Re: [Freesurfer] tracula and corona radiata
Hi Catherine - Sorry, no hidden options there! We currently have the 18 pathways listed in the tutorial and in our paper. To add another pathway, it'd have to be labeled manually in the subjects that are part of our atlas. a.y On Thu, 8 Dec 2011, Cat Chong wrote: > Hello Experts, > > I would like to be able to get measurements of the anterior portion of the > corona radiata using tracula. Is this a possibility? I did not see it as an > "option" in paths to reconstruct. > thank you very much for your help, > catherine > > ___ 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.
Re: [Freesurfer] trac-all flag for doing all 3 processing steps?
Nope, sorry about that. The reason for keeping them separate is that the middle step is running bedpostx. It's the lengthiest step and we typically run it on a cluster. When run on a cluster it's parallelized by slice, and the other 2 steps are parallelized by subject. One could try to queue up everything at once but it'd get crazy and probably cause more confusion than it solves. Not the most elegant solution, I know... On Thu, 8 Dec 2011, Scott Hayes wrote: > Hi, > I'm new to tracula, but I'm wondering if I'm overlooking or > misunderstanding the flags. It appears that one types in the trac-all > command 3 times to process a subject (or group of subjects) >> trac-all -prep -c ConfigFile >> trac-all -bedp -c ConfigFile >> trac-all -path -c ConfigFile > > Is there a way to specify all three steps w/ one command? That is, > could I specify: >> trac-all -all -C ConfigFile > (I don't see it stated in the help, but maybe it's implicitly > understood to work this way?) > > Thanks for your guidance. > Best, > Scott > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ 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.
Re: [Freesurfer] tracula and snow leopard: can't allocate region / memory error
Hi Scott - Sending to the list is always good so that others can find it
in the archives when they have similar problems.
Do you specify the .dcm or .mgz file in your dmrirc? Does dwi.nii.gz have
the right dimensions/frames?
a.y
On Mon, 12 Dec 2011, Scott Hayes wrote:
Thanks for the prompt response Anastasia--I ran it over the weekend
and it worked.
I've subsequently encountered a new issue (copied below from the
trac-all.log). The file (dwi.nii.gz) exists in the correct location
(it was written there by tracula). I use unpacksdcmdir for unpacking
the dicoms, and then point the config file to the appropriate .mgz
file, so I'm not doing anything particularly unusual in terms of
unpacking or messing w/ the headers (We scan on a Siemens 3T tim
trio.) I can send this to the listserv if you prefer.
Best,
Scott
fslstats -t /Volumes/RAID_4TB/futhink/nc331_recon/dmri/dwi.nii.gz -k
/Volumes/RAID_4TB/futhink/nc331_recon/dlabel/diff/White-Matter++.bbr.nii.gz
-m -s | awk '{print $1/$2}' >
/Volumes/RAID_4TB/futhink/nc331_recon/dmri/dwi_snr.txt
** ERROR (nifti_image_read): failed to find header file for '-t'
** ERROR: nifti_image_open(-t): bad header info
Error: failed to open file -t
ERROR: Could not open image -t
Image Exception : #22 :: Failed to read volume -t
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
On Fri, Dec 9, 2011 at 12:44 PM, Anastasia Yendiki
wrote:
Hi Scott - Here are the tracula executables for snow leopard that we posted
in response to that thread:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-snow-leopard-intel/dmri_5.1_snow_leopard.tar.gz
Let me know if this solves the memory errors.
a.y
On Fri, 9 Dec 2011, Scott Hayes wrote:
Hi Anastasia,
I've encountered an error using tracula w/ snow leopard OS that was
previously reported on the FS listserv:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18829.html
I'm wondering if there is a documented solution available?
Recompiling from source code would be beyond my expertise.
David: I'm cc'ing you just as a heads up--all of the workstations in
the imaging center run snow leopard OS.
Best,
Scott
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Re: [Freesurfer] tracula failed to find header file for -t
Hi Scott - Which version of FSL are you using? I cannot replicate this
behavior of fslstats on our data.
Thanks,
a.y
On Mon, 12 Dec 2011, Scott Hayes wrote:
> Hi,
> I have received the following error message (copied from trac-all.log file).
>
> fslstats -t /Volumes/RAID_4TB/futhink/nc331_recon/dmri/dwi.nii.gz -k
> /Volumes/RAID_4TB/futhink/nc331_recon/dlabel/diff/White-Matter++.bbr.nii.gz
> -m -s | awk '{print $1/$2}' >
> /Volumes/RAID_4TB/futhink/nc331_recon/dmri/dwi_snr.txt
> ** ERROR (nifti_image_read): failed to find header file for '-t'
> ** ERROR: nifti_image_open(-t): bad header info
> Error: failed to open file -t
> ERROR: Could not open image -t
> Image Exception : #22 :: Failed to read volume -t
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
>
>
> The file (dwi.nii.gz) exists in the correct location, and appears to
> have the correct number of frames (60 directions + 10 b0).
> We scan on a Siemens 3T tim trio. I unpack the data using
> unpacksdcmdir and I specify the resulting .mgz file in the tracula
> config file. Running locally on mac os 10.6.8.
>
> Any suggestions would be appreciated.
> Thanks,
> Scott
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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Re: [Freesurfer] tracula failed to find header file for -t
Ok, I just checked the 4.1.4 version of fslstats, and indeed it doesn't
have the -t option. We're using version 4.1.5.
On Mon, 12 Dec 2011, Scott Hayes wrote:
Hi,
I'm using FSL 4.1.4
On Mon, Dec 12, 2011 at 12:43 PM, Anastasia Yendiki
wrote:
Hi Scott - Which version of FSL are you using? I cannot replicate this
behavior of fslstats on our data.
Thanks,
a.y
On Mon, 12 Dec 2011, Scott Hayes wrote:
Hi,
I have received the following error message (copied from trac-all.log
file).
fslstats -t /Volumes/RAID_4TB/futhink/nc331_recon/dmri/dwi.nii.gz -k
/Volumes/RAID_4TB/futhink/nc331_recon/dlabel/diff/White-Matter++.bbr.nii.gz
-m -s | awk '{print $1/$2}' >
/Volumes/RAID_4TB/futhink/nc331_recon/dmri/dwi_snr.txt
** ERROR (nifti_image_read): failed to find header file for '-t'
** ERROR: nifti_image_open(-t): bad header info
Error: failed to open file -t
ERROR: Could not open image -t
Image Exception : #22 :: Failed to read volume -t
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
The file (dwi.nii.gz) exists in the correct location, and appears to
have the correct number of frames (60 directions + 10 b0).
We scan on a Siemens 3T tim trio. I unpack the data using
unpacksdcmdir and I specify the resulting .mgz file in the tracula
config file. Running locally on mac os 10.6.8.
Any suggestions would be appreciated.
Thanks,
Scott
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Re: [Freesurfer] bedpost failure using tracula
Hi Scott - Are there any files created directly under dmri.bedpostX? a.y On Fri, 16 Dec 2011, Scott Hayes wrote: > Hi, > After I run step 2 of tracula (>trac-all -c config_DTI_B.txt -bedp), I > am missing multiple bedpost output files (e.g., mergedph1samples.nii). > Examining the output, it looks like data from only one slice was > written (dmri.bedpostX/diff_slices/data_slice_0002). This issue has > replicated across multiple subjects. I'm processing data locally on > mac os 10.6.8 (16 GB RAM; two 3.2 quadcore processors, which should be > able to handle bedpost), using FSL 4.1.9. I don't see any errors in > the tracula log files (until I run -path), and no complaints in the > terminal window (which writes: Queuing parallel processing stage > 0 slices processed > 1 slices processed > 1 slices processed > etc... > > Any insight as to what might be causing the issue? > > Thanks, > Scott > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ 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.
Re: [Freesurfer] bedpost failure using tracula
Hi Scott - Could you try running bedpostx on the dmri/ directory directly and see what if any error you get? a.y On Fri, 16 Dec 2011, Scott Hayes wrote: > Hi, > The following files & directories are listed directly under dmri.bedpostX: > > bvals commands.txtlogs > nodif_brain_mask.nii.gz > bvecs diff_slices monitor xfms > > --Scott > > > Anastasia Yendiki > Fri, 16 Dec 2011 09:43:47 -0800 > > Hi Scott - Are there any files created directly under dmri.bedpostX? > > a.y > > On Fri, 16 Dec 2011, Scott Hayes wrote: > >> Hi, >> After I run step 2 of tracula (>trac-all -c config_DTI_B.txt -bedp), I >> am missing multiple bedpost output files (e.g., mergedph1samples.nii). >> Examining the output, it looks like data from only one slice was >> written (dmri.bedpostX/diff_slices/data_slice_0002). This issue has >> replicated across multiple subjects. I'm processing data locally on >> mac os 10.6.8 (16 GB RAM; two 3.2 quadcore processors, which should be >> able to handle bedpost), using FSL 4.1.9. I don't see any errors in >> the tracula log files (until I run -path), and no complaints in the >> terminal window (which writes: Queuing parallel processing stage >> 0 slices processed >> 1 slices processed >> 1 slices processed >> etc... >> >> Any insight as to what might be causing the issue? >> >> Thanks, >> Scott >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ 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.
Re: [Freesurfer] Tracula - bedpost failure
Hi Kiely - It's strange that bepostx would create ph2samples and not ph1samples. These are the orientation angles for the 2 anisotropic compartments, so if there's a 2nd there should be a 1st. Have you asked about it on the FSL list? a.y On Thu, 22 Dec 2011, Kiely Donnelly wrote: > Hi Everyone -- > > I've been having difficulty getting Tracula to run smoothly on our cluster. > Similar to others on the listserv, the bedpost step > was not creating the necessary files causing an error during the -path step. > Based on previous posts, I ran bedpostx on the dmri > directory. This initially seemed to work (I no longer received the message "1 > slice processed" over and over), but for some reason > the merged_ph1samples.nii.gz file is still not being created and I continue > to run into an error when I run -path. It does create > a merged_ph2samples.nii.gz output file. > > Any help would be greatly appreciated. > > Thanks, > > Kiely > > > > ___ 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.
[Freesurfer] trac-all update
Hi all - There is an updated version of trac-all here that's recommended for all users: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/allplatforms/trac-all This version switches on an option in the implementation that had not been fully tested at the time of the release last May, but that we now believe will make better use of the atlas data and thus give you more accurate paths. The change will affect the -prior and -path steps of the analysis. Also the tracula wiki pages have been modified to make some of the information there clearer, hopefully: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula This documentation is still a work in progress. Thank you for understanding and we appreciate your continuing feedback! a.y | Anastasia Yendiki, Ph.D. | Martinos Center for Biomedical Imaging | 149 13th St. Suite 2301 | Charlestown, MA 02129 | Tel: 617-726-9434 | Fax: 617-726-7422 ___ 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.
Re: [Freesurfer] rendering problem
Hi Gabriel - We don't develop slicer, so we don't know what the assumptions are but here's where you can find their tutorials, if that helps: http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training If you scroll down you'll find the one on importing freesurfer files. a.y On Wed, 18 Jan 2012, Gabriel Gonzalez Escamilla wrote: Yes, I did, they answer me just before you, and told me that exist a tutorial but, that was made time ago, so they're not sure if any of the assumptions that went into making the tutorial have changed. Do you know anything about it?? Regards, Gabriel. El 18/01/12, Bruce Fischl escribió: Hi Gabriel, have you asked the slicer folks about this? Bruce On Wed, 18 Jan 2012, Gabriel Gonzalez Escamilla wrote: > Dear FS experts, > > I'm trying to render the surfaces and volumetric data from FS into > 3D-slicer, Because I've read on the net that is compatible with FS surfs and > images; but something seem to be not right, I'm sending you an attached jpg > with my problem. > > The thing is that I've load the ?h.pial surface (gary render) and the > rawavg.mgz (gray-scale) and compare them with the original NIfTi images > (green render) which I've obtain from the reconstruction of the dicom files; > and is the image I'd used in FS to create the 001.mgz image as input for the > recon-all processes. > > As you may see in the attached image, each time I do load the images they > appear to be in different spaces, but they're supposed to be in the subjects > native space, > apparentely the mismatching between the two images (in 3D slicer) starts > from the conversion from NIfTI to the 001.mgz image; Because when I load it > into slicer is in the same space as the rawavg.mgz and the other mgz images > Is it a problem when images loading in slicer or could I've been doing > something wrong? > > And I don't really have idea for the mismatching between the surfaces and > the mgz images. > > I have created a fiber vtk file in another program, and the fibers load in > the same space as the NIfTI volume, which makes me think that the NIfTI has > been loaded correctly. > > Bests, > Gabriel. > > ___ 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. -- -- PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville - Spain - Email: ggon...@upo.es http://www.upo.es/neuroaging/es/ ___ 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.
Re: [Freesurfer] dividing a label into equal parts
See: mris_divide_parcellation --help On Wed, 18 Jan 2012, Ritobrato Datta wrote: > Is there a way to divide a surface label like V1 into equal parts (say 10 > parts) either along its length or width and save each part as a separate > label ? Drawing them in tkmedit is quite crude and not very accurate. > > Please let me know. > > Thanks > > Ri > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ 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.
Re: [Freesurfer] Two questions when using the new trac-all
Hi there - First of all, let me clarify that the new and old trac-all have no differences in terms of usage, so all of this applies to both. 1. Yes, we did come across the issue of jot not being part of some platforms. It'll be fixed in the next release. If you're getting this error, you'll just have to specify the runlist explicitly in your config file instead of relying on the default, i.e., set runlist = (1 2 3 ...), however many subjects you have. 2. There's no increase in compute time by having a separate config file for each subject. Being able to specify multiple subjects in the same file with all other options being the same was just done for convenience. Hope this helps, a.y On Wed, 1 Feb 2012, Xiangzhen Kong wrote: Hi, all I am using trac-all these days. But I came across two quetions: 1. If I don't Specify Subjects To Be Analyzed, which means running the analysis on all subjects, there is an error saying "jot: Command not found.". The OS I am using is CentOS and I think jot is not installed by default. And some one says jot is part of freeBSD. Do we need to replace 'jot' in trac-all with other commands, such as seq? 2. If I run trac-all for just one subject each time,(that is to say, one config-file each subject), I wonder whether the time loss will be increase too much, compared with that one config-file for all subjects. Thanks! conxz 2012-02-01 _ Xiangzhen Kong ___ 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.
Re: [Freesurfer] TRACULA bvecs question
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 > > > ___ 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.
Re: [Freesurfer] What does trac-all do on the file 'bvecs'?
When the DWIs are transformed to LAS and processed with eddy_correct, the same transformations are applied to the respective bvecs. On Fri, 3 Feb 2012, Xiangzhen Kong wrote: Hi, all~ I use trac-all with .nii data, not dicom. So I have to specify the bvecs and bvals in the config file. Trac-all requires a bvecs file in 3 columes, but FSL need that in 3 raws. I wonder what does trac-all do on the bvecs file that I specify. And I have check the code 'trac-preproc' and the log, but found nothing, except copy and Eddy-current "correction". ps: The orientation of my dicom and .nii fils are both LPS, and the bvecs is read from the DICOM header via nibabel. But FSL requires LAS. I thinks trac-all have done the transposition on the bvecs somewhere. What orientation of bvecs does trac-all need when run with .nii files? Thanks! Xiangzhen 2012-02-03 ___ 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.
Re: [Freesurfer] /path/to/dmri/dwi_orig_flip.mghdti.bvecs': No such file or directory
Unless your dicoms came from the same acquisition as the default MGH/Siemens one, you'll have to set bvecfile and bvalfile and provide those files yourself. On Fri, 3 Feb 2012, Xiangzhen Kong wrote: Hi all Now I am learning the trac-all using with DICOM data, but came across a problem. +++ mv -f /xxx/dmri/dwi_orig_flip.mghdti.bvecs //dmri/bvecs mv: cannot stat `/xxx/dmri/dwi_orig_flip.mghdti.bvecs': No such file or dir ectory +++ I check the dir /xxx/dmri/ and there are only two files 'dwi_orig_flip.nii.gz' , 'dwi_orig.nii.gz' and a dir 'xfms'. Does trac-all extract bvals/bvecs automatically when start with DICOM data? My data is from a siemens scanner. Thanks! Xiangzhen 2012-02-03 Xiangzhen Kong ___ 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.
Re: [Freesurfer] What does trac-all do on the file 'bvecs'?
Hi - It's hard to tell without access to the actual data, but it sounds like you've found the right way to reconcile your nifti volume and gradient directions, so you should pass those to trac-all directly instead of the dicom. Anastasia. On Tue, 7 Feb 2012, Xiangzhen Kong wrote: Hi Yendiki： Sorry to bother you again. The DWI volume and bvec orientation issues confused me very much, so I resort to you. In my case, DWI data were scanned from siemens 3T Trio system. The data were then unpacked using unpacksdcmdir command from FS, and the bvecs is directly read from dicom tag 'Private_0019_100e' with Matlab dicominfo function. After unpacked, DWI volume is in LPS orientation, so bvec is also LPS, am I right? If so, when we use fslswapdim to covert the volume to LAS using x, -y, z option, we should also reverse the bvecs with the same option (i.e. only swap the second dimension). But I found that trac-all uses –x –y z to bvecs, rather than x –y z as in converting volume data. The related code of trac-all is line 59 to line 100 in flip4fsl. Results from our data show that x –y z option to bvecs can give us the right tensor (attachment Fig1), but –x –y z gives us the tensor with left-right of reversed (attachment Fig2). These two figs both show the first eigenvector V1, with FA map as background. Can you give me some clues to understand the difference? Thanks you very much. Thanks. Xiangzhen 发件人： ayendiki 发送时间： 2012-02-04 15:22:09 收件人： Xiangzhen Kong 抄送： freesurfer 主题： Re: [Freesurfer] What does trac-all do on the file 'bvecs'? You don't have to multiply the bvecs with anything yourself, it will do it for you. Of course you should check that it does it correctly, check the help of the flip4fsl script for how to do that. > Could you give me something about the transpsition here? > I checked the code flip4fsl and found there are two kinds of sign. > line 59. set sign = `echo $inorient | sed "s/[LAS]/+\ /g; s/[RPI]/-\ > /g"` > line 99. set sign = `echo $inorient | sed "s/[RAS]/+\ /g; s/[LPI]/-\ > /g"` > e.g. > When the orientation of DWI is LPS, we have to transform data to RAS. > ($fslplipx=1) > The first sign = +-+ and the second sign = --+. > So I have to multiple the bvecs(extracted from DICOM) by [-1 -1 +1], but > NOT [+1 -1 +1]. > Why are they different? > > Thanks! > > > 2012-02-04 > > > > Xiangzhen Kong > > > > ·¢¼þÈË£º Anastasia Yendiki > ·¢ËÍʱ¼ä£º 2012-02-04 00:48:58 > ÊÕ¼þÈË£º Xiangzhen Kong > ³ËÍ£º freesurfer > Ö÷Ì⣺ Re: [Freesurfer] What does trac-all do on the file 'bvecs'? > When the DWIs are transformed to LAS and processed with eddy_correct, the > same transformations are applied to the respective bvecs. > On Fri, 3 Feb 2012, Xiangzhen Kong wrote: >> Hi, all~ >> ? >> I use trac-all with .nii data, not dicom. So I have to specify the bvecs >> and >> bvals in the config file. >> Trac-all requires a bvecs file in 3 columes, but FSL need that in 3 >> raws. >> I wonder what does trac-all do on the bvecs file that I specify. >> And I have check the code 'trac-preproc' and the log, but found >> nothing, >> except copy and Eddy-current "correction". >> ? >> ps: The orientation of my dicom and .nii fils are both LPS, and the >> bvecs is >> read from the DICOM header via nibabel. >> But FSL requires LAS. I thinks trac-all have done the transposition on >> the >> bvecs somewhere. >> What orientation of bvecs does trac-all need when run with .nii files? >> ? >> Thanks! >> ? >> Xiangzhen >> ? >> 2012-02-03 >> ? >> >> > 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. > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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.
Re: [Freesurfer] Tracula - bedpost failure
Hi Kiely - If part of the brain is cut off in dwi_orig.nii.gz, it means it was cut off in your original dicom. If there's actualy part of the brain missing in all the volumes in your diffusion series, you may not be able to reconstruct tracts that go through that part. a.y On Fri, 10 Feb 2012, Kiely Donnelly wrote: Hi Priti, Thanks for your help. I took another look at the original diffusion and anatomical images. The anatomical looks OK, but in the diffusion image a posterior region of the brain appears cutoff and when I view the image in freeview there is a green box in the lower left hand corner that I've never seen before (I've attached a shot). I'm new to Freesurfer so I would appreciate any help you may have. Thanks again, Kiely On Tue, Jan 24, 2012 at 1:21 PM, Priti Srinivasan wrote: Hi Kiely, I had a similar experience with one of my subjects, but I realized that the original diffusion image had a lot of signal loss in various regions and hence the subsequent registration steps failed. It can happen when either intra-subject or inter-subject registration fails. I would inspect the original diffusion image (dmri/dwi_orig.nii.gz) and the original anatomical (dlabel/anat_brain_mask.nii.gz) to see if they have any problems (signal loss etc) which could lead to failures in registration as a first step. If both your diffusion and anatomical are both good, then I'd try to do flirt seperately to see if you get the same results as the one produced by tracula. Hope this is helpful, Priti > Hi Anastasia, > > Sorry for my slow reply. I am working with data that I only have access to > intermittently. We were able to fix the problem by deleting the original files from the folder and re-running the bedpost step. The old files must > have been interfering in some way. > > I am hoping you can help me with a different problem I ran into. For several of our subjects, each pathway reconstruction fails and I get an error like the following for all 18 tracts: > > Processing pathway 16 of 18... > Initializing MCMC > INFO: Path from initial control points is not entirely in mask > INFO: or is self-intersecting > INFO: Attemping to perturb control points > ERROR: Path from initial control points is not entirely in mask > ERROR: or is self-intersecting > ERROR: Initialization failed > ERROR: Pathway reconstruction failed > Done in 0.216 sec. > > I am able to view the FA image in native space, but when I attempt to view > the FLIRT-registered FA image it's completely dark. Is there any reason you > can think of that this may be happening? > > Thanks in advance, > > Kiely > > > On Fri, Dec 23, 2011 at 2:42 PM, Anastasia Yendiki < > ayend...@nmr.mgh.harvard.edu> wrote: > >> Hi Kiely - It's strange that bepostx would create ph2samples and not ph1samples. These are the orientation angles for the 2 anisotropic compartments, so if there's a 2nd there should be a 1st. Have you asked about it on the FSL list? >> a.y >> On Thu, 22 Dec 2011, Kiely Donnelly wrote: >> Hi Everyone -- >>> I've been having difficulty getting Tracula to run smoothly on our cluster. Similar to others on the listserv, the bedpost step >>> was not creating the necessary files causing an error during the -path step. Based on previous posts, I ran bedpostx on the dmri >>> directory. This initially seemed to work (I no longer received the message "1 slice processed" over and over), but for some reason the merged_ph1samples.nii.gz file is still not being created and I continue to run into an error when I run -path. It does create a merged_ph2samples.nii.gz output file. >>> Any help would be greatly appreciated. >>> Thanks, >>> Kiely >> 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<http://www.partners.org/compliance line>. If the e-mail was sent to you in error >> but does not contain patient information, please contact t
Re: [Freesurfer] TRACULA bvecs question
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 > 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 >>> 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 >>>>> 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. >>>>>> >>>>> >>> >> > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] TRACULA bvecs question
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 > 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 >>> 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 >>>>> 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. >>>>>> >>>>> >>> >> > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] TRACULA bvecs question
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 wrote: >> 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 >>> # >>> 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 >>>> 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 >>>>>> 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 >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> &g
Re: [Freesurfer] trac-all -prep error
Hey Chris - That is strange. The FSLOUTPUTTYPE would've been my first guess, too. Does this lowb.nii.gz actually exist? Anything looks strange when you run mri_info/freeview/fslview on it? a.y On Wed, 15 Feb 2012, Chris Watson wrote: > Hello, in running trac-all -prep, I get an error saying that it can't > open "lowb.nii.gz.hdr": > > fslroi > /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/dwi.nii.gz > /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz > 0 1 > fslmaths > /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz > -Tmean > /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz > bet > /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz > /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb_brain.nii.gz > -m -f 0.3 > Can't open > /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz.hdr > Linux occipital.tch.harvard.edu 2.6.18-274.17.1.el5 #1 SMP Tue Jan 10 > 17:25:58 EST 2012 x86_64 x86_64 x86_64 GNU/Linux > > trac-preproc exited with ERRORS at Wed Feb 15 15:15:52 EST 2012 > > The variable FSLOUTPUTTYPE is set to NIFTI_GZ. I don't encounter this > problem with other subjects that I am processing. Any thoughts? > > Thanks, > Chris > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ 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.
Re: [Freesurfer] trac-all -prep error
When you run that bet command line outside of trac-all, does it give you the same error? On Wed, 15 Feb 2012, Chris Watson wrote: > Here's output from mri_info: > [freesurfer@occipital dmri]$ mri_info lowb.nii.gz > Volume information for lowb.nii.gz > type: nii > dimensions: 96 x 96 x 56 > voxel sizes: 2.5000, 2.5000, 2.5000 > type: FLOAT (3) > fov: 240.000 > dof: 0 >xstart: -120.0, xend: 120.0 >ystart: -120.0, yend: 120.0 >zstart: -70.0, zend: 70.0 > TR: 1000.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 > degrees > nframes: 1 > PhEncDir: UNKNOWN > ras xform present > xform info: x_r = -1., y_r = 0., z_r = 0., c_r = > 0.9450 > : x_a = 0., y_a = 1., z_a = 0., c_a = > 31.8560 > : x_s = 0., y_s = 0., z_s = 1., c_s = > 25.3936 > Orientation : LAS > Primary Slice Direction: axial > > voxel to ras transform: > -2.5000 0. 0. 120.9450 >0. 2.5000 0. -88.1440 >0. 0. 2.5000 -44.6064 >0. 0. 0. 1. > > voxel-to-ras determinant -15.625 > > ras to voxel transform: > -0.4000 0. 0.48.3780 > -0. 0.4000 -0.35.2576 > -0. -0. 0.400017.8426 >0. 0. 0. 1. > > It looks normal in fslview/freeview. > Chris > > Anastasia Yendiki wrote: >> Hey Chris - That is strange. The FSLOUTPUTTYPE would've been my first >> guess, too. Does this lowb.nii.gz actually exist? Anything looks strange >> when you run mri_info/freeview/fslview on it? >> >> a.y >> >> On Wed, 15 Feb 2012, Chris Watson wrote: >> >> >> > Hello, in running trac-all -prep, I get an error saying that it can't >> > open "lowb.nii.gz.hdr": >> > >> > fslroi >> > >> > /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/dwi.nii.gz >> > >> > /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz >> > 0 1 >> > fslmaths >> > >> > /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz >> > -Tmean >> > >> > /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz >> > bet >> > >> > /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz >> > >> > /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb_brain.nii.gz >> > -m -f 0.3 >> > Can't open >> > >> > /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz.hdr >> > Linux occipital.tch.harvard.edu 2.6.18-274.17.1.el5 #1 SMP Tue Jan 10 >> > 17:25:58 EST 2012 x86_64 x86_64 x86_64 GNU/Linux >> > >> > trac-preproc exited with ERRORS at Wed Feb 15 15:15:52 EST 2012 >> > >> > The variable FSLOUTPUTTYPE is set to NIFTI_GZ. I don't encounter this >> > problem with other subjects that I am processing. Any thoughts? >> > >> > Thanks, >> > Chris >> > >> > ___ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >> > >> > >> ___ >> 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. >> >> >> > > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] trac-all -prep error
Weird. Glad it got fixed, let us know if you have any more trouble. On Wed, 15 Feb 2012, Chris Watson wrote: > Actually, it now works when I re-source my .bash_profile and .bashrc files. > Not sure why that would be. > Chris > > Chris Watson wrote: >> Yes, the same error. >> Chris >> >> Anastasia Yendiki wrote: >> >> > When you run that bet command line outside of trac-all, does it give you >> > the same error? >> > >> > On Wed, 15 Feb 2012, Chris Watson wrote: >> > >> > >> > > Here's output from mri_info: >> > > [freesurfer@occipital dmri]$ mri_info lowb.nii.gz >> > > Volume information for lowb.nii.gz >> > > type: nii >> > > dimensions: 96 x 96 x 56 >> > > voxel sizes: 2.5000, 2.5000, 2.5000 >> > > type: FLOAT (3) >> > >fov: 240.000 >> > >dof: 0 >> > > xstart: -120.0, xend: 120.0 >> > > ystart: -120.0, yend: 120.0 >> > > zstart: -70.0, zend: 70.0 >> > >TR: 1000.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: >> > > 0.00 degrees >> > >nframes: 1 >> > >PhEncDir: UNKNOWN >> > > ras xform present >> > >xform info: x_r = -1., y_r = 0., z_r = 0., c_r = >> > > 0.9450 >> > > : x_a = 0., y_a = 1., z_a = 0., c_a = >> > > 31.8560 >> > > : x_s = 0., y_s = 0., z_s = 1., c_s = >> > > 25.3936 >> > > Orientation : LAS >> > > Primary Slice Direction: axial >> > > >> > > voxel to ras transform: >> > >-2.5000 0. 0. 120.9450 >> > > 0. 2.5000 0. -88.1440 >> > > 0. 0. 2.5000 -44.6064 >> > > 0. 0. 0. 1. >> > > >> > > voxel-to-ras determinant -15.625 >> > > >> > > ras to voxel transform: >> > >-0.4000 0. 0.48.3780 >> > >-0. 0.4000 -0.35.2576 >> > >-0. -0. 0.400017.8426 >> > > 0. 0. 0. 1. >> > > >> > > It looks normal in fslview/freeview. >> > > Chris >> > > >> > > Anastasia Yendiki wrote: >> > > >> > > > Hey Chris - That is strange. The FSLOUTPUTTYPE would've been my >> > > > first >> > > > guess, too. Does this lowb.nii.gz actually exist? Anything looks >> > > > strange >> > > > when you run mri_info/freeview/fslview on it? >> > > > >> > > > a.y >> > > > >> > > > On Wed, 15 Feb 2012, Chris Watson wrote: >> > > > >> > > > >> > > > >> > > > > Hello, in running trac-all -prep, I get an error saying that it >> > > > > >> > > > can't >> > > > >> > > > > open "lowb.nii.gz.hdr": >> > > > > >> > > > > > fslroi >> > > > > > >> > > > > >> > > > > >> > > > >> > > > /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/dwi.nii.gz >> > > > >> > > > >> > > > >> > > > > >> > > > > >> > > > >> > > > /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz >> > > > >> > > > >> > > > >> > > > > 0 1 >> > > > > fslmaths >> > > > > >> > > > > >> > > > >> > > > /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz >> > > > >> > > > >> > > > >> > > > > -Tmean >> > > > > >> > > > > >> > > > >> > > > /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz >> > > > >> > > > >> > > > >> > > > > bet >> > > > > >> > > > > >> &
Re: [Freesurfer] TRACULA bvecs question
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_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 > 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 >>> wrote: >>>> >>>> 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 >>>>> # >>>>> 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 >>>>>> 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 thi
Re: [Freesurfer] TRACULA question: pathstats.byvoxel.txt
Hi Minjie - There was no attachment to your email. The fmajor issue that you're describing sounds like an initialization issue. That single curve that you describe is where the algorithm starts at and b/c something is wrong with it, it doesn't move from there. Does the curve seem to go into a low anisotropy area? Can you rerun the dmri_paths command for just one of these fmajor paths with --debug and send us the log.txt file? Thanks! a.y On Mon, 20 Feb 2012, Minjie Wu wrote: > Hi Priti, > > Thank you very much for the detailed instructions. The tracts with > empty pathstat.byvoxel.txt files are slfp, slft, and unc tracts. > After your email, I have checked all 10+ subjects with such problems. > They all share similar motion problems (the parietal or temporal part > of brain is cut due to motion), which may be why TRACULA is not > working. > > The other issue is with fmajor. For many subjects (almost 1/3 of > overall subjects), the fiber tracking for fmajor (path.pd.nii.gz) > looks like a single fiber (or 2,3 fibers) instead of a bundle of > fibers. The volume from pathstats.overall.txt (195 voxels) is > significantly lower than the mean fmajor volume (1000 voxels) from the > population (see attached file). These brain images are complete (no > cutting issue at fmajor). Also I have checked the FA-MNI > co-registration, and the registration seems to be accurate. Any idea > of how to avoid this problem will be really appreciated. > > Thanks, > Minjie > > > > > [minjiewu@ccmfsl1 fmajor_PP_avg33_mni_bbr]$ more pathstats.overall.txt > # Title Pathway Statistics > # > # generating_program /ccm/pavuluri/imgsw/freesurfer/bin/dmri_pathstats > # cvs_version > # cmdline /ccm/pavuluri/imgsw/freesurfer/bin/dmri_pathstats --intrc > /ccm/pavuluri/rest/DTI/data/20191/dpath/fmajor_PP_avg33_mni_bbr > --dtbase /ccm/pavuluri/rest/DTI/data/20191/dmri/dtifit --path > fmajor --subj 20191 --out > /ccm/pavuluri/rest/DTI/data/20191/dpath/fmajor_PP_avg33_mni_bbr/pathstats.overall.txt > --outvox > /ccm/pavuluri/rest/DTI/data/20191/dpath/fmajor_PP_avg33_mni_bbr/pathstats > .byvoxel.txt > # sysname Linux > # hostname ccmfsl2.psych.uic.edu > # machine x86_64 > # user minjiewu > # anatomy_type pathway > # > # subjectname 20191 > # pathwayname fmajor > # > Count 1000 > Volume 195 > Len_Min 136 > Len_Max 179 > Len_Avg 149.767 > Len_Center 164 > AD_Avg 0.00145274 > AD_Avg_Weight 0.00149492 > AD_Avg_Center 0.00165127 > RD_Avg 0.000615351 > RD_Avg_Weight 0.00058665 > RD_Avg_Center 0.000529699 > MD_Avg 0.00089448 > MD_Avg_Weight 0.000889406 > MD_Avg_Center 0.000903556 > FA_Avg 0.475963 > FA_Avg_Weight 0.507926 > FA_Avg_Center 0.610243 > > > > > > > On Wed, Feb 15, 2012 at 9:25 AM, Priti Srinivasan > wrote: >> Hi Minjie, >> >> The pathstats.byvoxel.txt gives the statistics of the higest probability >> streamline of the posterior distribution of the tract and the >> pathstats.overall.txt gives you average diffusion values for the whole >> tract. >> >> Please refer to the following: >> >> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics >> >> Your pathstats.overall.txt does not look right. For instance the center >> streamline's length (Len_Center = 0). Did you open the posterior >> probability distribution of this tract? >> >> You can use the following command to do the same: >> >> freeview /dpath/path.pd.nii.gz >> >> If it does not look right then something probably went wrong during the >> path reconstruction. If you can send us your trac-all.log, we can check >> for anything that went wrong. >> >> Hope this is helpful., >> >> Priti >> >> >>> Hello Tracula Developer & User, >>> >>> I found a few subjects have pathstat.overall.txt information but with >>> blank voxel information in pathstats.byvoxel.txt. For such tracts, >>> they usually len_min = len_max = len_avg. Anyone know what happened >>> for the fiber tracking? Is it possible to extract the byvoxel >>> information along the tract? >>> >>> Thanks, >>> Minjie >>> >>> For example: >>> >>> [minjiewu@ccmfsl1 data]$ more >>> 22331/dpath/rh.slfp_PP_avg33_mni_bbr/pathstats.overall.txt >>> # Title Pathway Statistics >>> # >>> # generating_program /ccm/pavuluri/imgsw/freesurfer/bin/dmri_pathstats >>> # cvs_version >>> # cmdline /ccm/pavuluri/imgsw/freesurfer/bin/dmri_pathstats --intrc >>> /ccm/pavuluri/rest/DTI/data/22331/dpath/rh.slfp_PP_avg33_mni_bbr >>> --dtbase /ccm/pavuluri/rest/DTI/data/223 >>> 31/dmri/dtifit --path rh.slfp --subj 22331 --out >>> /ccm/pavuluri/rest/DTI/data/22331/dpath/rh.slfp_PP_avg33_mni_bbr/pathstats.overall.txt >>> --outvox /ccm/pavuluri/rest/DTI/data/ >>> 22331/dpath/rh.slfp_PP_avg33_mni_bbr/pathstats.byvoxel.txt >>> # sysname Linux >>> # hostname ccmfsl2.psych.uic.edu >>> # machine x86_64 >>> # user minjiewu >>> # anatomy_type pathway >>> # >>> # subjectname 22331 >>> # pathwayname rh.slfp >>> # >>> Count 1000 >>> Volume 86 >>> Len_Min 86 >>> Len_Max 86 >>> Len_Avg 86 >>> Len_Center 0 >>> AD_Avg 0.00112029 >>> AD_Avg_Weight 0.00112029
Re: [Freesurfer] tracula - submit via fsl_sub / qsub ?
Hi Andi - Thanks for your kind words! As explained on the trac-all wiki page (and also the help text you get from trac-all --help), the part about not submitting trac-all with pbsubmit is specific to our local Martinos Center users. That's b/c we've modified fsl_sub (and bedpostx) to work on our local compute clusters (that run PBS). So trac-all recognizes when it's run on one of our clusters and submits each subject as a job. If it's run on any other machine, it won't do that, so this doesn't affect you. You're free to make your own modifications to fsl_sub or otherwise make use of your own cluster. Let me know if you have any other questions, a.y On Wed, 29 Feb 2012, Andi Heckel wrote: Dear Tracula Team, recently i ran trac-all (-prep / -bedp / -path), but I happened to submit the commands to our SGE computer cluster using fsl_sub (which is fsl's wrapper for qsub) According to the header comments of the trac-all script, however, trac-all should not be submitted to a cluster. (it is self-submitting as i understand) Do I need to worry about the results being invalid when submitting the command with qsub/fsl_sub or would you suggest re-running trac-all without fsl_sub / qsub, although all processes finished without errors according to the logs ? Actually, i would really like to submit the trac-all command line using fsl_sub / qsub to a) make use of fsl_sub / qsub features and b) make full use of our cluster, so I can process multiple subjects in parallel, as it seems that not all time-consuming processing steps in the trac-all scripts are self-submitting (i guess only "trac-all -bedp" self-submits) Are there general concerns, why one should not use fsl_sub/qsub on the trac-all (-prep / - path) command ? (I used fsl_sub on other self-submitting scripts, which seemed to work so far.) Tracula is quite useful ! Thank you very much for your time ! Kind Regards, andi ___ 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.
Re: [Freesurfer] Tracula preproc failure
Hi Martijn - You could check how the ILF of the atlas subjects aligns with your subject's anatomical segmentation. These files are all in MNI space here: dlabel/mni/aparc+aseg.nii.gz dlabel/mni/aparc+aseg_mask.nii.gz (dilated version used as a brain mask) dlabel/mni/lh.ilf_*_histo.nii.gz Note that any ILF streamlines from the atlas that go off the brain mask of your subject have been removed before creating the *histo.nii.gz file, so you can compare with a healthy subject and see if there's much less left in the pathological subject, and if what's there goes through the same parts of the aparc+aseg in both cases. Hope this helps, a.y On Thu, 1 Mar 2012, Martijn Steenwijk wrote: Thanks for your reply, sorry for the delay. The problems appear in the left hemisphere ILF_AS. The subject has atrophy and a number of periventricular lesions. Does the error indicate that set of the endpoints could not be mached? In that case it could be that the points in the temporal pole give problems since the original FS segmentation is a bit too tight there. Is there a way to visualize the suspected points onto the subjects data? Best, Martijn On Mon, Feb 27, 2012 at 10:16 PM, wrote: Hi Martijn, Which pathway does it fail on? Is the pathology of your subject affecting the structures in the aparc+aseg that surround that pathway? a.y > Dear all, > > I'm running Tracula on a brain with some pathology. During the preproc > phase it fails with the following error: > > INFO: Rejected 843 streamlines for straying off mask > INFO: Rejected 0 streamlines for reversing direction > INFO: Rejected 10 streamlines as length outliers > INFO: Have 2748 total streamlines (min/mean/max length: 38/70/105) > Processing pathway 3 of 18... > Matching streamline ends > INFO: Have 0 non-truncated streamlines (min/mean/max length: 0/0/0) > INFO: Center of mass of start points: (nan+/-nan, nan+/-nan, nan+/-nan) > INFO: Center of mass of midpoints: (nan+/-nan, nan+/-nan, nan+/-nan) > INFO: Center of mass of end points: (nan+/-nan, nan+/-nan, nan+/-nan) > Segmentation fault (core dumped) > Linux lnx-rad-03 2.6.18-92.1.18.el5 #1 SMP Wed Nov 5 09:00:19 EST 2008 > x86_64 x86_64 x86_64 GNU/Linux > > trac-preproc exited with ERRORS at Mon Feb 27 19:41:00 CET 2012 > > I understand that no streamlines are available for initialization. Is that > correct? > > Best, > Martijn > ___ > 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. ___ 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.
Re: [Freesurfer] trac-all -path error
What's in the diff_slices directory? That's a temporary directory that bedpostx creates and that gets deleted after the results get "merged". So my guess would be that bedpostx didn't finish processing. On Fri, 23 Mar 2012, Chris Watson wrote: > Hello, I successfully ran trac-all -bedp, and when I run the next step I > get the following error: > > Loading BEDPOST parameter samples from > /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX > niiRead(): error opening file > /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz > ERROR: Could not read > /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz > Linux occipital.tch.harvard.edu 2.6.18-308.1.1.el5 #1 SMP Wed Mar 7 > 04:16:51 EST 2012 x86_64 x86_64 x86_64 GNU/Linux > > trac-paths exited with ERRORS at Fri Mar 23 11:24:11 EDT 2012 > > Word too long. > > > Indeed, the "merged" file doesn't exist. I am running Freesurfer 5.1.0 > and FSL 4.1.9. > Here's what's in the dmri.bedpostX directory: > > [freesurfer@occipital control]$ ls murphy_p/dmri.bedpostX/ > bvals bvecs commands.txt diff_slices logs monitor > nodif_brain_mask.nii.gz xfms > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ 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.
Re: [Freesurfer] trac-all -path error
Oh, ok. That's a known issue, it has to do with changes in the command line of the latest version of bedpostx. We've updated trac-all and it'll be working in our next release but for now you'll have to run bedpostx by itself and not through trac-all. Sorry for the inconvenience! On Fri, 23 Mar 2012, Chris Watson wrote: > [freesurfer@occipital dmri.bedpostX]$ ls diff_slices/data_slice_0002/ > dyads1.nii.gz f1samples.nii.gz logfile mean_dsamples.nii.gz > mean_f1samples.nii.gz mean_S0samples.nii.gz ph1samples.nii.gz > th1samples.nii.gz > > > Come to think of it, when I ran bedpostx, it only output "1 slice processed", > but repeated 70 times, or however many slices there are. The data is from a > Siemens 3T, by the way. > > On 03/23/2012 01:16 PM, Anastasia Yendiki wrote: >> >> What's in the diff_slices directory? That's a temporary directory that >> bedpostx creates and that gets deleted after the results get "merged". So >> my guess would be that bedpostx didn't finish processing. >> >> On Fri, 23 Mar 2012, Chris Watson wrote: >> >> > Hello, I successfully ran trac-all -bedp, and when I run the next step I >> > get the following error: >> > >> > Loading BEDPOST parameter samples from >> > /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX >> > niiRead(): error opening file >> > >> > /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz >> > >> > >> > ERROR: Could not read >> > >> > /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz >> > >> > >> > Linux occipital.tch.harvard.edu 2.6.18-308.1.1.el5 #1 SMP Wed Mar 7 >> > 04:16:51 EST 2012 x86_64 x86_64 x86_64 GNU/Linux >> > >> > trac-paths exited with ERRORS at Fri Mar 23 11:24:11 EDT 2012 >> > >> > Word too long. >> > >> > >> > Indeed, the "merged" file doesn't exist. I am running Freesurfer 5.1.0 >> > and FSL 4.1.9. >> > Here's what's in the dmri.bedpostX directory: >> > >> > [freesurfer@occipital control]$ ls murphy_p/dmri.bedpostX/ >> > bvals bvecs commands.txt diff_slices logs monitor >> > nodif_brain_mask.nii.gz xfms >> > >> > ___ >> > 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. >> >> > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] trac-all -path error
Yes. On Fri, 23 Mar 2012, Chris Watson wrote: > Ok. Do I run it with the defaults? > # fibers per voxel = 2 > ARD weight = 1 > burn-in period = 1000 > # jumps = 1250 > sample every = 25 > > On 03/23/2012 01:22 PM, Anastasia Yendiki wrote: >> >> Oh, ok. That's a known issue, it has to do with changes in the command >> line of the latest version of bedpostx. We've updated trac-all and it'll >> be working in our next release but for now you'll have to run bedpostx by >> itself and not through trac-all. Sorry for the inconvenience! >> >> On Fri, 23 Mar 2012, Chris Watson wrote: >> >> > [freesurfer@occipital dmri.bedpostX]$ ls diff_slices/data_slice_0002/ >> > dyads1.nii.gz f1samples.nii.gz logfile mean_dsamples.nii.gz >> > mean_f1samples.nii.gz mean_S0samples.nii.gz ph1samples.nii.gz >> > th1samples.nii.gz >> > >> > >> > Come to think of it, when I ran bedpostx, it only output "1 slice >> > processed", but repeated 70 times, or however many slices there are. The >> > data is from a Siemens 3T, by the way. >> > >> > On 03/23/2012 01:16 PM, Anastasia Yendiki wrote: >> > > >> > > What's in the diff_slices directory? That's a temporary directory >> > > that >> > > bedpostx creates and that gets deleted after the results get >> > > "merged". So >> > > my guess would be that bedpostx didn't finish processing. >> > > >> > > On Fri, 23 Mar 2012, Chris Watson wrote: >> > > >> > > > Hello, I successfully ran trac-all -bedp, and when I run the next >> > > step I >> > > > get the following error: >> > > > > Loading BEDPOST parameter samples from >> > > > >> > > /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX >> > > > niiRead(): error opening file >> > > > >> > > >> > > /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz >> > > >> > > > > ERROR: Could not read >> > > > >> > > >> > > /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz >> > > >> > > > > Linux occipital.tch.harvard.edu 2.6.18-308.1.1.el5 #1 SMP Wed >> > > Mar 7 >> > > > 04:16:51 EST 2012 x86_64 x86_64 x86_64 GNU/Linux >> > > > > trac-paths exited with ERRORS at Fri Mar 23 11:24:11 EDT 2012 >> > > > > Word too long. >> > > > >> > > >> > > >> > > >> > > > > Indeed, the "merged" file doesn't exist. I am running >> > > Freesurfer 5.1.0 >> > > > and FSL 4.1.9. >> > > > Here's what's in the dmri.bedpostX directory: >> > > > > [freesurfer@occipital control]$ ls murphy_p/dmri.bedpostX/ >> > > > bvals bvecs commands.txt diff_slices logs monitor >> > > > nodif_brain_mask.nii.gz xfms >> > > > > ___ >> > > > 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. >> > > >> > > >> > >> > >> > >> > > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] volume mapping
Hi Johnson - The aparc+aseg.mgz is in the same space as the T1 used as input to freesurfer. a.y On Mon, 26 Mar 2012, Johnson wrote: > Hi FS expert > I need to know the transformation matrix itself since I will do the > transformation in matlab. > I successfully transformed white matter fibers coordinates to T1 using AIR > 5.0 from LONI lab. > They provide a transformation matrix. > Now I want to transform the coordinates from T1 to Freesurfer space, so > my question is: what is the transformation matrix that relates the T1 > which FS have used for parcellation and segmentation with the aparc+aseg.mgz > file? > I searched the logs but couldn't find such matrix. > I don't want to do a registration step since it will be less accurate than > the one that was generated during the segmentation process. > Also is it just one transformation or a combination of transformations? > > thanks > > ___ 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.
Re: [Freesurfer] volume mapping
If you want to register your DWI to T1, you should register to mri/brain.mgz. You can do this with bbregister, or with any affine registration tool of your choice. On Mon, 26 Mar 2012, Johnson wrote: > Hi > I found it in a 256x256x256 space while the T1 we use is in different space, > I found this page on the registration step: > http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat > I wish to know how this script work? > > mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz > --regheader aseg.mgz > > what is the transformation used ? > JG > > > On 03/26/2012 12:24 PM, Anastasia Yendiki wrote: >> >> Hi Johnson - The aparc+aseg.mgz is in the same space as the T1 used as >> input to freesurfer. >> >> a.y >> >> On Mon, 26 Mar 2012, Johnson wrote: >> >> > Hi FS expert >> > I need to know the transformation matrix itself since I will do the >> > transformation in matlab. >> > I successfully transformed white matter fibers coordinates to T1 using >> > AIR 5.0 from LONI lab. >> > They provide a transformation matrix. >> > Now I want to transform the coordinates from T1 to Freesurfer space, so >> > my question is: what is the transformation matrix that relates the T1 >> > which FS have used for parcellation and segmentation with the >> > aparc+aseg.mgz file? >> > I searched the logs but couldn't find such matrix. >> > I don't want to do a registration step since it will be less accurate >> > than the one that was generated during the segmentation process. >> > Also is it just one transformation or a combination of transformations? >> > >> > thanks >> > >> > >> >> >> 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. >> > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] volume mapping
Actually, (1) should be more accurate, because bbregister uses the surface reconstruction obtained from the T1 to optimize the contrast across the gray/white boundary in the registered DWI. However if you want to convert to the 1mm, 256^3 voxel size that was used as input to freesurfer, see mri_convert --conform. On Mon, 26 Mar 2012, Johnson wrote: > Hi > Let me re-phrase my question: > I already did registration from DWI to T1, this step is OK. > Now I want to go from T1 to FreeSurfer space (aparc+aseg.mgz file not the > aparc+aseg-in-rawavg file). I know I have two choices: > 1) do registration using bbregister > 2) since Freesurfer during processing have already done this step, the > transformation matrix is there somewhere, the question is where to find it? > which log or which file? this choice is better since it is more accurate. > > Thanks > JG > > On 03/26/2012 12:41 PM, Anastasia Yendiki wrote: >> >> If you want to register your DWI to T1, you should register to >> mri/brain.mgz. You can do this with bbregister, or with any affine >> registration tool of your choice. >> >> On Mon, 26 Mar 2012, Johnson wrote: >> >> > Hi >> > I found it in a 256x256x256 space while the T1 we use is in different >> > space, I found this page on the registration step: >> > http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat >> > I wish to know how this script work? >> > >> > mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz >> > --regheader aseg.mgz >> > >> > what is the transformation used ? >> > JG >> > >> > >> > On 03/26/2012 12:24 PM, Anastasia Yendiki wrote: >> > > >> > > Hi Johnson - The aparc+aseg.mgz is in the same space as the T1 used >> > > as >> > > input to freesurfer. >> > > >> > > a.y >> > > >> > > On Mon, 26 Mar 2012, Johnson wrote: >> > > >> > > > Hi FS expert >> > > > I need to know the transformation matrix itself since I will do >> > > the > transformation in matlab. >> > > > I successfully transformed white matter fibers coordinates to T1 >> > > using > AIR 5.0 from LONI lab. >> > > > They provide a transformation matrix. >> > > > Now I want to transform the coordinates from T1 to Freesurfer >> > > space, so >> > > > my question is: what is the transformation matrix that relates >> > > the T1 >> > > > which FS have used for parcellation and segmentation with the > >> > > aparc+aseg.mgz file? >> > > > I searched the logs but couldn't find such matrix. >> > > > I don't want to do a registration step since it will be less >> > > accurate > than the one that was generated during the segmentation >> > > process. >> > > > Also is it just one transformation or a combination of >> > > transformations? >> > > > > thanks >> > > > > >> > > >> > > 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. >> > > >> > >> > >> > >> > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] trac-all -prep error
Ciao Sarina - The problem is here "fslorient: Command not found." You have to make sure that FSL is properly installed and the FSL executables are in your path, as trac-all calls a few of them. Hope this helps, a.y On Tue, 27 Mar 2012, Sarina Sacco wrote: quando avvio il trac-all (relase FS5.1) mi crea questo errore: /opt/freesurfer/bin/trac-preproc #- #@# Image corrections Tue Mar 27 11:17:27 CEST 2012 mri_convert /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz mri_convert /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm... Starting DICOMRead2() dcmfile = /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm dcmdir = /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig Ref Series No = 7 Found 2242 files, checking for dicoms Found 2240 dicom files in series. First Sorting Computing Slice Direction Vs: 0.029 0.321 1.9739 Vs: 0.0144997 0.160497 0.98693 Second Sorting Counting frames nframes = 28 nslices = 80 ndcmfiles = 2240 PE Dir = COL (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data TR=10050.00, TE=87.10, TI=0.00, flip angle=90.00 i_ras = (-0.999859, -0.0058291, -0.0157782) j_ras = (0.00830111, -0.987041, -0.160255) k_ras = (-0.0144997, -0.160497, 0.98693) writing to /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz... mri_probedicom --i /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dcminfo.dat flip4fsl /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 2 fslswapdim /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz x -y z /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.nii.gz fslorient -forceradiological /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.nii.gz fslorient: Command not found. mv -f /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.mghdti.bvecs /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/bvecs mv: cannot stat `/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.mghdti.bvecs': No such file or directory Linux thunder 2.6.38-8-generic #42-Ubuntu SMP Mon Apr 11 03:31:24 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Tue Mar 27 11:18:21 CEST 2012 Non riesco a capire perchè,da cosa può dipendere? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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.
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 (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 probabilistic tractography using > my previous results as mentioned above I can use TracVis. > > > Thank you. > Antonella > > > > ___ 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.
Re: [Freesurfer] TRACULA and CVS space
Note that tracula doesn't extract from the atlas the exact spatial location of the tracts. It only extracts which anatomical labels are the neighbors of the tract at each point along its trajectory. So it's not as sensitive to misregistration as a voxel-based analysis would be. Our paper discusses all this: http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2011.00023/abstract On Thu, 29 Mar 2012, Antonella Kis wrote: Hi, I would like to know if for a probabilistic tractrography using TRACULA I can use the CVS space as a common template to register the diffusion data instead of MNI template. How I should change for the CVS space the following: set doregmni = 1 which is the default for the MNI space. If I want to use bo th MNI template and CVS template for comparison purposes how this can be don e? THANKS. Antonella ___ 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.
Re: [Freesurfer] Tracula Siemens DTI
Hi Gabor - If you provide the DWI dicoms directly, tracula uses mri_convert to convert them to nifti, and mri_convert doesn't read directions from the header, it looks them up from: $FREESURFER_HOME/diffusion/mgh-dti-seqpack/ This should be fine assuming you use the same standard Siemens diffusion protocol that we use at MGH. If you're using anything different than that (including if you concatenate two DWI series into one), then you should set bvecfile, bvalfile, nb0. For more info see: http://www.freesurfer.net/fswiki/dmrirc If you have doubts about your bvecs is you can check the primary eigenvectors from dtifit (dmri/dtifit_V1.nii.gz) to make sure they're pointing the way you'd expect. Hope this helps, a.y On Sat, 31 Mar 2012, Gabor Perlaki wrote: Dear Freesurfers, I have DTI images acquired on a Siemens 3T TIM Trio (software version VB17A). 1, Is TRACULA able to extract the correct b-values and b-vectors from the DICOM headers of Siemens IMA files or do I need to specify them? 2, I'm not sure whether the gradient directions are stored in the image- or in the scanner coordinate system in the headers of Siemens IMA files. Does anybody have any experience with this version of Syngo software (VB17A)? Does TRACULA need the b-vecs in the image or in the scanner coordinate system? Is it able to reorient the bvecs if they are stored in the wrong coordinate system in the header? 3, My DTI protocol (30 diffusion weighted directions and 1 b0) was repeated twice (in separate series, the second right after the first one, same orientation). Because I'd like to correct for eddy current and movement I don't want to average them on the scanner. Is it possible to put the 62 volume (30+30 diffusion weighted directions and 2 b0) into the same TRACULA evaluation in dicom format or do I need to convert them into a single niftii file? Thanks a lot, Gabor ___ 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.
Re: [Freesurfer] TRACULA exited with errors
Hi Carolina - The bvecs and bvals in the tutorial data should have 3 lines and 1 line, respectively, with 70 entries in each line. Is that not what you have? For different possibilities for inputs, please see the tracula wiki page, and particularly the link to the example dmrirc file: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula a.y On Mon, 2 Apr 2012, Carolina Valencia wrote: Hi FS users I'm trying to run TRACULA tutorial without sucess. After setting the dmrirc_single_subject and run the first command step trac-all -prep -c $TUTORIAL_DATA/diffusion_tutorial/scripts/dmrirc_single_subject It exited with ERRORS, related to bvecs and bvals which is weird because I downloaded the data via wget and chech the size. #@# Tensor fit lun abr 2 13:23:46 COT 2012 dtifit -k /home/cvalencia/freesurfer/subjects/tracula_tutorial//diffusion_tutorial/Diff001/dmri/dwi.nii.gz -m /home/cvalencia/freesurfer/subjects/tracula_tutorial//diffusion_tutorial/Diff001/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -r /home/cvalencia/freesurfer/subjects/tracula_tutorial//diffusion_tutorial/Diff001/dmri/bvecs -b /home/cvalencia/freesurfer/subjects/tracula_tutorial//diffusion_tutorial/Diff001/dmri/bvals -o /home/cvalencia/freesurfer/subjects/tracula_tutorial//diffusion_tutorial/Diff001/dmri/dtifit Error: bvecs and bvals don't have the same number of entries Linux cvalencia-Precision-WorkStation-T3400 2.6.35-32-generic-pae #67-Ubuntu SMP Mon Mar 5 21:23:19 UTC 2012 i686 GNU/Linux trac-preproc exited with ERRORS at lun abr 2 13:23:49 COT 2012 Another question is related to process my own data. I have to recon-all my structural data and to have the orig DWI dicoms in order to use trac-all, right? Many thanks, Best regards -- -- Carolina Valencia M ___ 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.
Re: [Freesurfer] TRACULA exited with errors
Hi Carolina - The bvecs file that you're attaching has commas as the decimal separator. See this suggestion: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18395.html The input DWIs can be in a format other than dicom, but then some additional inputs must be specified, see: http://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc Also, from http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula: Note that, because TRACULA relies on the underlying anatomy as derived from the FreeSurfer cortical parcellation and subcortical segmentation, these need to be generated before running trac-all. This means that before you run trac-all you will have to analyze your subjects' anatomical images with recon-all and make sure that they have a good-quality mri/aparc+aseg.mgz. Hope this helps, a.y On Mon, 2 Apr 2012, Carolina Valencia wrote: I have under dmri folder of Diff001 2 files bvals and bvecs without an order of columns, in the same folder I found files called dwi_orig.mghdti.bvals andbvecs which have the rows and columns you said. I attached the files (I rename them to old in order to save the correct ones) Regarding the question to process my own data. I have to recon-all my structural data and to have the orig DWI dicoms in order to use trac-all, right? Thanks for the help! 2012/4/2 Anastasia Yendiki Hi Carolina - The bvecs and bvals in the tutorial data should have 3 lines and 1 line, respectively, with 70 entries in each line. Is that not what you have? For different possibilities for inputs, please see the tracula wiki page, and particularly the link to the example dmrirc file: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula a.y On Mon, 2 Apr 2012, Carolina Valencia wrote: Hi FS users I'm trying to run TRACULA tutorial without sucess. After setting the dmrirc_single_subject and run the first command step trac-all -prep -c $TUTORIAL_DATA/diffusion_tutorial/scripts/dmrirc_single_subject It exited with ERRORS, related to bvecs and bvals which is weird because I downloaded the data via wget and chech the size. #@# Tensor fit lun abr 2 13:23:46 COT 2012 dtifit -k /home/cvalencia/freesurfer/subjects/tracula_tutorial//diffusion_tutorial/Diff001/dmri/dwi.nii.gz -m /home/cvalencia/freesurfer/subjects/tracula_tutorial//diffusion_tutorial/Diff001/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -r /home/cvalencia/freesurfer/subjects/tracula_tutorial//diffusion_tutorial/Diff001/dmri/bvecs -b /home/cvalencia/freesurfer/subjects/tracula_tutorial//diffusion_tutorial/Diff001/dmri/bvals -o /home/cvalencia/freesurfer/subjects/tracula_tutorial//diffusion_tutorial/Diff001/dmri/dtifit Error: bvecs and bvals don't have the same number of entries Linux cvalencia-Precision-WorkStation-T3400 2.6.35-32-generic-pae #67-Ubuntu SMP Mon Mar 5 21:23:19 UTC 2012 i686 GNU/Linux trac-preproc exited with ERRORS at lun abr 2 13:23:49 COT 2012 Another question is related to process my own data. I have to recon-all my structural data and to have the orig DWI dicoms in order to use trac-all, right? Many thanks, Best regards -- -- Carolina Valencia M 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. -- -- Carolina Valencia M ___ 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.
Re: [Freesurfer] TRACULA "trac-all -path" does not generate all the paths
Hi Juke - Impossible to tell without looking at the output for the specific cases. Could you send the entire trac-all.log file for one of them? Thanks, a.y On Thu, 5 Apr 2012, Juke Cha wrote: > Hi all, > > Running "TRAC-ALL - PATH", I've got a error. Strangely trac-all reports all > jobs done without error as last, but actually it didn't > generate any reconstructed paths. > > When I looking through the 'trac-all.log' file, I found only one error on > "dmri_mergepaths" saying "ERROR: must specify input > volume(s)". But it looks like the function "dmri_paths", which is before the > 'mergepaths', was not successfully done as it didn't > generate any output. (but the log file didn't say anything about this.) > > This occurred in only 3 subjects out of ~70 total. I've rerun the trac-all > code on different machines to no avail. Can anyone help on > this matter? > > > Best, > Juke > > > ___ 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.
Re: [Freesurfer] trakula segmentation fault
Hi Viviana - If you upload this data set I'm happy to look at it. Also, I strongly recommend getting the updated version of trac-all from the wiki (I'm guessing from the log file that you're probably not using that?) See 2012/01/09 update here: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula Thanks, a.y On Wed, 4 Apr 2012, Viviana Siless wrote: Hello, I'm trying to run trac-all prec and I'm getting a segmentation fault error. Loading streamlines from /media/vivi/code/freesurfer/trctrain/trc032/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /media/vivi/code/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /media/vivi/code/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /media/vivi/code/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS.flt.trk INFO: Rejected 0 streamlines for straying off mask INFO: Rejected 0 streamlines for reversing direction Segmentation fault Linux vivi-ThinkStation-C20X 2.6.38-8-generic #42-Ubuntu SMP Mon Apr 11 03:31:24 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Wed Apr 4 18:24:21 CEST 2012 - When I look at the trak-all.error I see this error: -- SUBJECT 00112288Proc DATE Wed Apr 4 18:24:21 CEST 2012 USER vivi HOST vivi-ThinkStation-C20X PROCESSOR x86_64 OS Linux Linux vivi-ThinkStation-C20X 2.6.38-8-generic #42-Ubuntu SMP Mon Apr 11 03:31:24 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux $Id: trac-preproc,v 1.17.2.5 2011/05/20 06:51:51 ayendiki Exp $ /media/vivi/code/freesurfer/bin/trac-preproc PWD /media/vivi/code/freesurfer CMD /media/vivi/code/freesurfer/bin/dmri_train --outdir /media/vivi/images/freesurfer/00112288Proc/dlabel/mni --out lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt rh.ilf_AS_avg33_mni_flt fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt lh.atr_PP_avg33_mni_flt rh.atr_PP_avg33_mni_flt lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt lh.slfp_PP_avg33_mni_flt rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt --slist /tmp/subj33.00112288Proc.16360.txt --trk dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz dlabel/mni/lh.cst_AS_roi2.flt.nii.gz dlabel/mni/rh.cst_AS_roi1.flt.nii.gz dlabel/mni/rh.cst_AS_roi2.flt.nii.gz dlabel/mni/lh.unc_AS_roi1.flt.nii.gz dlabel/mni/lh.unc_AS_roi2.flt.nii.gz dlabel/mni/rh.unc_AS_roi1.flt.nii.gz dlabel/mni/rh.unc_AS_roi2.flt.nii.gz dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz dlabel/mni/fmajor_PP_roi1.flt.nii.gz dlabel/mni/fmajor_PP_roi2.flt.nii.gz dlabel/mni/fminor_PP_roi1.flt.nii.gz dlabel/mni/fminor_PP_roi2.flt.nii.gz dlabel/mni/lh.atr_PP_roi1.flt.nii.gz dlabel/mni/lh.atr_PP_roi2.flt.nii.gz dlabel/mni/rh.atr_PP_roi1.flt.nii.gz dlabel/mni/rh.atr_PP_roi2.flt.nii.gz dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz dlabel/mni/lh.cab_PP_roi1.flt.nii.gz dlabel/mni/lh.cab_PP_roi2.flt.nii.gz dlabel/mni/rh.cab_PP_roi1.flt.nii.gz dlabel/mni/rh.cab_PP_roi2.flt.nii.gz dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz dlabel/mni/lh.slft_PP_roi1.flt.nii.gz dlabel/mni/lh.slft_PP_roi2.flt.nii.gz dlabel/mni/rh.slft_PP_roi1.flt.nii.gz dlabel/mni/rh.slft_PP_roi2.flt.nii.gz --bmask /media/vivi/images/freesurfer/00112288Proc/dlabel/mni/aparc+aseg_mask.nii.gz --fa /media/vivi/images/freesurfer/00112288Proc/dmri/mni/dtifit_FA.flt.nii.gz --ncpts 5 --debug - If I run that command, I get the same (of course): INFO: Rejected 0 streamlines for straying off mask INFO: Rejected 0 streamlines for reversing direction Segmentation fault Can anybody give me an idea of the problem? I run recon-all and finished without errors. I attach the log file, the error file, and my dmrirc file. Please let me know if you need anything else. Thanks in advance! Viviana Siless -- Parietal Team, INRIA Saclay Neurospin, Centre CEA de Saclay 91191 Gif sur Yvette – FRANCE __
Re: [Freesurfer] trac-all -prep error
Hi Sarina - You'll have to specify the list of gradient directions (bvecfile) and b-values (bvalfile), see here for more info: http://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc Please send email to the freesurfer list and not to me directly. Emails sent to the freesurfer list are saved in a searchable archive so that other users can benefit from these pearls of wisdom. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/ a.y On Wed, 11 Apr 2012, Sarina Sacco wrote: Ciao Anastasia ho risolto il problema di FSL,ora l'installazione è corretta,però mi si presenta sempre un errore inerente al bvecs non li trova,potrebbe forse dipendere dai files DICOM che utilizzo? Questo è l'errore: sarina@thunder:/opt/freesurfer/subjects$ trac-all -prep -c $SUBJECTS_DIR/subjects_trac_all/scripts/dmrircFiles/dmrirc_Diff001_F.B. INFO: SUBJECTS_DIR is /opt/freesurfer/subjects/subjects_recon_all INFO: Diffusion root is /opt/freesurfer/subjects/subjects_trac_all Actual FREESURFER_HOME /opt/freesurfer trac-preproc -c /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./scripts/dmrirc.local -log /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./scripts/trac-all.log -cmd /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./scripts/trac-all.cmd #- /opt/freesurfer/bin/trac-preproc #- #@# Image corrections Wed Apr 11 18:01:15 CEST 2012 mri_convert /opt/freesurfer/subjects/subjects_trac_all//Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz mri_convert /opt/freesurfer/subjects/subjects_trac_all//Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /opt/freesurfer/subjects/subjects_trac_all//Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm... Starting DICOMRead2() dcmfile = /opt/freesurfer/subjects/subjects_trac_all//Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm dcmdir = /opt/freesurfer/subjects/subjects_trac_all//Diff001_F.B./orig Ref Series No = 7 Found 2242 files, checking for dicoms Found 2240 dicom files in series. First Sorting Computing Slice Direction Vs: 0.029 0.321 1.9739 Vs: 0.0144997 0.160497 0.98693 Second Sorting Counting frames nframes = 28 nslices = 80 ndcmfiles = 2240 PE Dir = COL (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data TR=10050.00, TE=87.10, TI=0.00, flip angle=90.00 i_ras = (-0.999859, -0.0058291, -0.0157782) j_ras = (0.00830111, -0.987041, -0.160255) k_ras = (-0.0144997, -0.160497, 0.98693) writing to /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz... mri_probedicom --i /opt/freesurfer/subjects/subjects_trac_all//Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dcminfo.dat flip4fsl /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 2 fslswapdim /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz x -y z /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.nii.gz mv -f /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.mghdti.bvecs /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/bvecs mv: cannot stat `/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.mghdti.bvecs': No such file or directory Linux thunder 2.6.38-8-generic #42-Ubuntu SMP Mon Apr 11 03:31:24 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Wed Apr 11 18:03:33 CEST 2012 2012/3/27 Anastasia Yendiki : Ciao Sarina - The problem is here "fslorient: Command not found." You have to make sure that FSL is properly installed and the FSL executables are in your path, as trac-all calls a few of them. Hope this helps, a.y On Tue, 27 Mar 2012, Sarina Sacco wrote: quando avvio il trac-all (relase FS5.1) mi crea questo errore: /opt/freesurfer/bin/trac-preproc #- #@# Image corrections Tue Mar 27 11:17:27 CEST 2012 mri_convert /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz mri_convert /opt/freesurfer/subjects/subje
Re: [Freesurfer] trakula segmentation fault
Hi Viviana - I suspect it may be b/c you're using the 2mm-resolution MNI template brain, and our atlas was built using the 1mm one. From your dmrirc file: # MNI template (the only option for inter-subject registration in this version) # Default: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz # #set mnitemp = /path/to/mni_template.nii.gz set mnitemp = /usr/share/fsl/4.1/data/standard/MNI152_T1_2mm_brain.nii.gz Can you please try changing the above from 2mm to 1mm and see if it works? If so, I'll make sure this is handled more elegantly in the next version. Hope this helps, a.y On Fri, 6 Apr 2012, Viviana Siless wrote: Hi Anastasia, Here is the data: https://transfert.inria.fr/fichiers/4531ddb4948dff7223febc5a5b4f7e7d/testData.tar.gz Let me know if you have any trouble. I changed to the other track-all, and the error is the same. Please let me know if I'm doing anything wrong! Thank you! Viviana Siless -- Parietal Team, INRIA Saclay Neurospin, Centre CEA de Saclay 91191 Gif sur Yvette – FRANCE On Thu, Apr 5, 2012 at 7:38 PM, Anastasia Yendiki wrote: Hi Viviana - If you upload this data set I'm happy to look at it. Also, I strongly recommend getting the updated version of trac-all from the wiki (I'm guessing from the log file that you're probably not using that?) See 2012/01/09 update here: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula Thanks, a.y On Wed, 4 Apr 2012, Viviana Siless wrote: Hello, I'm trying to run trac-all prec and I'm getting a segmentation fault error. Loading streamlines from /media/vivi/code/freesurfer/trctrain/trc032/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /media/vivi/code/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /media/vivi/code/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /media/vivi/code/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS.flt.trk INFO: Rejected 0 streamlines for straying off mask INFO: Rejected 0 streamlines for reversing direction Segmentation fault Linux vivi-ThinkStation-C20X 2.6.38-8-generic #42-Ubuntu SMP Mon Apr 11 03:31:24 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Wed Apr 4 18:24:21 CEST 2012 - When I look at the trak-all.error I see this error: -- SUBJECT 00112288Proc DATE Wed Apr 4 18:24:21 CEST 2012 USER vivi HOST vivi-ThinkStation-C20X PROCESSOR x86_64 OS Linux Linux vivi-ThinkStation-C20X 2.6.38-8-generic #42-Ubuntu SMP Mon Apr 11 03:31:24 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux $Id: trac-preproc,v 1.17.2.5 2011/05/20 06:51:51 ayendiki Exp $ /media/vivi/code/freesurfer/bin/trac-preproc PWD /media/vivi/code/freesurfer CMD /media/vivi/code/freesurfer/bin/dmri_train --outdir /media/vivi/images/freesurfer/00112288Proc/dlabel/mni --out lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt rh.ilf_AS_avg33_mni_flt fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt lh.atr_PP_avg33_mni_flt rh.atr_PP_avg33_mni_flt lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt lh.slfp_PP_avg33_mni_flt rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt --slist /tmp/subj33.00112288Proc.16360.txt --trk dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz dlabel/mni/lh.cst_AS_roi2.flt.nii.gz dlabel/mni/rh.cst_AS_roi1.flt.nii.gz dlabel/mni/rh.cst_AS_roi2.flt.nii.gz dlabel/mni/lh.unc_AS_roi1.flt.nii.gz dlabel/mni/lh.unc_AS_roi2.flt.nii.gz dlabel/mni/rh.unc_AS_roi1.flt.nii.gz dlabel/mni/rh.unc_AS_roi2.flt.nii.gz dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz dlabel/mni/fmajor_PP_roi1.flt.nii.gz dlabel/mni/fmajor_PP_roi2.flt.nii.gz dlabel/mni/fminor_PP_roi1.flt.nii.gz dlabel/mni/fminor_PP_roi2.flt.nii.gz dlabel/mn
Re: [Freesurfer] TRacula and Philips
Hi Fabricio - You can only use the formats supported by mri_convert: http://surfer.nmr.mgh.harvard.edu/fswiki/mri_convert Dicom or nifti is recommended. Hope this helps, Anastasia. On Thu, 19 Apr 2012, fabricio feltrin wrote: Hi Anastatia. Is it possible to use REC/PAR images from philips in tracula? Thanks. Fabrício. ___ 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.
Re: [Freesurfer] trakula segmentation fault
Hi Viviana - I cannot replicate this on our systems but I think I know
what your system may be fussy about and I'll amend it. For now, if you
don't get any outputs can you please try running bedpostx directly on
/media/vivi/images/freesurfer/00112288Proc/dmri and see if that works?
Thanks for bringing this to our attention,
a.y
On Mon, 23 Apr 2012, Viviana Siless wrote:
Hello Anastasia,
It fixed the bug. Thank you so much!
Now Im running trac-all -bedp -c
But it's been running for already 3 days, and it just printed that:
> trac-all -bedp -c /media/vivi/images/freesurfer/dmrirc.example
INFO: SUBJECTS_DIR is /media/vivi/images/freesurfer
INFO: Diffusion root is /media/vivi/images/freesurfer
Actual FREESURFER_HOME /media/vivi/code/freesurfer
ln -sf
/media/vivi/images/freesurfer/00112288Proc/dlabel/diff/anat_brain_mask.flt.nii.gz
/media/vivi/images/freesurfer/00112288Proc/dmri/nodif_brain_mask.nii.gz
ln -sf /media/vivi/images/freesurfer/00112288Proc/dmri/dwi.nii.gz
/media/vivi/images/freesurfer/00112288Proc/dmri/data.nii.gz
WARN: Running FSL's bedbost locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_seychelles /media/vivi/images/freesurfer/00112288Proc/dmri
subjectdir is /media/vivi/images/freesurfer/00112288Proc/dmri
Making bedpostx directory structure
Queuing preprocessing stages
[: 223: NONE: unexpected operator
[: 314: NONE: unexpected operator
[: 327: xbedpostx_pre: unexpected operator
[: 486: x: unexpected operator
[: 486: -le: argument expected
Queuing parallel processing stage
Is it normal?
Thanks for your help! (let me know if I should create another thread)
Viviana Siless
--
Parietal Team, INRIA Saclay
Neurospin, Centre CEA de Saclay
91191 Gif sur Yvette – FRANCE
On Wed, Apr 18, 2012 at 1:18 AM, Anastasia Yendiki
wrote:
Hi Viviana - I suspect it may be b/c you're using the 2mm-resolution MNI
template brain, and our atlas was built using the 1mm one. From your
dmrirc file:
# MNI template (the only option for inter-subject registration in this
version)
# Default: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
#
#set mnitemp = /path/to/mni_template.nii.gz
set mnitemp = /usr/share/fsl/4.1/data/standard/MNI152_T1_2mm_brain.nii.gz
Can you please try changing the above from 2mm to 1mm and see if it
works? If so, I'll make sure this is handled more elegantly in the next
version.
Hope this helps,
a.y
On Fri, 6 Apr 2012, Viviana Siless wrote:
Hi Anastasia,
Here is the data:
https://transfert.inria.fr/fichiers/4531ddb4948dff7223febc5a5b4f7e7d/testData.tar.gz
Let me know if you have any
trouble.
I changed to the other track-all, and the error is the same.
Please let me know if I'm doing anything wrong!
Thank you!
Viviana Siless
--
Parietal Team, INRIA Saclay
Neurospin, Centre CEA de Saclay
91191 Gif sur Yvette – FRANCE
On Thu, Apr 5, 2012 at 7:38 PM, Anastasia Yendiki
wrote:
Hi Viviana - If you upload this data set I'm happy to look at
it.
Also, I strongly recommend getting the updated version of
trac-all from the wiki (I'm guessing from the log file that
you're probably not using that?) See 2012/01/09 update here:
http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula
Thanks,
a.y
On Wed, 4 Apr 2012, Viviana Siless wrote:
Hello,
I'm trying to run trac-all prec and I'm getting a segmentation
fault error.
Loading streamlines from
/media/vivi/code/freesurfer/trctrain/trc032/dlabel/mni/lh.cst_AS.flt.trk
Loading streamline start ROI from
/media/vivi/code/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz
Loading streamline end ROI from
/media/vivi/code/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz
Loading streamlines from
/media/vivi/code/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS.flt.trk
INFO: Rejected 0 streamlines for straying off mask
INFO: Rejected 0 streamlines for reversing direction
Segmentation fault
Linux vivi-ThinkStation-C20X 2.6.38-8-generic #42-Ubuntu SMP
Mon Apr 11 03:31:24 UTC 2011 x86_64 x86_64 x86_64
GNU/Linux
trac-preproc exited with ERRORS at Wed Apr 4 18:24:21 CEST
2012
- When I look at the trak-all.error I see this error:
--
SUBJECT 00112288Proc
DATE Wed Apr 4 18:24:21 CEST 2012
USER vivi
Re: [Freesurfer] Running Tracula -bedpostx and -path
Hi Richard - I'd check your bedpostx output files, run mri_info on them to make sure they have the right number of slices. The monitoring script that produces the "slices processed" messages checks only every once in a while, so you won't see a separate message for each slice. The warnings from the -path part you can definitely ignore. Hope this helps, a.y On Tue, 24 Apr 2012, Richard Binney wrote: Hi Anastasia, I ran bedpost directly: bedpostx dmri It seemed to run fine, not exiting with any errors. the only thing that concerned me was that the last output in the terminal was 50 slices processed [when I have 54] queing post-processing stage then it exited. It seemed to run rather quicker than I expected and I expected it to at least output "all slices processed" and/or something after queing post Is there any reason to be concerned? Furthermore, in running the -path, the terminal window constantly outputting... ERROR: Degenerate spline segment 58 81 24 56 69 24 .. ERROR: Degenerate spline segment .. but it seems to continue on without exiting. Is there any reason to be concerned about this? what doe sit mean? Thanks for your help R ___ 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.
Re: [Freesurfer] trakula segmentation fault
Hi Viviana - Does it die at that point or does it keep running? If it's the latter it doesn't look wrong. For your first problem you should make sure that your path includes the bin/ directory under the FSL distribution. a.y On Wed, 25 Apr 2012, Viviana Siless wrote: Hi Anastasia, I ran: - bedpostx /media/vivi/images/freesurfer/00112288Proc/dmri and got the following output: subjectdir is /media/vivi/images/freesurfer/00112288Proc/dmri Making bedpostx directory structure Queuing preprocessing stages Queuing parallel processing stage But before it told me that /bin/fsl_sub was mising, so i copied from where i had it to there, and then it arrived at the same place than before then I ran - fsl4.1-bedpostx /media/vivi/images/freesurfer/00112288Proc/dmri I made symbolic link from fsl4.1-whatever to whatever. Im working in ubuntu 11.04 and I installed fsl from the package manager. and I got this: subjectdir is /media/vivi/images/freesurfer/00112288Proc/dmri Making bedpostx directory structure Queuing preprocessing stages Queuing parallel processing stage 0 slices processed What should I do? Thanks! Viviana On Wed, Apr 25, 2012 at 12:52 AM, Anastasia Yendiki wrote: Hi Viviana - I cannot replicate this on our systems but I think I know what your system may be fussy about and I'll amend it. For now, if you don't get any outputs can you please try running bedpostx directly on /media/vivi/images/freesurfer/00112288Proc/dmri and see if that works? Thanks for bringing this to our attention, a.y On Mon, 23 Apr 2012, Viviana Siless wrote: Hello Anastasia, It fixed the bug. Thank you so much! Now Im running trac-all -bedp -c But it's been running for already 3 days, and it just printed that: > trac-all -bedp -c /media/vivi/images/freesurfer/dmrirc.example INFO: SUBJECTS_DIR is /media/vivi/images/freesurfer INFO: Diffusion root is /media/vivi/images/freesurfer Actual FREESURFER_HOME /media/vivi/code/freesurfer ln -sf/media/vivi/images/freesurfer/00112288Proc/dlabel/diff/anat_brain_mask. flt.nii.gz /media/vivi/images/freesurfer/00112288Proc/dmri/nodif_brain_mask.nii.gz ln -sf /media/vivi/images/freesurfer/00112288Proc/dmri/dwi.nii.gz /media/vivi/images/freesurfer/00112288Proc/dmri/data.nii.gz WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_seychelles /media/vivi/images/freesurfer/00112288Proc/dmri subjectdir is /media/vivi/images/freesurfer/00112288Proc/dmri Making bedpostx directory structure Queuing preprocessing stages [: 223: NONE: unexpected operator [: 314: NONE: unexpected operator [: 327: xbedpostx_pre: unexpected operator [: 486: x: unexpected operator [: 486: -le: argument expected Queuing parallel processing stage Is it normal? Thanks for your help! (let me know if I should create another thread) Viviana Siless -- Parietal Team, INRIA Saclay Neurospin, Centre CEA de Saclay 91191 Gif sur Yvette – FRANCE On Wed, Apr 18, 2012 at 1:18 AM, Anastasia Yendiki wrote: Hi Viviana - I suspect it may be b/c you're using the 2mm-resolution MNI template brain, and our atlas was built using the 1mm one. From your dmrirc file: # MNI template (the only option for inter-subject registration in this version) # Default: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz # #set mnitemp = /path/to/mni_template.nii.gz set mnitemp = /usr/share/fsl/4.1/data/standard/MNI152_T1_2mm_brain.nii.gz Can you please try changing the above from 2mm to 1mm and see if it works? If so, I'll make sure this is handled more elegantly in the next version. Hope this helps, a.y On Fri, 6 Apr 2012, Viviana Siless wrote: Hi Anastasia, Here is the data:https://transfert.inria.fr/fichiers/4531ddb4948dff7223febc5a5b4f7e7d/testDa ta.tar.gz Let me know if you have any trouble. I changed to the other track-all, and the error is the same. Please let me know if I'm doing anything
Re: [Freesurfer] Trac-all on a cluster with PBS/torque
Hi Knut - If I understand correctly, your modification was replacing "fsl_sub_seychelles" with "fsl_sub"? a.y On Fri, 27 Apr 2012, Knut J Bjuland wrote: > Hi > > I am trying to run Trac-all on a cluster with PBS/torque. The trac-all > scripts was modified to run with qsub, but > the second stage in Trac-all crash without getting finished. This is tested > with the tutorial data. I am > enclosing the modified trac-all script. > > Best regard > > Knut J Bjuland > NTNU > > ___ 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.
Re: [Freesurfer] Trac-all on a cluster with PBS/torque
Hi Knut - I modified fsl_sub to work on our own PBS cluster. This modified version is fsl_sub_seychelles. Anything that works with the original fsl_sub should also work with fsl_sub_seychelles. You can modify either of the two to make it work on your cluster. If you do make it more general to work on more clusters, we'll be happy to incorporate the changes but there's no way for us to know what would work on every possible local setup. Good luck! a.y On Fri, 27 Apr 2012, Knut J Bjuland wrote: > Hi Anastasia > > > I think this hack was also added > > ## Steinar, steinar, commnet out this to fool the program to run under PBS > ## date 20 april 2012 > ## hack > > #if ($?PBS_JOBID) then > # echo "ERROR: Do not submit $ProgName as a job with pbsubmit or qsub." > # echo "ERROR: Run it directly on the command line." > # echo "ERROR: If run on the cluster, $ProgName will submit the jobs > for you." > # echo "ERROR: Each subject listed in your dmrirc will be submitted as a > job." > # exit 1 > #endif > > ## end hack > > Should I revert those changes? I changed to fsl_sub because the cluster I am > using had my modifcation to fsl_sub. Should I change back? > > Knut J > > > > > > > > On 04/27/2012 05:06 PM, Anastasia Yendiki wrote: >> >> Hi Knut - If I understand correctly, your modification was replacing >> "fsl_sub_seychelles" with "fsl_sub"? >> >> a.y >> >> On Fri, 27 Apr 2012, Knut J Bjuland wrote: >> >> > Hi >> > >> > I am trying to run Trac-all on a cluster with PBS/torque. The trac-all >> > scripts was modified to run with qsub, but >> > the second stage in Trac-all crash without getting finished. This is >> > tested with the tutorial data. I am >> > enclosing the modified trac-all script. >> > >> > Best regard >> > >> > Knut J Bjuland >> > NTNU >> > >> > >> >> >> 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. >> >> >> > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mutualinfo in flirt T1->MNI registration
Hi Andi - I'm pretty sure we were already planning to change some of the mutualinfo's to corratio's in the next release, so no, this is in no way an official endorsement! a.y On Tue, 1 May 2012, Andi Heckel wrote: Dear Tracula Team, i noticed that TRACULA uses fsl's flirt with "mutualinfo" as cost function to register the anatomical individual T1 brain (brain_anat.nii.gz) to the MNI152 space T1 template (MNI152_T1_1mm_brain.nii.gz), i.e. for an intramodal registration. I was wondering why "mutualinfo" (which is often used for intermodal registrations) is also used for a an intramodal registration in TRACULA'S implementation rather than e.g. least squares or correlation ratio, the latter being the fsl default. Is "mutualinfo" preferable not only for intermodal (e.g., b0 -> t1) but also for intramodal t1->t1 registrations for your purpose ? - I am just curious to know :) kind regards, andi ___ 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.
Re: [Freesurfer] tracula
Hi Carolina - Tracula is not an exploratory method for tractography from any seed region of your choice. It reconstructs a specific set of 18 tracts. http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula http://www.frontiersin.org/neuroinformatics/10.3389/fninf.2011.00023/abstract a.y On Fri, 4 May 2012, carolina.mr wrote: > Hello, > > Is it possible to track fibers with TRACULA from the cortical parcelation > masks obtained from recon-all or do we have to use the white matter > parcelation to do so? > Another question: if I use QDEC to find the areas with significant > difference in the cortical tickness between two groups, is it possible to > use those ROI's to launch the fiber track with TRACULA? > > Thank you, > Carolina Rimkus > ___ 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.
Re: [Freesurfer] TRACULA niftii file
Hi Gabor - The input DWIs can be in any format that can be read by mri_convert, including the NIfTI format. The gradient directions should be in voxel coordinates, like the ones used by FSL. I don't have experience with dcm2nii, but if you have original DICOM files, you can pass those as the input, too. Hope this helps, a.y On Thu, 10 May 2012, Gabor Perlaki wrote: Dear all, Is TRACULA able to handle 4D FSL niftii as input for DTI images? Are bves/bvalues extracted by dcm2nii and MRICro accurate for TRACULA? I think TRACULA needs the bvecs in the image coordinate system, which is not the same as scanner coordinate system in case of oblique acquisition. Do I need to use dcm2nii with correction for slice angulation to ___ 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.
Re: [Freesurfer] TRACULA niftii file
You can specify them by setting bvecfile and bvalfile in your configuration file. On Thu, 10 May 2012, Gabor Perlaki wrote: Dear Anastasia, I've the original DICOM files, but it is acquired with the standard Siemens DTI ep2_diff, and not with the MGH-DTI sequence. Is DTI images acquired with the standard DTI accurate and TRACULA able to extract the bvals and bvecs from the dicom files? Thanks, Gabor 2012/5/10 Anastasia Yendiki Hi Gabor - The input DWIs can be in any format that can be read by mri_convert, including the NIfTI format. The gradient directions should be in voxel coordinates, like the ones used by FSL. I don't have experience with dcm2nii, but if you have original DICOM files, you can pass those as the input, too. Hope this helps, a.y On Thu, 10 May 2012, Gabor Perlaki wrote: Dear all, Is TRACULA able to handle 4D FSL niftii as input for DTI images? Are bves/bvalues extracted by dcm2nii and MRICro accurate for TRACULA? I think TRACULA needs the bvecs in the image coordinate system, which is not the same as scanner coordinate system in case of oblique acquisition. Do I need to use dcm2nii with correction for slice angulation to 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. ___ 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.
Re: [Freesurfer] trac-all -path error
Hi Kiely - Looks like you used flirt for the intra-subject registration, so you can look in trac-all.log for the flirt command line that registers diffusion to anatomical and play around with the parameters. You can also use bbregister instead of flirt for the intra-subject registration - it has the option to initialize with flirt or with SPM. Hope this helps, a.y On Wed, 16 May 2012, Kiely Donnelly wrote: Hi Priti - Thanks for your help. The inter-subject registration seems to have run OK, but there must be something wrong with the intra-subject registration. When I try to view it using freeview, it's completely dark - I don't see a brain at all. Is there a way to troubleshoot this? Thanks, Kiely On Wed, May 9, 2012 at 2:08 PM, Priti Srinivasan wrote: Hi Kiely, Have you checked your inter and intra subject registrations? The control points going off the dwi is not only for one paths but for all the paths. If the registration goes terribly wrong, this can happen. You can take a look at /dmri/lowb_brain_anat.flt.nii.gz (For intra subject registration diff-anat) and /dmri/brain_anat_mni.nii.gz (For inter-subject registration anat-mni) I would start by checking that first. Priti > Hello-- > > I have run Tracula successfully for ~75 healthy subjects. However, the > pathway reconstruction seems to fail for a handful of people. I've > attached > the log file for one of these subjects. It appears that the control points > are not within the dwi. A similar problem occurred in a subject with > substantial signal loss in the dwi, but that doesn't seem to be the case > for this particular person. I have been creating the entire set of tracts, > but at this point, I'm only interested in the SLFt and SLFp. > > Thanks, > > Kiely > ___ > 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. -- Kiely M. Donnelly, M.A. Doctoral Candidate, Clinical Neuropsychology University of Cincinnati ___ 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.
Re: [Freesurfer] trac-all -path error
No, this is something you have to try yourself on the command line. If you want to make the change permanent, you can edit the relevant line in $FREESURFER_HOME/bin/trac-preproc. On Wed, 16 May 2012, Kiely Donnelly wrote: Is this something I can change in my dmrirc file or do I need to run flirt on it's own? Thanks, Kiely On Wed, May 16, 2012 at 9:27 AM, Priti Srinivasan wrote: Kiely, For flirt, try using corratio, cost function instead of mutualinfo (which is the default in trac-all) to see if that solves your registration problem. > Hi Kiely - Looks like you used flirt for the intra-subject registration, > so you can look in trac-all.log for the flirt command line that registers > diffusion to anatomical and play around with the parameters. > > You can also use bbregister instead of flirt for the intra-subject > registration - it has the option to initialize with flirt or with SPM. > > Hope this helps, > a.y > > On Wed, 16 May 2012, Kiely Donnelly wrote: > >> Hi Priti - Thanks for your help. The inter-subject registration seems to >> have run OK, but there must be something wrong with the intra-subject >> registration. When I try to view it using freeview, it's completely dark >> - I >> don't see a brain at all. Is there a way to troubleshoot this? >> Thanks, >> >> Kiely >> >> On Wed, May 9, 2012 at 2:08 PM, Priti Srinivasan >> wrote: >> Hi Kiely, >> >> Have you checked your inter and intra subject registrations? The >> control >> points going off the dwi is not only for one paths but for all >> the paths. >> If the registration goes terribly wrong, this can happen. You >> can take a >> look at >> >> /dmri/lowb_brain_anat.flt.nii.gz (For intra subject registration >> diff-anat) >> >> and >> >> /dmri/brain_anat_mni.nii.gz (For inter-subject registration >> anat-mni) >> >> I would start by checking that first. >> >> Priti >> >> > Hello-- >> > >> > I have run Tracula successfully for ~75 healthy subjects. >> However, the >> > pathway reconstruction seems to fail for a handful of people. >> I've >> > attached >> > the log file for one of these subjects. It appears that the >> control points >> > are not within the dwi. A similar problem occurred in a >> subject with >> > substantial signal loss in the dwi, but that doesn't seem to >> be the case >> > for this particular person. I have been creating the entire >> set of tracts, >> > but at this point, I'm only interested in the SLFt and SLFp. >> > >> > Thanks, >> > >> > Kiely >> > ___ >> > 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. >> >> >> >> >> -- >> Kiely M. Donnelly, M.A. >> Doctoral Candidate, Clinical Neuropsychology >> University of Cincinnati >> >>___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Kiely M. Donnelly, M.A. Doctoral Candidate, Clinical Neuropsychology University of Cincinnati ___ 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 contai
Re: [Freesurfer] trac-all -path error
The .mat registration matrix should be saved under dmri/xfms/. On Wed, 16 May 2012, Kiely Donnelly wrote: I tried using corratio and it seems to have fixed the registration issue. I'm very new to this so just want to make sure I did it correctly before I move forward. Should the command line look something like this if I am running it in this individuals dmri directory: flirt -in dwi_orig.nii.gz -ref brain_anat.nii.gz -out lowb_brain_anat.flt.nii.gz -omat diff2anat.flt.mat -cost corratio Thanks so much for your help. Kiely On Wed, May 16, 2012 at 10:12 AM, Priti Srinivasan wrote: you have to run flirt commandline separately to check if it solves your problem. > Is this something I can change in my dmrirc file or do I need to run flirt > on it's own? > > Thanks, > > Kiely > > On Wed, May 16, 2012 at 9:27 AM, Priti Srinivasan < > rspr...@nmr.mgh.harvard.edu> wrote: > >> Kiely, For flirt, try using corratio, cost function instead of >> mutualinfo >> (which is the default in trac-all) to see if that solves your >> registration >> problem. >> >> >> > Hi Kiely - Looks like you used flirt for the intra-subject >> registration, >> > so you can look in trac-all.log for the flirt command line that >> registers >> > diffusion to anatomical and play around with the parameters. >> > >> > You can also use bbregister instead of flirt for the intra-subject >> > registration - it has the option to initialize with flirt or with SPM. >> > >> > Hope this helps, >> > a.y >> > >> > On Wed, 16 May 2012, Kiely Donnelly wrote: >> > >> >> Hi Priti - Thanks for your help. The inter-subject registration seems >> to >> >> have run OK, but there must be something wrong with the intra-subject >> >> registration. When I try to view it using freeview, it's completely >> dark >> >> - I >> >> don't see a brain at all. Is there a way to troubleshoot this? >> >> Thanks, >> >> >> >> Kiely >> >> >> >> On Wed, May 9, 2012 at 2:08 PM, Priti Srinivasan >> >> wrote: >> >> Hi Kiely, >> >> >> >> Have you checked your inter and intra subject registrations? >> The >> >> control >> >> points going off the dwi is not only for one paths but for all >> >> the paths. >> >> If the registration goes terribly wrong, this can happen. You >> >> can take a >> >> look at >> >> >> >> /dmri/lowb_brain_anat.flt.nii.gz (For intra subject >> registration >> >> diff-anat) >> >> >> >> and >> >> >> >> /dmri/brain_anat_mni.nii.gz (For inter-subject registration >> >> anat-mni) >> >> >> >> I would start by checking that first. >> >> >> >> Priti >> >> >> >> > Hello-- >> >> > >> >> > I have run Tracula successfully for ~75 healthy subjects. >> >> However, the >> >> > pathway reconstruction seems to fail for a handful of people. >> >> I've >> >> > attached >> >> > the log file for one of these subjects. It appears that the >> >> control points >> >> > are not within the dwi. A similar problem occurred in a >> >> subject with >> >> > substantial signal loss in the dwi, but that doesn't seem to >> >> be the case >> >> > for this particular person. I have been creating the entire >> >> set of tracts, >> >> > but at this point, I'm only interested in the SLFt and SLFp. >> >> > >> >> > Thanks, >> >> > >> >> > Kiely >> >> > ___ >> >> > 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. >> >> >> >> >>
Re: [Freesurfer] trac-all -path error
Were the old .mat files replaced with the new ones? On Fri, 18 May 2012, Kiely Madhavan wrote: That seemed to fix the registration issue, but I'm still unable to reconstruct the tracts using trac-all -path. I'm getting the same error that the control points are not within the mask. THis happens for all tracts. Thanks, Kiely On Wed, May 16, 2012 at 11:39 AM, Anastasia Yendiki wrote: The .mat registration matrix should be saved under dmri/xfms/. On Wed, 16 May 2012, Kiely Donnelly wrote: I tried using corratio and it seems to have fixed the registration issue. I'm very new to this so just want to make sure I did it correctly before I move forward. Should the command line look something like this if I am running it in this individuals dmri directory: flirt -in dwi_orig.nii.gz -ref brain_anat.nii.gz -out lowb_brain_anat.flt.nii.gz -omat diff2anat.flt.mat -cost corratio Thanks so much for your help. Kiely On Wed, May 16, 2012 at 10:12 AM, Priti Srinivasan wrote: you have to run flirt commandline separately to check if it solves your problem. > Is this something I can change in my dmrirc file or do I need to run flirt > on it's own? > > Thanks, > > Kiely > > On Wed, May 16, 2012 at 9:27 AM, Priti Srinivasan < > rspr...@nmr.mgh.harvard.edu> wrote: > >> Kiely, For flirt, try using corratio, cost function instead of >> mutualinfo >> (which is the default in trac-all) to see if that solves your >> registration >> problem. >> >> >> > Hi Kiely - Looks like you used flirt for the intra-subject >> registration, >> > so you can look in trac-all.log for the flirt command line that >> registers >> > diffusion to anatomical and play around with the parameters. >> > >> > You can also use bbregister instead of flirt for the intra-subject >> > registration - it has the option to initialize with flirt or with SPM. >> > >> > Hope this helps, >> > a.y >> > >> > On Wed, 16 May 2012, Kiely Donnelly wrote: >> > >> >> Hi Priti - Thanks for your help. The inter-subject registration seems >> to >> >> have run OK, but there must be something wrong with the intra-subject >> >> registration. When I try to view it using freeview, it's completely >> dark >> >> - I >> >> don't see a brain at all. Is there a way to troubleshoot this? >> >> Thanks, >> >> >> >> Kiely >> >> >> >> On Wed, May 9, 2012 at 2:08 PM, Priti Srinivasan >> >> wrote: >> >> Hi Kiely, >> >> >> >> Have you checked your inter and intra subject registrations? >> The >> >> control >> >> points going off the dwi is not only for one paths but for all >> >> the paths. >> >> If the registration goes terribly wrong, this can happen. You >> >> can take a >> >> look at >> >> >> >> /dmri/lowb_brain_anat.flt.nii.gz (For intra subject &
Re: [Freesurfer] trac-all -path error
The other registration files depend on diff2anat. For example, diff2mni is composed of diff2anat and anat2mni. If you're using the old diff2mni, it's like you didn't change anything. The -intra step creates all these. You need to edit the command that generates the diff2anat in your version of trac-preproc. Either comment that line out so that it runs everything but that, or change that line to the options that worked for you. On Fri, 18 May 2012, Kiely Madhavan wrote: I only created a diff2anat.flt.mat file which replaced the old one. Do they all need to be recreated? If so, is that something I add to the command line? On Fri, May 18, 2012 at 10:55 AM, Anastasia Yendiki wrote: Were the old .mat files replaced with the new ones? On Fri, 18 May 2012, Kiely Madhavan wrote: That seemed to fix the registration issue, but I'm still unable to reconstruct the tracts using trac-all -path. I'm getting the same error that the control points are not within the mask. THis happens for all tracts. Thanks, Kiely On Wed, May 16, 2012 at 11:39 AM, Anastasia Yendiki wrote: The .mat registration matrix should be saved under dmri/xfms/. On Wed, 16 May 2012, Kiely Donnelly wrote: I tried using corratio and it seems to have fixed the registration issue. I'm very new to this so just want to make sure I did it correctly before I move forward. Should the command line look something like this if I am running it in this individuals dmri directory: flirt -in dwi_orig.nii.gz -ref brain_anat.nii.gz -out lowb_brain_anat.flt.nii.gz -omat diff2anat.flt.mat -cost corratio Thanks so much for your help. Kiely On Wed, May 16, 2012 at 10:12 AM, Priti Srinivasan wrote: you have to run flirt commandline separately to check if it solves your problem. > Is this something I can change in my dmrirc file or do I need to run flirt > on it's own? > > Thanks, > > Kiely > > On Wed, May 16, 2012 at 9:27 AM, Priti Srinivasan < > rspr...@nmr.mgh.harvard.edu> wrote: > >> Kiely, For flirt, try using corratio, cost function instead of >> mutualinfo >> (which is the default in trac-all) to see if that solves your >> registration >> problem. >> >> >> > Hi Kiely - Looks like you used flirt for the intra-subject >> registration, >> > so you can look in trac-all.log for the flirt command line that >> registers >> > diffusion to anatomical and play around with the parameters. >> > >> > You can also use bbregister instead of flirt for the intra-subject >> > registration - it has the option to initialize with flirt or with SPM. >> > >> > Hope this helps, >> > a.y >> > >> > On Wed, 16 May 2012, Kiely Donnelly wrote: >> > >> >> Hi Priti - Thanks for your help. The inter-subject registration seems >> to >> >> have run O
Re: [Freesurfer] trac-all -path error
This is a script, it's in the directory where all freesurfer scripts are. You can find it by doing "which trac-preproc". On Fri, 18 May 2012, Kiely Madhavan wrote: OK - Can you point me in the direction of the trac-preproc file that I should edit? On Fri, May 18, 2012 at 12:18 PM, Anastasia Yendiki wrote: The other registration files depend on diff2anat. For example, diff2mni is composed of diff2anat and anat2mni. If you're using the old diff2mni, it's like you didn't change anything. The -intra step creates all these. You need to edit the command that generates the diff2anat in your version of trac-preproc. Either comment that line out so that it runs everything but that, or change that line to the options that worked for you. On Fri, 18 May 2012, Kiely Madhavan wrote: I only created a diff2anat.flt.mat file which replaced the old one. Do they all need to be recreated? If so, is that something I add to the command line? On Fri, May 18, 2012 at 10:55 AM, Anastasia Yendiki wrote: Were the old .mat files replaced with the new ones? On Fri, 18 May 2012, Kiely Madhavan wrote: That seemed to fix the registration issue, but I'm still unable to reconstruct the tracts using trac-all -path. I'm getting the same error that the control points are not within the mask. THis happens for all tracts. Thanks, Kiely On Wed, May 16, 2012 at 11:39 AM, Anastasia Yendiki wrote: á á áThe .mat registration matrix should be saved under dmri/xfms/. á á áOn Wed, 16 May 2012, Kiely Donnelly wrote: á á á á á áI tried using corratio and it seems to have fixed á á á á á áthe registration issue. á á á á á áI'm very new to this so just want to make sure I did á á á á á áit correctly before I á á á á á ámove forward. Should the command line look something á á á á á álike this if I am á á á á á árunning it in this individuals dmri directory:á á á á á á áflirt -in dwi_orig.nii.gz -ref brain_anat.nii.gz á á á á á á-out á á á á á álowb_brain_anat.flt.nii.gz -omat diff2anat.flt.mat á á á á á á-cost corratio á á á á á áThanks so much for your help. á á á á á áKiely á á á á á áOn Wed, May 16, 2012 at 10:12 AM, Priti Srinivasan á á á á á á wrote: á á á á á áá á áyou have to run flirt commandline separately to á á á á á ácheck if it á á á á á áá á ásolves your á á á á á áá á áproblem. á á á á á áá á á> Is this something I can change in my dmrirc á á á á á áfile or do I need á á á á á áá á áto run flirt á á á á á áá á á> on it's own? á á á á á áá á á> á á á á á áá á á> Thanks, á á á á á áá á á> á á á á á áá á á> Kiely á á á á á áá á á> á á á á á áá á á> On Wed, May 16, 2012 at 9:27 AM, Priti á á á á á áSrinivasan < á á á á á áá á á> rspr...@nmr.mgh.harvard.edu> wrote: á á á á á áá á á> á á á á á áá á á>> Kiely, For flirt, try using corratio, cost á á á á á áfunction instead á á á á á áá á áof á á á á á áá á á>> mutualinfo á á á á á áá á á>> (which is the default in trac-all) to see if á á á á á áthat solves your á á á á á áá á á>> registration á á á á á áá á á>> problem. á á á á á áá á á>> á á á á á áá á á>> á á á á á áá á á>> > Hi Kiely - Looks like you used flirt for á á á á á áthe intra-subject á á á á á áá á á>> registration, á á á á á áá á á>> > so you can look in trac-all.log for the á á á á á áflirt command line á á á á á áá á áthat á á á á á áá á á>> registers á á á á á áá á á>> > diffusion to anatomical and play around á á á á á áwith the á á á á á áá á áparameters. á á á á á áá á á>> > á á á á á áá á á>> > You can also use bbregister instead of á á á á á áflirt for the á á á á á áá á áintra-subject á á á á á áá á á>> > registration - it has the option to á á á á á áinitialize with flirt á á á á á áá á áor with SPM. á á á á á áá á á>> > á á á á á áá á á>> > Hope this helps, á á á á á áá á á>> > a.y á á á á á áá á á>> > á á á á á áá á á>> > On Wed, 16 Ma
Re: [Freesurfer] trac-all -path error
This is the help text that you get when you run the script. You need to
open the script in a text editor.
On Fri, 18 May 2012, Kiely Madhavan wrote:
That's where I looked, but all I see is the following (I don't see the command
line that creates the diff2anat for me to edit):
Last login: Fri May 18 13:45:47 on ttys000
/Applications/freesurfer/bin/trac-preproc ; exit;
Kielys-MacBook-Air:~ kielydonnelly$ /Applications/freesurfer/bin/trac-preproc ;
exit;
USAGE: trac-preproc
Required arguments:
-c : dmrirc file (see dmrirc.example)
Other arguments:
-log : default is trac-all.log in the same dir as dmrirc
-nolog : do not save a log file
-cmd : default is trac-all.cmd in the same dir as dmrirc
-nocmd : do not save a cmd file
-no-isrunning : do not check whether this subject is currently being
processed
-umask umask : set unix file permission mask (default 002)
-grp groupid : check that current group is alpha groupid
-allowcoredump : set coredump limit to unlimited
-debug : generate much more output
-dontrun : do everything but execute each command
-version : print version of this script and exit
-help : print full contents of help
logout
[Process completed]
On Fri, May 18, 2012 at 1:59 PM, Anastasia Yendiki
wrote:
This is a script, it's in the directory where all freesurfer scripts are. You
can find it by doing "which
trac-preproc".
On Fri, 18 May 2012, Kiely Madhavan wrote:
OK - Can you point me in the direction of the trac-preproc file
that I should edit?
On Fri, May 18, 2012 at 12:18 PM, Anastasia Yendiki
wrote:
The other registration files depend on diff2anat. For example,
diff2mni is composed of diff2anat
and anat2mni. If
you're using the old diff2mni, it's like you didn't change
anything.
The -intra step creates all these. You need to edit the
command that generates the diff2anat in
your version of
trac-preproc. Either comment that line out so that it runs
everything but that, or change that line
to the options
that worked for you.
On Fri, 18 May 2012, Kiely Madhavan wrote:
I only created a diff2anat.flt.mat file which replaced the old
one. Do they all need to be
recreated? If so,
is that something I
add to the command line?
On Fri, May 18, 2012 at 10:55 AM, Anastasia Yendiki
wrote:
Were the old .mat files replaced with the new ones?
On Fri, 18 May 2012, Kiely Madhavan wrote:
That seemed to fix the registration issue, but I'm
still unable to
reconstruct the tracts using trac-all -path. I'm
getting the same error that
the control points are not within the mask. THis
happens for all tracts.
Thanks,
Kiely
On Wed, May 16, 2012 at 11:39 AM, Anastasia Yendiki
wrote:
á á áThe .mat registration matrix should be saved under
dmri/xfms/.
á á áOn Wed, 16 May 2012, Kiely Donnelly wrote:
á á á á á áI tried using corratio and it seems to have
fixed
á á á á á áthe registration issue.
á á á á á áI'm very new to this so just want to make
sure I did
á á á á á áit correctly before I
á á á á á ámove forward. Should the command line look
something
á á á á á álike this if I am
á á á á á árunning it in this individuals dmri
directory:á
á á á á á áflirt -in dwi_orig.nii.gz -ref
brain_anat.nii.gz
á á á á á á-out
á á á á á álowb_brain_anat.flt.nii.gz -omat
diff2anat.flt.mat
á á á á á á-cost corratio
á á á á á áThanks so much for your help.
á á á á á áKiely
á á á á á áOn Wed, May 16, 2012 at 10:12 AM, Priti
Srinivasan
á á á á á á wrote:
á á á á á áá á áyou have to run flirt commandline
separately to
á á á á á ácheck if it
á á á á á áá á ásolves your
á á á á á áá á áproblem.
á á á á á áá á á> Is this something I can change in my
dmrirc
á á á á á áfile or do I need
á á á á á áá á áto run flirt
á á á á á áá á á> on it's own?
Re: [Freesurfer] trac-all -bedp error
This is going to be updated in the next version of freesurfer. There have
been some compatibility issues with the latest version of bedpostx that
we've had to fix. For now please run bedpostx by itself. Thanks!
On Fri, 25 May 2012, Gabor Perlaki wrote:
> Dear Priti
>
> The bedpostx works fine on the data if I run it outside of tracula.
>
> The command "/home/kutato12/freesurfer/bin/fsl_sub_seychelles -T 60 -m a -N
> bedpostx_pre -l
> /home/kutato12/freesurfer/subjects/my_subject/dmri.bedpostX/logs
> ${FSLDIR}/bin/bedpostx_preproc.sh
> /home/kutato12/freesurfer/subjects/my_subject/dmri"
>
> gives the following error:
>
> [: 224: NONE: unexpected operator
> [: 315: NONE: unexpected operator
> [: 328: xbedpostx_pre: unexpected operator
> [: 487: x: unexpected operator
> [: 487: -le: argument expected
>
> But "/usr/lib/fsl/4.1/fsl_sub -T 60 -m a -N bedpostx_pre -l
> /home/kutato12/freesurfer/subjects/my_subject/dmri.bedpostX/logs
> ${FSLDIR}/bin/bedpostx_preproc.sh
> /home/kutato12/freesurfer/subjects/my_subject/dmri"
>
> works.
>
> So I think there is a problem with fsl_sub_seychelles. Any idea how to solve
> this thing?
>
> Thanks,
> Gabor
>
> 2012/5/24 Priti Srinivasan
> Hi Gabor,
>
> If you run bedpostX on the data outside of tracula using the
> default
> options, do you get the same error?
>
> Priti
>
> > Dear all,
> >
> > I've the following error right after starting trac-all -bedp
> -c
> > configuration_file:
> >
> > Making bedpostx directory structure
> > Queuing preprocessing stages
> > [: 223: NONE: unexpected operator
> > [: 314: NONE: unexpected operator
> > [: 327: xbedpostx_pre: unexpected operator
> > [: 486: x: unexpected operator
> > [: 486: -le: argument expected
> > Queuing parallel processing stage
> > [: 223: NONE: unexpected operator
> > 0 slices processed
> > [: 327: xbedpostx: unexpected operator
> > [: 486: x70: unexpected operator
> > Queuing post processing stage
> > [: 223: NONE: unexpected operator
> > [: 314: NONE: unexpected operator
> > [: 327: xbedpostx_post: unexpected operator
> > [: 486: x: unexpected operator
> > [: 486: -le: argument expected
> >
> >>From the created files it seems that the first error occurs at
> > "preprocid=`${BPDIR}/fsl_sub_seychelles -T 60 -m a -N
> bedpostx_pre -l
> > ${subjdir}.bedpostX/logs ${FSLDIR}/bin/bedpostx_preproc.sh
> ${subjdir}`"
> >
> > Any idea how to fix this error?
> >
> > Trac-all -prep finished without error.
> > I've Freesurfer 5.1.0, Ubuntu 11.04 and FSL 4.1.8 installed
> using
> > Neurodebian and I don't use SGE.
> >
> > I'd appreciate an early answer.
> >
> > Thanks,
> > Gabor
> > ___
> > 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.
>
>
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] 回复: Re: /path/to/dmri/dwi_orig_flip.mghdti.bvecs': No such file or directory
Hi Xiangzhen - Currently mri_convert does not support extracting gradients and b-values from dicom files. If you can get the gradients and b-values from the dicom header yourself, that's great. Save them in text files and enter the path in your dmrirc file. a.y On Thu, 7 Jun 2012, Xiangzhen Kong wrote: Thank you very much, Anastasia. I have checked the related mails in the list and found not me came across this problem. As you said, I know how I can run my data. But I have a question. Why would we make trac-all compatible to other scanner or acquisitions, since we can get bvecs and bval from the DICOM header? thank in advance. Xiangzhen Kong From: Anastasia Yendiki Date: 2012-02-04 00:52 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] /path/to/dmri/dwi_orig_flip.mghdti.bvecs': No such file or directory Unless your dicoms came from the same acquisition as the default MGH/Siemens one, you'll have to set bvecfile and bvalfile and provide those files yourself. On Fri, 3 Feb 2012, Xiangzhen Kong wrote: > Hi all > Now I am learning the trac-all using with DICOM data, but came across a > problem. > +++ > mv?f?xxx/dmri/dwi_orig_flip.mghdti.bvecs?/dmri/bvecs > mv:燾annot爏tat燻/xxx/dmri/dwi_orig_flip.mghdti.bvecs':燦o爏uch爁ile爋r ?? ??ir > ectory > +++ > I check the dir /xxx/dmri/ and there are only two files > 'dwi_orig_flip.nii.gz' , 'dwi_orig.nii.gz'?and a dir 'xfms'. > Does trac-all extract bvals/bvecs automatically when start with DICOM dat a? > My data is from a siemens scanner. > ? > Thanks! > ? > Xiangzhen > ? > 2012-02-03 > > _ ___ > Xiangzhen Kong > > The information in this e-mail is intended only for the person to whom it i s addressed. If you believe this e-mail was sent to you in error and the e-ma il contains patient information, please contact the Partners Compliance HelpLi ne at http://www.partners.org/complianceline . If the e-mail was sent to you in e rror but does not contain patient information, please contact the sender and pro perly dispose of the e-mail. ___ 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.
Re: [Freesurfer] [Fwd: Re: TRACULA dpath problem]
Hi XJ - In your configuration file, you've set both doregflt and doregbbr
to 0. You have to set one of them to 1, otherwise no intra-subject
registration will be done and every step that relies on it will fail.
a.y
On Fri, 15 Jun 2012, XJ Kang wrote:
> Hi Priti,
>
> I removed the NaNs in the 4D images and re-ran trac-all -prep. The
> warning message is gone (of course) but the error message of
> dlable/diff/White-Matter++.flt.nii.gz is still there since no
> "White-Matter++.flt.nii.gz" in the diff directory. Only one image in
> dlabel/diff/: lowb_brain_mask.nii.gz.
>
> fslstats -t /home/xkang/DTI//S0001/dmri/dwi.nii.gz -k
> /home/xkang/DTI//S0001/dlabel/diff/White-Matter++.flt.nii.gz -m -s |
> awk '{print $1/$2}' > /home/xkang/DTI//S0001/dmri/dwi_snr.txt
> ** ERROR (nifti_image_read): failed to find header file for
> '/home/xkang/DTI//S0001/dlabel/diff/White-Matter++.flt'
> ** ERROR:
> nifti_image_open(/home/xkang/DTI//S0001/dlabel/diff/White-Matter++.flt):
> bad header info
> ERROR: failed to open file
> /home/xkang/DTI//S0001/dlabel/diff/White-Matter++.flt
> ERROR: Could not open image
> /home/xkang/DTI//S0001/dlabel/diff/White-Matter++.flt
> Image Exception : #22 :: Failed to read volume
> /home/xkang/DTI//S0001/dlabel/diff/White-Matter++.flt.nii.gz
>
> I am not sure if the error will affect the next steps of -bedp and
> -path. I want to make sure before run -bedp since that will take several
> hours.
>
> Also there is no dpath directory yet. Probably it will be created during
> the -path processing?
>
> Thanks.
>
> XJ
>
>
> On 6/15/2012 12:15 PM, Priti Srinivasan wrote:
>> Hi XJ,
>>
>> I'm just starting to look at your log files. Just curious, did you decide
>> to not do eddy current correction and b0 inhomogenity correction or
>> accidentally left it out?
>>
>> When I look at the configuration file, you've given all the parameters for
>> b0 inhomogenity correction, but it is set to '0' (set dob0 = 0) and the
>> same is the case for eddy current correction too (set doeddy = 0). Just
>> wanted to make sure you did not set that '0' accidentally. Eddy current
>> correction is definitely one of the recommended preprocessing steps, so
>> you might want to consider doing that.
>>
>> Also looks like your original input dwi file (with NaNs) may be the root
>> cause of the problem. If you do have the original dicoms, you can give
>> that as an input. I'm not sure if you can give a series of 3D Nifti DWI
>> files as an input in the configurations file...Anastasia (cc'd) might be
>> able to answer that question.
>>
>> Hope that helps,
>> Priti
>>> Original Message
>>> Subject: Re: [Freesurfer] TRACULA dpath problem
>>> From:"XJ Kang"
>>> Date:Fri, June 15, 2012 2:22 pm
>>> To: "Priti Srinivasan"
>>> --
>>>
>>> Hi Priti,
>>>
>>> Attached are the tracula conf file and log files from two subjects.
>>>
>>> I ran the two subjects. The results are almost the same. Here are what I
>>> found so far:
>>>
>>> 1. There are NaN values in the 4D image. I created it from 3D images
>>> using "fslmerge -a", and the 3G images have no NaNs.
>>> 2. The image "dlabel/diff/White-Matter++.flt" was not found. Probably
>>> this is the origin of all the problems?
>>>
>>> Do you want me to send the email to you or to the mailing list? Probably
>>> many people are not interested in my email if I post on the whole list.
>>>
>>> Thank you.
>>>
>>> XJ
>>>
>>> On 6/15/2012 11:02 AM, Priti Srinivasan wrote:
Can you send us your configuration file (mytracula.conf) and log file
(it
should be under scripts/trac-all.log). I can take a look.
Priti
> Hi,
>
> I am trying to run the last step of TRACULA. I used the command line:
>
> % trac-all -path -c mytracula.conf
>
> Here is all the info I got on the screen:
>
> INFO: SUBJECTS_DIR is /home/sata2/FreeSurfer/Subjects.Verio
> INFO: Diffusion root is /home/xkang/DTI/
> Actual FREESURFER_HOME /home/local/freesurfer-v510
> trac-paths -c /home/xkang/DTI//S0006/scripts/dmrirc.local -log
> /home/xkang/DTI//S0006/scripts/trac-all.log -cmd
> /home/xkang/DTI//S0006/scripts/trac-all.cmd
> #-
> /usr/local/freesurfer/bin/trac-paths
> #-
> #@# Path reconstruction Fri Jun 15 10:47:44 PDT 2012
> #-
> trac-paths finished without error at Fri Jun 15 10:47:44 PDT 2012
>
>
>
> I didn't see "dpath" under the subject's directory. Seems nothing has
> been done. I already ran the "trac-all -prep" and "trac-all -bedp". I
> have the directories dlable, dmri and dmir.bedpostX, but not dpath. Can
> any body help where the problems are?
>
> I use DTI images in NIFTI format and the resolution is 2x2x2, which is
> not the same as
Re: [Freesurfer] -inter error
Hi Maria - Do you at any point get the following warning? "WARN: CVS template is not unavailable in the current version" Thanks, a.y On Wed, 20 Jun 2012, Maria Gemzicka wrote: Hi, I run -corr and -intra with no errors. -inter finishes without errors if does not use doregcvs. When I want to use cvs for registration, I get error: iterating done with candidates Active BCs = 91494 Total BCs = 548640 no-eqs = 245610 surf2vol(26656) malloc: *** mmap(size=295714816) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug [0]PETSC ERROR: - Error Message [0]PETSC ERROR: Out of memory. This could be due to allocating [0]PETSC ERROR: too large an object or bleeding by not properly [0]PETSC ERROR: destroying unneeded objects. [0]PETSC ERROR: Memory allocated 0 Memory used by process 0 [0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info. [0]PETSC ERROR: Memory requested 29571! trac-all.error in scripts: .. PROCESSOR x86_64 OS Darwin Darwin shemp.mri.yorku.ca 11.4.0 Darwin Kernel Version 11.4.0: Mon Apr 9 19:32:15 PDT 2012; root:xnu-1699.26.8~1/RELEASE_X86_64 x86_64 $Id: trac-preproc,v 1.17.2.5 2011/05/20 06:51:51 ayendiki Exp $ /Users/Maria/Applications/freesurfer/bin/trac-preproc PWD /Users/Maria CMD mri_cvs_register --mov mgFS6 --template cvs_avg35 --outdir /Users/maria/Desktop/mgFS/mgFS6/dmri/xfms/cvs Thank you. ___ 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.
Re: [Freesurfer] -inter error
Oops, that's a typo, meant "is unavailable". In any case something like this should show up early in the logs. On Wed, 20 Jun 2012, Bruce Fischl wrote: "not unavailable"???? On Wed, 20 Jun 2012, Anastasia Yendiki wrote: Hi Maria - Do you at any point get the following warning? "WARN: CVS template is not unavailable in the current version" Thanks, a.y On Wed, 20 Jun 2012, Maria Gemzicka wrote: > Hi, > I run -corr and -intra with no errors. -inter finishes without errors if > does not use doregcvs. > When I want to use cvs for registration, I get error: > > iterating > > done with candidates > > Active BCs = 91494 > > Total BCs = 548640 > > no-eqs = 245610 > > surf2vol(26656) malloc: *** mmap(size=295714816) failed (error code=12) > > *** error: can't allocate region > > *** set a breakpoint in malloc_error_break to debug > > [0]PETSC ERROR: - Error Message > > > [0]PETSC ERROR: Out of memory. This could be due to allocating > > [0]PETSC ERROR: too large an object or bleeding by not properly > > [0]PETSC ERROR: destroying unneeded objects. > > [0]PETSC ERROR: Memory allocated 0 Memory used by process 0 > > [0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info. > > [0]PETSC ERROR: Memory requested 29571! > > > > trac-all.error in scripts: > > > .. > > PROCESSOR x86_64 > > OS Darwin > > Darwin shemp.mri.yorku.ca 11.4.0 Darwin Kernel Version 11.4.0: Mon Apr > 9 > 19:32:15 PDT 2012; root:xnu-1699.26.8~1/RELEASE_X86_64 x86_64 > > $Id: trac-preproc,v 1.17.2.5 2011/05/20 06:51:51 ayendiki Exp $ > > /Users/Maria/Applications/freesurfer/bin/trac-preproc > > PWD /Users/Maria > > CMD mri_cvs_register --mov mgFS6 --template cvs_avg35 --outdir > /Users/maria/Desktop/mgFS/mgFS6/dmri/xfms/cvs > > > Thank you. > > ___ 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.
Re: [Freesurfer] trac-all: error during trac-paths due to tract missing
Hi Torben - I just scrolled to the end of your log file. The last invocation of trac-all -prep is the one that failed b/c of the bvecs error. Did you rerun trac-all -prep after you fixed the bvecs? Thanks, a.y On Tue, 26 Jun 2012, Torben Prokscha wrote: > Hi Priti, > > thank you for your reply, but I'm afraid you didn't scroll to the end of > the log file: Yes, we had that bvecs/bvals error in the first run, but we > corrected it and got the error I reported in my previous mail (it is also > printed at the end of the log file): > > ERROR: Could not open > /Users/torben/Desktop/tracon/fs_diff/s001/dlabel/diff/lh.cst_AS_avg33_mni_flt_cpts_5.txt > > Could you or anybody else please help with this problem which is obviously > related to missing tracts? > > Thanks in advance > Torben > > >> Hi Torben, >> >> Your trac-preproc exited with errors because of the following error. >> >> Error: bvecs and bvals don't have the same number of entries >> >> You should check to see if your bvals and bvecs have the same no.of lines >> and then rerun trac-all -prep. >> >> Priti >> >> >>> Dear all, >>> >>> while running trac-all, I got the following error: >>> >>> ERROR: Could not open >>> /Users/torben/Desktop/tracon/fs_diff/s001/dlabel/diff/lh.cst_AS_avg33_mni_flt_cpts_5.txt >>> >>> Obviously, a similar problem was discussed before (here: >>> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019570.html). >>> However, no general solution was publicly mailed. Since it was requested >>> then, I attach the trac-all.log file. >>> >>> Thanks in advance for any help! >>> >>> Best >>> Torben Prokscha >>> >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> ___ >> 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. >> >> > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] DTI question
Not sure if this is the simplest way but mri_convert --split, followed by mri_concat, should do it. You'll also have to remove the respective gradient directions from the gradient file. Hope this helps, a.y On Wed, 27 Jun 2012, Drottar, Marie wrote: > I have a DTI dataset with 10 b0 and gradient 30 directions. I would like > to remove one or two volumes from the dataset and then repackage the data. > How do I do this? > thank you > > > Marie Drottar, MA > > Research Assistant > > Division of Newborn Medicine > > Fetal-Neonatal Neuroimaging & Developmental Science Center > > Boston Childrens Hospital > > 1 Autumn St > > Boston, MA 02115 > > http://childrenshospital.org/FNNDSC > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ 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.
Re: [Freesurfer] TRACULA question: pathstats.overall.txt
Hi Minjie - These commonly used measures are provided for your convenience. You can always use the reconstructed path distribution volume path.pd.nii.gz, thresholded or not, as a mask to average your measurement of choice. a.y On Thu, 28 Jun 2012, Minjie Wu wrote: > Dear TRACULA Developer & User, > > I am wondering if it is possible to add other DTI measurements to the > pathstats.overall.txt along with those DTI parameters already included > (FA, MD, AD, RD)? > > Thank you very much. > Minjie > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ 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.
Re: [Freesurfer] TRACULA question: pathstats.overall.txt
Yes, if you wanted to do a weighted average of your measure. Or you could just theshold and binarize path.pd and use it a simple ROI to do an unweighted average. On Thu, 28 Jun 2012, Minjie Wu wrote: > Dear Dr. Yendiki, > > Thank you very much for your quick response. To calculate the weighted > DTI measure, per your previous emails, we would need to normalize > path.pd.nii.gz, right? If this is the case, we could use the following > equation correct for weighted measurement: > > dti_para (DTI parameter image) > path_pd (path.pd.nii.gz) > > sum(dti_para.*path_pd))/sum(path_pd) > > Thank you very much. > > Minjie > > > > > On Thu, Jun 28, 2012 at 11:05 AM, Anastasia Yendiki > wrote: >> >> Hi Minjie - These commonly used measures are provided for your convenience. >> You can always use the reconstructed path distribution volume >> path.pd.nii.gz, thresholded or not, as a mask to average your measurement of >> choice. >> >> a.y >> >> >> On Thu, 28 Jun 2012, Minjie Wu wrote: >> >>> Dear TRACULA Developer & User, >>> >>> I am wondering if it is possible to add other DTI measurements to the >>> pathstats.overall.txt along with those DTI parameters already included >>> (FA, MD, AD, RD)? >>> >>> Thank you very much. >>> Minjie >>> ___ >>> 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. >> > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] trac-all: error during trac-paths due to tract missing
Hi Torben - I'm looking at all the invocations of "trac-all -prep" in your log file, and they've both exited with an error (the same bvecs error). > grep prep trac-all.log -prep -c /Users/torben/Desktop/tracon/tracon New invocation of trac-preproc /Applications/MRSoftware/freesurfer/bin/trac-preproc trac-preproc exited with ERRORS at Do 21 Jun 2012 20:34:41 CEST ... -prep -c /Users/torben/Desktop/tracon/tracon New invocation of trac-preproc /Applications/MRSoftware/freesurfer/bin/trac-preproc trac-preproc exited with ERRORS at So 24 Jun 2012 22:37:30 CEST After that you've ran "trac-all -bedp" and "trac-all -path", but obviously these are going to fail if "trac-all -prep" has failed. I hope this makes sense. a.y On Fri, 29 Jun 2012, Torben Prokscha wrote: > Hi Anastasia! > > Yes, we reran trac-all -prep after fixing the bvec issue. I am still > surprised how you know that the latest failure was due to a bvecs problem, > because the last error message was the one about the missing tract ...? > > Thank you for your help! > > Best > Torben > > >> >> Hi Torben - I just scrolled to the end of your log file. The last >> invocation of trac-all -prep is the one that failed b/c of the bvecs >> error. Did you rerun trac-all -prep after you fixed the bvecs? >> >> Thanks, >> a.y >> >> On Tue, 26 Jun 2012, Torben Prokscha wrote: >> >>> Hi Priti, >>> >>> thank you for your reply, but I'm afraid you didn't scroll to the end of >>> the log file: Yes, we had that bvecs/bvals error in the first run, but >>> we >>> corrected it and got the error I reported in my previous mail (it is >>> also >>> printed at the end of the log file): >>> >>> ERROR: Could not open >>> /Users/torben/Desktop/tracon/fs_diff/s001/dlabel/diff/lh.cst_AS_avg33_mni_flt_cpts_5.txt >>> >>> Could you or anybody else please help with this problem which is >>> obviously >>> related to missing tracts? >>> >>> Thanks in advance >>> Torben >>> >>> Hi Torben, Your trac-preproc exited with errors because of the following error. Error: bvecs and bvals don't have the same number of entries You should check to see if your bvals and bvecs have the same no.of lines and then rerun trac-all -prep. Priti > Dear all, > > while running trac-all, I got the following error: > > ERROR: Could not open > /Users/torben/Desktop/tracon/fs_diff/s001/dlabel/diff/lh.cst_AS_avg33_mni_flt_cpts_5.txt > > Obviously, a similar problem was discussed before (here: > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019570.html). > However, no general solution was publicly mailed. Since it was > requested > then, I attach the trac-all.log file. > > Thanks in advance for any help! > > Best > Torben Prokscha > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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. >>> >>> >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> > > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Memory allocation problem trac-all -prior
Hi Rui - How many voxels are in your diffusion volume? How many of them are inside the mask? a.y On Thu, 12 Jul 2012, Rui Lavrador wrote: > Hi all, > I'm running tracula and when doing the step: > trac-all -prior -c single_subject > > After some time it gives this error: > > MRIalloc(218, 182, 182): could not allocate 158704 bytes for 49th slice > > Cannot allocate memory > > I' m running tracula on Ubuntu 10.04, with 4GB ram. The diffusion data is > DTI with 64 directions. > > This happens many times? I need more memory? > > Best regards, > > -- > Rui Lavrador > > > ___ 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.
Re: [Freesurfer] trac all - cant allocate memory
Hi Michael and Jürgen - This issue has been resolved, see "Updates": http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula It had to do with the original mac executables having been compiled on an older version of MacOS, which was not smart about utilizing all the memory on your computer. If you download the updated version, you should not have this problem. Please try that instead of downsizing the tract atlas by editing trainlist.txt - that was just meant as a temporary work-around. Hope this helps, a.y On Tue, 17 Jul 2012, Jürgen Hänggi wrote: Hi Michael This is a Mac specific problem. You can reduce the number of a priori tracts used by reducing the entries in the list found in freesurfer/trctrain/trainlist.txt. On my Mac it works with 26 a priori tracts. Cheers Jürgen On [DATE], "Michael Scheel" <[ADDRESS]> wrote: Dear FS experts, when running tracula I get the following error (see below and trac-all.log attached to this mail). It seems that memory cannot be allocated but I have a PowerMac with 12 GB RAM and I suppose this should be enough. Any ideas how I can solve this problem? Thanks, Michael dmri_train(50487) 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 fslmachine.charite.de 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 trac-preproc exited with ERRORS at Tue Jun 26 15:12:03 CEST 2012 ___ 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. Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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.
Re: [Freesurfer] Memory allocation problem trac-all -prior
Hi Rui - Just keep in mind that when you're removing lines from trainlist.txt, you're removing subjects from the atlas. So instead of using a tract atlas that's based on 33 subjects, you are now using a tract atlas based on as many subjects as the lines that remain in trainlist.txt. a.y On Tue, 17 Jul 2012, Rui Lavrador wrote: > Hi all, > > I think I found the problem. I reduced the number of train files in the > trainlist.txt file and it ran without errors. Maybe I will need more memory > to run with all train files. > > > thanks > > > > 2012/7/16 Rui Lavrador > > > -- Forwarded message -- > From: Rui Lavrador > Date: 2012/7/16 > Subject: Re: [Freesurfer] Memory allocation problem trac-all > -prior > To: Anastasia Yendiki > > > Hi Anastasia, > Each diffusion volume has 128x128x60 voxels, and there are > 182138 voxels inside of the brain mask. > > Rui > 2012/7/12 Anastasia Yendiki > > Hi Rui - How many voxels are in your diffusion > volume? How many of them are inside the mask? > > a.y > > On Thu, 12 Jul 2012, Rui Lavrador wrote: > > Hi all, > I'm running tracula and when doing the > step: > trac-all -prior -c single_subject > > After some time it gives this error: > > MRIalloc(218, 182, 182): could not > allocate 158704 bytes for 49th slice > > Cannot allocate memory > > I' m running tracula on Ubuntu 10.04, > with 4GB ram. The diffusion data is > DTI with 64 directions. > > This happens many times? I need more > memory? > > Best regards, > > -- > Rui Lavrador > > > > > > 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. > > > > > -- > Rui Lavrador > > Visual Neuroscience Laboratory > IBILI-Faculdade de Medicina > Azinhaga de Santa Comba > 3000-548 Coimbra, Portugal > Phone: +351 964985485 > e-mail: rui.lavra...@fmed.uc.pt > e-mail2: ruilavra...@gmail.com > > > > > -- > Rui Lavrador > > Visual Neuroscience Laboratory > IBILI-Faculdade de Medicina > Azinhaga de Santa Comba > 3000-548 Coimbra, Portugal > Phone: +351 964985485 > e-mail: rui.lavra...@fmed.uc.pt > e-mail2: ruilavra...@gmail.com > > > > > -- > Rui Lavrador > > Visual Neuroscience Laboratory > IBILI-Faculdade de Medicina > Azinhaga de Santa Comba > 3000-548 Coimbra, Portugal > Phone: +351 964985485 > e-mail: rui.lavra...@fmed.uc.pt > e-mail2: ruilavra...@gmail.com > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] running trac-all -path missing files
Hi Rui - You can ignore the message about spline segments, it's fine. For the directory structure and where to find your files, I'll refer you to the trac-all wiki page (see section "Outputs from trac-all -path"): http://surfer.nmr.mgh.harvard.edu/fswiki/trac-all Hope this helps, a.y On Wed, 18 Jul 2012, Rui Lavrador wrote: Hi FS users, I'm running “trac-all –path ” and when running it, it constantly gives the output ERROR: Degenerate spline segment 58 81 24 56 69 24 … But it runs until the end without exiting and says that it ran without errors. It’s normal? Plus, it seems that it fails to create the output files. When looking at the created folder “…/Diff001/dpath” there is only one folder “5cpts”, so I cannot visualize the WM pathways, with freeview, that should be located, for example at “…/dpath/lh.ilf_AS_avg32_mni_flt/path.pd.nii.gz” Any suggestions? -- Rui Lavrador ___ 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.
Re: [Freesurfer] tracula RAM memory ?...
Hi Gonzalo - You'll find some recent emails on this in the archives. In short, you can try deleting a few lines from the file: $FREESURFER_HOME/trctrain/trainlist.txt For every line you're deleting, you're removing a subject from the tract atlas that tracula uses. There are currently 33 subjects included in there, and as many lines in this text file. Sorry, we don't have official memory and CPU time estimates right now. It depends on the tract and various configuration parameters. Hopefully we'll get around to it for the new version that we're working on. Hope this helps, a.y On Tue, 24 Jul 2012, Gonzalo Rojas Costa wrote: Hi: How much memory needs tracula to process a DTI study ?... Because my PC (Ubuntu Linux, 4GB RAM) exit because it can't allocate memory in trac-preproc... There exist any tip & trick in such a case?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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.
Re: [Freesurfer] Issues with Tracula
Hi Sergio - Thank you for your kind words, and also thank you for taking
the time to search the archives for answers!
The first problems you had with running bedpostx through trac-all have to
do with trac-all assuming an older version of FSL than the current one,
and this'll be fixed in the upcoming release of trac-all. Indeed the thing
to do in the meantime is to run bedpostx by itself, as you did. I
apologize for the inconvenience.
About the problem you had when you ran bedpostx directly: do you get the
other outputs of bedpostx, listed here? Are there any other, temporary
files left over as well?
http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_bedpostx.html
The merged_ph?samples are the orientation angles of the each of the two
anisotropic compartments ("sticks", "fibers", whatever you want to call
them) that bedpostx fit in each voxel. So "1" is the orientation angle of
the largest stick/fiber, and "2" the one of the 2nd largest. If there's a
"2", there should be a "1"!
Also, I looked at your dmrirc file and noticed that you decreased the # of
control points b/c you hate waiting :) I just wanted to warn you that
decreasing that # might make you wait longer b/c make fitting a spline
with fewer control points to initialize the algorithm is sometimes more
challenging.
Hope this helps,
a.y
On Thu, 26 Jul 2012, Sergio Medina wrote:
Hi!
First of all let me thank you for having put at our disposal such great
tools as FreeSurfer and Tracula!
I am trying to run Tracula on the sample data that is on the website, but
I've been running into some issues.
I am attaching the configuration file just in case
(dmrirc_single_subject-serch).
The first step "trac-all -prep" seems to run fine.
The first problem comes with the second step "trac-all -bedp". The complete
trace is included in the attached file 1-error-trac-all-bedp.txt
After finding this on the FreeSurfer mailing
listhttps://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/024042.html
I changed the lines
${BPDIR}/fsl_sub_seychelles
for
${FSL_BIN}/fsl_sub
in the bedpostx_seychelles and I could continue, until the script seems to
be stuck
Queuing parallel processing stage
/volatile/tracula/results/Diff001/dmri.bedpostX/monitor
0 slices processed
1 slices processed
1 slices processed
1 slices processed <== this line keeps on repeating
Following a suggestion I found on this other archived email
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20815.html
I ran bedpostx on the dmri directory and seemed to succeed. I am attaching
the output (2-bedpostx-dmri.txt).
Then I tried to run trac-all -path but it stops with the following error:
niiRead(): error opening file
/volatile/tracula/results/Diff001/dmri.bedpostX/merged_ph1samples.nii.gz
ERROR: Could not read
/volatile/tracula/results/Diff001/dmri.bedpostX/merged_ph1samples.nii.gz
I searched for that file everywhere but it doesn't exist. The closest I
found was
results/Diff001/dmri.bedpostX/merged_ph2samples.nii.gz
Just in case I tried once again to run trac-all -bedp and this time, after
having run bedpostx on the dmri directory, I get the following error (the
whole output is in the attached 4-error-trac-all-bedp-2.txt file):
[...]
slice 62 has already been processed
slice 63 has already been processed
wc: /volatile/tracula/results/Diff001/dmri.bedpostX/commands.txt: No such
file or directory
Queuing post processing stage
64 slices processed
For some reason the bedpostX process DOES NOT appear
to have successfully completed. Please examine your
results carefully.
kill: 390: No such process
I tried searching for a file named commands.txt but I couldn't find any.
Here is the output of bugr:
FREESURFER_HOME: /i2bm/local/freesurfer
Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
Debian version: squeeze/sid
Kernel info: Linux 2.6.38-14-generic x86_64
and the output of source $FREESURFER_HOME/SetUpFreeSurfer.sh
freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /i2bm/local/freesurfer
FSFAST_HOME /i2bm/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /volatile/tracula/data/buckner_data/tutorial_subjs/
MNI_DIR /i2bm/local/freesurfer/mni
FSL_DIR /usr/share/fsl/4.1
Thanks in advance for your help, any hint would be highly appreciated.
Best,
Sergio.
--
Sergio Medina
Engineer
INRIA Parietal - Neurospin
Bât 145, Point Courrier 156
91191 Gif/Yvette, France
Tel.: (+33) 1 69 08 80 85
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Re: [Freesurfer] tracula -bedp - path
Hi Keith - This seems to be a different problem here, since all the bedpostx outputs are there and are loaded in without a problem. The error occurs after that. What's the size of your images? Does the mask file look normal? Thanks, a.y On Thu, 26 Jul 2012, Keith Yoder wrote: Hi, Was there any resolution to this issue? I'm having a similar problem running trac-all on a Linux cluster. I think bedpostx works if I call it directly from the command line twice. The first time, bedpostx_postproc.sh doesn't seem to work and the *samples.nii.gz files are only created if I rerun bedpostx. However, trac-all...-path fails. I've attached the trac-all-path output and pasted the relevant section below: Creating output directory/mnt/ide0/home/kjyoder/research/conduct_disorder/fs/1001/dpath/lh.cst_AS_av g33_mni_flt Loading DWIs from /mnt/ide0/home/kjyoder/research/conduct_disorder/fs/1001/dmri/dwi.nii.gz Loading mask from/mnt/ide0/home/kjyoder/research/conduct_disorder/fs/1001/dlabel/diff/aparc+ aseg_mask.flt.nii.gz Loading BEDPOST parameter samples from /mnt/ide0/home/kjyoder/research/conduct_disorder/fs/1001/dmri.bedpostX Loading segmentation map from/mnt/ide0/home/kjyoder/research/conduct_disorder/fs/1001/dlabel/mni/aparc+a seg.nii.gz Loading b-values from /mnt/ide0/home/kjyoder/research/conduct_disorder/fs/1001/dmri/bvals Loading gradients from /mnt/ide0/home/kjyoder/research/conduct_disorder/fs/1001/dmri/bvecs Segmentation fault (core dumped) Here are the contents of the subjects bedpostX directory: bvals bvecs commands.txt diff_slices dyads1_dispersion.nii.gz dyads1.nii.gz dyads2_dispersion.nii.gz dyads2.nii.gz logs mean_dsamples.nii.gz mean_f1samples.nii.gz mean_f2samples.nii.gz mean_ph1samples.nii.gz mean_ph2samples.nii.gz mean_S0samples.nii.gz mean_th1samples.nii.gz mean_th2samples.nii.gz merged_f1samples.nii.gz merged_f2samples.nii.gz merged_ph1samples.nii.gz merged_ph2samples.nii.gz merged_th1samples.nii.gz merged_th2samples.nii.gz monitor nodif_brain_mask.nii.gz xfms Also, I'm attaching the bvals, bvecs, dmrirc.local, trac-all.error, and trac-all.log for the subject. Let me know if there is any other information you need. Thanks in advance, Keith -- Keith YoderPhD Candidate, Integrative Neuroscience Social Cognitive Neuroscience Laboratory The University of Chicago 5846 S. University Avenue, Kelly 312 Chicago, IL 60637 Phone: 574-215-9678 kjyo...@uchicago.edu On Fri, Oct 7, 2011 at 10:04 AM, Anastasia Yendiki wrote: Hi Judit, 1. If you can run bedpostx directly then you should do: bedpostx /usr/local/freesurfer/subjects/C001/dmri Note that this dmri directory and the one you tried to run bedpostx_single_slice.sh on are different, so I'm not sure which location is the right one where your data is, but in any case you don't need to run bedpostx_single_slice.sh. 2. The error seems to occur either when it's reading the bvecs file, or right after that when it's accessing the bedpostx outputs. So I'd try to look those for that subject and see if everything is ok. Hope this helps, a.y On Fri, 7 Oct 2011, Judit Haasz wrote: Hi, I ran into 2 problems related to tracula. 1. trac-all -bedp command exits with following message. WARN: Running FSL's bedbost locally - this might take a while >> > WARN: It is recommended to run this step on a cluster >> > bedpostx_seychelles /usr/local/freesurfer/subjects/C001/dmri >> > subjectdir is /usr/local/freesurfer/subjects/C001/dmri >> > Making bedpostx directory structure >> > Queuing preprocessing stages >> > [: 223: NONE: unexpected operator >> > [: 314: NONE: unexpected operator >> > [: 327: xbedpostx_pre: unexpected operator >> > [: 486: x: unexpected operator >> > [: 486: -le: argument expected >> > Queuing parallel processing stage >> > [: 223: NONE: unexpected operator >> > [: 327: xbedpostx: unexpected operator >> > [: 486: x53: unexpected operator >> > 0 slices processed >> > Queuing post processing stage >> > [: 223: NONE: unexpected operator >> > [: 314: NONE: unexpected operator >> > [: 327: xbedpostx_post: unexpected operator >> > [: 486: x: unexpected operator >> > [: 486: -le: argument expected >> > This problem has been posted in May and June. bedpostx from command line runs perfectly and tha
Re: [Freesurfer] Issues with Tracula
Hi Sergio - As with any imminent new version release, it's happening
"soon". I'd say in a month, I'm just not sure a month from when :P
The fact that the temporary files (everything with *slice* in the name)
are still in your bedpostx directory means that bedpostx didn't finish
running properly. You can try running the last step of bedpostx and see if
you get any error messages that give you any clues:
bedpostx_postproc.sh /volatile/tracula/results/Diff001/dmri
Normally this step merges the individual slices into volumes and deletes
the temporary files. If all else fails, I'd ask the FSL gurus.
Hope this helps,
a.y
On Fri, 27 Jul 2012, Sergio Medina wrote:
Anastasia,
Thanks for such a quick reply!
Please find my answers inline...
2012/7/26 Anastasia Yendiki
Hi Sergio - Thank you for your kind words, and also thank you
for taking the time to search the archives for answers!
The first problems you had with running bedpostx through
trac-all have to do with trac-all assuming an older version of
FSL than the current one, and this'll be fixed in the upcoming
release of trac-all. Indeed the thing to do in the meantime is
to run bedpostx by itself, as you did. I apologize for the
inconvenience.
Great! By any chance, do you know when that release will happen?
About the problem you had when you ran bedpostx directly: do you
get the other outputs of bedpostx, listed here? Are there any
other, temporary files left over as well?
http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_bedpostx.html
I have all of them, except for nodif_brain. And I only have the ones with
i=2 while I should have the ones with i=1 too.
Attached you can find two files, the output of ls -Rah on both dmri and
dmri.bedpostX directories.
The merged_ph?samples are the orientation angles of the each of
the two anisotropic compartments ("sticks", "fibers", whatever
you want to call them) that bedpostx fit in each voxel. So "1"
is the orientation angle of the largest stick/fiber, and "2" the
one of the 2nd largest. If there's a "2", there should be a "1"!
But there are not :(
Also, I looked at your dmrirc file and noticed that you
decreased the # of control points b/c you hate waiting :) I just
wanted to warn you that decreasing that # might make you wait
longer b/c make fitting a spline with fewer control points to
initialize the algorithm is sometimes more challenging.
Hehe, thanks! I changed it back to 5 now...
Thanks!
Sergio.
Hope this helps,
a.y
On Thu, 26 Jul 2012, Sergio Medina wrote:
Hi!
First of all let me thank you for having put at our
disposal such great
tools as FreeSurfer and Tracula!
I am trying to run Tracula on the sample data that is on
the website, but
I've been running into some issues.
I am attaching the configuration file just in case
(dmrirc_single_subject-serch).
The first step "trac-all -prep" seems to run fine.
The first problem comes with the second step "trac-all
-bedp". The complete
trace is included in the attached file
1-error-trac-all-bedp.txt
After finding this on the FreeSurfer
mailinglisthttps://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/024042.
html
I changed the lines
${BPDIR}/fsl_sub_seychelles
for
${FSL_BIN}/fsl_sub
in the bedpostx_seychelles and I could continue, until the
script seems to
be stuck
Queuing parallel processing stage
/volatile/tracula/results/Diff001/dmri.bedpostX/monitor
0 slices processed
1 slices processed
1 slices processed
1 slices processed <== this line keeps on repeating
Following a suggestion I found on this other archived email
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20815.html
I ran bedpostx on the dmri directory and seemed to succeed. I am
attaching
the output (2-bedpostx-dmri.txt).
Then I tried to run trac-all -path but it stops with the
following error:
niiRead(): error opening file
/volatile/tracula/results/Diff001/dmri.bedpostX/merged_ph1samples.nii.gz
ERROR: Could not read
/volatile/tracula/results/Diff001/dmri.bedpostX/merged_ph1samples.nii.gz
I searched for that file everywhere but it doesn't exist. The
closest I
found was
results/Diff001/dmri.bedpostX/merged_ph2samples.nii.gz
Just in case I tried once again to run trac-all -bedp and this
time, after
having run bedpostx on the dmri directory, I get the following
error (the
whole output is in the attached 4-error-trac-all-bedp-2.txt
file):
[...]
slice 62 has already been processed
slice 63 has already been processed
wc:
/volatile/tracula/results/Diff001/dmri.bedpostX/commands.txt: No
such
file or directory
Queuing post processing stage
64 slices processed
For
Re: [Freesurfer] Issues with Tracula
The monitoring script that bedpostx runs and tells you if things have or
haven't finished properly can't always be trusted. So if that's the only
error message you see, I wouldn't worry about it. Have the *ph1* and *th1*
files appeared this time?
On Fri, 27 Jul 2012, Sergio Medina wrote:
What a coincide! Our teams have both chosen the same release cycle strategy
:P
I ran bedpostx_postproc and I've got so many errors that makes me think the
problem is before this step (see output in attached
n1-bedpostx-postproc.txt).
So, I ran again bedpostx on the dmri directory, which the first run *seemed*
to finish and didn't throw any error (I attached the output in the first
email).
This run did finish, and it did throw errors (full output in
n2-bedpostx-dmri.txt):
[...]
slice 63 has already been processed
wc: /volatile/tracula/results/Diff001/dmri.bedpostX/commands.txt: No such
file or directory
Queuing post processing stage
64 slices processed
For some reason the bedpostX process DOES NOT appear
to have successfully completed. Please examine your
results carefully.
kill: 276: No such process
Then I started wondering whether I do have the right data to actually run
bedpostx, so I run the script that checks that: bedpostx_datacheck, the
output (n3-bedpostx-datacheck.txt) doesn't show any signs of errors so I
would like to assume everything is ok with the input data...
Any idea?
Thanks, once again.
Sergio.
2012/7/27 Anastasia Yendiki
Hi Sergio - As with any imminent new version release, it's
happening "soon". I'd say in a month, I'm just not sure a month
from when :P
The fact that the temporary files (everything with *slice* in
the name) are still in your bedpostx directory means that
bedpostx didn't finish running properly. You can try running the
last step of bedpostx and see if you get any error messages that
give you any clues:
bedpostx_postproc.sh
/volatile/tracula/results/Diff001/dmri
Normally this step merges the individual slices into volumes and
deletes the temporary files. If all else fails, I'd ask the FSL
gurus.
Hope this helps,
a.y
On Fri, 27 Jul 2012, Sergio Medina wrote:
Anastasia,
Thanks for such a quick reply!
Please find my answers inline...
2012/7/26 Anastasia Yendiki
Hi Sergio - Thank you for your kind words, and
also thank you
for taking the time to search the archives for
answers!
The first problems you had with running
bedpostx through
trac-all have to do with trac-all assuming an
older version of
FSL than the current one, and this'll be fixed
in the upcoming
release of trac-all. Indeed the thing to do in
the meantime is
to run bedpostx by itself, as you did. I
apologize for the
inconvenience.
Great! By any chance, do you know when that release
will happen?
About the problem you had when you ran
bedpostx directly: do you
get the other outputs of bedpostx, listed
here? Are there any
other, temporary files left over as well?
http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_bedpostx.html
I have all of them, except for nodif_brain. And I
only have the ones with
i=2 while I should have the ones with i=1 too.
Attached you can find two files, the output of ls
-Rah on both dmri and
dmri.bedpostX directories.
The merged_ph?samples are the orientation
angles of the each of
the two anisotropic compartments ("sticks",
"fibers", whatever
you want to call them) that bedpostx fit in
each voxel. So "1"
is the orientation angle of the largest
stick/fiber, and "2" the
one of the 2nd largest. If there's a "2",
there should be a "1"!
But there are not :(
Also, I looked at your dmrirc file and noticed
that you
decreased the # of control points b/c you hate
waiting :) I just
wanted to warn you that decreasing that #
might make you wait
longer b/c make fitting a spline with fewer
control points to
initialize the algorithm is sometimes more
challenging.
Hehe, thanks! I changed it back to 5 no
Re: [Freesurfer] Issues with Tracula
Hi Sergio - Sorry, if this occurs independently of trac-all, whenever you
run bedpostx directly, you're better off asking for help on the FSL list.
We've never run into this problem with bedpostx up till now.
a.y
On Mon, 30 Jul 2012, Sergio Medina wrote:
Nope, I have the same files as before :(
2012/7/27 Anastasia Yendiki
The monitoring script that bedpostx runs and tells you if things
have or haven't finished properly can't always be trusted. So if
that's the only error message you see, I wouldn't worry about
it. Have the *ph1* and *th1* files appeared this time?
On Fri, 27 Jul 2012, Sergio Medina wrote:
What a coincide! Our teams have both chosen the same
release cycle strategy
:P
I ran bedpostx_postproc and I've got so many errors
that makes me think the
problem is before this step (see output in attached
n1-bedpostx-postproc.txt).
So, I ran again bedpostx on the dmri directory,
which the first run *seemed*
to finish and didn't throw any error (I attached the
output in the first
email).
This run did finish, and it did throw errors (full
output in
n2-bedpostx-dmri.txt):
[...]
slice 63 has already been processed
wc:
/volatile/tracula/results/Diff001/dmri.bedpostX/commands.txt:
No such
file or directory
Queuing post processing stage
64 slices processed
For some reason the bedpostX process DOES NOT appear
to have successfully completed. Please examine your
results carefully.
kill: 276: No such process
Then I started wondering whether I do have the right
data to actually run
bedpostx, so I run the script that checks that:
bedpostx_datacheck, the
output (n3-bedpostx-datacheck.txt) doesn't show any
signs of errors so I
would like to assume everything is ok with the input
data...
Any idea?
Thanks, once again.
Sergio.
2012/7/27 Anastasia Yendiki
Hi Sergio - As with any imminent new version
release, it's
happening "soon". I'd say in a month, I'm just
not sure a month
from when :P
The fact that the temporary files (everything
with *slice* in
the name) are still in your bedpostx directory
means that
bedpostx didn't finish running properly. You
can try running the
last step of bedpostx and see if you get any
error messages that
give you any clues:
bedpostx_postproc.sh
/volatile/tracula/results/Diff001/dmri
Normally this step merges the individual
slices into volumes and
deletes the temporary files. If all else
fails, I'd ask the FSL
gurus.
Hope this helps,
a.y
On Fri, 27 Jul 2012, Sergio Medina wrote:
Anastasia,
Thanks for such a quick reply!
Please find my answers inline...
2012/7/26 Anastasia Yendiki
Hi Sergio - Thank you for your
kind words, and
also thank you
for taking the time to search the
archives for
answers!
The first problems you had with
running
bedpostx through
trac-all have to do with trac-all
assuming an
older version of
FSL than the current one, and
this'll be fixed
in the upcoming
release of trac-all. Indeed the
thing to do in
the meantime is
to run bedpostx by itself, as you
did. I
apologize for the
inconvenience.
Great! By any chance, do you know when
that release
will happen?
About the problem you had when you
ran
bedpostx directly: do you
get the other outputs of bedpostx,
listed
Re: [Freesurfer] tracula error...
Hi Gonzalo - This has come up a few times recently. Please see here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23064.html Hope this helps, a.y On Mon, 30 Jul 2012, Gonzalo Rojas Costa wrote: > Hi: > > I ran "trac-all -prep -c dmrirc" and it finished ok... Then, when I > tried to run the command "trac-all -bedp -c dmrirc", I got the error: > > ln -sf > /usr/local/freesurfer/subjects/bmvf_23_7_2012/dlabel/diff/anat_brain_mask.bbr.nii.gz > /usr/local/freesurfer/subjects/bmvf_23_7_2012/dmri/nodif_brain_mask.nii.gz > ln -sf /usr/local/freesurfer/subjects/bmvf_23_7_2012/dmri/dwi.nii.gz > /usr/local/freesurfer/subjects/bmvf_23_7_2012/dmri/data.nii.gz > WARN: Running FSL's bedbost locally - this might take a while > WARN: It is recommended to run this step on a cluster > bedpostx_seychelles /usr/local/freesurfer/subjects/bmvf_23_7_2012/dmri > subjectdir is /usr/local/freesurfer/subjects/bmvf_23_7_2012/dmri > Making bedpostx directory structure > Queuing preprocessing stages > [: 223: NONE: unexpected operator > [: 314: NONE: unexpected operator > [: 327: xbedpostx_pre: unexpected operator > [: 486: x: unexpected operator > [: 486: -le: argument expected > Queuing parallel processing stage > [: 223: NONE: unexpected operator > [: 327: xbedpostx: unexpected operator > [: 486: x27: unexpected operator > 0 slices processed > Queuing post processing stage > [: 223: NONE: unexpected operator > [: 314: NONE: unexpected operator > [: 327: xbedpostx_post: unexpected operator > [: 486: x: unexpected operator > [: 486: -le: argument expected > > That problem occurr because my PC is not a parallelized environment?... > > Sincerely, > > > > ___ 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.
Re: [Freesurfer] tracula error...
Yes, default is fine! Just run bedpostx with the path to the dmri directory as the only argument, that should work. On Mon, 30 Jul 2012, Gonzalo Rojas Costa wrote: > Hi Anastasia: > > And, which options do you think I must use with bedpostx ?... The default > ?... > > Sincerely, > > > Gonzalo Rojas Costa > > > On Mon, Jul 30, 2012 at 5:36 PM, Anastasia Yendiki r.mgh.harvard.edu> wrote: >> >> Hi Gonzalo - This has come up a few times recently. Please see here: >> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23064.html >> >> Hope this helps, >> a.y > > ___ 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.
Re: [Freesurfer] Issues with Tracula
Well, when the current version of tracula was being developped we had FSL
4.1.5 installed here. But now that the next version (you know, the one
that will be available "soon") is being developped we have FSL 4.1.9. So
I'd suggest going with the latest version of FSL. The only thing that
should give you trouble with the latest version of FSL until the next
version of trac-all is released will be the trac-all -bedp step.
On Tue, 31 Jul 2012, Sergio Medina wrote:
Anastasia,
We might try installing FSL + FreeSurfer in another machine, because the one
we were using was too slow anyway.
Would you mind telling us exactly which versions of FreeSurfer and FSL I
need to install?
As I will mostly/only use Tracula then I would rather install the version of
FSL that you used to develop and test Tracula.
Thanks,
Sergio.
2012/7/31 Sergio Medina
Ok I will. Thanks for your help! :)
Sergio.
2012/7/30 Anastasia Yendiki
Hi Sergio - Sorry, if this occurs independently of
trac-all, whenever you run bedpostx directly, you're
better off asking for help on the FSL list. We've never
run into this problem with bedpostx up till now.
a.y
On Mon, 30 Jul 2012, Sergio Medina wrote:
Nope, I have the same files as before :(
2012/7/27 Anastasia Yendiki
The monitoring script that bedpostx runs
and tells you if things
have or haven't finished properly can't
always be trusted. So if
that's the only error message you see, I
wouldn't worry about
it. Have the *ph1* and *th1* files
appeared this time?
On Fri, 27 Jul 2012, Sergio Medina
wrote:
What a coincide! Our teams have
both chosen the same
release cycle strategy
:P
I ran bedpostx_postproc and I've
got so many errors
that makes me think the
problem is before this step (see
output in attached
n1-bedpostx-postproc.txt).
So, I ran again bedpostx on the
dmri directory,
which the first run *seemed*
to finish and didn't throw any
error (I attached the
output in the first
email).
This run did finish, and it did
throw errors (full
output in
n2-bedpostx-dmri.txt):
[...]
slice 63 has already been
processed
wc:
/volatile/tracula/results/Diff001/dmri.bedpostX/commands.txt:
No such
file or directory
Queuing post processing stage
64 slices processed
For some reason the bedpostX
process DOES NOT appear
to have successfully completed.
Please examine your
results carefully.
kill: 276: No such process
Then I started wondering whether I
do have the right
data to actually run
bedpostx, so I run the script that
checks that:
bedpostx_datacheck, the
output (n3-bedpostx-datacheck.txt)
doesn't show any
signs of errors so I
would like to assume everything is
ok with the input
data...
Any idea?
Thanks, once again.
Sergio.
2012/7/27 Anastasia Yendiki
Hi Sergio - As with any
imminent new version
release, it's
happening "soon". I'd say in
a month, I'm just
not sure a month
from when :P
The fact that the temporary
files (everything
with *slice* in
the name) are still in your
bedpostx directory
means that
bedpostx didn't finish
running properly. You
can try running the
last step of bedpostx and
see if you get any
Re: [Freesurfer] asking about seed/target ROIs in TRACULA
Hi Juke - The end ROIs are obtained by dilating the end points of the training streamlines from the tract atlas and finding their intersection with the cortex of the test subject. Hope this helps, a.y On Thu, 9 Aug 2012, Juke Cha wrote: > Hi, > > I'm wondering if I can get any information about ROIs being used in the > global tractography procedure in TRACULA. I'm particularly interested in the > uncinate fasciculus. I've searched for such information in the website and > the article, to no avail. Thanks for your help! > > > Best, > Juke > > > > ___ 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.
Re: [Freesurfer] Freesurfer 5.2 or new trac_all
There will not be any intermediate releases of trac-all before the freesurfer 5.2 release. A few different things are being changed at the same time and releasing a half-tested version would possibly cause more problems than it'd solve. ETA of 5.2 is within the next few months but I can't give you an exact date. On Fri, 10 Aug 2012, Knut J Bjuland wrote: When will FreeSurfer 5.2 be release. Is is possible to download the news version of trac-all and fsl_sub and use them in FreeSurfer 5. since I am using fsl 4.1.9. Knut Jørgen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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.
Re: [Freesurfer] Tracula question
Do these files that it's trying to load exist? If not, the actual error happened earlier, when they were being generated. Looking at the entire trac-all.log instead of just the end might shed some light on this. On Fri, 10 Aug 2012, Natalia Sánchez wrote: Hi!I am running tracula for the first time and I am encountering the following error: Loading brain mask of output subject from/Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dlabel/mni/lowb_brain _mask.flt.nii.gz niiRead(): error opening file/Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dlabel/mni/lowb_brain _mask.flt.nii.gz Loading FA map of output subject from/Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dmri/mni/dtifit_FA.fl t.nii.gz niiRead(): error opening file/Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dmri/mni/dtifit_FA.fl t.nii.gz Segmentation fault Darwin dhcp-165-124-9-95.phystherapy.northwestern.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 trac-preproc exited with ERRORS at Fri Aug 10 16:19:17 CDT 2012 what file is lowb_brain_mask.flt.nii.gz? should this have been created during tracula or is this file my nodiff image? Thanks! -- Natalia Sánchez PhD Candidate Departments of Biomedical Engineering & Physical Therapy and Human Movement Sciences Northwestern University 645 North Michigan Ave, Suite 1100 Chicago, IL 60611 ___ 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.
Re: [Freesurfer] Tracula question
Hi Natalia - This is an error that will occur if lowb_brain_mask does not exist. The command that generates lowb_brain_mask is "bet" - can you find that line in the log file and run it directly on the command line and see if you get an error? On a separate note, have you opted to use a DWI mask instead of an anatomical mask by setting usemaskanat = 0? If not, then it may be that it's trying to use the DWI mask b/c it can't find the anatomicals, in which case I'd check if SUBJECTS_DIR has been set properly and a freesurfer recon of the same subject exists there. But this is a separate issue than the DWI mask not being generated. Hope this helps, a.y On Fri, 10 Aug 2012, Natalia Sánchez wrote: The required files were not generated. the error occurs at rh.slft_PP_roi2.flt.nii.gz --bmask/Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dlabel/mni/lowb_brain _mask.flt.nii.gz --fa/Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dmri/mni/dtifit_FA.fl t.nii.gz --ncpts 5 --trunc --debug ERROR: fio_pushd: /Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dlabel/mni ERROR: Must specify brain mask volume for output subject does the brain mask have to be input manually in the configuration file, or is this part of the pre-processing? since I set the bet thr to 0.23 in the config file i thought the brain mask was also created during the preprocessing stage. Attached is my log file. I am familiar with FSL but I am using Free surfer since i think automating the entire process, including tracking is a great advantage, but I'm just starting to get the hang of it Thanks! -- Natalia Sánchez PhD Candidate Departments of Biomedical Engineering & Physical Therapy and Human Movement Sciences Northwestern University 645 North Michigan Ave, Suite 1100 Chicago, IL 60611 On Fri, Aug 10, 2012 at 4:28 PM, Anastasia Yendiki wrote: dtifit_FA.fl t.nii.gz ___ 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.
Re: [Freesurfer] Tracula: pathway #7
Hi Chris - That's probably the corpus callosum forceps major or minor. It's the highest-curvature path and that makes it harder to initialize the tractography. If it looks right visually, and it took 90 tries to do that, then it's doing its job as it's supposed to :) a.y On Mon, 13 Aug 2012, Chris Watson wrote: > Hello, > When I go through trac-prep, pathway #7 always takes much much longer than > any of the others. And for that pathway it always displays this: > INFO: Distances between consecutive points are 34 37 34 40 > WARN: Could not find satisfactory control point fit - try 90 > > > Has anyone else had this problem? Visually, they look right to me. > > Thanks, > Chris > > ___ 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.
Re: [Freesurfer] TRACULA -prep error
Hi Richard - In the listing you sent below I do see the a nodif_brain_mask.nii.gz and a control.dat, although I have no idea what control.dat is. As for data.nii.gz, it should be created as a symbolic link to dwi.nii.gz, since bedpostx indeed expects it to be called "data". I have not seen this problem before, but does it occur only when you rerun and overwrite things in the same directory, or also when you start a fresh run on a previously non-existent directory? a.y On Thu, 16 Aug 2012, Richard Binney wrote: Hi Anastasia et al., I previously had TRACULA running wonderfully on a test dataset. I was tasked with writing an in-house step-by-step manual for dummies. Since then, a colleague has followed my manual with a new dataset and had problems. After trying to determine whether it was her install or something about her data and failing to find anything, I returned to re-run the subject I had already successfully processed. Nothing has changed in my install (TRAC-all version etc) ODDLY, this re-run is suffering from the same problem as my colleague. We ran trac-all -prep -dmrirc and it exited without any errors. However, there seem to be some files missing from the output: control.dat data.nii.gz nodif_brain_mask.nii.gz Bedpostx will not run due to the data file being missing and I'm sure the other missing files will cause problems. What is going on? I knew to look for these files as at some point I found the following list for the \dmri\. I can not re-find a post with this list so I'm sorry if it related to a solution to our current problem. Please help Richard brain_anat_mni.nii.gz dtifit_L2.nii.gz dwi_orig_flip.nii.gz brain_anat.nii.gz dtifit_L3.nii.gz dwi_orig.mghdti.bvals brain_anat_orig.nii.gz dtifit_MD.nii.gz dwi_orig.mghdti.bvecs bvals dtifit_MO.nii.gz dwi_orig.nii.gz bvecs dtifit_S0.nii.gz dwi_snr.txt bvecs.norot dtifit_V1.nii.gz lowb_brain.nii.gz control.dat dtifit_V2.nii.gz lowb.nii.gz data.nii.gz dtifit_V3.nii.gz mni dtifit_FA.nii.gz dwi.ecclog nodif_brain_mask.nii.gz dtifit_L1.nii.gz dwi.nii.gz xfms ___ 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.
Re: [Freesurfer] TRACULA -prep error
The symlinks are actually created in the -bedp step, not the -prep step. If you're running bedpostx outside of trac-all, you need to create them yourself. On Thu, 16 Aug 2012, Watson, Christopher wrote: > I've just taken to making the sym links myself after running trac-prep and > before running bedpostx. Then everything should run normally. > > 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, August 16, 2012 4:24 PM > To: Richard Binney > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] TRACULA -prep error > > Hi Richard - In the listing you sent below I do see the a > nodif_brain_mask.nii.gz and a control.dat, although I have no idea what > control.dat is. As for data.nii.gz, it should be created as a symbolic > link to dwi.nii.gz, since bedpostx indeed expects it to be called "data". > I have not seen this problem before, but does it occur only when you rerun > and overwrite things in the same directory, or also when you start a fresh > run on a previously non-existent directory? > > a.y > > On Thu, 16 Aug 2012, Richard Binney wrote: > >> Hi Anastasia et al., >> >> I previously had TRACULA running wonderfully on a test dataset. I was tasked >> with writing an in-house step-by-step manual for dummies. Since then, a >> colleague has followed my manual with a new dataset and had problems. After >> trying to determine whether it was her install or something about her data >> and failing to find anything, I returned to re-run the subject I had already >> successfully processed. Nothing has changed in my install (TRAC-all version >> etc) ODDLY, this re-run is suffering from the same problem as my colleague. >> >> We ran trac-all -prep -dmrirc and it exited without any errors. However, >> there seem to be some files missing from the output: >> >> control.dat >> >> data.nii.gz >> >> nodif_brain_mask.nii.gz >> >> >> >> Bedpostx will not run due to the data file being missing and I'm sure the >> other missing files will cause problems. >> >> What is going on? >> >> I knew to look for these files as at some point I found the following list >> for the \dmri\. I can not re-find a post with this list so I'm sorry if it >> related to a solution to our current problem. >> >> Please help >> >> Richard >> >> brain_anat_mni.nii.gz >> >> dtifit_L2.nii.gz dwi_orig_flip.nii.gz >> >> brain_anat.nii.gz >> >> dtifit_L3.nii.gz >> >> dwi_orig.mghdti.bvals >> >> brain_anat_orig.nii.gz dtifit_MD.nii.gz >> >> dwi_orig.mghdti.bvecs >> >> bvals >> >> dtifit_MO.nii.gz dwi_orig.nii.gz >> >> bvecs >> >> dtifit_S0.nii.gz dwi_snr.txt >> >> bvecs.norot >> >> dtifit_V1.nii.gz lowb_brain.nii.gz >> >> control.dat >> >> dtifit_V2.nii.gz >> >> lowb.nii.gz >> >> data.nii.gz >> >> dtifit_V3.nii.gz >> >> mni >> >> dtifit_FA.nii.gz >> >> dwi.ecclog >> >> nodif_brain_mask.nii.gz >> >> dtifit_L1.nii.gz >> >> dwi.nii.gz >> >> xfms >> >> >> >> > > > ___ 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.
Re: [Freesurfer] TRACULA -prep error
I'm thinking now maybe it's a good idea to move the symlink creation to
the -prep part, to make it easier for anyone who ever needs to run
bedpostx outside trac-all. Thanks for bringing this up.
On Thu, 16 Aug 2012, Richard Binney wrote:
Yes, because of the directions given previous listing I am running bedpost
outside of trac-all (is this not necessary anymore - have we a new update?)
I do not remember having to manually create the symlinks last time around
but I have just done that now and bedpost is whirring away happily.
For future reference to other TRACULA users:
dmri/data.nii.gz should be a symlink to dmri/dwi.nii.gz
presumably only if you have usemaskanat=1, then:
dmri/nodif_brain_mask.nii.gz should be linked to
dlabel/diff/aparc+aseg_mask.bbr.nii.gz
Otherwise I guess it would be linked to the dmri/lowb_brain.nii.gz, but
someone may correct me on that and some of the above.
Thanks for your help eveyone
Richard
On Thu, Aug 16, 2012 at 2:24 PM, Anastasia Yendiki
wrote:
The symlinks are actually created in the -bedp step, not the
-prep step. If you're running bedpostx outside of trac-all, you
need to create them yourself.
On Thu, 16 Aug 2012, Watson, Christopher wrote:
I've just taken to making the sym links myself after
running trac-prep and before running bedpostx. Then
everything should run normally.
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, August 16, 2012 4:24 PM
To: Richard Binney
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] TRACULA -prep error
Hi Richard - In the listing you sent below I do see
the a
nodif_brain_mask.nii.gz and a control.dat, although
I have no idea what
control.dat is. As for data.nii.gz, it should be
created as a symbolic
link to dwi.nii.gz, since bedpostx indeed expects it
to be called "data".
I have not seen this problem before, but does it
occur only when you rerun
and overwrite things in the same directory, or also
when you start a fresh
run on a previously non-existent directory?
a.y
On Thu, 16 Aug 2012, Richard Binney wrote:
Hi Anastasia et al.,
I previously had TRACULA running
wonderfully on a test dataset. I was
tasked
with writing an in-house step-by-step
manual for dummies. Since then, a
colleague has followed my manual with a
new dataset and had problems. After
trying to determine whether it was her
install or something about her data
and failing to find anything, I returned
to re-run the subject I had already
successfully processed. Nothing has
changed in my install (TRAC-all version
etc) ODDLY, this re-run is suffering
from the same problem as my colleague.
We ran trac-all -prep -dmrirc and it
exited without any errors. However,
there seem to be some files missing from
the output:
control.dat
data.nii.gz
nodif_brain_mask.nii.gz
Bedpostx will not run due to the data
file being missing and I'm sure the
other missing files will cause problems.
What is going on?
I knew to look for these files as at
some point I found the following list
for the \dmri\. I can not re-find a post
with this list so I'm sorry if it
related to a solution to our current
problem.
Please help
Richard
brain_anat_mni.nii.gz
dtifit_L2.nii.gz dwi_orig_flip.nii.gz
brain_anat.nii.gz
dtifit_L3.nii.gz
dwi_orig.mghdti.bvals
brain_anat_orig.nii.gz dtifit_MD.nii.gz
dwi_orig.mghdti.bvecs
bvals
dtifit_MO.nii.gz dwi_orig.nii.gz
bvecs
dtifit_S0.nii.gz dwi_snr.txt
bvecs.norot
dtifit_V1.nii.gz lowb_brain.nii.gz
control.dat
dtifit_V2.nii.gz
lowb.nii.gz
data.nii.gz
Re: [Freesurfer] trac-all -path unable to open merged_ph1samples.nii.gz
Hi Knut - Does merged_ph1samples.nii.gz exist in your dmri.bedpostX directory? It's one of the bedpostx output files. If not, it means bedpostx did not finish running properly. You can try running bedpostx directly on the dmri directory, not through trac-all -bedp. Output files of bedpostx are listed here: http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_bedpostx.html a.y On Fri, 17 Aug 2012, Knut J Bjuland wrote: The Tracula script has been modifed and adopted to a local cluster. I am now able to run trac-all -prep, but trac-all bails out when I am running trac-all -bedp. Is there any work around since I am using FSL 4.1.9 with Fressurfer 5.1 I am not able to see what went wrong when I am running trac-all -bedp., but when I ran trac-all -path I get this error niiRead(): error opening file merged_ph1samples.nii.gz. Should I adjust the patch I have used to get around this error or should I run bedpostx ro another command before running trac-all -path? Will I be able to use Tracula from Freesurfer 5.2 with recon-all data used with Freesurfer 5.1? ___ 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.
Re: [Freesurfer] Tracula question
Hi Natalia - I'd need to see at which point in the processing the error
occurs, since this is a very generic error message. Can you please include
your trac-all.log and dmrirc?
Thanks,
a.y
On Thu, 23 Aug 2012, Natalia Sánchez wrote:
Hi Anastasia!I finally made tracula -prep work without errors, using the 1mm
T1 MNI template (i tried using the 2mm one but the vertices for registering
white matter came out as NaN). However, I was not able to get bedpost to
work. After looking at other posts on the FS archive, I think the reason why
-bedp does not work is because of my FSL version. I tried running bedpost on
FSL and then just copying those files on my dmri.bedpost folder and using
those files for reconstructing the white matter tracts. However, I get a
"Segmentation Fault" error. Do you have any idea what this error may mean?
My dpath folder is empty and I my trac-all.log file has no errors related to
-path
Thanks!
-- Natalia Sánchez
PhD Candidate
Departments of Biomedical Engineering &
Physical Therapy and Human Movement Sciences Northwestern University
645 North Michigan Ave, Suite 1100
Chicago, IL 60611
On Fri, Aug 10, 2012 at 5:05 PM, Anastasia Yendiki
wrote:
Hi Natalia - This is an error that will occur if lowb_brain_mask
does not exist. The command that generates lowb_brain_mask is
"bet" - can you find that line in the log file and run it
directly on the command line and see if you get an error?
On a separate note, have you opted to use a DWI mask instead of
an anatomical mask by setting usemaskanat = 0? If not, then it
may be that it's trying to use the DWI mask b/c it can't find
the anatomicals, in which case I'd check if SUBJECTS_DIR has
been set properly and a freesurfer recon of the same subject
exists there. But this is a separate
issue than the DWI mask not being generated.
Hope this helps,
a.y
On Fri, 10 Aug 2012, Natalia Sánchez wrote:
The required files were not generated.
the error occurs at
rh.slft_PP_roi2.flt.nii.gz--bmask/Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dlabel/mni/low
b_brain
_mask.flt.nii.gz--fa/Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dmri/mni/dtifit_F
A.fl
t.nii.gz --ncpts 5 --trunc --debug
ERROR: fio_pushd:
/Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dlabel/mni
ERROR: Must specify brain mask volume for output subject
does the brain mask have to be input manually in the
configuration file, or
is this part of the pre-processing? since I set the bet
thr to 0.23 in the
config file i thought the brain mask was also created
during the
preprocessing stage. Attached is my log file.
I am familiar with FSL but I am using Free surfer since i
think automating
the entire process, including tracking is a great
advantage, but I'm just
starting to get the hang of it
Thanks!
-- Natalia Sánchez
PhD Candidate
Departments of Biomedical Engineering &
Physical Therapy and Human Movement Sciences
Northwestern University
645 North Michigan Ave, Suite 1100
Chicago, IL 60611
On Fri, Aug 10, 2012 at 4:28 PM, Anastasia Yendiki
wrote:
dtifit_FA.fl
t.nii.gz
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.
___
Freesurfer mailing list
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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
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Re: [Freesurfer] Tracula question
Can you please check that the x-y-z dimensions of the bedpostx output files are the same as the dimensions of the DWIs? On Thu, 23 Aug 2012, Natalia Sánchez wrote: Thanks for your response!Attached are the requested files The error occurs here are shown on my terminal: Loading b-values from/Users/Natalia/Desktop/freesurfer/subjects/Justin/diff_tutorial/cJD/dmri/bv als Loading gradients from/Users/Natalia/Desktop/freesurfer/subjects/Justin/diff_tutorial/cJD/dmri/bv ecs Segmentation fault Darwin dhcp-165-124-9-141.phystherapy.northwestern.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 -- Natalia Sánchez PhD Candidate Departments of Biomedical Engineering & Physical Therapy and Human Movement Sciences Northwestern University 645 North Michigan Ave, Suite 1100 Chicago, IL 60611 On Thu, Aug 23, 2012 at 1:48 PM, Anastasia Yendiki wrote: Hi Natalia - I'd need to see at which point in the processing the error occurs, since this is a very generic error message. Can you please include your trac-all.log and dmrirc? Thanks, a.y On Thu, 23 Aug 2012, Natalia Sánchez wrote: Hi Anastasia!I finally made tracula -prep work without errors, using the 1mm T1 MNI template (i tried using the 2mm one but the vertices for registering white matter came out as NaN). However, I was not able to get bedpost to work. After looking at other posts on the FS archive, I think the reason why -bedp does not work is because of my FSL version. I tried running bedpost on FSL and then just copying those files on my dmri.bedpost folder and using those files for reconstructing the white matter tracts. However, I get a "Segmentation Fault" error. Do you have any idea what this error may mean? My dpath folder is empty and I my trac-all.log file has no errors related to -path Thanks! -- Natalia Sánchez PhD Candidate Departments of Biomedical Engineering & Physical Therapy and Human Movement Sciences Northwestern University 645 North Michigan Ave, Suite 1100 Chicago, IL 60611 On Fri, Aug 10, 2012 at 5:05 PM, Anastasia Yendiki wrote: Hi Natalia - This is an error that will occur if lowb_brain_mask does not exist. The command that generates lowb_brain_mask is "bet" - can you find that line in the log file and run it directly on the command line and see if you get an error? On a separate note, have you opted to use a DWI mask instead of an anatomical mask by setting usemaskanat = 0? If not, then it may be that it's trying to use the DWI mask b/c it can't find the anatomicals, in which case I'd check if SUBJECTS_DIR has been set properly and a freesurfer recon of the same subject exists there. But this is a separate issue than the DWI mask not being generated. Hope this helps, a.y On Fri, 10 Aug 2012, Natalia Sánchez wrote: The required files were not generated. the error occurs at rh.slft_PP_roi2.flt.nii.gz--bmask/Users/Natalia/Desktop/freesurfer/subjects /Justin/cJD/dlabel/mni/low b_brain _mask.flt.nii.gz--fa/Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/d mri/mni/dtifit_F A.fl t.nii.gz --ncpts 5 --trunc --debug ERROR: fio_pushd: /Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dlabel/mni ERROR: Must specify brain mask volume for output subject does the brain mask have to be input manually in the configuration file, or is this part of the pre-processing? since I set the bet thr to 0.23 in the config file i thought the brain mask was also created during the preprocessing stage. Attached is my log file. I am familiar with FSL but I am using Free surfer since i think automating the entire process, including tracking is a
Re: [Freesurfer] Tracula question
This probably means that bedpostx didn't process all the slices in your DWIs. Someone else reported something like that recently, not sure what may be causing it, but since it's independent of trac-all, I'd check on the FSL list archives. On Thu, 23 Aug 2012, Natalia Sánchez wrote: they are not. The z dimension of the bedpost images is 52 (from FSL) and for the dmri FS images it is 72. -- Natalia Sánchez PhD Candidate Departments of Biomedical Engineering & Physical Therapy and Human Movement Sciences Northwestern University 645 North Michigan Ave, Suite 1100 Chicago, IL 60611 On Thu, Aug 23, 2012 at 2:08 PM, Anastasia Yendiki wrote: Can you please check that the x-y-z dimensions of the bedpostx output files are the same as the dimensions of the DWIs? On Thu, 23 Aug 2012, Natalia Sánchez wrote: Thanks for your response!Attached are the requested files The error occurs here are shown on my terminal: Loading b-valuesfrom/Users/Natalia/Desktop/freesurfer/subjects/Justin/diff_tutorial/cJD/dmr i/bv als Loading gradientsfrom/Users/Natalia/Desktop/freesurfer/subjects/Justin/diff_tutorial/cJD/dmr i/bv ecs Segmentation fault Darwin dhcp-165-124-9-141.phystherapy.northwestern.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 -- Natalia Sánchez PhD Candidate Departments of Biomedical Engineering & Physical Therapy and Human Movement Sciences Northwestern University 645 North Michigan Ave, Suite 1100 Chicago, IL 60611 On Thu, Aug 23, 2012 at 1:48 PM, Anastasia Yendiki wrote: Hi Natalia - I'd need to see at which point in the processing the error occurs, since this is a very generic error message. Can you please include your trac-all.log and dmrirc? Thanks, a.y On Thu, 23 Aug 2012, Natalia Sánchez wrote: Hi Anastasia!I finally made tracula -prep work without errors, using the 1mm T1 MNI template (i tried using the 2mm one but the vertices for registering white matter came out as NaN). However, I was not able to get bedpost to work. After looking at other posts on the FS archive, I think the reason why -bedp does not work is because of my FSL version. I tried running bedpost on FSL and then just copying those files on my dmri.bedpost folder and using those files for reconstructing the white matter tracts. However, I get a "Segmentation Fault" error. Do you have any idea what this error may mean? My dpath folder is empty and I my trac-all.log file has no errors related to -path Thanks! -- Natalia Sánchez PhD Candidate Departments of Biomedical Engineering & Physical Therapy and Human Movement Sciences Northwestern University 645 North Michigan Ave, Suite 1100 Chicago, IL 60611 On Fri, Aug 10, 2012 at 5:05 PM, Anastasia Yendiki wrote: Hi Natalia - This is an error that will occur if lowb_brain_mask does not exist. The command that generates lowb_brain_mask is "bet" - can you find that line in the log file and run it directly on the command line and see if you get an error? On a separate note, have you opted to use a DWI mask instead of an anatomical mask by setting usemaskanat = 0? If not, then it may be that it's trying to use the DWI mask b/c it can't find the anatomicals, in which case I'd check if SUBJECTS_DIR has been set properly and a freesurfer recon of the same subject exists there. But this is a separate issue than the DWI mask not being generated. Hope this helps, a.y On Fri, 10 Aug 2012, Natalia Sánchez wr
Re: [Freesurfer] [TRACULA] trac-preproc error while reruning with an 'init=1' option
Hi Juke - I apologize for the late response. I was away and I'm still catching up on email. It looks like it fails while it's loading the atlas data (here the 4th out of 33 atlas subjects). Does this happen in other cases? Are the cases that fail running on a machine with less memory than the cases that don't? a.y PS: I'm assuming you mean "reinit=1". On Tue, 11 Sep 2012, Juke Cha wrote: Hi Anastasia, After an intial tracula pipeline procedure, I found some tracts were not successfully reconstructed. Their aparc+aseg looked fine to me. So I reran the trac-preproc -prior and trac-path with an option, 'init=1' in a dmrirc file. Now, the analysis's running well on some, but not the other. I've got an error in trac-preproc -prior: INFO: Rejected 536 streamlines for straying off mask INFO: Rejected 36 streamlines for reversing direction INFO: Rejected 0 streamlines as length outliers INFO: Have 4722 total streamlines (min/mean/max length: 8/57/104) Loading list of excluded streamlines from /home/brain/F/JOSH/fs/1006/dlabel/mni/lh.unc_AS_avg33_mni_flt_cpts_all.bad.txt INFO: Found 3 streamlines to be excluded Loading segmentation from /usr/local/freesurfer//trctrain/trc001/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /usr/local/freesurfer//trctrain/trc001/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /usr/local/freesurfer//trctrain/trc002/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /usr/local/freesurfer//trctrain/trc002/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /usr/local/freesurfer//trctrain/trc003/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /usr/local/freesurfer//trctrain/trc003/dlabel/mni/cortex+2mm.nii.gz Loading segmentation from /usr/local/freesurfer//trctrain/trc004/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /usr/local/freesurfer//trctrain/trc004/dlabel/mni/cortex+2mm.nii.gz trac-preproc exited with ERRORS at Tue Sep 11 11:03:52 EDT 2012 What would cause this and how can I fix this? Thanks for your help in advance. -Jiook ___ 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.
Re: [Freesurfer] [TRACULA] short thin tracks
Hi Akvile - Sorry for the late response, I was out of town for a bit. At first glance it looks like all the tracts are stuck where they're initialized. This might happen occasionally for a tract if initializing it is tricky (i.e., if the subject is not well aligned to the atlas, if the brain mask has a hole, etc), which is why the reinit option exists. But I've never seen it happen to all tracts, so something's fishy here. If you upload all the tracula-related directories for this subject (dmri, dlabel, dpath, scripts), I'll take a look. http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange a.y On Thu, 13 Sep 2012, Akvile Lukose wrote: Hello Freesurfers, I ran into a problem running TRACULA that I couldn't solve myself, and I would really appreciate if you could have a look. I am running a FS 5.1 on mac os x 10.7.4 (intel 64bit) machine with 16GB RAM. I extracted the bvals and bvecs with the dcm2nii converter and adjusted the format to what FS expects (scans acquired on a non-Siemens scanner). I attach the dmrirc file as well. First, I had a memory problem (cannot alloc memory) during the –prep stage. The new compiled update from here (http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula )helped and –prep stage finished without any errors. I was not able to run bedpostx from dmrirc configuration file. I could work around it by running bedpostx directly on dmri directory (as described here http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20815.html). Then I had a problem with symlinks, I created them manually and after that it worked fine, I had all the output files as listed here (http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_bedpostx.html). -path worked also without any errors, but I keep getting very short thin tracks (all tracks) (snapshot attached). There is nothing wrong with the aparc+aseg.mgz. I tried rerunning every stage after I added option "set reinit=1" (as described here http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21990.html), but unfortunately it didn't help. Do you have any ideas how to fix it? Thank you very much in advance! Kind regards, Akvile Lukose ___ 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.
Re: [Freesurfer] TRACULA - failed corpus callosum forceps major
Hi Clare - Sorry for responding late to any email that was sent while I was away. The fmajor and slft are sometimes tricky in their initialization b/c of their high curvature. The initial guess for the path is chosen from the atlas and if it's not well-aligned and veers off the subject's white matter somewhere the initialization will fail. In those cases the path.pd.nii.gz will contain only the initial path, so you can overlay it on the subject's FA map and see if that's what's happening. If you try the reinit trick a few times (if you keep doing it, it'll try different initializations each time) and it doesn't work, you can also try increasing the number of controls points (say, set ncpts = 7) for these cases. If none of this works, I can try to take a look at one of these data sets. Hope this helps, a.y On Fri, 14 Sep 2012, Gibbard, Clare wrote: Hello, I have tried out running TRACULA on 20 subjects. It all seemed to work well except that in 8 of the subjects the corpus callosum forceps major was either missing or was a very small cluster. The same happened for the temporal SLF of 2 subjects. I read previous posts related to this and tried re-running the affected subjects with set reinit =1. However, the results were very similar to before. I have checked the registrations and they are not perfect, but not wildly inaccurate. Are you able to suggest any options for me to try? I have attached the dmrirc file I used for the first run (called dmrirc-original) as well as the one for re-running the subjects whose CC was not segmented (called dmrirc). Thank you. Best wishes, Clare ___ 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.
Re: [Freesurfer] TRACULA Question
Hi Gabor - Tracula doesn't use the BA labels, only the labels in the aparc+aseg. I hope this answers your question. a.y On Sun, 16 Sep 2012, Gabor Perlaki wrote: > Dear Anastasia, > > Earlier I was posted an issue about BA44/pars triangular: > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23706.html > > Because TRACULA also uses the cortical parcellation it may be > important to handle this issue somehow. Is it handled in TRACULA > analysis? Does it affect the result of WM-volumes? > > Thank you for your answer, > Gabor > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ 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.
Re: [Freesurfer] Tracula Error: bvecs and bvals don't have the same number of entries
Hi Joy - How were your bvecs and bvals files generated? In the past some people have had problems with files exported from Excel b/c it generates text files with Windows-specific end-of-line characters that cannot be read properly on Linux. Do the files look normal when you run "more" on them on the system where you ran trac-all? a.y On Wed, 26 Sep 2012, Loi wrote: > Dear FreeSurfers, > > I am trying to run trac-all -prep on a single subject, and get the > following error: > > dtifit -k > /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/dwi.nii.gz > -m > /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dlabel/diff/aparc+aseg_mask.flt.nii.gz > -r > /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvecs > -b > /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvals > -o > /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/dtifit > Error: bvecs and bvals don't have the same number of entries > > I have searched the message thread, and cannot seem to find a solution > applicable to my situation: it seems that the trac-all process > generates transposed bvec and bval files. > Therefore, I tried transposing these manually and specifying the > location to these files (as explained in the tutorial: > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula), but > attempting to run trac-all again still leads to the same result: new > bval and bvec files are generated, and I receive the same error > message. > > Does anyone know how I can solve this problem? > > Thank you, > Joy-Loi > > > * > My configuration file: > > > setenv SUBJECTS_DIR > /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_recons > > set dtroot = > /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data > > set subjlist = id101 > set runlist = 1 > > set dcmroot = > /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data > set dcmlist = id101/orig/1.dcm > > set bvalfile = > /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvals.txt > > set bvecfile = > /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvecs.txt > > set nb0 = 10 > > set doeddy = 1 > set dorotbvecs = 1 > set thrbet = 0.3 > set doregflt = 1 > set doregbbr = 0 > set doregmni = 1 > set mnitemp = /psyklab/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz > > #set trainfile = > /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/subj,train,difftutorial123.txt > > set pathlist = (lh.cst_AS rh.cst_AS \ >lh.ilf_AS rh.ilf_AS \ > lh.unc_AS rh.unc_AS \ >fmajor_PP fminor_PP \ >lh.atr_PP rh.atr_PP \ >lh.cab_PP rh.cab_PP \ >lh.ccg_PP rh.ccg_PP \ >lh.slfp_PP rh.slfp_PP \ >lh.slft_PP rh.slft_PP) > > > set ncpts = 5 > > set usetrunc = 1 > > > > > > * > My bvals: > > 0.00 > 0.00 > 0.00 > 0.00 > 0.00 > 0.00 > 0.00 > 0.00 > 0.00 > 0.00 > 700.00 > 700.00 > 700.00 > 700.00 > 700.00 > 700.00 > 700.00 > 700.00 > 700.00 > 700.00 > 700.00 > 700.00 > 700.00 > 700.00 > 700.00 > 700.00 > 700.00 > 700.00 > 700.00 > 700.00 > 700.00 > 700.00 > 700.00 > 700.00 > 700.00 > 700.00 > 700.00 > 700.00 > 700.00 > 700.00 > > * > My bvecs: > > 0.000 0.000 0.000 > 0.000 0.000 0.000 > 0.000 0.000 0.000 > 0.000 0.000 0.000 > 0.000 0.000 0.000 > 0.000 0.000 0.000 > 0.000 0.000 0.000 > 0.000 0.000 0.000 > 0.000 0.000 0.000 > 0.000 0.000 0.000 > -0.9998760 0.0011040 0.0157340 > -0.7705615 0.6320276 0.0823114 > -0.2461791 0.0273479 0.9688392 > -0.7953558 0.1076421 0.5965091 > 0.4620816 -0.8755928 0.1407778 > 0.2261090 -0.8553081 -0.4661796 > 0.2601186 0.4095102 -0.8744363 > -0.7969547 -0.5877791 0.1392076 > -0.5028073 -0.5104712 0.6975709 > -0.3073035 0.1334521 -0.9422074 > 0.7957742 0.1950272 -0.5733304 > 0.8041493 0.5924478 -0.0484727 > -0.1867079 -0.9528833 0.2390659 > 0.3898569 -0.1063898 0.9147088 > 0.1341999 -0.6614532 0.7378819 > 0.3382555 0.8823941 0.3270553 > -0.7688307 -0.3139264 -0.5570900 > -0.4086013 0.6653325 0.6248017 > -0.2933309 0.7581020 -0.5824408 > 0.7689370 -0.4282441 0.4747016 > 0.1800972 0.5296402 0.8288835 > 0.7680658 0.3158178 0.5570763 > -0.2214999 0.9744585 0.0370050 > -0.4175692 -0.8418782 -0.3418731 > -0.1784475 -0.4817282 -0.8579599 > 0.3361637 0.8554551 -0.3939400 > 0.7858656 -0.5091907 -0.3509137 > 0.4194232 -0.2589429 -0.8700761 > -0.7760561 0.3511497 -0.5238622 > 0.9987836 -0.0413076 0.0269219 > __
