to
be something within Tracula that is not working for me as expected.
On Fri, Sep 21, 2018 at 12:27 PM Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> wrote:
Thank you. Can you also send screenshots of your original DWIs, if they don't
look like this?
__
Hi Carissa – Don’t set variables to “None” in the config file. Just remove
those lines from the config file altogether – that’s the same as not having any
inputs for them.
Hope this helps,
a.y
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Carissa Nicole Weis mailto:cnw...
Did you look at the nifti volumes? Are they 2 sets of diffusion-weighted
images? If so, you can concatenate them into 1 volume with mri_concat. You will
also have to concatenate the text files that contain the b-values of the 2
scans, and those that contain the gradient directions of the 2 scans
External Email - Use Caution
Yes, here is the log file.
Thanks for your help!
-Jon
On Tue, Oct 30, 2018 at 5:34 PM Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Jon - I suspect that the source of the problem is before the -path step, but
your trac-all.log on
They are not random, they are 20% of the maximum value. If you want to generate
stats at a different threshold, you can find the dmri_pathstats command line in
trac-all.log and add the --pthr option (the default 20% would be --pthr .2).
On Nov 1, 2018 9:01 PM, June Kang wrote:
External
ith more directions?
Bests,
J.
On Nov 2, 2018, at 10:44 AM, Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> wrote:
They are not random, they are 20% of the maximum value. If you want to generate
stats at a different threshold, you can find the dmri_pathstats command line in
trac-all.l
We are actively working on it, but it's a time consuming process that involves
many tracts. A few months, probably.
On Nov 9, 2018 4:40 AM, "Hayek, Dayana"
wrote:
External Email - Use Caution
Dear all,
In my research work, I am using Freesurfer for both grey and white matter
segment
have
motion artifact, but I couldn’t find any special points in the protocol.
http://protocols.humanconnectome.org/HCP/3T/imaging-protocols.html
J.
On Nov 4, 2018, at 4:21 AM, Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi June - Not in principle, any number of dire
Have you checked if the registered segmentation and the FA map align correctly
in freeview?
On Nov 23, 2018 1:27 PM, "Winkelbeiner, Stephanie A"
wrote:
External Email - Use Caution
Hi,
I try to extract FA values from the FSL FA skeleton using the freesurfer
aparc.a2009s+aseg+2mm parc
he parcels from the FA skeletons with fslmaths to
make sure that only the area of the skeleton is read out. But that doesn't give
convincing results either.
Anyone having other suggestions?
Thanks,
Steph
Sent from my Samsung Galaxy smartphone.
Original message --------
From:
values are around 0.1…
Could you think of a reason why that is?
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Monday, November 26, 2018 1:58 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] [EX
https://www.ismrm.org/jobs/j06670.pdf
The Connectome 2.0 Project is a new BRAIN initiative-funded effort at the
Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General
Hospital and Harvard Medical School. Building on our experience designing the
first Connectome scanner, we
Yes, you can register other modalities to the T1 using bbregister. Then you can
use that registration to transform any volume from T1 space to the space of the
other modality. Check out the multimodal integration tutorials on the
freesurfer wiki.
On Dec 5, 2018 2:36 AM, Maedeh Khalilian wrote
Hi Nick - This likely means that it got stuck at the initial path for a while,
but eventually got unstuck and explored the space successfully. If you don't
like this look, you can try setting the nburnin parameter in the config file,
to something higher than the default 200. This sets the number
pushing
through to reconstruct the paths and just check the final posterior
distribution output?
Thank you so much for the help!
Nick
On Jan 4, 2019, 4:12 PM -0600, Yendiki, Anastasia ,
wrote:
Hi Nick - This likely means that it got stuck at the initial path for a while,
but eventually got unst
Hi Ainara - What do you mean by default freesurfer files? Can you describe how
you created each subject's recon-all style directory under SUBJECTS_DIR?
TRACULA looks for $SUBJECTS_DIR/$subjectid/mri/aparc+aseg.mgz for each subject
ID.
a.y
On Jan 11, 2019 8:30 AM, Ainara Gomez wrote:
IR/$subjectid/) so TRACULA can find all the files from Freesurfer
that are needed in trac-all prep step.
Thanks a lot again,
Ainara
El vie., 11 ene. 2019 a las 14:49, Yendiki, Anastasia
(mailto:ayend...@mgh.harvard.edu>>) escribió:
Hi Ainara - What do you mean by default freesurfer files? Ca
Hi Donald - Both your input and output reference volume are in diffusion space
and there is no transformation specified, so the output is also in diffusion
space. These are voxel, not RAS, coordinates.
Best,
a.y
On Jan 22, 2019 7:14 AM, "Krieger, Donald N." wrote:
External Email - Us
Hi Lorenzo - If you are still having this problem, please send the trac-all.log
file from one of the 4 subjects.
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Lorenzo Pini
Sent: Friday, May 10, 2019 4:35:50 PM
To: freesurfer@nmr.mgh.harvard.
Hi Jim - Units of diffusivity are mm^2 / sec.
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Alexopoulos, Dimitrios
Sent: Thursday, May 9, 2019 4:33:27 PM
To: Freesurfer support list
Subject: [Freesurfer] units for tracula output
Exte
Dear all - The IronTract tractography challenge is now open. For more
information on challenge tasks, ranking criteria, and how to participate,
please visit: https://irontract.mgh.harvard.edu
There will be 2 winners:
* Overall winner: The goal is to find the tractography method that achiev
Hi Costanza - can you please attach your configuration file?
Best,
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Costanza Gianni'
Sent: Wednesday, June 5, 2019 6:49:02 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] running recon -al
ternal Email - Use Caution
Hi Anastasia,
I've attached the configuration file.
Best,
Costanza
Il giorno mer 5 giu 2019 alle ore 15:07 Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> ha scritto:
Hi Costanza - can you please attach your configuration file?
Best,
a.y
__
g fsl version: 5.0.9
thanks a lot,
Costanza
Il giorno mer 5 giu 2019 alle ore 18:36 Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> ha scritto:
Hi Costanza - When you use "\" in a shell script to continue a command onto the
next line, make sure that the "\" is the v
Hi Daniel - Yes, this seems to be the problem: " tkregister2: Command not
found." What version of freesurfer are you using?
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Daniel Callow
Sent: Wednesday, July 3, 2019 2:06:27 PM
To: Freesurfer su
udent, Neuroscience and Conitive Science
Exercise for Brain Health Lab
University of Maryland, College Park
ddcc2...@gmail.com<mailto:ddcc2...@gmail.com>
443-254-6298
On Thu, Jul 4, 2019 at 4:26 AM Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Daniel - Yes, this see
Hi Daniel - What is the age range you're interested in? We have used tracula
with children as young as 5 (see example ref below). Keep in mind that tracula
is not a traditional template-based approach that needs perfect alignment to a
template, because it finds tracts based on their relative pos
es that mean my suggested edit of
changing the mni template to a different template wouldn’t work. I appreciate
your input and quick response!
Kind regards,
Daniel Callow
On Mon, Jul 29, 2019 at 6:43 PM Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Daniel - What is the age ra
Hi Daniel - It'll be easier to just preprocess the data before passing them to
trac-all. Topup will be incorporated to the preprocessing for the next version
release. Of course you can replace that part of the script yourself if you
prefer - you'll have to also combine the AP and PA outputs etc
Hi Fred - What program are you using to display these? Any chance that the
volumes are not actually all zero but that they're just not displayed correctly
for whatever reason?
Have you tried opening these two volumes in freeview at the same time?
/usr/share/fsl/5.0/data/standard/MNI152_T1_1mm
Hi Daniel - Can you please attach the dmrirc and trac-all.log files in their
entirety? Thanks!
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Daniel Callow
Sent: Thursday, August 8, 2019 9:07:31 AM
To: Freesurfer support list
Subject: [Freesu
Hi Daniel - You can confirm if the orientation is different from your other
scans by running mri_info directly on the dicom. If these two subjects were
scanned in a completely different orientation than the rest of the subjects in
your study, e.g. coronal vs. axial, if does raise the question of
Yes. Please check out the instructions in the tutorial on how to specify your
input DWIs and let us know if you have any questions:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Daniel Call
@gmail.com<mailto:ddcc2...@gmail.com>
443-254-6298
On Fri, Sep 27, 2019 at 11:26 AM Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> wrote:
Yes. Please check out the instructions in the tutorial on how to specify your
input DWIs and let us know if you have any questions:
https://surf
Hi Juan - You can see usage info for dt_recon if you run it without arguments:
USAGE: dt_recon
Required Aruments:
--i invol
--b bvals bvecs
--s subjectid
--o outputdir
...
So --b takes both bvals and bvecs one after the other, and --s is the subject
name as found under $SUBJECTS_DIR
Hi Cecilia - Does the number of entries in the bvals and bvecs files match the
number of volumes in data.nii.gz?
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Mazzetti, C. (Cecilia)
Sent: Saturday, October 5, 2019 3:23:23 AM
To: freesurfer@nmr.
How many volumes does this file have?
/myfolder/freesurfer/subject02_C/dmri/data.nii.gz
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Mazzetti, C. (Cecilia)
Sent: Sunday, October 6, 2019 5:56 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Fr
There's a line break after:
set dcmlist = (APOE.124.dwi.nii.gz APOE.158.dwi.nii.gz APOE.215.dwi.nii.gz
APOE.269.dwi.nii.gz
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Daniel Callow
Sent: Monday, October 7, 2019 10:21 AM
To: Freesurfer support list
Does this file exist?
niiRead(): error opening file
/autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/dwi.nii.gz
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Juan Rivas
Sent: Tuesday, October 8, 2019 6:11:39 PM
To: freesurfer@n
13
External Email - Use Caution
Hi, thank you for your answer. This file does exist, it contains 59.3 MB.
JC.
Message: 10
Date: Tue, 8 Oct 2019 22:23:11 +
From: "Yendiki, Anastasia"
mailto:ayend...@mgh.harvard.edu>>
Subject: Re: [Freesurfer] Tracula
Hi Daniel - is this an error in recon-all? Then I wouldn't put "tracula error"
in the subject line if you want the developers of the structural stream to look
into it.
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Daniel Callow
Sent: Thursday,
k
ddcc2...@gmail.com<mailto:ddcc2...@gmail.com>
443-254-6298
On Thu, Oct 10, 2019 at 9:14 AM Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Daniel - is this an error in recon-all? Then I wouldn't put "tracula error"
in the subject line if you want the developers
Hi Cecilia - this commnd tells it to do the preprocessing (-prep), but then not
to do any of the steps of the preprocessing (-no...)
trac-all -prep -c config_01C.txt -nocorr -noqa -nointra -nointer -nomasks
-notensor -noprior -no-isrunning
So this command won't do anything. Have you run those st
Hi Alan - It looks like it may be due to a mismatch between the bvals/bvecs
files and the number of volumes in your DWI data. I think it's expecting to
find a b=0 volume as the 64th volume, but your DWI nifti has only 63 volumes.
a.y
From: freesurfer-boun...@nmr.
Hi, you need to run recon-all on the T1, not on the diffusion scan. This will
produce an anatomical segmentation of each subject based on the T1s, which
TRACULA will then use to extract anatomical priors on white matter tracts, to
aid tractography. When you run trac-all to do the actual tractogr
Hi Don - Diffusivity and FA depend on the b-value. Even if you just scan a
subject with multiple b-values on a single scanner, and you compute FA etc from
each shell, you'll get different values in the same voxel. So this is unrelated
to what tractography method you use, tracula or other. There
Hi Nayan - Try using /Applications instead of $Applications everywhere. Also,
the config file seems to be in rich text format - not sure how that'll work.
Try converting it to plain text (if you use mac, from the Format menu of the
text editor).
Best,
Anastasia.
my iPhone
On 22-Oct-2019, at 8:01 AM, Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Nayan - Try using /Applications instead of $Applications everywhere. Also,
the config file seems to be in rich text format - not sure how that'll work.
Try converting it to plain t
y, October 22, 2019 2:32 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] trac-all error
External Email - Use Caution
I have attached the log-file from the trac-all command
Thanks and Regards
Nayan Wadhwani
On Mon, Oct 21, 2019 at 10:26 PM Yendiki, Anastasia
ma
You could register another subject's segmentation to your subjects, but having
the individual segmentations is ideal.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Renew Andrade
Sent: Thursday, October 24, 2019 9:53 AM
To: freesurfer@nmr.mgh.harvard
You are using some forward slashes ("/") where you should be using backslashes
("\").
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Renew Andrade
Sent: Saturday, October 26, 2019 5:11 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] ERRO
Hi Cecilia - Can you please attach your configuration file?
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Mazzetti, C. (Cecilia)
Sent: Friday, November 22, 2019 11:30:29 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] TRACULA: Too m
When you set a variable to a list of multiple things, you need parentheses
around them (see the example config file for this). My recommendation to make
things simpler for yourself is to remove any variables where you are just using
the default settings, and only keep the ones where you define w
Hi Benxamín - Those can occasionally arise due to noise. You're more likely to
see them if you're looking at single voxel values than average values over
multiple voxels. That sequence of values in the .9-1 range does look quite high
though. Another possibility would be miscalculation due to inc
Hi Andrade - You have some forward slashes ("/") at the ends of lines in the
config file that should be backslashes ("\") instead.
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Renew Andrade
Sent: Saturday, December 21, 2019 9:11 AM
To: Freesur
Hi Sam - You can use mri_vol2vol to apply the transformation that was saved in
the registration file nodiffb2orif.dat to any volume that's in the same space
as nodif.nii.gz.
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Sam W
Sent: Saturday, Ja
Hi Ameen - diffusion_recons/elmo.2005 should have the freesurfer recon of the
T1 data and diffusion_tutorial/elmo.2005 should have the diffusion data. Can
you confirm if this was in what you downloaded?
Thanks!
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
o
Hi Nayan - The plan is to make it available with the next release but it needs
to undergo more testing. At the moment you can use it from the dev version and,
as with anything in the dev version, keep in mind that things may change by the
time they're in the official release. We appreciate any f
econd method than
please help me how to use that.
Thanks and Regards
Nayan Wadhwani
On Wed, Jan 29, 2020 at 5:40 PM Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Nayan - The plan is to make it available with the next release but it needs
to undergo more testing. At the moment
een
On Tue, Jan 28, 2020 at 8:48 PM Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Ameen - diffusion_recons/elmo.2005 should have the freesurfer recon of the
T1 data and diffusion_tutorial/elmo.2005 should have the diffusion data. Can
you confirm if this was
Hi Renew - I think it's just because of using "/" instead of "\" at the end of
lines for bveclist and bvallist. If the problem persists after you change that,
let us know.
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Renew Andrade
Sent: Wedne
Hi Markus - If you were to find longitudinal changes in this study, you would
have no way of knowing if they are changes in the brain or changes in the
instrument used to measure the brain.
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Markus Gs
:10, Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> a écrit :
Hi Markus - If you were to find longitudinal changes in this study, you would
have no way of knowing if they are changes in the brain or changes in the
instrument used to measure the brain
The answer depends on how you want to correct susceptibility artifacts. Do you
have a field map, or do you have DWIs acquired with reverse polarities?
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Adam Rytina
Sent: Thursday, February 6, 2020 2:02 PM
rrect susceptibility artefacts?
Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Yendiki, Anastasia
Sent: Thursday, February 6, 2020 9:27:51 PM
To:
ether there are
some possibilities to perform diffusion data correction in Freesurfer, too.
Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Yendiki, Anastasia
Sen
from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Yendiki, Anastasia
Sent: Thursday, February 6, 2020 9:35:16 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] DWI EPI cor
Hi Jason - Please save the config file as a simple text file, not a rich text
file (rtf). When you view it with the more command on the command line, it
should just show you the text that you typed, and not all the other stuff.
Best,
Anastasia.
From: freesurfer-b
Hi Lily - No, you should search for dmri_pathstats in the log file
(scripts/trac-all.log) and follow the syntax for the command that you'll see
there. Only change the threshold, and potentially the output file, if you don't
want to overwrite the existing one.
a.y
___
rd.edu/a-y
From: Renew Andrade
Sent: Tuesday, March 17, 2020 4:13 PM
To: Yendiki, Anastasia ;
freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] format bvalues bvectors tracula
External Email - Use Caution
Dear Yendiki Anastasia:
I am replying for second time. I haven’t received
Hi Salah - It looks like it didn't find your subject's freesurfer recon when it
was doing the pre-processing, so it skipped some steps that you need to go
beyond that point. Based on your SUBJECTS_DIR and your subject name, it looked
for this file:
/Volumes/HD/Post_HARDI/PAH_Clinical_110/07/C07/
Hi Nazife - That is correct, the lengths are numbers of voxels along a tract in
each subject's native DWI space, so if you were to compare them across subjects
you'd probably want to correct for total intracranial volume. (This is just as
you would do for any other length/area/volume measurement
!
NB: log file is attached.
Regards,
Salah
On Thu, Apr 9, 2020 at 12:35 PM Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Salah - It looks like it didn't find your subject's freesurfer recon when it
was doing the pre-processing, so it skipped some steps that you ne
Hi Jessica - Please send us your trac-all.log file as an attachment. It's hard
to guess what went wrong just from the output of one command, without seeing
the output of all commands before it. Thanks!
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf
Can you please also send your bvecs and bvals files? I can't see anything else
going wrong, so I'm guessing it has to do with those.
From: Hua, Jessica
Sent: Monday, April 13, 2020 12:10 PM
To: Yendiki, Anastasia ;
freesurfer@nmr.mgh.harvard.edu
S
n open it in a linux text editor and
save it again.
Hope this helps!
a.y
From: Hua, Jessica
Sent: Tuesday, April 14, 2020 4:38 PM
To: freesurfer@nmr.mgh.harvard.edu ; Yendiki,
Anastasia
Subject: Re: Trac-All Error
External Email - Use Caution
At
Thanks Freesurfer developer
I have followed what you have suggested and it did work for me.
Thanks once again for your help.
Regards
Salah
On Sat, 11 Apr 2020, 5:54 am Yendiki, Anastasia,
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Salah - You're probably running into this problem:
- 1 n9800093 staff454934 17 Apr 22:22 wm.seg.mgz
-rw-rw-r-- 1 n9800093 staff468036 18 Apr 05:43 wmparc.mgz
QUT-gonzo:mri n9800093$
Regards,
Salah
On Tue, Apr 21, 2020 at 5:17 AM Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> wrote:
When you run the following command,
Those values are at the endpoints of the tracts. As the median tract may be a
bit longer or shorter in different subjects, the endpoints don't always have
corresponding points in all subjects
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Hua, Jessica
Hi Maria Gabriela - This does not look like a diffusion dicom:
PulseSeq tfl_me3d4_16ns
Protocol T1
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Figueiro Longo, Maria
Gabriela
Sent: Monday, April 27, 2020 9:49 AM
To: freesurfer
You cannot have multiple SUBJECTS_DIR's. It is supposed to be the base
directory under which all subjects' dirs are saved. You could have a different
configuration file for each subject if you want each of them to have a
different SUBJECTS_DIR, but this hack won't work for longitudinal analyses
Yes, this is fine.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Zeng, Qi
Sent: Thursday, April 30, 2020 2:22 PM
To: Freesurfer support list
Subject: [Freesurfer] trac-all -bedp error
External Email - Use Caution
Hi,
I run trac-all, the
ake a look? From what you
say, I have some suspicion that my individual configuration could also have
some problem.
Thank you so much !
Best,
Qi
On Thu, Apr 30, 2020 at 4:41 PM Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> wrote:
You cannot have multiple SUBJECTS_DIR&#
You exceeded the memory limit:
TERM_MEMLIMIT: job killed after reaching LSF memory usage limit.
Exited with exit code 1.
How big is are your diffusion data sets (matrix size and number of directions)?
Your cluster probably has a way for you to request more memory when you submit
jobs - you'd hav
DWIs, assuming the remaining DICOM files from the
same series are in the same directory."
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Batra, Vinita R.
Sent: Monday, May 4, 2020 9:24 AM
To: Freesurfer support list ; Yendiki,
Anastasia
Subject: [
;:
1) log file: "queuing post processing"
However, 2) I have all needed outputs generated in
SUBJ1_ses1.long.SUBJ1_base/bedpostX and SUBJ1_ses2.long.SUBJ1_base/bedpostX
I have attached the trac-all -path log file below.
Thank you so much!
Best,
Qi
On Fri, May 1, 2020 at 10:01 PM Yendiki,
If you're not happy with the output of tractstats2table and want something
custom, you can just do a search in the stats files. They're simple text files.
You can see how these files are named and what their contents look like here:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStat
DICOMs may save each slice or each volume separately. This is not a problem per
se, it's just a format, but it suggests that something may have changed in the
protocol, which begs the question if other things changed in the protocol. I'd
start by checking the converted nifti (dmri/dwi.nii.gz) to
It can't find the freesurfer recon of your subject.
Your SUBJECTS_DIR is /Users/ahn/Downloads/9211720/ and your subject name is
freesurfer. This means that you have saved the output from running recon-all on
this subject's T1 scan at this location:
/Users/ahn/Downloads/9211720/freesurfer/
___
Hi Jocelyn - It's strange to get this in the tutorial data, it's the kind of
thing you might get if the FS recon was missing part of the brain or if the
alignment between datasets was not good. So I'm surprised you're getting this
in the tutorial data. Can you please send your entire trac-all.lo
Hi Jason - Did this file get created?
/home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi.nii.gz
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Jason Silva Rudberg
Sent: Sunday, July 12, 2020 2:45 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject:
here:
http://irontract.mgh.harvard.edu/compete-round2/
See you at ISMRM!
On behalf of the organizers,
Anastasia Yendiki.
| Anastasia Yendiki, Ph.D.
| Associate Professor, Harvard Medical School
| Associate Investigator, Massachusetts General Hospital
| Martinos Center for Biomedical Imaging
|
ce my previous attempts to post it were rejected by the Freesurfer mailing
list moderators.
Thank you once again!
Sincerely,
Jocelyn
On Tue, Jun 30, 2020 at 12:51 AM Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Jocelyn - It's strange to get this in the tutorial data,
Dear all - Please see below for a unique opportunity to join the Haber lab in
Boston. While the amazing work of the Haber lab speaks for itself, I will also
add here the questionable perk that you might have me as a collaborator. If
interested, please contact Dr. Haber directly (see below).
Be
] Error in Trac-All Pre-Processing step
External Email - Use Caution
Hi Anastasia,
I'm using FSL 6!
Hope this helps,
Jocelyn
On Thu, Jul 23, 2020 at 8:47 AM Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Jocelyn - I'm having a hard time replicating
Hi Jason - Without looking at your trac-all.log I can only guess what error
you're seeing, so here it goes. You should save the config file as a simple
text file, not a rich text file. If you're using TextEdit by any chance, you
can convert from the Format menu before saving.
a.y
_
Hi Qi - Are those two images in the same space, or in different spaces (the
aparc+aseg_mask in T1 space and the FA map in diffusion space)? If the latter
is true, there is no reason to expect them to have the same orientation.
Checking the registration between T1 and diffusion space is a sensibl
Qi
On Wed, Aug 26, 2020 at 10:22 PM Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Qi - Are those two images in the same space, or in different spaces (the
aparc+aseg_mask in T1 space and the FA map in diffusion space)? If the latter
is true, there is no reason to ex
Hi Qi - Correcting for overall brain size is important when you are comparing
measures of length/area/volume. As in, you want to know if a region
specifically is bigger in population A vs. B, and not just because the whole
brain is bigger. In that case, use eTIV (estimated total intracranial vol
easurement, for example, FA, if a subject has lower FA in general in
the brain, should I adjust the whole brain FA or average FA for that matter?
Best,
Qi
On Mon, Aug 31, 2020 at 6:53 PM Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Qi - Correcting for overall brain size i
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