nday, August 31, 2020 10:57 PM
To: Yendiki, Anastasia
Cc: Freesurfer support list
Subject: Re: [Freesurfer] group level analysis
External Email - Use Caution
Hi Anastasia,
Thank you for the clarification! As you said, if I regress out the global FA, I
could wipe out the regional FA.
Hi Jim - There should not be any differences in TRACULA between recent stable
releases. I've been committing the new features described on the wiki to the
tracula beta branch on github, so they are available there only. Let us know if
you run into any issues!
Anastasia.
list
Jasons-MacBook-Pro:XXX7.24.14 jasonledesma$
Sincerely,
Jason Ledesma
Staff Research Associate
Phone: 1(424)571-7755
E-mail: jason.lede...@lundquist.org
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Yendiki, Anastasia
Sent: Monday, August 24
Hi Qi - Please see under "Output directories and files":
https://surfer.nmr.mgh.harvard.edu/fswiki/trac-all
Anastasia.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Zeng, Qi
Sent: Wednesday, September 9, 2020 1:23 AM
To: Freesurfer support list
Su
Hi Qi - Please see under "Anisotropy and diffusivity along the trajectory of a
pathway":
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics
Anastasia.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Zeng, Qi
Sent: Wednesday, Sep
s for FS 7 as FS 6, for example\
using a generic dmrirc parameter file ?
Best.
Jim
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Yendiki, Anastasia
Sent: Thursday, September 17, 2020 12:42 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula FS 6 vs FS 7.1.1
wants tracts using the stable FS7.1 release, we should using
the tracula.beta instead?
Jim
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Yendiki, Anastasia
Sent: Thursday, September 17, 2020 12:07 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula FS 6 vs FS 7.1.1
release?
In other words, the beta only has new features but the stable version is OK.
Jim
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Yendiki, Anastasia
Sent: Thursday, September 17, 2020 12:27 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula FS 6 vs FS
Hi Keita - Instead of setting variables to "None", just delete or comment out
those lines altogether.
Anastasia.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of ksak...@yahoo.co.jp
Sent: Monday, September 28, 2020 12:28 AM
To: freesurfer@nmr.mgh.harv
Hi Yasemin - It looks like the unix shell doesn't like that there are spaces
after the "\" in a few lines:
1723_base \
1741_base \
1725-2/eddy_with_repol.nii.gz \
Best,
Anastasia.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Hasimoglu, Yasemin
Dear FreeSurfers - Join us today at 12pm EDT / 6pm CET for the IronTract
Challenge webinar/happy hour! Learn about this effort to assess tractography
methods objectively and get up to speed on how to participate by the deadline
of November 8. The webinar will include demos on how to submit your
Hi Ileana - It looks like it fails on the left uncinate. Is there any artifact
or missing part of the brain or brain mask, either in the diffusion scan or the
T1 scan, in a location that would affect the uncinate?
Anastasia.
From: freesurfer-boun...@nmr.mgh.harva
Yes, they are all the same in terms of the command line. If your shells are in
separate scans and you want to combine them, that can be done with the new beta
version.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Zeng, Qi
Sent: Thursday, October 1
Hi Samar - Can you please attach your trac-all.log file and your configuration
file? It's hard to guess what's going on just from the line where the error
occurs without seeing everything that came before it.
Thanks!
Anastasia.
From: freesurfer-boun...@nmr.mgh.ha
Fouda
Sent: Friday, October 16, 2020 6:04 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Help!
External Email - Use Caution
Hi Anastasia,
Thank you so much for responding, please find the log attached!
On Fri, Oct 16, 2020 at 3:24 PM Yendiki, Anastasia
mailto:ayend
Make sure to use "subjlist", not "sublist". If that is not the issue, then
please attach your log file and configuration file - it's hard to guess the
issue without more information.
Best,
Anastasia.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Sha
digest Vol 200, Issue 28 error
trac all prep (Yendiki, Anastasia)
External Email - Use Caution
Hi Anastasia,
Thank you so much for your reply.
I omitted a very important information. I am working with left hemisphere
stroke data. On a visual check I see that recon all worked well on
-boun...@nmr.mgh.harvard.edu
on behalf of Shanika Jayakody
Sent: Monday, October 26, 2020 10:06 AM
To: Freesurfer support list ; Yendiki,
Anastasia
Subject: [Freesurfer] Fw: Tracula error: run list is longer than subject list
External Email - Use Caution
Hi Anastasia
Thanks again for he
Hi Zhen - We do not have a date for the next FreeSurfer release yet. The code
for the infant stream has been merged into the main TRACULA code base, but
there is some work still to be done to finalize the new atlas that we've been
working on. In the meantime, you can try running the infant T1 se
Hi Cat - The FA/MD/RD/AD at a specific voxel comes from first fitting a tensor
to the intensity values of all the DWIs at that voxel and then finding the
eigenvalues of the tensor at that voxel. The tracts work like ROIs - the
FA/MD/RD/AD values are averaged over all the voxels in a tract.
Best
What goes after "-c" in the trac-all command should be the configuration file,
not the nifti file.
From: Shanika Jayakody
Sent: Monday, October 26, 2020 5:01 PM
To: Yendiki, Anastasia
Subject: Fw: Tracula error: run list is longer than su
tract do
not necessarily have a ‘precise’ relationship to one another?
With warm Regards,
Cat
From: on behalf of "Yendiki,
Anastasia"
Reply-To: Freesurfer support list
Date: Monday, October 26, 2020 at 8:26 AM
To: "freesurfer@nmr.mgh.harvard.edu"
Subject: [EXTERNAL] Re:
s trac-all -prep -c /path/to/configuration
file- is that what you meant?
Thanks,
Oshadi
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Yendiki, Anastasia
Sent: Monday, October 26, 2020 5:12 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfe
-0.2799370.976579 0.920768
Which one is the correct version?
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Shanika Jayakody
Sent: Tuesday, October 27, 2020 4:06 PM
To: Freesurfer support list ; Yendiki,
Anastasia
Subject: Re: [Freesurfer
Hi Yasemin - If you upload all the tracula output files for me here, I'll take
a look:
https://gate.nmr.mgh.harvard.edu/filedrop2/
Please include all the output directories for this one subject in one zip file.
Thanks!
Anastasia.
From: freesurfer-boun...@nmr.mgh
Hi Michele - Do you get any other output on the screen? Can you attach your
configuration file and trac-all.log? Thanks!
Anastasia.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Michele Valotti
Sent: Friday, October 30, 2020 12:44 PM
To: Freesurfer
Hi Oshadi - That does not sound normal. Is there anything wrong with the
FreeSurfer segmentation of this subject?
Anastasia.
From: Shanika Jayakody
Sent: Monday, November 2, 2020 10:33 AM
To: Freesurfer support list ; Yendiki,
Anastasia
Subject: Re
Hi Rita - From the log file, the first error occurs when it tries to convert
your DWI nifti volume to LAS orientation:
mri_convert -oni 128 -onj 128 -onk 62 -oid 0 0 0 -ojd 0 0 0 -okd 0 0 0 -oc -2
24 35 -rt nearest
/home/rita/Desktop/test/diffusion_output/MRI_20160226_2_PHD003/dmri/dwi_orig.nii
o-ras determinant -8
ras to voxel transform:
-0.4990 -0.0252 -0.018763.9202
-0.0235 0.4975 -0.043853.3510
-0.0208 0.0428 0.497712.3162
-0. -0. -0. 1.0000
Yendiki, Anastasia mailto:ayend...@mgh.harvar
Hi Shanika - Can you please send the full log file from scripts/trac-all.log?
It's hard to figure out what causes the error without seeing the full output.
Nothing looks unusual in the config file.
Thanks,
Anastasia.
From: freesurfer-boun...@nmr.mgh.harvard.edu
thing else.
Regards,
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Yendiki, Anastasia
Sent: Wednesday, March 17, 2021 5:40 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA error: missing output volume name
Hi Shanika - Can you please sen
Hi Carissa - Any QA issues aside, the first reason for a difference that I can
think of is that the same % threshold for the tract probability distribution
(e.g., 20% of the max) would not be equivalent between cross and long streams.
In the long stream I'd expect the distributions to be tighter
How about an aseg volume? The left and right are labeled with different numbers
🙂
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Arman Avesta
Sent: Wednesday, March 31, 2021 5:24 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Left-Right
Hi Qi - This is documented here:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics
Anastasia.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Zeng, Qi
Sent: Monday, April 19, 2021 1:40 PM
To: Freesurfer support list
Subject: [Fre
Hi Marena - How does the T1 of this subject and its freesurfer segmentation
(aparc+aseg) look? In the image the brain looks truncated, is that the case
with the T1?
Anastasia.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Marena Manierka
Sent: Tue
lobes is cut off.
Let me know if there are other files/ screenshots I can provide to help with
solving this issue.
Best,
Marena
On Wed, May 26, 2021 at 1:04 PM Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Marena - How does the T1 of this subject and its freesurfer seg
Hi Daniel - Can you track down which command does this? I suspect that it's
something in the pre- or post-processing, because I haven't added
multi-threading to the main TRACULA executables (yet).
Best,
Anastasia.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on
Hi Daniel - That makes sense. You can set the number of threads that
eddy_openmp uses with the OMP_NUM_THREADS environment variable:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=fsl;f42cb2e6.1611
Hope this helps,
Anastasia.
From: freesurfer-boun...@nmr.mgh.harv
Hi Akila - The new atlas indeed includes the 42 tracts shown here:
https://dmri.mgh.harvard.edu/tract-atlas/ Others will be coming in future
versions. Indeed one of the summer students this year will be working on one of
the other cerebellar peduncles that you mention, so those are high on the l
Hi Jürgen - In principle they can be any format that mri_convert reads, so they
could be nifti. I suspect there's some glitch with where it's looking for the
files vs. where they are. Can you please attach your config file?
I have a grant deadline tomorrow, but will look after that. Thanks!
Ana
FS archive, but did not find any hint.
The whole trac-all.log file and the config file are attached.
Thanks in advance and good luck with your grant submission.
Regards
Jürgen
Am 29.06.2021 um 16:32 schrieb Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>>:
Hi Jürgen - In principle the
s and
therefore the difference in TE cannot be extracted.
Is there an easy work around to provide —tediff or the file b0info.dat to
trac-all -prep? I tried to define —tediff in the config file, but it does not
work.
Thanks for any advise
Best,
Jürgen
Am 02.07.2021 um 19:09 schrieb Yendiki, Ana
Hi Fanny - The meaning of the statistics is explained in this section of the
TRACULA tutorial:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics#Anisotropyanddiffusivityaveragedatcross-sectionsalongapathway
Please note that the instructions in the tutorial have now been updat
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
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
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
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
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
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
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
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
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
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
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
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.
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
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:
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
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
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.
__
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
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
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
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
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
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
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.
__
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
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
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
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...@
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
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
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
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
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
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
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,
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
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
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
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-
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
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
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
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
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
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
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
______
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
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
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
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
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
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
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
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
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
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,
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
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