On 10/30/2023 9:50 PM, Mirsol Choi wrote:
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Hi there,
I am currently going through the dt_recon tutorial on your website and
I just have a quick question regarding the recon-all and dt_recon
commands on freesurfer.
For me to process dt_recon, my
External Email - Use Caution
Hi there,
I am currently going through the dt_recon tutorial on your website and I
just have a quick question regarding the recon-all and dt_recon commands on
freesurfer.
For me to process dt_recon, my understanding is that I must process
recon-all
Do you see a filed called dwi-ec.nii.gz? That should be the output of
eddy_correct. The log file says it is running it. Two min does seem a
little fast for 60 directions; I have another case that does 340 in
about 40min. Try running eddy_correct outside of dt_recon and see what
happens.,
On
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Dear Freesurfer Developers,
I am trying to perform the dt_recon command for a single participant of my
dataset. The original data comes from a philips scanner and was in the PAR/REC
format. I converted these files to nifti’s using dcm2niix. This
There might be something wrong with the dicom, so first, try to convert
the dicom to nii.gz with mri_convert
On 5/10/2022 3:23 AM, m-maiw...@web.de wrote:
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Hi all,
I try to run dt_recon on my dicom files, acquired with a siemens
scanner unsing the command
External Email - Use CautionHi all,
I try to run dt_recon on my dicom files, acquired with a siemens scanner unsing the command from the wiki.
The dwi.nii.gz and the dwi-ec.nii.gz as well as the bval and bvec files are generated without problems. Then following error massage
are arising.
Best,
Matt
From: freesurfer-boun...@nmr.mgh.harvard.edu
Date: Saturday, January 9, 2021 at 9:06 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] dt_recon error: dimension mismatch between y and X
External Email - Use Caution
Dear FS experts,
I’m attempting to run
External Email - Use CautionDear FS experts,I’m attempting to run dt_recon on my own DWI DICOM file with registration to corresponding structural data, as described in FS diffusion tutorial (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to
External Email - Use Caution
It might be an issue with the current freesurfer dev version because when I
change it back to the Freesurfer 6.0 version it works perfectly fine? And
has no issues reading them.
On Tue, Apr 2, 2019 at 1:51 PM Greve, Douglas N.,Ph.D. <
It is having problems reading both the bvals and the bvecs
On 4/2/19 9:34 AM, Daniel Callow wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I am running dt_Recon with the following specifications and am running
> into this issue? I wasn't running into this issue previously. Two
>
External Email - Use Caution
Hello,
I am running dt_Recon with the following specifications and am running into
this issue? I wasn't running into this issue previously. Two changes I made
are I added the --eres-save flag and I am running the code on the dev
version instead of the
We don't really have a good way to do this. In theory, you could
concatenate them together and then let the motion correction fix the
misalignment, but I could imagine it would create some problems.
On 3/14/19 8:00 AM, Daniel Callow wrote:
>
> External Email - Use Caution
>
> Hello
External Email - Use Caution
Hello Doug,
If I collected 3 dti scans at each time point and I wanted to know how
would I go about incorporating them all into dt_recon to improve my SNR?
Could I just pull all the DICOMS into 1 folder? Or process each one
separately?
Thanks,
Daniel
I don't know, probably a better question for the FSL group
On 3/1/19 8:57 AM, Daniel Callow wrote:
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Hi Doug,
I was looking at the dt_recon code and was wondering if it would be possible to
incorporate a field map into the eddy_correct portion? I tried to
External Email - Use Caution
Hi Doug,
I was looking at the dt_recon code and was wondering if it would be
possible to incorporate a field map into the eddy_correct portion? I tried
to test it on one subject and tried to add --field=$pathtofieldmap to the
eddy_correct command
External Email - Use Caution
I was also running an ROI analysis based on the recon-all segmentations so
I figured I could use the FA results and skip the process of running
through the whole tbss process. I also found dt_recon's ability to
determine bvals and bvecs from the dcm
no idea. If you want to use tbss, why not use FSL to do the dti analysis
from the start?
On 2/26/19 10:27 AM, Daniel Callow wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I am working through dt_recon troubleshooting (One subjects
> registration to anatomical is skewed leading
Did you check the registration? My guess is that the registration failed
because the initial FSL registration failed. I've put a new version here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/dt_recon
it has a better initializer. Just copy it over the one in
$FREESURFER_HOME/bin (make a
External Email - Use Caution
Hello,
I am working through dt_recon troubleshooting (One subjects registration
to anatomical is skewed leading to incorrect masking of that subjects FA
image). I would like to use the dt_recon's FA outputs and input them into
FSL's tbss pipeline. My
External Email - Use Caution
Hello freesurfer experts,
I am running dt_recon with the following script
dt_recon --sd /Volumes/DANIEL/dti_freesurf/diffusion_recons --i
/Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/image01.dcm
--s ${subj}.${cond} --b dwi.bvals
See here
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalRegistration_freeview
On 2/21/19 3:01 PM, Daniel Davidson Callow wrote:
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Hello,
I have run through dt_recon and want to use anatomically based segmentations
(aseg) to create ROIs for
External Email - Use Caution
Hello,
I have run through dt_recon and want to use anatomically based
segmentations (aseg) to create ROIs for the diffusion-weighted data using
mri_vol2vol.
I ran
mri_vol2vol --mov $subj_dir/dtrecon/${subj}.${cond}./lowb.nii.gz --targ
External Email - Use Caution
Thanks!
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com *
443-254-6298
On Fri, Feb 15, 2019 at 11:18 AM Greve, Douglas N.,Ph.D. <
Can you do this in two steps? First, convert the dicom to a volume format (eg,
mgz or nii.gz) with
mri_convert image001.dcm dwi.nii.gz
This may or may not create bvals and bvecs. If not, then you will have to
supply them. If they are created, look at them and make sure they are right.
Next
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Hello, running the following command line script for dt_recon
dt_recon --debug --i
/Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/image01.dcm
--s ${subj}.${cond} --o /Volumes/DANIEL/tutorial_data/dtrecon
MatrixReadTxT: could not
you can only give it one dicom file from the series, it will find the rest.
On 2/14/19 4:11 PM, Daniel Callow wrote:
>
> External Email - Use Caution
>
> As you can see the folder has 65 DICOM images labeled
> images01.dcm-images65.dcm.
>
> I tried
>
> dt_recon --i
>
I never saw an email with the result of the ls -l command
On 2/14/19 3:36 PM, Daniel Callow wrote:
>
> External Email - Use Caution
>
> Hi Douglas,
>
> I was unsure if the emails I had been replying with were going
> through. They did not seem to come up on the mailing list so I wasn’t
External Email - Use Caution
Hi Douglas,
I was unsure if the emails I had been replying with were going through.
They did not seem to come up on the mailing list so I wasn’t sure if they
had reached you. I recently responded to your question about the ls -l path
output and the
what happens when you run
ls -l /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
On 2/13/19 6:45 PM, Daniel Callow wrote:
>
> External Email - Use Caution
>
> Here it is.
>
>
> [hlhp-105:DANIEL/scripts/dti_freesurfer] administrator% dt_recon
> --debug --i
>
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Here it is.
[hlhp-105:DANIEL/scripts/dti_freesurfer] administrator% dt_recon --debug
--i /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm --s
AES101.Ex --o /Volumes/DANIEL/tutorial_data/dtrecon
set echo = 1 ;
breaksw
breaksw
end
what happens when you run
ls -l /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
On 2/13/19 6:27 PM, Daniel Callow wrote:
>
> External Email - Use Caution
>
> The error output that accompanies the command.
>
>
> administrator% dt_recon --debug --i
>
Yes. Can you run it with --debug with the slash in front of "Volumes"?
On 2/13/19 6:25 PM, Daniel Callow wrote:
>
> External Email - Use Caution
>
>
> Is this what you mean by no variables??
>
> dt_recon --debug --i
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm --s
External Email - Use Caution
The error output that accompanies the command.
administrator% dt_recon --debug --i
/Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm --s
AES101.Ex --o /Volumes/DANIEL/tutorial_data/dtrecon
set echo = 1 ;
breaksw
breaksw
end
end
External Email - Use Caution
Is this what you mean by no variables??
dt_recon --debug --i
/Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm --s
AES101.Ex --o /Volumes/DANIEL/tutorial_data/dtrecon
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
can you send the command line without the variables?
On 2/13/19 5:19 PM, Daniel Davidson Callow wrote:
>
> External Email - Use Caution
>
> Thanks for pointing that out! Unfortunately after making the change
>
> dt_recon --debug --i
>
External Email - Use Caution
Thanks for pointing that out! Unfortunately after making the change
dt_recon --debug --i
/Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/1-65.dcm --s
${subj}.${cond} --o /Volumes/DANIEL/tutorial_data/dtrecon
I still get the error.
External Email - Use Caution
Hello Daniel.
It looks like you need a slash in front of Volumes for the path after —I/Volumes
- R.
On Feb 13, 2019, at 14:44, Daniel Davidson Callow dcal...@umd.edu
wrote:External Email - Use
CautionHello,I am trying to run
dt_recon on my dtidata
External Email - Use Caution
Hello,
I am trying to run dt_recon on my dti data using the following script.
dt_recon --debug --i
Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/1-65.dcm --s
${subj}.${cond} --o /Volumes/DANIEL/tutorial_data/dtrecon
with the
Hello FreeSurfer Developers,
I am trying to follow the diffusion processing pipeline describe in this
tutorial:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/DiffusionV6.0#dMRIDataAnalysisProcessingStream
However, I keep getting an error when using dt_recon. For background, my
input is
Hello FreeSurfer Developers,
I'm trying to pre-process some diffusion data based on the tutorial:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/DiffusionV6.0
I am getting the following warning followed by the program hanging
--
Creating output directory
Dear Doug,
I figured out the mistake I was making, which was that I ran:
> freeview -v orig.mgz wmparc2diff.mgz:colormap=lut
> lowb.nii.gz:reg=register.dat -f lh.white:edgecolor=green
> rh.white:edgecolor=green -viewport coronal &
Here the lowb, orig, and white surfaces were consistent.
Can you send the command line and terminal output?
On 11/10/17 1:34 PM, Mehta, Chintan wrote:
Dear FreeSurfer users,
Sorry for adding the questions, I found most of my answers at
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/DiffusionV6.0#dMRIDataAnalysisProcessingStream
I used
Dear FreeSurfer users,
Sorry for adding the questions, I found most of my answers at
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/DiffusionV6.0#dMRIDataAnalysisProcessingStream
I used FreeView and found that registrations of the lowb.nii, orig.mgz,
lh.white, and rh.white aligned very
Dear FreeSurfer users,
I've been using FreeSurfer and Tracula versions 6.0. I've run Tracula on DWI
scans, and now I am seeking to run dt_recon on them as well. As a new user, it
seems both programs follow similar initial pre-processing steps (eddy current &
motion correction), which the
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
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 retrieved the associated *bval, *bvec
and *nii.gz files that come out.
In the tutorial it mentions the -i flag requiring a dcm image. Is it possible
to pass a *.nii.gz
” to describe the
analysis?
Thanks
Mohamad
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve
Sent: Monday, September 28, 2015 11:26 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] dt_recon
On 9/25/15 9:28 AM
urfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve
Sent: Monday, September 28, 2015 11:26 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] dt_recon
On 9/25/15 9:28 AM, Alshikho, Mohamad J. wrote:
Hi Doug and Bruce,
After running the command :
dt_recon --i 6-1025.dcm --s M87
rm " DTI morphometry" to describe the
analysis?
Thanks
Mohamad
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve
Sent: Monday, September 28, 2015 11:26 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer]
On 9/25/15 9:28 AM, Alshikho, Mohamad J. wrote:
Hi Doug and Bruce,
After running the command :
dt_recon --i 6-1025.dcm --s M87102113 --o dti dt_recon --i f.nii --b
f.bvals f.bvecs --s M87102113 --o dti <<< source: Freesurfer wiki>>>
I need to generate the final statistics ( FA for
Hi Doug and Bruce,
After running the command :
dt_recon --i 6-1025.dcm --s M87102113 --o dti dt_recon --i f.nii --b f.bvals
f.bvecs --s M87102113 --o dti <<< source: Freesurfer wiki>>>
I need to generate the final statistics ( FA for every parcellate and segment
in aseg and
Thanks, Doug!
Pedro Rosa
On Monday, May 11, 2015 at 6:51 PM, Douglas N Greve wrote:
It sounds like you did the right thing.
On 05/10/2015 02:41 PM, Pedro Rosa - GMail wrote:
Dear developers,
I am running an analysis with dt_recon, and it seems that my DWI files
are organized into
It sounds like you did the right thing.
On 05/10/2015 02:41 PM, Pedro Rosa - GMail wrote:
Dear developers,
I am running an analysis with dt_recon, and it seems that my DWI files
are organized into three series (one larger, and two smaller, that I
believe are ADC and Trace). Inputing a DICOM
Dear developers,
I am running an analysis with dt_recon, and it seems that my DWI files are
organized into three series (one larger, and two smaller, that I believe are
ADC and Trace). Inputing a DICOM file to dt_recon generates a .nii file from
one of the series only (the larger one, once it
Hi All,
I ran dt_recon and got the following error. Can someone suggest how to fix this
? I have attached the dwi-infodump.dat file for more information.
Thanks a lot for the help.
Best
Rito
#@#---
Fitting Tensors
Mon Aug 11 07:29:29 EDT 2014
cd
Greve
Sent: Tuesday, May 27, 2014 6:45 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] dt_recon error
Did it actually fail? If not, does the registration look ok? That msg should
just be a warning doug
On 05/27/2014 02:06 PM, Weber, Wade (weberw) wrote:
Hi all,
I have been
...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Tuesday, May 27, 2014 6:45 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] dt_recon error
Did it actually fail? If not, does the registration look ok? That msg should
just
The registration completed fine.
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Wednesday, May 28, 2014 11:30 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] dt_recon error
Hi all,
I have been trying to work with DTI data in FreeSurfer for the first time. We
acquire our data on a 4T Varian and reconstruct into AFNI format (BRIK/HEAD
files). I set up the bval and bvec files successfully and ran the dt_recon
script. It seemed to run fine until I got an
Did it actually fail? If not, does the registration look ok? That msg
should just be a warning
doug
On 05/27/2014 02:06 PM, Weber, Wade (weberw) wrote:
Hi all,
I have been trying to work with DTI data in FreeSurfer for the first
time. We acquire our data on a 4T Varian and reconstruct
Dear freesurfer experts,
As far as I understand, dt_recon uses linear least squares method as
default to estimate the diffusion tensor. Is it possible to use weighted
linear least squares in dt_recon?
Thank you.
Estephan Moana-Filho, DDS, MS, PhD
Clinical Fellow, Oral Maxillofacial Pain
In principle if you knew the weights you could weight each direction
(but not across weights). But it will not compute such weights for you
doug
On 4/17/14 7:35 PM, Estephan Moana wrote:
Dear freesurfer experts,
As far as I understand, dt_recon uses linear least squares method as
default
has it been anonymized?
On 02/11/2014 02:23 PM, Gennan Chen wrote:
HI! All,
I got an error when I ran dt_recon
WARNING: file /Users/gnchen/tmp/3011_DTI/orig/MR01.dcm does not
contain a Siemens ASCII header
has this file been anonymized?
ERROR: cannot unpack mosiacs without ASCII
Subject: Re: [Freesurfer] dt_recon error for Siemens mosaics image
has it been anonymized?
On 02/11/2014 02:23 PM, Gennan Chen wrote:
HI! All,
I got an error when I ran dt_recon
WARNING: file /Users/gnchen/tmp/3011_DTI/orig/MR01.dcm does not
contain a Siemens ASCII header
has
@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] dt_recon error for Siemens mosaics image
has it been anonymized?
On 02/11/2014 02:23 PM, Gennan Chen wrote:
HI! All,
I got an error when I ran dt_recon
WARNING: file /Users/gnchen/tmp/3011_DTI/orig/MR01.dcm does not
contain a Siemens ASCII
HI! All,
I got an error when I ran dt_recon
WARNING: file /Users/gnchen/tmp/3011_DTI/orig/MR01.dcm does not contain a
Siemens ASCII header
has this file been anonymized?
ERROR: cannot unpack mosiacs without ASCII header
I can confirm it is Siemens mosaics format. Any idea how to by pass
Howdy,
I'm trying to run *dt_recon* on some DTI data but seem to be having some
trouble with the number of b-values and b-vectors not matching the number
of data frames we have (see dt_recon logfile below).
Some basic parameters of our sequence are as follows:
- TR = 10 s
- TE = 96.2 ms
Dear FS experts,
I would like to know if for a Diffusion tensor imaging (DTI) tractography study
with TRACULA I can use my previous results from FSTutorial/Diffusion more
exactly my results after running dt_recon and registrations on the CVS space.
If not can you please advise me if for a DTI
Trackvis does deterministic tractography, not probabilistic.
Which previous results do you want to use and why?
On Wed, 28 Mar 2012, Antonella Kis wrote:
Dear FS experts,
I would like to know if for a Diffusion tensor imaging (DTI) tractography
study
with TRACULA I can use my previous
, 2012 2:07 PM
Subject: Re: [Freesurfer] dt_recon and tractography
Trackvis does deterministic tractography, not probabilistic.
Which previous results do you want to use and why?
On Wed, 28 Mar 2012, Antonella Kis wrote:
Dear FS experts,
I would like to know if for a Diffusion tensor imaging
___
From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
To: Antonella Kis ator...@yahoo.com
Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, March 28, 2012 2:07 PM
Subject: Re: [Freesurfer] dt_recon and tractography
Trackvis does
Hi John,
Could you send us the terminal output containing the error you receive
when running dt_recon?
-Louis
On Fri, 9 Mar 2012, John Fredy wrote:
Hello all, I am trying to process siemen dti data from a skyra model in the
dt_recon software. But the software fails in the conversion from
Hello all, I am trying to process siemen dti data from a skyra model in the
dt_recon software. But the software fails in the conversion from Dicom.
Anyone had experience with the DTI sequence from a skyra model?
Any suggestion is welcome
Thanks in advance
John Ochoa
Bioingeniería
Universidad de
Hi Doug,
I thought I figured this out, but I was wrong...
my b-values are 700, and number of directions is 64.
Number of images with b=0 is 1.
Text file for bvals has 65 rows, first row has 0, followed by 64 of 700.
0
700
700
700
...
Text file for bvecs has 65 rows and three columns. The
Hi Yuko, i'm guessing that something is fishy with your bval and bvec
files. Make sure that there is a new line after the last entry. How did
you make the files?
doug
On 12/13/11 11:22 PM, Yuko Yotsumoto wrote:
Hi Doug,
I thought I figured this out, but I was wrong...
my b-values are 700,
Thanks Doug,
In the dt_recon help,
The bvalues are in a simple text file, one for each direction
(including b=0). The bvectors (gradient directions) are also in a
simple text file with three components on each row. These also include
the b=0 values. There must be as many rows in the
Doug,
Never mind. I think I just figured it out!0
Yuko
On Dec 12, 2011, at 6:18 PM, Yuko Yotsumoto wrote:
Thanks Doug,
In the dt_recon help,
The bvalues are in a simple text file, one for each direction
(including b=0). The bvectors (gradient directions) are also in a
simple text
Hi Yuko, your dicom file might be from a different versioned scanner
than dt_recon is used to seeing. If so, then it cannot extract the bvecs
and bvals. If you supply them in a file on the command line, it should
run properly.
doug
Yuko Yotsumoto wrote:
Hello,
I'm having a problem with
Hi Doug,
Thank you for your reply.
If so, then it cannot extract the bvecs and bvals. If you supply them in a
file on the command line
I don't quite understand how --b works with dt_recon.
I did:
dt_recon --i
/Users/yuko/Documents/FreeSurfer/raw/AGY11ADTI/DTIs/IM-0011-0001.dcm --s AGY11
Hi Yuko, it will get the bvals and bvecs from a set of tables
distributed with FS. But the dicom has to have some information in it
that tells it which table to use. It looks like your dicom did not have
this information (it is not in the info dump created from the dicom). So
you'll have to
Hello,
I'm having a problem with dt_recon on data scanned by Siemens TrioTim.
I'm using v4.5.0, with Mac OS 10.6.8.
dt_recon ran for a while, and stopped with an error ERROR: cannot extract
sWiPMemBlock.alFree[8] from
/Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat
I
for your time and help.
Best regards,
Antonella
From: Lilla Zollei lzol...@nmr.mgh.harvard.edu
To: Antonella Kis ator...@yahoo.com
Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
Sent: Monday, November 14, 2011 4:13 PM
Subject: Re: [Freesurfer
lzol...@nmr.mgh.harvard.edu
To: Antonella Kis ator...@yahoo.com
Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
Sent: Monday, November 14, 2011 4:13 PM
Subject: Re: [Freesurfer] dt_recon registration
Hi Antonella,
1) I will be very grateful if you can confirm if my coding is write
Hi Antonella,
1) I will be very grateful if you can confirm if my coding is write. First can
you please let me know if by default dt_recon is re-sample FA to talairch
space? In this case because I want to register on CVS should I add the
--no-tal flag? I am asking this question
because
Hi all,
I use dt_recon on DTI scans from Siemens machine.
The command I used is
dt_recon --i k1/ep2d/81678191 --s k1 --o k1_DTI
The error message is as follows
sysname Linux
hostname movado-laptop
machine x86_64
user movado
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
:11 -0300
From: MRI CDPI //m...@cdpi.com.br/ mailto:m...@cdpi.com.br/
Subject: [Freesurfer] dt_recon stage 3
To: //freesurfer@nmr.mgh.harvard.edu/
mailto:freesurfer@nmr.mgh.harvard.edu/
Message-ID: //002601c8f892$f992cbc0$0100a...@cdpi.local/
mailto:002601c8f892$f992cbc0$0100a...@cdpi.local
I am using Freesurfer and I am having difficulties in coregistration of a DTI
volume to the anatomy image. I have been running
recon-all -i anatomy1.nii -i anatomy2.nii -s 2005_anatomy
followed by
recon-all -autorecon1 -s 2005_anatomy
and then
dt_recon --i dti/subj_539_dti.nii --b
The answer is in the help, I think: dt_recon --help
doug
Kjell Inge wrote:
I am using Freesurfer and I am having difficulties in coregistration
of a DTI volume to the anatomy image. I have been running
recon-all -i anatomy1.nii -i anatomy2.nii -s 2005_anatomy
followed by
recon-all
It will probably be the case that it just gives the entire volume (the
masking routine just looks for 0-valued voxels). I don't think it
actually uses the mask for anything, though.
glmfit is run because that's what the tensor analysis is.
Siddharth Srivastava wrote:
Hi everyone,
Hi Douglas,
Thanks for the reply. can i get a link to a publication or
report that describes the GLM analysis applied to tensors?
thanks,
sid.
On Mon, Feb 9, 2009 at 10:22 AM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
It will
All standard tensor analysis use a glm, they just don't often call it
that. The design matrix are columns formed from the cross products of
the gradients (of which there are 6) plus a column of 1s, and the log()
of the input data is taken before the glm. After that, it's just a glm.
Siddharth
Hi everyone,
I have recently started using the dt_recon processing
pipeline
in freesurfer. I just ran a dataset through it, and had a few questions
about
the methodology
1) How does the script calculate the mask from the DW data set. Is there any
way
to influence the mask
Dear group,
i am trying to run dt_recon on some dti data, the first two steps: image
transformation, eddy_correction, run fine.
In the third stage, the glmfit, the process stops after giving the ERROR
message:
cannot extract sWiPMemBlock.alFree[8] from .../ dwi-infodump.dat
And indeed, there is
What's your cmd line? Is this from a Siemens scanner?
MRI CDPI wrote:
Dear group,
i am trying to run dt_recon on some dti data, the first two steps:
image transformation, eddy_correction, run fine.
In the third stage, the glmfit, the process stops after giving the
ERROR message:
cannot
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