Hello folks,

We are in the processing of writing a paper on cortical thickness. The cluster-wise simulation that we use is it similar to alphasim monte-carlo simulation by afni? Do you have any paper on it?

Best Regards, Manish Dalwani Instructor Dept. of Psychiatry Univ. of CO

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 '/' and since you're adding an extra '/', it's giving an error. I've edited your dmrirc file and removed those trailing slashes. Could you run this again and let us know if it solves the problem?

Hope this is helpful, Priti

Thank you Priti and Anastasia,

Anastasia, just wanted to clarify, I meant $dtroot/$subjectname/dmri/bvecs, when I wrote /dmri/bvecs, sorry for this misunderstanding.

I attach my configuration file and the command I use is < trac-all -prep -c /Applications/freesurfer/subjects/TRACULA/DTI/scripts/dmrirc

...

.

I also attach a picture of my file tree and a track-all.log file.

Thank you for your time and help, Tanja.

On Fri, Feb 3, 2012 at 2:21 AM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:

...

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

On Thu, 2 Feb 2012, Tetiana Dadakova wrote:

...

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 file. Should I create it myself using dcm2nii or is it supposed to be created automatically?

Thank you, Tanja. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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 specify it explicitly in the dmrirc file.

Please refer to the following page for instructions on how to specify your bvals and bvecs for tracula:

http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula

Hope this helps, Priti

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 rspriti@nmr.mgh.harvard.edu wrote:

...

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 '/' and since you're adding an extra '/', it's giving an error. I've edited your dmrirc file and removed those trailing slashes. Could you run this again and let us know if it solves the problem?

Hope this is helpful, Priti

...

Thank you Priti and Anastasia,

Anastasia, just wanted to clarify, I meant $dtroot/$subjectname/dmri/bvecs, when I wrote /dmri/bvecs, sorry for this misunderstanding.

I attach my configuration file and the command I use is < trac-all -prep -c /Applications/freesurfer/subjects/TRACULA/DTI/scripts/dmrirc

...

.

I also attach a picture of my file tree and a track-all.log file.

Thank you for your time and help, Tanja.

On Fri, Feb 3, 2012 at 2:21 AM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:

...

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

On Thu, 2 Feb 2012, Tetiana Dadakova wrote:

...

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 file. Should I create it myself using dcm2nii or is it supposed to be created automatically?

Thank you, Tanja. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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 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

On Fri, Feb 3, 2012 at 5:52 PM, Priti Srinivasan rspriti@nmr.mgh.harvard.edu wrote:

...

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 specify it explicitly in the dmrirc file.

Please refer to the following page for instructions on how to specify your bvals and bvecs for tracula:

http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula

Hope this helps, Priti

...

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 rspriti@nmr.mgh.harvard.edu wrote:

...

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 '/' and since you're adding an extra '/', it's giving an error. I've edited your dmrirc file and removed those trailing slashes. Could you run this again and let us know if it solves the problem?

Hope this is helpful, Priti

...

Thank you Priti and Anastasia,

Anastasia, just wanted to clarify, I meant $dtroot/$subjectname/dmri/bvecs, when I wrote /dmri/bvecs, sorry for this misunderstanding.

I attach my configuration file and the command I use is < trac-all -prep -c /Applications/freesurfer/subjects/TRACULA/DTI/scripts/dmrirc

...

.

I also attach a picture of my file tree and a track-all.log file.

Thank you for your time and help, Tanja.

On Fri, Feb 3, 2012 at 2:21 AM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:

...

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

On Thu, 2 Feb 2012, Tetiana Dadakova wrote:

> 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 file. > Should I create it myself using dcm2nii or is it supposed to be > created automatically? > > Thank you, > Tanja. > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

I see, thank you :)

On Tue, Feb 14, 2012 at 6:50 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu 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 # set nb0 = 10

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 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

On Fri, Feb 3, 2012 at 5:52 PM, Priti Srinivasan rspriti@nmr.mgh.harvard.edu wrote:

...

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 specify it explicitly in the dmrirc file.

Please refer to the following page for instructions on how to specify your bvals and bvecs for tracula:

http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula

Hope this helps, Priti

...

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 rspriti@nmr.mgh.harvard.edu wrote:

...

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 '/' and since you're adding an extra '/', it's giving an error. I've edited your dmrirc file and removed those trailing slashes. Could you run this again and let us know if it solves the problem?

Hope this is helpful, Priti

...

Thank you Priti and Anastasia,

Anastasia, just wanted to clarify, I meant $dtroot/$subjectname/dmri/bvecs, when I wrote /dmri/bvecs, sorry for this misunderstanding.

I attach my configuration file and the command I use is < trac-all -prep -c /Applications/freesurfer/subjects/TRACULA/DTI/scripts/dmrirc > > .

I also attach a picture of my file tree and a track-all.log file.

Thank you for your time and help, Tanja.

On Fri, Feb 3, 2012 at 2:21 AM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote: > > > 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 > > > On Thu, 2 Feb 2012, Tetiana Dadakova wrote: > >> 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 file. >> Should I create it myself using dcm2nii or is it supposed to be >> created automatically? >> >> Thank you, >> Tanja. >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > > The information in this e-mail is intended only for the person to > whom > it is > addressed. If you believe this e-mail was sent to you in error and > the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you > in > error > but does not contain patient information, please contact the sender > and > properly > dispose of the e-mail. >

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 the archives. You'll have to make sure you have text files that can be read properly on unix.

On Wed, 15 Feb 2012, Tetiana Dadakova wrote:

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 at 7:31 PM, Tetiana Dadakova tetiana.d@gmail.com wrote:

...

I see, thank you :)

On Tue, Feb 14, 2012 at 6:50 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu 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 # set nb0 = 10

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 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

On Fri, Feb 3, 2012 at 5:52 PM, Priti Srinivasan rspriti@nmr.mgh.harvard.edu wrote:

...

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 specify it explicitly in the dmrirc file.

Please refer to the following page for instructions on how to specify your bvals and bvecs for tracula:

http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula

Hope this helps, Priti

...

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 rspriti@nmr.mgh.harvard.edu wrote: > > 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 '/' and since you're adding an extra '/', > it's > giving an error. I've edited your dmrirc file and removed those > trailing > slashes. Could you run this again and let us know if it solves the > problem? > > Hope this is helpful, > Priti > > > > > >> Thank you Priti and Anastasia, >> >> Anastasia, just wanted to clarify, I meant >> $dtroot/$subjectname/dmri/bvecs, when I wrote /dmri/bvecs, sorry for >> this misunderstanding. >> >> I attach my configuration file and the command I use is < trac-all >> -prep -c /Applications/freesurfer/subjects/TRACULA/DTI/scripts/dmrirc >>> >>> . >> >> I also attach a picture of my file tree and a track-all.log file. >> >> Thank you for your time and help, >> Tanja. >> >> On Fri, Feb 3, 2012 at 2:21 AM, Anastasia Yendiki >> ayendiki@nmr.mgh.harvard.edu wrote: >>> >>> >>> 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 >>> >>> >>> On Thu, 2 Feb 2012, Tetiana Dadakova wrote: >>> >>>> 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 file. >>>> Should I create it myself using dcm2nii or is it supposed to be >>>> created automatically? >>>> >>>> Thank you, >>>> Tanja. >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>> >>> >>> The information in this e-mail is intended only for the person to >>> whom >>> it is >>> addressed. If you believe this e-mail was sent to you in error and >>> the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to >>> you >>> in >>> error >>> but does not contain patient information, please contact the sender >>> and >>> properly >>> dispose of the e-mail. >>> >>

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 used "tr '\r' '\n\ <bvec_dos_file> bvec_unix_file" to convert dos end-of-line character into unix ones. But something is wrong again (I attach log file):

dmri_train(82757) malloc: *** mmap(size=159744) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(218, 182, 182): could not allocate 158704 bytes for 14th slice

Cannot allocate memory Darwin 130-229-40-185.cns.ki.se 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64

trac-preproc exited with ERRORS at Thu Feb 16 11:45:26 CET 2012

I run TRACULA on Mac OS X 10.6.8, and I have 4GB of memory. Is it really a memory error or something else? Thank you, Tanja.

On Wed, Feb 15, 2012 at 8:02 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:

...

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 the archives. You'll have to make sure you have text files that can be read properly on unix.

On Wed, 15 Feb 2012, Tetiana Dadakova wrote:

...

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 at 7:31 PM, Tetiana Dadakova tetiana.d@gmail.com wrote:

...

I see, thank you :)

On Tue, Feb 14, 2012 at 6:50 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu 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 # set nb0 = 10

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 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

On Fri, Feb 3, 2012 at 5:52 PM, Priti Srinivasan rspriti@nmr.mgh.harvard.edu wrote: > > > 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 > specify > it explicitly in the dmrirc file. > > Please refer to the following page for instructions on how to specify > your > bvals and bvecs for tracula: > > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula > > Hope this helps, > Priti > > >> 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 >> rspriti@nmr.mgh.harvard.edu wrote: >>> >>> >>> 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 '/' and since you're adding an extra '/', >>> it's >>> giving an error. I've edited your dmrirc file and removed those >>> trailing >>> slashes. Could you run this again and let us know if it solves the >>> problem? >>> >>> Hope this is helpful, >>> Priti >>> >>> >>> >>> >>> >>>> Thank you Priti and Anastasia, >>>> >>>> Anastasia, just wanted to clarify, I meant >>>> $dtroot/$subjectname/dmri/bvecs, when I wrote /dmri/bvecs, sorry >>>> for >>>> this misunderstanding. >>>> >>>> I attach my configuration file and the command I use is < trac-all >>>> -prep -c >>>> /Applications/freesurfer/subjects/TRACULA/DTI/scripts/dmrirc >>>>> >>>>> >>>>> . >>>> >>>> >>>> I also attach a picture of my file tree and a track-all.log file. >>>> >>>> Thank you for your time and help, >>>> Tanja. >>>> >>>> On Fri, Feb 3, 2012 at 2:21 AM, Anastasia Yendiki >>>> ayendiki@nmr.mgh.harvard.edu wrote: >>>>> >>>>> >>>>> >>>>> 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 >>>>> >>>>> >>>>> On Thu, 2 Feb 2012, Tetiana Dadakova wrote: >>>>> >>>>>> 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 file. >>>>>> Should I create it myself using dcm2nii or is it supposed to be >>>>>> created automatically? >>>>>> >>>>>> Thank you, >>>>>> Tanja. >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> The information in this e-mail is intended only for the person to >>>>> whom >>>>> it is >>>>> addressed. If you believe this e-mail was sent to you in error and >>>>> the >>>>> e-mail >>>>> contains patient information, please contact the Partners >>>>> Compliance >>>>> HelpLine at >>>>> http://www.partners.org/complianceline . If the e-mail was sent to >>>>> you >>>>> in >>>>> error >>>>> but does not contain patient information, please contact the >>>>> sender >>>>> and >>>>> properly >>>>> dispose of the e-mail. >>>>> >>>> >> >