[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] 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>>

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] 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] 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 - 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 - 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

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

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] 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 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] 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.

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 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 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 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

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

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 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] 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] 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

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

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] 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] 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] 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] 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] 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] 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] 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 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

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] 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] "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] 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] 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] 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] 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] 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

[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

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

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] 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] error with trac-all -prep in FS7.2 tracula

Hi Jim - Thanks for pointing this out. I'll make sure to add $ANTSPATH before every ants command. In the meantime, if you include $ANTSPATH in your own Unix path, this should be enough for it to work. Best, Anastasia. From: freesurfer-boun...@nmr.mgh.harvard.edu

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

Hi Bryna - Any chance you can attach your config file and trac-all.log to your message here? These are just text files so they should be pretty light. Thanks, Anastasia. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Goeckner, Bryna Sent: Tuesday,

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

Hi Kayti - Yes, there is a way to get stats from other maps, in 7.2. We just haven't had a chance to document it yet 🙂 If you look in your trac-all.log or trac-all.cmd file, you'll find the dmri_pathstats command lines that produce the stats. You can use a modified version of those commands to

Re: [Freesurfer] TRACULA longitudinal - weird tracts

Hi Donovan - That's interesting, is there a way you can share the cross and long dirs of this subject with me? The data look good based on the cross tracts, so I suspect there might be an issue with a registration or other step that comes before the tract reconstruction, and that affects only t

Re: [Freesurfer] Tracula -prep error: cannot stat dwi_orig_las.1.bvecs

ink> On Thu, Jan 20, 2022 at 6:00 AM Yendiki, Anastasia mailto:ayend...@mgh.harvard.edu>> wrote: Hi Ioannis - Any chance that you're running into this previously reported (and addressed) problem? MailScanner has detected a possible fraud attempt from "secure-web.cisco.co

Re: [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized

bility for mri_glmfit-sim). I would greatly appreciate for your further clarifications. Thank you so much for your help. Best regards, Taka On Thu, Jan 20, 2022 at 1:09 PM Yendiki, Anastasia mailto:ayend...@mgh.harvard.edu>> wrote: Hi Taka - Does it work when you remove the "--1d&q

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

ror setting the registration method as bbregister but we get error when we change it to Flirt. This is at least true for the freesurfer 7.2.0 that we installed on our server using freesurfer-linux-centos7_x86_64-7.2.0.tar.gz package. My best wishesm Ela From: Yendiki, Anastasia<https://se

Re: [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized

Hi Taka - Does it work when you remove the "--1d" from the command line? I think that must be an error in the documentation. Anastasia. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Tarumi Takashi Sent: Wednesday, January 12, 2022 7:04 PM To: frees

Re: [Freesurfer] Tracula -prep error: cannot stat dwi_orig_las.1.bvecs

Hi Ioannis - Any chance that you're running into this previously reported (and addressed) problem? https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg71427.html Anastasia. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of John Pap Sent: Sun

Re: [Freesurfer] TRACULA Question

Hi Ela - When you overlay the aparc+aseg from 6.0 and the one from 7.2, is there a notable difference? Is there any chance that the brain is cut off? The error happened in the anterior commissure, that's a tract that does goes fairly close to the ventral surface of the brain, and in the part of

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

alarming)? Thank you for your time and constant help, Ela ________ From: Yendiki, Anastasia Sent: Monday, January 3, 2022 To: elaheh.salard...@yale.edu Subject: Trac-all -prep -c error Hi Ela - Is there a specific reason why you ar

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

I ask you to check if my configuration file is correct? And if the attached trac-all.log file looks good (not alarming)? Thank you for your time and constant help, Ela ______

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

Hi Ela - Is there a specific reason why you are not using the default method for dMRI-to-T1 registration (bbregister, a.k.a. boundary-based registration in the config file)? Anastasia. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Salar Dini, Elaheh

Re: [Freesurfer] Trac-all -Prep -C Error

Hi Elizabeth - If you're using launchpad, just switch to the dev version. It has the latest bug fixes. Happy new year! Anastasia. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Kaplan, Elizabeth Sent: Friday, December 31, 2021 1:56 PM To: freesurfer

Re: [Freesurfer] Tracula error

00 -0.59.1168 -0. 0.5000 -0.60.3009 -0. -0. 0.500037.0859 -0. -0. -0. 1. On Dec 14, 2021, at 12:50 PM, Yendiki, Anastasia mailto:ayend...@mgh.harvard.edu>> wrote: Is there a dmri/data.ni

Re: [Freesurfer] trac-all -prep error

e version of freesurfer is 7.2.0 and the installed package is freesurfer-linux-centos7_x86_64-7.2.0.tar.gz. The installed fsl version is 6.0.5.1 . Thank you as always. Kindly, Ela From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Yendiki, Anas

Re: [Freesurfer] Tracula error

How much space would I need to run this? Thanks, Mona On Dec 14, 2021, at 12:40 PM, Yendiki, Anastasia mailto:ayend...@mgh.harvard.edu>> wrote: Any chance you're low on disk space? From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:f

Re: [Freesurfer] Tracula error

slslice ${subjdir}/data /usr/pubsw/packages/fsl/6.0.4/bin/bedpostx_preproc.sh: line 78: 9837 Illegal instruction (core dumped) ${FSLDIR}/bin/fslslice ${subjdir}/nodif_brain_mask On Dec 8, 2021, at 6:37 PM, Yendiki, Anastasia mailto:ayend...@mgh.harvard.edu>> wrote: Hi Mona - Here's h

Re: [Freesurfer] Tracula error

legal instruction (core dumped) ${FSLDIR}/bin/fslslice ${subjdir}/nodif_brain_mask On Dec 8, 2021, at 6:37 PM, Yendiki, Anastasia mailto:ayend...@mgh.harvard.edu>> wrote: Hi Mona - Here's how you add something to your Unix path: https://unix.stackexchange.com/questions/3809/how-can-

Re: [Freesurfer] Fieldmap Images in Nifti Format

Hi Elizabeth - From your log file, I see that you're using FreeSurfer 6. Please use the latest version (7.2), as TRACULA has undergone a drastic overhaul in this version. The TRACULA tutorials and documentation on the wiki apply to this new version. To use field maps, you need one more acquisit

Re: [Freesurfer] trac-all -prep error

Hi Ela - Do you know what phase-encode direction your DWIs were collected with (e.g. AP, PA, LR, etc.)? Then add it to the config file like this: "set pedir = (AP)" Otherwise, if your data are stored in BIDS format, there's a new script that will figure all this out and generate the configurati

[Freesurfer] auto-configure TRACULA for BIDS data

Dear FreeSurfers - There's a new script in the development version called dmri_bids_config. You can get it here: https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/dmri_bids_config There is documentation here: https://surfer.nmr.mgh.harvard.edu/fswiki/dmri_bids_config It will pa

Re: [Freesurfer] Tracula error

w/packages/ANTS/2.3.4/bin to the .csh file which has all the TRACULA configuration info, and also to the bash script that I’m running the trac-all from: export ANTSPATH=/usr/pubsw/packages/ANTS/2.3.4/bin Is there anything else I should do? Thanks, Mona On Dec 6, 2021, at 10:44 AM, Yendiki,

Re: [Freesurfer] Tracula error

Hi Mona - You need to add the location of the ANTs executables to your path. Best, Anastasia. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Nasiriavanaki, Zahra,M.D. Sent: Sunday, December 5, 2021 12:21 PM To: freesurfer@nmr.mgh.harvard.edu Subjec

Re: [Freesurfer] follow-up on trac-all -prep -c error

Hi Ela - From the log file it looks like it fails when it tries to do the eddy-current correction, because it can't find this file: /pet/apps/fsl6.0/fslpython/envs/fslpython/lib/python3.7/site-packages/mkl/../../../libmkl_core.so I'd check with your sysadmin to see if FSL was installed properly

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

Hi Ela - The example config file that you used is from the old version, not the new version. That's why the old version doesn't give you an error and the new one does. Take the example config file from the new version (in $FREESURFER_HOME/bin/), then adapt it accordingly for your data. This wik

Re: [Freesurfer] TRACULA error

Hi Stephanie - Please send along your configuration file and the log file from scripts/trac-all.log. It's hard to guess just by seeing the error message. Thanks! Anastasia. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Stephanie Otto Sent: Thursda

Re: [Freesurfer] trac-all -prep error

You're running the old version, you should install 7.2 🙂 From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Arman Avesta Sent: Wednesday, December 1, 2021 10:35 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] trac-all -prep error Ex

Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file

nal Email - Use Caution Dear Anastasia cat $FSLDIR/etc/fslversion reported 6.0.5.1:57b01774 I guess its the newest version available Thanks Jürgen Am 24.11.2021 um 15:53 schrieb Yendiki, Anastasia mailto:ayend...@mgh.harvard.edu>>: Hi Jürgen - Can you check what's in this fi

Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file

r FSL commands. Best Jürgen Am 24.11.2021 um 01:20 schrieb Yendiki, Anastasia mailto:ayend...@mgh.harvard.edu>>: Hi Jürgen - What's your $FSLDIR set to? Anastasia. From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@

Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file

le possible to run bedpostx_mgh also locally or do we have to run bedpostx directly as suggested in the link? Best Jürgen Am 23.11.2021 um 01:14 schrieb Yendiki, Anastasia mailto:ayend...@mgh.harvard.edu>>: Ah yes, I did say that this would be feasible in 7.2, before 7.2 came out �� One

Re: [Freesurfer] Converting .trk files in mini space to nifti using dorm_trk2trk

From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Yendiki, Anastasia Sent: Tuesday, November 23, 2021 5:46 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Converting .trk files in mini space to nifti using dorm_trk2trk Hi Judith - The files under hcp/mni/ are in the

Re: [Freesurfer] Freeview grey matter, white matter and Tracula outputs

ii:reg=dmri/xfms/anatorig2diff.bbr.dat:edgecolor=red >> dmri/dtifit_AD.nii:reg=dmri/xfms/anatorig2diff.bbr.dat:edgecolor=yellow... FA.nii RD.nii [FA2.JPG] [RD1.JPG] Thank you! Best, Jackie On Mon, Nov 22, 2021 at 7:27 PM Yendiki, Anastasia mailto:ayend...@mgh.h

Re: [Freesurfer] Converting .trk files in mini space to nifti using dorm_trk2trk

Hi Judith - The files under hcp/mni/ are in the space of the actual MNI template. The files under hcp/syn/ are in the space of MGH35_HCP_FA_template.nii.gz. Also, there is no need to use version 7.2.0-beta any more, the official 7.2.0 is out. Hope this helps, Anastasia. __

Re: [Freesurfer] Freeview grey matter, white matter and Tracula outputs

See "viewing volumes with freeview" in the tutorial: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData_freeview When you view the aseg, aparc+aseg, or any other FreeSurfer segmentation volume, make sure that the colormap is not grayscale but "look-up table". You can get the AD and

Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file

attached. Is there any work around for this problem? Thanks in advance Best, Jürgen Am 20.11.2021 um 18:11 schrieb Yendiki, Anastasia mailto:ayend...@mgh.harvard.edu>>: Hi Jürgen - You have diagnosed the problem correctly. It's specific to the case when you have 1 DWI run only. I

Re: [Freesurfer] Tracula 7.2 using older structural outputs

Hi Jim and Luis - The only change between versions of recon-all that would mess things up for TRACULA would be if the IDs of the structures in the aparc+aseg changed (e.g., the left thalamus changed from 10 to 100) or a new structure got added to the aparc+aseg that wasn't there in the previous

Re: [Freesurfer] TRACULA configuration file for bash

Hi Luis - Not sure if you've tried this already, but the instructions on the wiki should work regardless of what your default shell is, because trac-all will source the configuration file from within a c shell. Best, Anastasia. From: freesurfer-boun...@nmr.mgh.ha

Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file

Hi Jürgen - You have diagnosed the problem correctly. It's specific to the case when you have 1 DWI run only. I committed a bug fix for this. For now you can get it from here (and it should get merged into the dev version in a couple of days): https://raw.githubusercontent.com/ayendiki/freesurfe

Re: [Freesurfer] Tracula -- Segmentation Fault

Hi Elizabeth - Have you tried running this with the latest version (7.2)? It looks from the log file like you used 6.0. The tutorial and other info on the wiki apply to the newest version only. Let us know if you are still having this issue. Thanks, Anastasia. F

Re: [Freesurfer] Dracula 7.2 -bedp error

Not sure why, could be a specific version of FSL. You can try running the step that merges everything separately: bedpostx_postproc.sh /path/to/your/tracula/dir/subjname/dmri On a separate note: I have to do some emergency travel so I will not be monitoring the list through the next week. __

Re: [Freesurfer] Using only a aparc+aseg input file for TRACULA

arvard.edu On Behalf Of Yendiki, Anastasia Sent: Wednesday, October 20, 2021 2:12 PM To: Freesurfer support list Subject: Re: [Freesurfer] Using only a aparc+aseg input file for TRACULA * External Email - Caution * Hi Jim - If the file was called $SUBJECTS_DIR/$subj/mri/aparc+aseg.mgz, inc

Re: [Freesurfer] Using only a aparc+aseg input file for TRACULA

Hi Jim - If the file was called $SUBJECTS_DIR/$subj/mri/aparc+aseg.mgz, included the same labels and followed the same lookup table as the OG aparc+aseg, this could work. Note that, for the new TRACULA (in FS 7.2), we recommend also running the thalamic nuclei segmentation, as it helps with the

Re: [Freesurfer] unpacking Diffusion data

and I can go through all the slices in freeview. Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Department of Psychiatry | MGH/HMS 149 13th Street, 149-2615 Boston, MA, USA, 02129 On Sep 30, 2021, at 12:52 PM, Yendiki, Anastasia mailto:ayend...@mgh.harvard.edu>> wrote:

Re: [Freesurfer] unpacking Diffusion data

Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Department of Psychiatry | MGH/HMS 149 13th Street, 149-2615 Boston, MA, USA, 02129 On Sep 30, 2021, at 12:27 PM, Yendiki, Anastasia mailto:ayend...@mgh.harvard.edu>> wrote: Hi Zahra - What scanner/sequence was this scan collecte

Re: [Freesurfer] unpacking Diffusion data

Hi Zahra - What scanner/sequence was this scan collected with? From your scan info below, it looks like run IM01113 has dimensions: 110 x 110 x 74 x 1. This means only 1 volume, so it's not a full diffusion series. What does it look like when you open it in a viewer, like freeview? Anastasia.

Re: [Freesurfer] Freesurfer: Version of development version?

Hi Tobias - You can see the dates of official version releases here: https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes The dev version is a "work in progress" and not an official release, so it doesn't have a number. Based on the release dates, you downloaded yours between the 7.1.1 and 7.2

Re: [Freesurfer] TRACULA Locating Bvecs Error

Hi John - Did the topup command near the end of the logfile work? For example was this file created: /autofs/cluster/bang/TAW_New/tracula/180515_4PR00065/dmri/lowb_topup.nii.gz Anastasia. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Jacoby, John S

Re: [Freesurfer] TRACULA mri_convert error

Hi John - You're using a config file set up for the new TRACULA (in FS 7.2) and running an older version of TRACULA (from FS 6.0). You won't be able to take advantage of all the new TRACULA features with this old version. It's OK if your T1's were run through FS 6.0, you can still process your D

Re: [Freesurfer] Tracula on a stand alone workstation

Hi Alan - The only way to find out is to try 😄 Let us know how it goes! Anastasia. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Alan Francis Sent: Saturday, July 24, 2021 1:36 PM To: Freesurfer Subject: [Freesurfer] Tracula on a stand alone workst

Re: [Freesurfer] dwi_orig_las issue trac-all -prep

DEAL_WITH_IT" to the first line of the "jobs" file but the issue remained. Should I add value after it? Maybe "export MY_MORPHS_DO_NOT_CONFORM_DEAL_WITH_IT=1"? I am using parallel like this: cat jobs_prep | parallel -j 10 (to allocate 10 cores). On Thu, Jul 2

Re: [Freesurfer] dwi_orig_las issue trac-all -prep

ne [and continues without error] The log file for one of the subjects is also attached plus the config file. I'll be glad to know your opinion. Bests, Amir On Wed, Jul 21, 2021 at 5:47 PM Yendiki, Anastasia mailto:ayend...@mgh.harvard.edu>> wrote: Hi Amir - I should make it clearer i

Re: [Freesurfer] dwi_orig_las issue trac-all -prep

fault settings which is $FREESURFER_HOME/trctrain/trainlist.txt. I couldn't find a place to type in the pathlist.txt so I manually copied all the 42 paths into the config. I have also attached the config file. Bests, Amir On Tue, Jul 20, 2021 at 11:37 PM Yendiki, Anastasia ma

Re: [Freesurfer] dwi_orig_las issue trac-all -prep

rored with a syntax error, and I had to change the first line of bedpostx_mgh into /bin/bash. I hope they've been addressed in the released 7.2 version. Bests, Amir On Mon, Jul 19, 2021 at 6:06 AM Yendiki, Anastasia mailto:ayend...@mgh.harvard.edu>> wrote: Hi Amir - You can check t

[Freesurfer] Announcing the new version of TRACULA, included in FreeSurfer 7.2

Hi all - After a year of lockdown coding, and a couple more years of tireless work by the tract annotation team, we are pleased to share the new version of TRACULA. For a summary of new features see: https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates Of note, new protocols were developed

Re: [Freesurfer] dwi_orig_las issue trac-all -prep

Hi Amir - You can check the build stamp in your log file: build-stamp.txt: freesurfer-linux-ubuntu18_x86_64-dev-20210207-440e8c2 You're using a development version of freesurfer that was built on Feb 7th, 2021 ("dev-20210207") . This is neither 7.1.1 (which was released on July 27th, 2020: http

Re: [Freesurfer] dwi_orig_las issue trac-all -prep

Hi Amir - Are you using the official 7.1.1 FreeSurfer release or a beta version? The config file that you are using seems to be newer than 7.1.1. Please attach your entire trac-all.log file, this will help answer this and other questions. Thanks, Anastasia. Fro

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