If you're using version 5.2, you don't have to set nb0. Version 5.1
assumed that there were nb0 images acquired with b=0 in the very beggining
of the DWI series, but 5.2 doesn't make that assumption.
On Tue, 2 Apr 2013, std...@virgilio.it wrote:
Hi Anastasia,
my subjects have gradient=0 on
Hi Anastasia,
my subjects have gradient=0 only in first or last line.
I'm noting that the subjects having 0.000 0.000 0.000 in the first line of
bvecs.txt (0 in vals.txt) show correct tracts.
The subjects that having 0.000 0.000 0.000 as last line of bvecs.txt show wrong
or lacking tracts.
For t
Do you have a freesurfer recon of your subject's T1 in the $SUBJECTS_DIR?
On Sun, 3 Feb 2013, std...@virgilio.it wrote:
> I think that I have resolved the bvecs error by using sudo nano option but
> now in the next step I visualize this error:
> ERROR: fio_pushd:
> /Applications/freesurfer/subje
I think that I have resolved the bvecs error by using sudo nano option but now
in the next step I visualize this error:
ERROR: fio_pushd:
/Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/mniERROR: must
specify brain mask volume for output subject
Thanks,
Stefano
Hi Anastasia,
Any news?
I checked my environment and it's ok.
LANG="en_US.UTF-8"LC_COLLATE="en_US.UTF-8"LC_CTYPE="en_US.UTF-8"LC_MESSAGES="en_US.UTF-8"LC_MONETARY="en_US.UTF-8"LC_NUMERIC="en_US.UTF-8"LC_TIME="en_US.UTF-8"
I have previously used the files that I send to you to perform FSL analysis
This is because the mac executables in freesurfer where compiled on the
leopard verion of OSX. There's an update here compiled on snow leopard
that should solve this error:
https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula
On Thu, 16 Feb 2012, Tetiana Dadakova wrote:
> Thanks for the note. I
When I look at them with the more command on a linux machine, I see 2
lines in bval and 6 lines in bvec. Most likely this is a problem with the
text files being created with a windows program like excel and not having
unix-compatible end-of-line characters. It's been discussed a few times in
t
Sorry for bothering you again,
I have another error now: "Error: bvecs and bvals don't have the same
number of entries".
Visually my bval/bvec files seem ok to me. I can't find the problem.
I attach the files, could you please take a look on them?
Thank you very much,
Tanja.
On Tue, Feb 14, 2012
I see, thank you :)
On Tue, Feb 14, 2012 at 6:50 PM, Anastasia Yendiki
wrote:
>
> PS: The info on what you need to set it here:
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc
>
> # Number of low-b images
> # Must be specified if inputs are not DICOM
> # Default: Read from DICOM header
> #
PS: The info on what you need to set it here:
https://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc
# Number of low-b images
# Must be specified if inputs are not DICOM
# Default: Read from DICOM header
#
set nb0 = 10
On Tue, 14 Feb 2012, Tetiana Dadakova wrote:
> Dear Priti, Anastasia,
>
> Thank
You need to set the nb0 parameter (number of low-b volumes in the
beginning of your DWI series).
On Tue, 14 Feb 2012, Tetiana Dadakova wrote:
> Dear Priti, Anastasia,
>
> Thank you for your help, I created bvec and bval files and it went fine.
> But now I have another error in preprocessing ste
Dear Priti, Anastasia,
Thank you for your help, I created bvec and bval files and it went fine.
But now I have another error in preprocessing step.
I attach a log file. Could you please take a look at that?
Thank you,
Tanja.
trac-preproc exited with ERRORS at Fri Feb 10 10:52:37 CET 2012
O
Hi Tanja,
Can you check if the $dtroot/$subjectname/dmri/dwi_orig_flip.mghdti.bvecs
was created at all? It looks like that may not have been created and
that's why it can't find "dwi_orig_flip.mghdti.bvecs". If your bvals and
bvecs information is not encoded in the dicom header, then you can speci
Hi Priti,
I changed the dmrirc file to the one you sent, but unfortunately got
the same error. I attach the log (although it is basically the same).
Do you have any ideas what else can cause it?
Thanks again,
Tanja.
On Fri, Feb 3, 2012 at 4:51 PM, Priti Srinivasan
wrote:
> Hi Tanja,
>
> I think
Hi Tanja,
I think the problem may be due to the trailing slash you've included while
specifying $dtroot, $SUBJECTS_DIR etc.
setenv SUBJECTS_DIR /Applications/freesurfer/subjects/TRACULA/T1/
should be
setenv SUBJECTS_DIR /Applications/freesurfer/subjects/TRACULA/T1
trac-all usually adds the '
Hi Tanja - The file is supposed to be created under
$dtroot/$subjectname/dmri/bvecs. If it's trying to create it as
/dmri/bvecs, this means that something wasn't defined correctly. What is
the exact trac-all command line that you're using? And your configuration
file if you're using one?
a.y
Hi Tanja,
It is supposed to be created automatically. Can you send your
configuration file and log file for us to see what's going on?
Thanks,
Priti
> Dear list,
>
> I try to run TRACULA pre-processing step and I get the following
> error: /dmri/bvecs: No such file or directory.
>
> I have a fol
Dear list,
I try to run TRACULA pre-processing step and I get the following
error: /dmri/bvecs: No such file or directory.
I have a folder with reconstructed T1 data and a folder with raw dicom
DTI data. When I start trac-all -prep, it creates directory /dmri/,
but it doesn't create the bvecs fil
Dear Knut,
Here it is: setenv LC_ALL en_US
Good luck, Joana
2011/10/1 Knut J Bjuland
> Dear Joana
>
> Could you please send me proposed line to the .tcshrc file. You got from Priti
> and Anastasia.
>
>
> Best regards
>
> Knut J
>
>
>
> On 01. okt. 2011 16:52, Joana Braga Pereira wrote:
>
> De
Dear Joana
Could you please send me proposed line to the .tcshrc file. You got from
Priti and Anastasia.
Best regards
Knut J
On 01. okt. 2011 16:52, Joana Braga Pereira wrote:
Dear Priti and Anastasia,
Many thanks for your reply!
Priti, i did what you suggested by adding the proposed li
Dear Priti and Anastasia,
Many thanks for your reply!
Priti, i did what you suggested by adding the proposed line to the .tcshrc
file and it worked!
The process finished without any errors!
Thanks once again for your help!
Joana
2011/9/30 Anastasia Yendiki
>
> Hi Joana - Can you please
Hi Joana - Can you please send your dmrirc file too?
Thanks,
a.y
On Fri, 30 Sep 2011, Joana Braga Pereira wrote:
> Dear Freesurfers,
>
> I'm pre-processing my DTI data with Tracula and i found the following error
> while running trac-all -prep -c dmrirc_H_P01:
>
> dtifit -k /home/joana/FIU/H_
Dear Freesurfers,
I'm pre-processing my DTI data with Tracula and i found the following error
while running trac-all -prep -c dmrirc_H_P01:
dtifit -k /home/joana/FIU/H_P01/dmri/dwi.nii.gz -m
/home/joana/FIU/H_P01/dlabel/diff/aparc+aseg_mask.flt.nii.gz -r
/home/joana/FIU/H_P01/dmri/bvecs -b /home/
Great, good to know. My LANG is en_US.UTF-8, everything else is not set.
On Thu, 7 Jul 2011, Franz Liem wrote:
> Dear Anastasia & all.
>
> I fixed it.
>
> The problem was my LOCALE setting which leads to different handling of
> decimal separators by awk (for further details see
> http://object
Dear Anastasia & all.
I fixed it.
The problem was my LOCALE setting which leads to different handling of decimal
separators by awk (for further details see
http://objectmix.com/awk/716715-awk-different-decimal-separator-different-linux-distros.html).
My original setting was:
% locale
LANG="de_
Hi again,
I found out that, if I change the flip4fsl line
printf '%s ' `cat $inbvecs | awk -v sgn=$sign[$k]1 -v n=$k
'{print sgn*$n}'` \
to
printf '%s ' `cat $inbvecs | awk -v sgn=$sign[$k]1 -v n=$k
'{print $n}'` \
(deleting the sgn*) the values in the out-bvecs a
I'm attaching what I get when I run it. Only the trailing zeros are
missing.
On Wed, 6 Jul 2011, Franz Liem wrote:
If i flip4fsl my fake file the the numbers after the decimal point are missing
in the output (bvecs_bvecs_onezero3decpoint1_western_out).
I have attached a fake bvecs fitting
If i flip4fsl my fake file the the numbers after the decimal point are missing
in the output (bvecs_bvecs_onezero3decpoint1_western_out).
I have attached a fake bvecs fitting your tutorial data (70 lines). Would you
be so kind, as to run this.
Thank you so much for your help,
Franz
bvecs_bv
I'd need the nifti file to run flip4fsl. Can you try it on your data?
On Wed, 6 Jul 2011, Franz Liem wrote:
> does your flip4fsl convert this file correctly (with the numbers after the
> decimal point)?
>
> Thank you,
> Franz
>
> Am 06.07.2011 um 18:06 schrieb Anastasia Yendiki:
>
>>
>> Yes!
>>
does your flip4fsl convert this file correctly (with the numbers after the
decimal point)?
Thank you,
Franz
Am 06.07.2011 um 18:06 schrieb Anastasia Yendiki:
>
> Yes!
>
> On Wed, 6 Jul 2011, Franz Liem wrote:
>
>> Hi Anastasia,
>> thank you. I created this file from scratch with osx' TextEdi
Yes!
On Wed, 6 Jul 2011, Franz Liem wrote:
> Hi Anastasia,
> thank you. I created this file from scratch with osx' TextEdit and saved it
> as western european (Mac OS Roman).
> Are you able to read this?
>
> Thanks,
> Franz
>
___
Freesurfer mailing li
Hi Anastasia,
thank you. I created this file from scratch with osx' TextEdit and saved it as
western european (Mac OS Roman).
Are you able to read this?
Thanks,
Franz
bvecs_onezero3decpoint1_western
Description: Binary data
Am 06.07.2011 um 17:42 schrieb Anastasia Yendiki:
>
> Hi Franz - Look
Hi Franz - Looks like it may be a windows vs. unix text file issue.
Looking at dwi_orig.mghdti.bvecs under unix, it seems that it has
windows-specific carriage returns (they look like "^M" in unix). Actually,
I could only see this on a darwin machine, on a centos machine I can only
read the fi
Hi Franz - As long as you have a good aparc+aseg, the exact version of the
recon should not matter.
a.y
On Wed, 6 Jul 2011, Franz Liem wrote:
> and another question.
> Is it OK to run tracula with recons done with an earlier version (5.0.0)?
>
> Thank you,
> Franz
>
> Am 06.07.2011 um 00:05 sc
and another question.
Is it OK to run tracula with recons done with an earlier version (5.0.0)?
Thank you,
Franz
Am 06.07.2011 um 00:05 schrieb Anastasia Yendiki:
>
> Hi Franz - Which of the files that you sent us are the original files (the
> bvalfile and bvecfile from your dmrirc)? I could n
Hi Priti and Anastasia.
Thank you very much for your replies.
Prit, I ran you modified_bvecs. This resulted in zeros (see bvecs_out). I also
tried the modified_bvecs in a tab-deliniated version. same result.
Anastasia, the original bvecs file is attached as bvecs_orig. I imported this
into exc
Hi Franz - Which of the files that you sent us are the original files (the
bvalfile and bvecfile from your dmrirc)? I could not find any files that
had 33 lines among your attachments so I'm not sure what your input files
look like.
Thanks,
a.y
On Tue, 5 Jul 2011, Franz Liem wrote:
> Hello a
Hi Franz,
Sorry I just saw your previous email now. The problem could be due to the
variable decimal places you've used in your input bvecs file. I've
modified your bvecs file from the previous email to 3 decimal places
constantly for all the gradient values (See Attached!!). Can you check to
see
Hi Franz,
Please refer to the following page:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula
Specifically Step7.2 for the format in which bvals/bvecs files should be
given as an input.
If your input bvals/bvecs are in the right format flip4fsl should not give
you an error.
Also if
Hello again.
I dug into the code and could locate the problem (I don't have a solution,
though. My coding skills are quite amateurish.) I think the problem somehow
lies in the format of my bvecs file.
flip4fsl is not able to read it correctly:
---
if (-e $inbvecs) then
echo "INFO: found
Dear Freesurfers.
I am trying to run trac-all on one subject and have a problem with the bvecs
file at the -prep stage.
After dtifit is started an error massage occurs: Error: bvecs and bvals don't
have the same number of entries.
I checked the dmri/bvals and dmri/bvecs. There seems to be a prob
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