Hi Marissa - You have to specify as many b-values and gradient vectors as
there are volumes in your DWI data file. This means that, if you combine
the AP and PA volumes, you also have to concatenate the bvals from the two
into one file, and do the same with the bvecs. Make sure that the order
You're right that this looks fine. Can you upload the entire DWI series
for me here? Nifti is fine. Thanks!
https://gate.nmr.mgh.harvard.edu/filedrop2/
On Mon, 12 Sep 2016, Lars M. Rimol wrote:
Re: [Freesurfer] Tracula movement
Anastasia Yendiki Mon, 12 Sep 20
Hi Lars - This sounds like the subject was trying to climb out of the
scanner: 3cm average translational motion and 24% of the slices in the
series have drop-out. How do the images look?
a.y
On Mon, 12 Sep 2016, Lars M. Rimol wrote:
HI,
Is there a rule-of-thumb upper level of acceptable he
Good to know, thanks for sharing this trick!
On Sat, 3 Sep 2016, Chung, Yoonho wrote:
I found out why it didn't work. One of the script that bedpostx_postproc.sh
calls is written in python2. I set my default to python3 and therefore
caused the error in the last step. After I loaded python2 e
Hi Yoon - It sounds like FSL's bedpostx postprocessing script
failed. You can run it like this:
bedpostx_postproc.sh /path/to/your/subject/dmri
This script merges the results from all the slices. It's possible that
something went wrong with the slices (you ran out disk space for exam
Hi Kristina - I suspect there's some misregistration, or part of the brain
mask (and hence the anatomical segmentation) missing or something like
that. Do you mind uploading the tracula directories of this subject for me
to take a look at?
https://gate.nmr.mgh.harvard.edu/filedrop2/
Thanks!
Hi there - If you upload the tracula directories for me, I'm happy to try
to figure out what's going on. Although honestly at this point it's worth
waiting for the new version.
Thanks!
a.y
On Tue, 30 Aug 2016, Kang, XJ wrote:
Hi,
I am trying to computer the changes of cortical parcellat
Dear FreeSurfers - If you're attending the Resting-State and Brain
Connectivity Conference in Vienna, you can now register for satellite
symposia, including one on diffusion MRI.
Hope to see you there!
a.y
--
We are pleased to inform you that registration for the six Satellite
Sym
No need to rerun anything. It's an issue with the format of those mean
path files. Just view them in the standard 5.3 version of freeview for
now.
On Fri, 26 Aug 2016, Elijah Mak wrote:
Hi Anastasia,
Yes indeed. I am using a dev version of freeview. I could give it another go
with the fre
Hi Elijah - Glad to hear that things worked out! Are you by any chance
using the dev version of freeview?
a.y
On Fri, 26 Aug 2016, Elijah Mak wrote:
Hi Anastasia and others,
I am trying to visualise the *.path.mean.txt on MNI template after running
trac-all -stat. I used this
command:
fre
Hi Vasudev - These regions are part of the subcortical segmentation (aseg)
volume:
http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.roi.ppt
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI
a.y
On Thu, 25 Aug 2016, Dev vasu wrote:
Dear all,
After running through recon-al
can help to do tractography for the
corticospinal tract when T1 images are not available?
Thank you for any advice
Mohamad
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Anastasia Yendiki
Sent: Wednesday, Aug
Hi Mohamad - This tool is *way* deprecated. It should not have been
included in beta releases. Thanks for bringing this to our attention.
a.y
On Wed, 24 Aug 2016, Alshikho, Mohamad J. wrote:
Dear Freesurfer experts,
I would like to inquire about the tool “dmri_poistats”
https://surfer.nm
id Ave.Tel: 314-747-6173
St. Louis, MO 63110Email: mha...@wustl.edu
On 8/23/16, 5:09 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Anastasia Yendiki" wrote:
Hi Michael - Even if it starts very close to the true max of the
distribution, in practice it'll never stay pu
nter for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO 63110Email: mha...@wustl.edu
On 8/23/16, 4:44 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Anastasi
Hi Dillan - There's a work-around for this, see the reinit variable at the
bottom of the sample config file:
http://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc
I'm hoping to make this happen automatically soon!
Best,
a.y
On Tue, 23 Aug 2016, Newbold, Dillan wrote:
Dear Anastasia,
I’
Hi Yoon - The wmparc and aseg ROIs are in the subject's native T1 space,
so you don't need to register across subjects to get ROI-based diffusion
measures. You just need to register between the subject's own T1 and DWIs
- the recommended method for that is bbregister. You can find more in the
Hi Elijah - Does the directory in the error message exist?
a.y
On Fri, 19 Aug 2016, Elijah Mak wrote:
Hi Anastasia,
The error message occurs for other control points too, but it does not kill the
-prior stage.
I have attached the full trac-all.log file.
This error message is also found in
Hi Elijah - This error occurs with one number of control points but not
another? That would be very strange. I'd have to look at the full
trac-al.log to figure it out, I can't guess what's going on just from this
one line unfortunately.
a.y
On Fri, 19 Aug 2016, Elijah Mak wrote:
Hi Anasta
Mmm, it sounds like the shape of the tract is too convoluted for it to
find a good fit. I'd try increasing the # of control points.
On Fri, 19 Aug 2016, Elijah Mak wrote:
Hi Anastasia,
Thank you for looking into that subject. I have tried reinitiliasation a few
times and in all cases, it
ju
Hi Elijah - It looks to me like the forceps major had the same problem for
both MNI and CVS in this subject, right? This subject has a relatively
thin and somewhat convoluted forceps major, so you can try increasing the
number of control points, say from 7 to 8. (But I'd try reinitialization
very much!
Best,
Taha
On Fri, Aug 19, 2016 at 9:49 AM, Anastasia Yendiki
wrote:
Hi Taha - Trying getting a .dat registration file from bbregister
and using that as the input to mri_vol2surf. There's a multimodal
tutorial on the freesurfer wiki that might be of help.
Hi Eun Young - Not sure if anyone has a more elegant solution but it
sounds like you could split your positive and negative activations into 2
volumes and use the 2 different colormaps for them.
Best,
a.y
On Thu, 18 Aug 2016, Eun Young Choi wrote:
> Hi all,
>
> I'd like to have a freeview co
Hi Taha - Trying getting a .dat registration file from bbregister and
using that as the input to mri_vol2surf. There's a multimodal tutorial on
the freesurfer wiki that might be of help.
Best,
a.y
On Thu, 18 Aug 2016, Taha Abdullah wrote:
Hello All,
I am trying to project FA map (dtifit_F
Hi Elijah - You add "set reinit =1" to the config file, (and remember to
set the pathlist and subjlist to only what you want to rerun), and then
rerun the -prior and -path steps in that order.
Best,
a.y
On Thu, 18 Aug 2016, Elijah Mak wrote:
Thanks for the tips on reinitialisation of tract
Hi Elijah - It looks like the CVS case needs to be reinitialized. In
principle you're right that if the registration is good this shouldn't be
a problem. It's hard to tell what might've caused this in an individual
case without looking at the data. If you want me to look into it you can
uploa
-- Forwarded message --
Date: Tue, 16 Aug 2016 22:55:47 +
From: Sasha Klistorner
Research Fellow - Neuroimaging
Save Sight Institute and Brain and Mind Centre
Sydney Medical School
Reference no. 1332/0816
· Join a collaborative and supportive research team
· Bri
Hi Yoon - Please see "FA ROI analysis" in the diffusion tutorial on the
freesurfer wiki:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Diffusion_DtiIntegration#FAROIAnalysis
Best,
a.y
On Mon, 15 Aug 2016, Chung, Yoonho wrote:
Hi Anastasia,
Is it possible to extract diffusion mea
Hi - Check out the dmri_trk2trk command. In your case, you'd need to pass
it a transformation file from the registration between your diffusion and
structural data, which you can compute with bbregister.
Best,
a.y
On Mon, 15 Aug 2016, "김재명" wrote:
Dear expert.
Hi. I'm a newbie using Fr
Once more thank you very much for your
initial response and your time!
Best,
Nasia Metoki
On Sat, Aug 13, 2016 at 8:03 PM, Anastasia Yendiki
wrote:
Hi Athanasia - TRACULA expects certains files named a certain
way to be
there at the end of each preprocessing step. These are
Hi Athanasia - TRACULA expects certains files named a certain way to be
there at the end of each preprocessing step. These are described here:
https://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Outputdirectoriesandfiles
If you are using pre-existing files, you have to make sure that they
follo
Hi - Does this directory exist?
ERROR: fio_pushd:
/cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/mni
I'd have to see the entire trac-all.log file to tell you for sure. The
first error may show up earlier than the one that causes the crash.
Thanks,
a.y
On Mon, 8 Aug 20
Hi Barbara - This can be done with mri_vol2surf. The projection that's
described in that passage can be done with --projdist-max -6 6 1, and the
surface smoothing with --surf-fwhm 6. There are other options in
mri_vol2surf, I'd recommend playing with the settings to see what works
better for y
icine
**
2016-07-31 22:49 GMT+09:00 Anastasia Yendiki :
Hi Anri - Instead of hard-coding some ROIs in the white matter that the
tract is forced to go
through, TRACULA uses information like "what is the probability that this
tract goes
Hospital, Kyoto Prefectural University of Medicine
**
2016-07-31 13:22 GMT+09:00 Anastasia Yendiki :
Hi Anri - TRACULA does not use deterministic ROIs. It uses a probabilistic
model of how likely each tract is to go thr
Anastasia Yendiki :
Hi Anri - The problem is in this line:
set cmd = ($cmd --ref $cvstempdir/$cvstemp)
It should be changed to this:
set cmd = ($cmd --ref $cvstempdir/$cvstemp/mri/norm.mgz)
For this to take effect, you need to run "
-boun...@nmr.mgh.harvard.edu on behalf of
Anastasia Yendiki" wrote:
Hi Dillan - Thank you for your support!
Because the maximum value can sometimes be an outlier, we use the values
of the 99th percentile instead. In the absence of an outlier this would be
very close to the maximum.
Best,
a.y
On T
>
>
> On 27/07/2016 06:25, Anastasia Yendiki wrote:
>> Hi Barbara - We're working on a new atlas for TRACULA that will include
>> the fornix. We've already done the manual labeling for it.
>>
>> Best,
>>
>> a.y
>>
>> On Mon, 25 J
Hi Dillan - Thank you for your support!
Because the maximum value can sometimes be an outlier, we use the values
of the 99th percentile instead. In the absence of an outlier this would be
very close to the maximum.
Best,
a.y
On Tue, 26 Jul 2016, Newbold, Dillan wrote:
Hi everyone,
I’m h
Hi Barbara - Your hack sounds like the right idea. One option would be to
switch the FA values between the pathstats.byvoxel.txt files in the lh.*
and rh.* output directories, by editing the text files without renaming
the directories.
Hope this helps,
a.y
On Mon, 25 Jul 2016, Barbara Kreilk
Hi Barbara - We're working on a new atlas for TRACULA that will include
the fornix. We've already done the manual labeling for it.
Best,
a.y
On Mon, 25 Jul 2016, Barbara Kreilkamp wrote:
> Dear Anastasia,
>
> As we are analyzing DTI data acquired in patients with epilepsy we are
> especially
Hi Michael - Which build of freesurfer do you use? I can send you the new
version of dmri_paths so you can try it out.
Best,
a.y
On Wed, 20 Jul 2016, Harms, Michael wrote:
Hi Anastasia,
I was wondering what the resolution to this thread was:
http://www.mail-archive.com/freesurfer%40nmr.m
ellent for both timepoints, for
> all subjects... Any other thoughts about what might be causing this?
>
> Kind regards,
> -Derek
> ________
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anasta
心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**
2016-07-13 6:16 GMT+09:00 Anastasia Yendiki :
Hi A
/home/knutjbj/subjects/4_test/dmri/xfms/diff2anatorig.bbr.mat
Can you please try running this with the 5.3 version?
Thanks!
a.y
On Wed, 13 Jul 2016, Knut J Bjuland wrote:
Hi Anastasia
Thanks. I am sending my entire trac-all.log
Knut Jøgen
On 07/12/2016 11:19 PM, Anastasia Yendiki wrote
Hi Knut Jørgen - Can you please send your entire trac-all.log? Thanks!
a.y
On Mon, 11 Jul 2016, Knut J Bjuland wrote:
flirt.fsl -ref
/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/refvol.fslregister.nii
-in
/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**
2016-07-07 20:12 GMT+09:00 Anastasia Yendiki :
Hi Anri - Is there an error in the stats/*.log files fo
uestion as well please?
>
> How would I be able to use a different colormap under point sets please?
> I can only find "solid color" and "heatmap" but for example a
> blue-yellow-to-red colormap would suit my needs more.
>
> Thank you,
>
> Best wishes,
>
et me know.
Thanks
Shashwath
On Mon, Jul 4, 2016 at 3:25 AM, Anastasia Yendiki
wrote:
Hi Shashwath - It looks like you have modified the directory structure of
the output files.
Normally the dpath/ directory is right under the directory with subject's
name. From your fil
txt file is attached.
>
>
> Thanks a bunch,
> -Derek
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki
> [ayend...@nmr.mgh.harvard.edu]
> Sent: Thursday, Jul
Hi Barbara - I don't believe that freeview has an option to show colorbars
for heat maps that are loaded onto waypoints (if that's what you're
trying to display). We should definitely add it in the future.
Best,
a.y
On Wed, 6 Jul 2016, Barbara Kreilkamp wrote:
> Dear Freesurfers,
>
> I am loo
> -stat
>
> -Derek
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki
> [ayend...@nmr.mgh.harvard.edu]
> Sent: Monday, July 04, 2016 12:47 AM
> To: F
属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**
2016-06-02 3:03 GMT+09:00 An
Hi there - I think I know what it is, but it's a problem that should be
solved if you have the last tracula update. It means that your LANG
environment variable needs to be set to en_US.UTF-8, which the update does
for you.
a.y
On Tue, 5 Jul 2016, Lars M. Rimol wrote:
Hi Anastasia,
I ha
idea what this could be ?
Thanks,
Ismail
On Jul 4, 2016, at 3:15 PM, Koubiyr, Ismail
wrote:
It says 1 … I don’t understand why I get that knowing that when I open
the nifti I can go through the frames …
Ismail
On Jul 4, 2016, at 3:11 PM, Anastasia Yendiki
wrote:
.
Also why the DICOMs wouldn’t work at the beginning ?
Thanks,
Ismail
On Jul 4, 2016, at 2:41 PM, Anastasia Yendiki
wrote:
Hi Ismail - You can see from the log file that the command that causes the
error is this:
mri_convert --frame 31
/Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri
nastasia,
Here it is.
But how could the problem be related to the nifti volume since I have errors
when using the DICOMs too ?
Thanks again,
Ismail
> On Jul 4, 2016, at 1:44 PM, Anastasia Yendiki
wrote:
>
>
> Hi Ismail - It sounds like the error has to do with the nifti volume, n
ors.
The bvecs and bvals are obtained from dcm2nii and then corrected to avoid
any additional space.
Thank you in advance for your help.
Best,
Ismail
P.S : 3T2_bvecs.txt and 3T2_bvals.txt are the original files used.
On Jul 4, 2016, at 3:32 AM, Anastasia Yendiki
wrote:
Hi Ism
uroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO 63110Email: mha...@wustl.edu
On 7/4/16, 2:41 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Anastasia Yendiki" w
Hi Lars - At first glance, these files look fine to me. Do the dmri/bvals
and dmri/bvecs files that get generated look fine too?
a.y
On Sat, 2 Jul 2016, Lars M. Rimol wrote:
Hi,
Trying to run trac-all -c dmric_file -prep, I get an error message stating
that there are different numbers of
Hi Derek - Are you by any chance using the dev version of freeview?
a.y
On Fri, 1 Jul 2016, Derek Pisner wrote:
Dear Anastasia,
I am running into an issue with the trac-all -stat option on our longitudinal
TRACULA data.
Everything runs smoothly through all earlier stages, and I checked ind
Hi Michael - Indeed it should not be too difficult to add the feature of
specifying the b-value table for each scan and I can add this in the next
version.
However, I would be a bit careful with removing different DWI volumes for
different time points. The acquisition should be as consistent
Hi Ismail - Are you passing the nifti volume as input to trac-all? It's
hard to tell without looking at your configuration file.
Best,
a.y
On Tue, 28 Jun 2016, Koubiyr, Ismail wrote:
> Hi everyone,
>
> I have some problems trying to run TRACULA on some DWI data. It is a mosaic
> Siemens DWI.
Hi Yang - Have you followed the instructions on how to set up the
freesurfer environment?
https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall#Setup.26Configuration
Best,
a.y
On Mon, 13 Jun 2016, yangfuxing wrote:
Hi professor?? When I finished setting up the configuration file "
Hi Shashwath - It looks like you have modified the directory structure of
the output files. Normally the dpath/ directory is right under the
directory with subject's name. From your file of inputs, it looks like
you've created some other subdirectories and now dpath/ is a few levels
down the
Hi Yang - TRACULA does not assume that the shape, size, or integrity of
the tracts is the same in the study subjects as in the atlas subjects. It
just assumes that the relative position of the tracts with respect to the
cortical and subcortical segmentation labels from freesurfer. For example,
Hi - It's hard to predict in advance what will happen without trying it
out. A lot will depend on the size/position/nature of the tumor. Some
tumor patients will go through just fine, other will have issues. If the
freesurfer segmentation works, then tracula will work too.
Best,
a.y
On Thu,
**
2016-05-31 22:55 GMT+09:00 Anastasia Yendiki :
Hi Anri - Can you also send your log file (scripts/trac-all.log)? I'll
need to see what
exactly was running when the error occurred. Thanks!
a.y
On Sat, 28 May 2016, Anri WAT
different metrics (FA, MD,..)
Is there a way I can use the trac-all on these files?
On 5/31/16, 9:26 PM, "Anastasia Yendiki"
wrote:
Some of the errors make me suspect that your input DWI files contain only
one volume. Could this be the case?
On Tue, 31 May 2016, Jacobs H (NP) wrote:
Hmm, w
much
Heidi
On 5/31/16, 8:13 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Anastasia Yendiki" wrote:
Hi Heidi - It knows where to find the freesurfer recons of the T1's from
SUBJECTS_DIR (see example config file). Based on your log file, it looks
like you haven't
mmand knows where to find the T1 data?
Thanks
Heidi
On 5/31/16, 5:07 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Anastasia Yendiki" wrote:
No, it should be pointed to the DWI data, which can be corrected niftis
instead of the original dicoms. I would recommend turning
configuration file. You
will see that I tried the inter and intra option, because I thought that
for the inter it would not need anything else than the MNI template and
the DTI images.
Thanks
Best
Heidi
On 5/31/16, 4:01 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Anastasia Ye
Hi Heidi - The intra-subject registration step that you're trying to run
registers your subject's DWI and T1 images. It expects to find those
images. It doesn't use the FA, MD, etc in any way.
Did the log file get created in scripts/trac-all.log? If so, can you
please send that file and your
artment of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**
2016-05-27 22:57 GMT+09:00 Anastasia Yendiki :
Hi Anri - I do not know what command line you ran and what your
configuration file look
05-21 6:48 GMT+09:00 Anastasia Yendiki :
Hi Anri - The FA values are extracted in the native space of each
subject, which is why those are the only
coordinates that you see. If you want to display the results of your
analysis on an average path, after
running trac-all -stat, y
wrote:
Correct.
On Sunday, May 22, 2016, Anastasia Yendiki
wrote:
No idea, sorry. You used the -c option with the previous steps of
trac-all and didn't see this
error, correct?
On Sun, 22 May 2016, Jasmin Alves wrote:
Hi
g the following error:
ERROR: flag –c unrecognized -path –c dmrirc1_sim.txt
This occurs when I do trac-all -path –c dmrirc1_sim.txt
I tried looking at posts from previous mailing lists, and found no match to
this problem.
Thank you,
Jasmin
On Sun, May 22, 2016 at 5:53 PM, Anastasia Yendiki
Ok, then you can ignore the error that you see when you run the bedpost
step.
`On Sun, 22 May 2016, Jasmin Alves wrote:
Sorry for the mix-up. All of the bedpost output files are generated as well
both 1 and 2 of each file.
On Sun, May 22, 2016 at 4:22 PM, Anastasia Yendiki
wrote
p won't work. I have ran it a few times and the bedpost step ends at the
same point.
On Sun, May 22, 2016 at 3:24 PM, Anastasia Yendiki
wrote:
But do you see the output files from the previous step? The
outputs from each step are described on the wiki.
On Sun, 22 May
dmrirc1_sim.txt
I get the following error:
ERROR: flag –c unrecognized
-path –c dmrirc1_sim.txt
Thanks,
Jasmin
On Sun, May 22, 2016 at 1:51 AM, Anastasia Yendiki
wrote:
Hi Jasmin - Check if things are running despite that error. Are
output files being generated?
a.y
On Sat
Hi Jasmin - Check if things are running despite that error. Are output
files being generated?
a.y
On Sat, 21 May 2016, Jasmin Alves wrote:
Dear Freesurfer,
While doing the bedpost step for TRAC-all ( trac-all -bedp -c
dmrirc1_sim.txt) I received the following error:
/Applications/freesur
(I'm assuming the configuration file
> only looks for dcm images)? Would we also need to run bedpostX again
> separately with the concatenated images?
>
> Thanks again for your help!
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
>
Hi Kristina - I'm assuming the 2 data sets were acquired in the same
session and with the same acquisition parameters, other than the b-values?
Then you can just concatenate the DWIs from the 2 runs (e.g. with
mri_concat) and also concatenate the b-value and gradient vector tables
(and make s
Hi Anri - The FA values are extracted in the native space of each subject,
which is why those are the only coordinates that you see. If you want to
display the results of your analysis on an average path, after running
trac-all -stat, you can use the stats/*.path.mean.txt files (see also the
Hi Qi - Is /Studies/*/DTI/dmrirc_subject a single file or multiple files?
What are the contents of that file?
a.y
On Fri, 6 May 2016, Zeng, Qi wrote:
Hi,
I am running dti data with trac-all. I followed the command:
trac-all -prep -c /Studies/*/DTI/dmrirc_subject
but it exited with erro
Hi Elijah - Since the error occurs in the CST, is any of the brainstem cut
off for this subject? It's hard to tell from the screenshot, but the field
of view seems a bit cropped inferiorly.
Best,
a.y
On Thu, 5 May 2016, Elijah Mak wrote:
> Dear Anastasia Yendiki,
> I ran into a
Hi Xiaofu - It's hard to tell but it looks like the brain mask (which
comes from the structural data) is a bit too large in the temporal lobe,
so it's possible that the structural-to-diffusion registration didn't go
so well for this subject. You can check on this by overlaying the
structural
Hi Peggy - If it looks like a single path, it definitely is an
initialization error. If you reinitialize repeatedly and it doesn't get
fixed, it might be that something went wrong earlier in the processing
(for example some part of brain that the tract goes through is missing
from the brain m
Hi Marissa - If your bvecs/bvals files are in row format, you need to make
sure that you have the most recent update that supports this. It was a
feature that was added later on:
http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates
Best,
a.y
On Fri, 15 Apr 2016, Marissa Pifer wrote:
H
Hi Elijah - Are the bvec/bval files located in the current directory from
where you are running trac-all? This is where it seems to be looking for
them:
cp 16084.bvec
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig.mghdti.bvecs
cp 16084.bval
/Users/MacPro/Documen
Hi Bryan - It'll convert whatever input you give it to nifti, so it's fine
if your input is already nifti.
Best,
a.y
On Wed, 6 Apr 2016, Chiu, Bryan (PHTH) wrote:
Hi,
I’m looking to do some DTI analysis with dt_recon. I have Philips acquired DTI
images in par/rec. I ran dcm2nii
and have r
.
Do you have other suggestions regarding how to change the script, so it will
create the data.nii without the
symbolic link (there are plenty "ln" commands uses in the script)?
Many thanks,
Efrat
On Wed, Mar 30, 2016 at 12:39 AM, Anastasia Yendiki
wrote:
Hi Efrat - This app
i, MD
---
Research Fellow in Radiology
Massachusetts General Hospital
Harvard Medical School
25 New Chardon Street, Suite 400
Boston, MA 02114
Tel: 617 726 5237
Email: e...@nmr.mgh.harvard.edu
On Apr 1, 2016, at 10:49 AM, Anastasia Yendiki
wrote:
Hi Emad - The error happens at the very beginning, s
Hi Emad - The error happens at the very beginning, so I'm wondering if
something went wrong in the previous steps, before -path. Can you please
send me the entire trac-all.log of one of your subjects? Thank you!
a.y
On Wed, 30 Mar 2016, Emad Ahmadi wrote:
Hi Anastasia,
I hope you’re enjoy
Hi Efrat - This appears to be a virtual machine problem:
https://communities.vmware.com/thread/312591?tstart=0
There are some solutions suggested in that thread. I'm wondering if using
a relative instead of an absolute path for the symlink works, i.e.,
ln -sf dwi.nii.gz /mnt/hgfs/linux_share
Hi Elijah - I suggest looking at the axial diffusivity (AD) and radial
diffusivity (RD) to help you interpret these results. These are the
diffusivity parallel and perpendicular to the main budnle going through a
voxel, respectively. Essentially, FA tells you how different the AD and RD
are f
.
However, I am not getting an error during the prep or the bedpost stage, and
so I am still completely lost any advice would be deeply appreciated!
Thank you,
KD
On Wed, Jan 13, 2016 at 6:07 PM, Anastasia Yendiki
wrote:
Hi Katherine - Do the freesurfer segmentations look ok? What
about
hem on different machines or is because I
> had to run the bedpostx command directly ?
>
> Thanks!
> -Prad
> _______
>
> _
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> on behalf of Anastasia Yendiki
>
> Sent: Monday, March 7, 2016
-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki
> [ayend...@nmr.mgh.harvard.edu]
> Sent: Monday, March 07, 2016 12:20 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] path.pd.trk format
>
> What to you want to display it on? If you want to display in on the FA
anatorig..mat or
> /dmri/xfms/diff2anat..mat transformation matrices?
>
> Thanks again,
> Noam
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki
> [ayend...@nmr.m
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