAIN Initiative funded center for Large-scale Imaging of Neural Circuits (LINC) is seeking to name 2 undergrads and 2 postdocs from diverse backgrounds and/or under-resourced institutions “LINC fellows” for 2024-25. The applicants are ex

Re: [Freesurfer] [TRACULA] Auto-BIDS Config Variables Question

Hi Steven - Indeed you are right that the values from your scanner protocol are the ones to use. In this case it sounds like what it finds in the json files does not agree with the scanner protocol, and this is good to know. I will look into this. Glad to hear it worked well otherwise! Anastasi

Re: [Freesurfer] Tracula error in path construction

Could be that you reached a memory limit? If the same analysis runs fine on your computer, then it's probably a cloud issue, not a TRACULA issue. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Shanika Jayakody Sent: Thursday, July 21, 2022 3:58 PM To

Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

Hi King-Wai - You are not supposed to run trac-preproc directly. Run trac-all -c configfile, like before. Anastasia. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of kingwai@gmail.com Sent: Monday, July 25, 2022 2:11 PM To: 'Freesurfer support li

Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Yendiki, Anastasia Sent: Monday, August 1, 2022 12:03 AM To: 'Freesurfer support list' Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3 Hi King-Wai - You are not supposed to run trac-preproc directly. Run trac-all -c configfile,

Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

placing the original one with the modified one Doug sent, trac-all -prep -c config.file runs w/o problem. Thanks, King-Wai From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Yendiki, Anastasia Sent: Monday, August 1, 2022 12:15 AM To: 'Freesurfer support list' Subjec

Re: [Freesurfer] TRACULA in FreeSurfer version 7.3

From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Yendiki, Anastasia Sent: Monday, August 1, 2022 12:15 AM To: 'Freesurfer support list' Subject: Re: [Freesurfer] TRACULA in FreeSurfer version 7.3 Indeed. Doug sent you a modified version of trac-preproc, which is a script that's

Re: [Freesurfer] Tracula error in path construction

ted Oshadi From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Yendiki, Anastasia Sent: Thursday, July 21, 2022 4:30 PM To: Freesurfer support list Subject: Re: [Freesurfer] Tracula error in path construction Could be that you reached a memory limit? I

Re: [Freesurfer] Tracula Config file.

Hi Alan - dcmroot is the root directory under which the dicom files are saved. It's actually optional. In your case, either of the following will have the same, correct effect: set dcmroot = /home/afrancis/Imaging set dcmlist = (109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz) OR set dcmlist = (/h

Re: [Freesurfer] Tracula Config file.

aution Good morning Anastasia - I made the changes you suggested and removed "extraneous" commands. But the error message still persists. Could you please shed some light on this? Attached - latest RC file. The error message is : unmatched ' " ' Thank you Alan On

Re: [Freesurfer] Tracula Config file.

mailto:alandarkene...@gmail.com>> wrote: External Email - Use Caution Good morning Anastasia - I made the changes you suggested and removed "extraneous" commands. But the error message still persists. Could you please shed some light on this? Attached - latest RC file.

Re: [Freesurfer] segmentation of thalamic nuclei: possibility of generating connectome

Hi Lauren - What you want is to replace the thalamus labels in aparc+aseg.mgz with the thalamic nuclei labels. This is a bit less straightforward than it may first seem because the outer boundaries of the thalamus in the two segmentations are not necessarily the same. However, we've implemented

Re: [Freesurfer] Tracula - Preproc

Yes that's from FSL. It's needs to be in $FSLDIR. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Alan Francis Sent: Thursday, August 11, 2022 3:30 PM To: Freesurfer Subject: [Freesurfer] Tracula - Preproc External Email - Use Caution Hi An

Re: [Freesurfer] Tracula - Preproc

sia said, bet is part of FSL. If you don’t have it installed already, you need to install FSL. Best, King-Wai From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Yendiki, Anas

Re: [Freesurfer] Tracula - Preproc

already, you need to install FSL. Best, King-Wai From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Yendiki, Anastasia Sent: Thursday, August 11, 2022 3:42 PM T

Re: [Freesurfer] Tracula - Preproc

n Fri, Aug 12, 2022 at 5:54 PM Alan Francis mailto:alandarkene...@gmail.com>> wrote: External Email - Use Caution Hi Anastasia : I installed ANTS and tried this set ANTSPATH = /home/afrancis/Imaging/ANTs but it did not work. Is there a different set path? Thanks, Alan On Fr

Re: [Freesurfer] TRACULA - custom tracts and path labelling

Hi Liliana - Please see here for info on TRACULA and the tracts included so far: https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula https://dmri.mgh.harvard.edu/tract-atlas/ We do not include the IFOF because it is controversial. Many anatomists believe that it is an artifact of tractography metho

Re: [Freesurfer] TRACULA - preprocessing error

Hi Liliana - It looks like you are using a very old FreeSurfer build (from 2016) and an old TRACULA configuration file. You should update to the latest version of FreeSurfer and follow the instructions on the wiki for how to set up TRACULA. We have many more tracts now and the naming has changed

Re: [Freesurfer] primary diffusion direction & surface normal vector

The principal eigenvector of the tensor, which is the primary direction of diffusion, is V1. The magnitude of that vector is L1, i.e., AD. The normal vector of a surface is a vector perpendicular to the tangent plane to the surface at a certain point. It's a characteristic of a surface, rather

Re: [Freesurfer] primary diffusion direction & surface normal vector

& surface normal vector External Email - Use Caution Hi Anastasia, Thanks for your prompt reply. So can the normal vector of a surface be found in the outputs of recon-all? Best, Qi On Sat, Aug 20, 2022 at 8:28 AM Yendiki, Anastasia mailto:ayend...@mgh.harvard.edu>>

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