Re: [Freesurfer] Tracula Error: bvecs and bvals don't have the same number of entries
Can you please send the original bvals and bvecs files (the ones that you specify in the configuration file), and the configuration file itself? Thanks! a.y On Thu, 27 Sep 2012, Loi wrote: > Hello, > > I generate the files in Linux (using gedit) and they look normal (I > have compared them to the files in the tutorial). > > So far I have tried ending both with and without .txt, transposing the > files, changing to equal number of decimals and adding 'setenv LC_ALL > en_US' to the .tchsrc file. > > The inputs I am using are dicoms, and even though I specify a path to > the b-value files and gradient tables I make (I originally didn't > specify these, and got the same error message), new bvecs and bvals > are generated in the trac-all -prep process, leading to the error. > > Thank you, > Joy-Loi > > > > > On Thu, Sep 27, 2012 at 7:30 PM, Anastasia Yendiki > wrote: >> >> 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) >>> >>> >>
Re: [Freesurfer] Tracula Error: bvecs and bvals don't have the same number of entries
There are 10 empty lines at the end of your Tbvecs.txt file. Can you try removing those and reruning? Hope this helps, a.y On Fri, 28 Sep 2012, Loi wrote: > Hello again, > > Here is the configuration file and some variations of the bvec and > bval files I have tried using. > > Also, I have noticed that the first time I run trac-all (without > specifying the bvecs and bvals), the bval file generated seems to list > the values twice. ie: > > 0 > 0 > 7 > 7 > 7 > 7 > 0 > 0 > 7 > 7 > 7 > 7 > > I hope this make sense. Thank you, > > Joy-Loi > > > On 9/27/12, Anastasia Yendiki wrote: >> >> Thanks, no problem. I'd like to see the actual files on one of our >> machines just to make sure. >> >> On Thu, 27 Sep 2012, Loi wrote: >> >>> Hello Anastasia, >>> >>> I am in Norway and home from work for the evening, but will send you >>> the files first thing tomorrow morning. >>> Meanwhile, here is a copy of the contents in the files (as included in >>> my original e-mail). >>> Thank you for your help! >>> >>> * >>> 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: >>> >>> 0.000 >>> 0.000 >>> 0.000 >>> 0.000 >>> 0.000 >>> 0.000 >>> 0.000 >>> 0.000 >>> 0.000 >>> 0.000 >>> 700.000 >>> 700.000 >>> 700.000 >>> 700.000 >>> 700.000 >>> 700.000 >>> 700.000 >>> 700.000 >>> 700.000 >>> 700.000 >>> 700.000 >>> 700.000 >>> 700.000 >>> 700.000 >>> 700.000 >>> 700.000 >>> 700.000 >>> 700.000 >>> 700.000 >>> 700.000 >>> 700.000 >>> 700.000 >>> 700.000 >>> 700.000 >>> 700.000 >>> 700.000 >>> 700.000 >>> 700.000 >>> 700.000 >>> 700.000 >>> >>> * >>> 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 >>> 0.22610
Re: [Freesurfer] TRACULA Question
Hi Gabor - The info that tracula uses is which aparc+aseg labels each pathway neighbors at each point along its trajectory. It learns this information from the 33 subjects in the atlas, where the pathways were labeled manually, and then applies that knowledge to reconstruct the pathways in your subject. As long as the aparc+aseg of your subject is consistent with the ones in the atlas, you're fine. But if you think that the version you used to generate your aparc+aseg, and the latest version, that the aparc+aseg's in the atlas were generated with, have significant differences, this *may* be a problem. The extent of the problem will depend on how often the problematic label occurs next to one of the 18 pathways that tracula reconstructs and how different the label is b/w the versions. A small diference will probably not affect tracula at all. Your aparc+aseg's were generated with freesurfer 4.5, and there was no tracula atlas generated with that version of aparc+aseg's. Hope this helps, a.y On Fri, 28 Sep 2012, Gabor Perlaki wrote: > Dear Anastasia, > > Thanks a lot your answer. My fear is that the pars triangular > segmentation also seems bad, because it is right lateralized in most > of our analyzed data. Here is the post about this issue: > https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024541.html > > Is it also OK with Tracula? > > Thank you in advance, > Gabor > > 2012/9/27 Anastasia Yendiki : >> >> 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 >>> >>> >>> >> >> >> 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 Error: bvecs and bvals don't have the same number of entries
In the files that you sent me earlier, the final bvecs had a set of 10 all-zero directions in the end (which I thought may have been caused by the 10 empty lines at the end of your input Tbvecs.txt) Are those zeros still there in bvecs? On Fri, 28 Sep 2012, Loi wrote: > Hello again, > > I have tried removing the empty lines and rerunning trac-all -prep, > but the error persists. > > > Joy-Loi > > On 9/28/12, Anastasia Yendiki wrote: >> >> There are 10 empty lines at the end of your Tbvecs.txt file. Can you try >> removing those and reruning? >> >> Hope this helps, >> a.y >> >> On Fri, 28 Sep 2012, Loi wrote: >> >>> Hello again, >>> >>> Here is the configuration file and some variations of the bvec and >>> bval files I have tried using. >>> >>> Also, I have noticed that the first time I run trac-all (without >>> specifying the bvecs and bvals), the bval file generated seems to list >>> the values twice. ie: >>> >>> 0 >>> 0 >>> 7 >>> 7 >>> 7 >>> 7 >>> 0 >>> 0 >>> 7 >>> 7 >>> 7 >>> 7 >>> >>> I hope this make sense. Thank you, >>> >>> Joy-Loi >>> >>> >>> On 9/27/12, Anastasia Yendiki wrote: >>>> >>>> Thanks, no problem. I'd like to see the actual files on one of our >>>> machines just to make sure. >>>> >>>> On Thu, 27 Sep 2012, Loi wrote: >>>> >>>>> Hello Anastasia, >>>>> >>>>> I am in Norway and home from work for the evening, but will send you >>>>> the files first thing tomorrow morning. >>>>> Meanwhile, here is a copy of the contents in the files (as included in >>>>> my original e-mail). >>>>> Thank you for your help! >>>>> >>>>> * >>>>> 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: >>>>> >>>>> 0.000 >>>>> 0.000 >>>>> 0.000 >>>>> 0.000 >>>>> 0.000 >>>>> 0.000 >>>>> 0.000 >>>>> 0.000 >>>>> 0.000 >>>>> 0.000 >>>>> 700.000 >>>>> 700.000 >>>
Re: [Freesurfer] tracula question
Hola Fernando - Please send questions about tracula to the freesurfer list
and not me personally, so that all users may benefit.
This issue will be resolved in the next version. For now, if you're on a
unix system that doesn't have the jot command, you'll just have to specify
the runlist in your configuration file, even if you want to process all
subjects on your list. So if you have 5 subjects for example:
set runlist = (1 2 3 4 5)
Hope this helps,
a.y
On Fri, 5 Oct 2012, Fernando Ventrice wrote:
Dear Anastasia Yendiki,
I have been trying to use TRACULA and I think I'm doing something wrong.
Because it keeps on giving me this error (I tried within tcsh and bash):
fventrice@xubuntu1204x64fleni:~$ trac-all -prep -c
${TUTORIAL_DATA}/diffusion_tutorial/scripts/dmrirc_single_subject
jot: Command not found.
INFO: SUBJECTS_DIR is
/media/LEVIATAN01/LaboINEBA/testing_TRACULA/diffusion_recons
INFO: Diffusion root is
/media/LEVIATAN01/LaboINEBA/testing_TRACULA/diffusion_tutorial
Actual FREESURFER_HOME /home/fventrice/CONTAINER_FLENI/Programs/freesurfer
I use freesurfer and fsl perfectly well. I have also tried with the new version
of trac-all. But keeps on giving the same error.
Best regards and thanks!
Fernando Ventrice
El contenido del presente mensaje y el de sus adjuntos, es confidencial,
privado y de uso exclusivo de los destinatarios a los cuales está dirigido,
pudiendo contener información legalmente protegida. Queda prohibida la
revisión, divulgación, publicación, modificación, copia, distribución o acción
en relación con esta información, por personas o entidades distintas al
destinatario. Si usted, por alguna razón, lo ha recibido por error, por favor
tenga la amabilidad de eliminarlo de su sistema. Las opiniones contenidas, son
exclusivas de su autor, y no representa necesariamente, la opinión de FLENI.
http://www.fleni.org.ar
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Re: [Freesurfer] TRACULA: multiple bvecs files in one configuration file
Hi Joy-Loi - No, all updates that happened since the 5.1 release are listed here: http://www.freesurfer.net/fswiki/Tracula For now it's assumed that all your subjects were scanned with the same protocol, which is usually the case, unless you're comparing different protocols. If you want to specify a different set of gradients for some subjects, you have to create a different configuration file for them. Hope this helps, a.y On Thu, 11 Oct 2012, Loi wrote: > Hello, > > I see in the message thread that as of July 2011 there was no support > for multiple bvecs files in one configuration file. Have any changes > been made regarding this? And if so, how can I include multiple paths > to bvecs files? > > Thank you, > > Joy-Loi > ___ > 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 trac-all -path ERROR
Hi Fernando - Can you please send your scripts/trac-all.log file? My guess is something went wrong earlier in the process that caused those files not to be created. Thanks, a.y On Thu, 11 Oct 2012, Fernando Ventrice wrote: Dear Freesurfer-Tracula users, I'm trying to use Tracula to analyze some DTI images. I already used Freesurfer and FSL without problems. First of all, my system is the following: Linux Xubuntu 12.04 LTS x86_64 - Intel i7 - 8Gb RAM - Nvidia GeForce GT 520 1GB Freesurfer version 5.1.0 (freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0.tar.gz) FSL version 5.0.1 (from Neurodebian) The first problem I had was with the first command: "trac-all -prep -c dmrirc_file" gave an error about not finding the 'job' command. This was solved (thanks to Anastasia Yendiki) using: "set runlist=(1)" in the 'dmrirc_file'. Then, I had some problems with the second command: "trac-all -bedp -c dmrirc_file", which gave this error: Queuing preprocessing stages /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 216: [: NONE: unexpected operator /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 263: [: NONE: unexpected operator /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 321: [: xbedpostx_pre: unexpected operator /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 458: [: x: unexpected operator /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 472: [: -le: argument expected Queuing parallel processing stage /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 216: [: NONE: unexpected operator /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 321: [: xbedpostx: unexpected operator /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 458: [: x43: unexpected operator 0 slices processed Queuing post processing stage /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 216: [: NONE: unexpected operator /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 263: [: NONE: unexpected operator /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 321: [: xbedpostx_post: unexpected operator /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 458: [: x: unexpected operator /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 472: [: -le: argument expected Reading about this on the freesurfer mailing-list I got to the conclusion of running directly: bedpostx /home/labneuroimg/STATION_FLENI/Tensores/subject/TRACULA/subject/dmri (in the middle I learned how to use condor!) It finished without errors. So I went to the last command: "trac-all -path -c dmrirc_file" which complained about not finding the following file: ERROR: Could not open /home/labneuroimg/STATION_FLENI/Tensores/subject/TRACULA/subject/dlabel/diff/lh.cst_AS_avg33_mni_flt_cpts_5.txt These files were at "/home/labneuroimg/STATION_FLENI/Tensores/subject/TRACULA/subject/dlabel/mni"... should I copy them to the diff folder?? I send as attachments the error output from "trac-all -path -c dmrirc_file" and the "dmrirc_file" I used. Best regards and thanks a lot! Fernando Ventrice El contenido del presente mensaje y el de sus adjuntos, es confidencial, privado y de uso exclusivo de los destinatarios a los cuales está dirigido, pudiendo contener información legalmente protegida. Queda prohibida la revisión, divulgación, publicación, modificación, copia, distribución o acción en relación con esta información, por personas o entidades distintas al destinatario. Si usted, por alguna razón, lo ha recibido por error, por favor tenga la amabilidad de eliminarlo de su sistema. Las opiniones contenidas, son exclusivas de su autor, y no representa necesariamente, la opinión de FLENI. http://www.fleni.org.ar ___ 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 ERROR
Hi Fernando - You need to provide you bvecs and bvals files explicitly in your configuration file. The first error occurs b/c these files are missing. a.y On Thu, 11 Oct 2012, Fernando Ventrice wrote: Yes, of course. Here I send it. Best regards, Fernando From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] Sent: Thursday, October 11, 2012 1:50 PM To: Fernando Ventrice Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] TRACULA trac-all -path ERROR Hi Fernando - Can you please send your scripts/trac-all.log file? My guess is something went wrong earlier in the process that caused those files not to be created. Thanks, a.y On Thu, 11 Oct 2012, Fernando Ventrice wrote: Dear Freesurfer-Tracula users, I'm trying to use Tracula to analyze some DTI images. I already used Freesurfer and FSL without problems. First of all, my system is the following: Linux Xubuntu 12.04 LTS x86_64 - Intel i7 - 8Gb RAM - Nvidia GeForce GT 520 1GB Freesurfer version 5.1.0 (freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0.tar.gz) FSL version 5.0.1 (from Neurodebian) The first problem I had was with the first command: "trac-all -prep -c dmrirc_file" gave an error about not finding the 'job' command. This was solved (thanks to Anastasia Yendiki) using: "set runlist=(1)" in the 'dmrirc_file'. Then, I had some problems with the second command: "trac-all -bedp -c dmrirc_file", which gave this error: Queuing preprocessing stages /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 216: [: NONE: unexpected operator /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 263: [: NONE: unexpected operator /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 321: [: xbedpostx_pre: unexpected operator /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 458: [: x: unexpected operator /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 472: [: -le: argument expected Queuing parallel processing stage /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 216: [: NONE: unexpected operator /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 321: [: xbedpostx: unexpected operator /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 458: [: x43: unexpected operator 0 slices processed Queuing post processing stage /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 216: [: NONE: unexpected operator /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 263: [: NONE: unexpected operator /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 321: [: xbedpostx_post: unexpected operator /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 458: [: x: unexpected operator /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 472: [: -le: argument expected Reading about this on the freesurfer mailing-list I got to the conclusion of running directly: bedpostx /home/labneuroimg/STATION_FLENI/Tensores/subject/TRACULA/subject/dmri (in the middle I learned how to use condor!) It finished without errors. So I went to the last command: "trac-all -path -c dmrirc_file" which complained about not finding the following file: ERROR: Could not open /home/labneuroimg/STATION_FLENI/Tensores/subject/TRACULA/subject/dlabel/diff/lh.cst_AS_avg33_mni_flt_cpts_5.txt These files were at "/home/labneuroimg/STATION_FLENI/Tensores/subject/TRACULA/subject/dlabel/mni"... should I copy them to the diff folder?? I send as attachments the error output from "trac-all -path -c dmrirc_file" and the "dmrirc_file" I used. Best regards and thanks a lot! Fernando Ventrice El contenido del presente mensaje y el de sus adjuntos, es confidencial, privado y de uso exclusivo de los destinatarios a los cuales está dirigido, pudiendo contener información legalmente protegida. Queda prohibida la revisión, divulgación, publicación, modificación, copia, distribución o acción en relación con esta información, por personas o entidades distintas al destinatario. Si usted, por alguna razón, lo ha recibido por error, por favor tenga la amabilidad de eliminarlo de su sistema. Las opiniones contenidas, son exclusivas de su autor, y no representa necesariamente, la opinión de FLENI. http://www.fleni.org.ar 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. El contenido del presente mensaje y el de sus adjuntos, es confidencial, privado y de uso exclusivo de los destinatarios a lo
Re: [Freesurfer] FW: TRACULA some fiber volumes being too small
Hi Fernando - Thank you for your kind words. You can indeed try the reinit
option as Christofer suggested when one of the pathways looks like a
single curve and not like a volume.
However, because some of your other pathways in the screenshots look a bit
funky too, I would also check that there was nothing wrong with the
gradient directions. An easy way to check that is by looking at the
eigenvectors from the tensor fit (dmri/dtifit_V1.nii.gz). Although tracula
itself doesn't use tensors, if there's something wrong with the gradient
directions, it'll show up in the tensor fit.
If you're not sure how to check, you can upload all tracula-related
directories of your subject here and I'll take a look:
http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
Hope this helps,
a.y
On Thu, 18 Oct 2012, Fernando Ventrice wrote:
Dear Freesurfer/Tracula users,
Finally I could successfully test Tracula and I think it is amazing what it can
do automatically. These are the commands I used:
export FREESURFER_HOME=${HOME}/Programs/freesurfer_510 && source
$FREESURFER_HOME/SetUpFreeSurfer.sh
source /etc/fsl/fsl.sh
export FSLPARALLEL=condor
trac-all -prep -c
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/dmrirc_Fernando_Ventrice
trac-all -bedp -c
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/dmrirc_Fernando_Ventrice
# "trac-all -bedp" gave some errors so I used bedpostx directly:
bedpostx
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/20120112_VENTRICE_FERNANDO/dmri
trac-all -path -c
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/dmrirc_Fernando_Ventrice
freeview -tv
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/20120112_VENTRICE_FERNANDO/dpath/merged_avg33_mni_flt.mgz
-v
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/20120112_VENTRICE_FERNANDO/dmri/dtifit_FA.nii.gz
&
All finished without errors, but there seems to be a problem with CC Forceps
Mayor volume, which gave very small values. Is this OK or I made some mistake?
First I tested with some patient and other fiber tracks also gave very small
volumes. I attached some pictures and the dmrirc and trac-all log files.
Best,
Fernando Ventrice
El contenido del presente mensaje y el de sus adjuntos, es confidencial,
privado y de uso exclusivo de los destinatarios a los cuales está dirigido,
pudiendo contener información legalmente protegida. Queda prohibida la
revisión, divulgación, publicación, modificación, copia, distribución o acción
en relación con esta información, por personas o entidades distintas al
destinatario. Si usted, por alguna razón, lo ha recibido por error, por favor
tenga la amabilidad de eliminarlo de su sistema. Las opiniones contenidas, son
exclusivas de su autor, y no representa necesariamente, la opinión de FLENI.
http://www.fleni.org.ar
___
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 during inter-subject registration with mri_cvs_register
Hi Verena - Which version of freesurfer are you using? In the public release of 5.1 the CVS registration option in trac-all is disabled. a.y On Tue, 23 Oct 2012, Verena Gramse wrote: > > > From: Verena Gramse > Sent: Monday, October 22, 2012 8:19 PM > To: freesur...@nmr.mgh.harvard > Subject: trac-all -prep error during inter-subject registration with > mri_cvs_register > > Dear Tracula Team, > > I have been running into problems during Inter-subject registration at the > mri_cvs_register step: it aborts with Image Exception : #22 :: ERROR: Could > not open image /gablab/p/BGFU/data/freesurfer/cvs_avg35/mri//norm.mgz. But > norm.mgz exists at the specified location and it can be opened with freeview > without problems. > > Did I oversee anything? > Thanks in advance! > Verena > > > Find attached my dmrirc and the error.log > > > > ___ 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 during inter-subject registration with mri_cvs_register
Yes. Using affine vs. nonlinear registration to the atlas shouldn't be as big a deal for tracula as, say, for a voxel-based analysis. That's because the anatomical priors used by tracula don't use the exact spatial location of the tracts but the IDs of the anatomical labels neighboring the tracts. On Tue, 23 Oct 2012, Verena Gramse wrote: > Hi Anastasia, > > Ahh.. I used the regular 5.1 and pointed to our dev folder where the > cvs_avg35 (and cvs_avg_inMNI152) live. > So, do you recommend skipping cvs registration for now? > > Thanks in advance! > Verena > > > ________ > From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] > Sent: Tuesday, October 23, 2012 12:00 PM > To: Verena Gramse > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] trac-all -prep error during inter-subject > registration with mri_cvs_register > > Hi Verena - Which version of freesurfer are you using? In the public > release of 5.1 the CVS registration option in trac-all is disabled. > > a.y > > On Tue, 23 Oct 2012, Verena Gramse wrote: > >> >> >> From: Verena Gramse >> Sent: Monday, October 22, 2012 8:19 PM >> To: freesur...@nmr.mgh.harvard >> Subject: trac-all -prep error during inter-subject registration with >> mri_cvs_register >> >> Dear Tracula Team, >> >> I have been running into problems during Inter-subject registration at the >> mri_cvs_register step: it aborts with Image Exception : #22 :: ERROR: Could >> not open image /gablab/p/BGFU/data/freesurfer/cvs_avg35/mri//norm.mgz. But >> norm.mgz exists at the specified location and it can be opened with freeview >> without problems. >> >> Did I oversee anything? >> Thanks in advance! >> Verena >> >> >> Find attached my dmrirc and the error.log >> >> >> >> > > > 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
Hi Crystal - This is because of the way the B0 dewarping script is called during the pre-processing. It assumes that you have 2 phase images instead of the difference of 2 phase images (which is what you have). The next version actually accommodates both cases but for now you have 2 options: 1. Edit the script $FREESURFER_HOME/bin/trac-preproc and change this line: set cmd = ($cmd --ph $dwidir/b0pha.nii.gz) to this: set cmd = ($cmd --dph $dwidir/b0pha.nii.gz) 2. Be lazy and skip B0 dewarping! Hope this helps, a.y On Wed, 24 Oct 2012, Franklin, Crystal G wrote: Freesurfer, I am trying to run trac-all –prep and trac-preproc keeps exiting with errors. It keeps saying the unwrappedphasemaps must contain at least two volumes. My data only contains one phase image and 2 magnitude images. Do you know what could be causing this error or how to get around it? Thanks in advance, Crystal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] FW: TRACULA some fiber volumes being too small
Hi Fernando - Thanks for uploading your data. Looking at the primary
directions from tensor fit on the data that you sent me (see screenshot),
they seem to be off by a 90 degree angle from what you'd expect them. This
means that your gradient table is probably off as well.
Hope this helps,
a.y
On Thu, 18 Oct 2012, Fernando Ventrice wrote:
Dear Freesurfer/Tracula users,
Finally I could successfully test Tracula and I think it is amazing what it can
do automatically. These are the commands I used:
export FREESURFER_HOME=${HOME}/Programs/freesurfer_510 && source
$FREESURFER_HOME/SetUpFreeSurfer.sh
source /etc/fsl/fsl.sh
export FSLPARALLEL=condor
trac-all -prep -c
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/dmrirc_Fernando_Ventrice
trac-all -bedp -c
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/dmrirc_Fernando_Ventrice
# "trac-all -bedp" gave some errors so I used bedpostx directly:
bedpostx
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/20120112_VENTRICE_FERNANDO/dmri
trac-all -path -c
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/dmrirc_Fernando_Ventrice
freeview -tv
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/20120112_VENTRICE_FERNANDO/dpath/merged_avg33_mni_flt.mgz
-v
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/20120112_VENTRICE_FERNANDO/dmri/dtifit_FA.nii.gz
&
All finished without errors, but there seems to be a problem with CC Forceps
Mayor volume, which gave very small values. Is this OK or I made some mistake?
First I tested with some patient and other fiber tracks also gave very small
volumes. I attached some pictures and the dmrirc and trac-all log files.
Best,
Fernando Ventrice
El contenido del presente mensaje y el de sus adjuntos, es confidencial,
privado y de uso exclusivo de los destinatarios a los cuales está dirigido,
pudiendo contener información legalmente protegida. Queda prohibida la
revisión, divulgación, publicación, modificación, copia, distribución o acción
en relación con esta información, por personas o entidades distintas al
destinatario. Si usted, por alguna razón, lo ha recibido por error, por favor
tenga la amabilidad de eliminarlo de su sistema. Las opiniones contenidas, son
exclusivas de su autor, y no representa necesariamente, la opinión de FLENI.
http://www.fleni.org.ar
___
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 - posterior density just one-dimensional curve
Hi Andi - The most common problem that would cause all or almost all pathways to fail is an incorrect gradient table. You can do a sanity check on that by looking at the primary eigenvectors from your tensor fit (dmri/dtifit_V1.nii.gz). See also my answer to Fernando earlier today. Hope this helps, a.y On Tue, 30 Oct 2012, Andi Heckel wrote: Dear Tracula team, I have noticed in a multisubject tracula analysis, that the posterior density in many if not all paths in the path.pd.nii.gz file is just a bright one-dimensional curve, rather than a true distribution. The path.map.nii.gz is empty. This is true for both flirt and bbreg registered versions in many subjects. Trac-all finished wiithout errors. So did Recon-all. Could it actually be a memory (RAM) problem ? We are running tracula on a cluster with only 2.5 GB per core. thx for any help and 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] FW: TRACULA some fiber volumes being too small
If FSL isn't happy with the directions, that's going to be fatal b/c
trac-all relies on bedpostx running properly. I'm going to look into this
further to try to figure out what it is about this data that's causing
the discrepancy.
On Wed, 31 Oct 2012, Fernando Ventrice wrote:
Dear Anastasia,
When I open the dtifit_V1 and dtifit_FA with Freeview the vector directions
actually are OK, but when I open them with FSLview they are similar to your
screen-shot. Here I also send a screen-shot with the comparison between the two
softwares in each monitor.
Best,
Fernando
________
From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
Sent: Tuesday, October 30, 2012 1:24 PM
To: Fernando Ventrice
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] FW: TRACULA some fiber volumes being too small
See screenshot now :)
On Tue, 30 Oct 2012, Anastasia Yendiki wrote:
Hi Fernando - Thanks for uploading your data. Looking at the primary
directions from tensor fit on the data that you sent me (see screenshot),
they seem to be off by a 90 degree angle from what you'd expect them. This
means that your gradient table is probably off as well.
Hope this helps,
a.y
On Thu, 18 Oct 2012, Fernando Ventrice wrote:
Dear Freesurfer/Tracula users,
Finally I could successfully test Tracula and I think it is amazing what
it can do automatically. These are the commands I used:
export FREESURFER_HOME=${HOME}/Programs/freesurfer_510 && source
$FREESURFER_HOME/SetUpFreeSurfer.sh
source /etc/fsl/fsl.sh
export FSLPARALLEL=condor
trac-all -prep -c
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/dmrirc_Fernando_Ventrice
trac-all -bedp -c
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/dmrirc_Fernando_Ventrice
# "trac-all -bedp" gave some errors so I used bedpostx directly:
bedpostx
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/20120112_VENTRICE_FERNANDO/dmri
trac-all -path -c
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/dmrirc_Fernando_Ventrice
freeview -tv
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/20120112_VENTRICE_FERNANDO/dpath/merged_avg33_mni_flt.mgz
-v
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/20120112_VENTRICE_FERNANDO/dmri/dtifit_FA.nii.gz
&
All finished without errors, but there seems to be a problem with CC
Forceps Mayor volume, which gave very small values. Is this OK or I made
some mistake? First I tested with some patient and other fiber tracks also
gave very small volumes. I attached some pictures and the dmrirc and
trac-all log files.
Best,
Fernando Ventrice
El contenido del presente mensaje y el de sus adjuntos, es confidencial,
privado y de uso exclusivo de los destinatarios a los cuales está
dirigido, pudiendo contener información legalmente protegida. Queda
prohibida la revisión, divulgación, publicación, modificación, copia,
distribución o acción en relación con esta información, por personas o
entidades distintas al destinatario. Si usted, por alguna razón, lo ha
recibido por error, por favor tenga la amabilidad de eliminarlo de su
sistema. Las opiniones contenidas, son exclusivas de su autor, y no
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tenga la amabilidad de eliminarlo de su sistema. Las opiniones contenidas, son
exclusivas de su autor, y no representa necesariamente, la opinión de FLENI.
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El contenido del presente mensaje y el de sus adjuntos, es confidencial,
privado y de uso exclusivo de los destinatarios a los cuales está dirigido,
pudiendo contener información legalmente protegida. Queda prohibida la
revisión, divulgación, publicación, modificación, copia, distribución o acción
en relación con esta información, por personas o entidades distintas al
destinatario. Si usted, por alguna razón, lo ha recibido por error, por favor
tenga la amabilidad de eliminarlo de su sistema. Las opiniones contenidas, son
exclusivas de su autor, y no representa necesariament
Re: [Freesurfer] Interpretation of voxel values in TRACULA "path.pd" images
Hi Jon - The path.pd volumes are indeed the posterior probability distributions of each pathway. They are not normalized to a sum of 1 though b/c they're estimated by a sampling algorithm (drawing sample paths from this unknown distribution and adding up the sample paths, instead of estimating the distribution directly). Hope this helps, a.y On Fri, 9 Nov 2012, Jon Clayden wrote: > Dear all, > I understand that the various "path.pd" image files that are created by > TRACULA represent a posterior > distribution over the corresponding tract location, but I was wondering if > someone could explain to me > exactly what the values in these images mean. I assume that they are not > probabilities as such, since they > have values ranging up to several hundreds. > > Thanks in advance, > Jon > > ___ 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 -bedp post processing e-mail notification
Hi Joy-Loi, You can edit the bedpostx script (make sure you figure out which version of that script trac-all is calling). Find this line and delete the "@fmrib.ox.ac.uk" part: mailto=`whoami`@fmrib.ox.ac.uk Hope this helps, a.y On Tue, 20 Nov 2012, Loi wrote: > Hello FreeSurfer experts, > > I am wondering if it is possible to run trac-all -bedp without > generating the email notification at the end of the post-processing > stage? > After submitting a long list of -bedp jobs to the local cluster, I > received a message from our IT center reporting being spammed by the > Mail Delivery System with the following message: > > - - > > This message was created automatically by mail delivery software. > A message that you sent could not be delivered to one or more of its > recipients. This is a permanent error. The following address(es) failed: > 'myusername'@fmrib.ox.ac.uk > > - - > > I am assuming it is the -bedp e-mail notification that is bouncing. > > Thanks for the help > > > Joy-Loi > ___ > 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] Pixelated DTI mask from Tracula
Hi Alessia - I'm not sure what you're referring to as "the dti mask". Can you give me the file name of the image that you're displaying in the screehshot? It does look like noise. Thanks, a.y On Wed, 21 Nov 2012, Alessia Sarica wrote: Dear Freesurfer Users,I'm a Ph.D. Student and I'm working on tractography using Tracula, with the aim of conducting statistical analysis on the FA values. I have a cohort of 18 Amyotrophic Lateral Sclerosis Patients, and i'm doing all the process phases, starting from recon-all, ending to trac-all path. I've attached a text file with info about DTI DICOM extracted by ImageJ. Now, my problem is about the dti mask, as you can see on the attached image, a pixelated one is obtained, even if the left and right cst tracts seem good. This problem only occurs in few patients, not in all of them, even if the script is the same for all. This is the script i'm using: #Patient_name setenv SUBJECTS_DIR $TUTORIAL_DATA/Patient_recons set dtroot = $TUTORIAL_DATA/Patient_tracula set subjlist = (Patient_name) set runlist = (1) set dcmroot = $TUTORIAL_DATA/Patient_tracula set dcmlist = (Patient_name/orig/MR00) set bvalfile = $TUTORIAL_DATA/Patient_tracula/Patient_name/bfiles/Patient_name.bval set bvecfile = $TUTORIAL_DATA/Patient_tracula/Patient_name/bfiles/Patient_name.bvec set nb0 = 1 set dob0 = 0 set doeddy = 1 set dorotbvecs = 1 set usemaskanat = 0 set thrbet = 0.3 set doregflt = 1 set doregbbr = 0 set doregmni = 1 set mnitemp = $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz 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 nburnin = 200 set usetrunc = 1 set nkeep = 5 set nsample = 5000 I want to highlight that bval and bvec files are obtained from the tool dicom2nift, because Tracula is not able to extract them from DICOM header. I will really appreciate your help. Best regards, Alessia. -- Alessia Sarica Ph.D. Student Biomedical and Informatics Engineering, Bioinformatics Laboratory, Department of Surgical and Medical Sciences, University "Magna Græcia" of Catanzaro, Viale Europa (Località Germaneto), 88100 CATANZARO, ITALY. Phone: +3909613694193 ___ 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] Pixelated DTI mask from Tracula
Hi Alessia - So it's the FA map. Yes, this doesn't look like a correct FA map, there's no contrast between the white matter and everything else. The calculation of the FA has nothing to do with the freesurfer or tracula algorithms. It just uses your DWI data set, the gradient directions and the b-values, so these 3 things must be in disagreement if the FA doesn't come out right. I'd look into whether the subjects that have this problem were scanned with a different protocol or if the gradient directions and b-values were not extracted properly for them. Hope this helps, a.y On Wed, 21 Nov 2012, Alessia Sarica wrote: Hi Anastasia,thanks for your fast reply. I mean the file named dtifit_FA.nii I've re-run twice recon-all and tracula both, but it doesn't change the result. Best regards, Alessia. 2012/11/21 Anastasia Yendiki Hi Alessia - I'm not sure what you're referring to as "the dti mask". Can you give me the file name of the image that you're displaying in the screehshot? It does look like noise. Thanks, a.y On Wed, 21 Nov 2012, Alessia Sarica wrote: Dear Freesurfer Users,I'm a Ph.D. Student and I'm working on tractography using Tracula, with the aim of conducting statistical analysis on the FA values. I have a cohort of 18 Amyotrophic Lateral Sclerosis Patients, and i'm doing all the process phases, starting from recon-all, ending to trac-all path. I've attached a text file with info about DTI DICOM extracted by ImageJ. Now, my problem is about the dti mask, as you can see on the attached image, a pixelated one is obtained, even if the left and right cst tracts seem good. This problem only occurs in few patients, not in all of them, even if the script is the same for all. This is the script i'm using: #Patient_name setenv SUBJECTS_DIR $TUTORIAL_DATA/Patient_recons set dtroot = $TUTORIAL_DATA/Patient_tracula set subjlist = (Patient_name) set runlist = (1) set dcmroot = $TUTORIAL_DATA/Patient_tracula set dcmlist = (Patient_name/orig/MR00) set bvalfile = $TUTORIAL_DATA/Patient_tracula/Patient_name/bfiles/Patient_name.bval set bvecfile = $TUTORIAL_DATA/Patient_tracula/Patient_name/bfiles/Patient_name.bvec set nb0 = 1 set dob0 = 0 set doeddy = 1 set dorotbvecs = 1 set usemaskanat = 0 set thrbet = 0.3 set doregflt = 1 set doregbbr = 0 set doregmni = 1 set mnitemp = $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz 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 nburnin = 200 set usetrunc = 1 set nkeep = 5 set nsample = 5000 I want to highlight that bval and bvec files are obtained from the tool dicom2nift, because Tracula is not able to extract them from DICOM header. I will really appreciate your help. Best regards, Alessia. -- Alessia Sarica Ph.D. Student Biomedical and Informatics Engineering, Bioinformatics Laboratory, Department of Surgical and Medical Sciences, University "Magna Græcia" of Catanzaro, Viale Europa (Località Germaneto), 88100 CATANZARO, ITALY. Phone: +3909613694193 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. -- Alessia Sarica Ph.D. Student Biomedical and Informatics Engineering, Bioinformatics Laboratory, Department of Surgical and Medical Sciences, University "Magna Græcia" of Catanzaro, Viale Europa (Località Germaneto), 88100 CATANZARO, ITALY. Phone: +3909613694193 ___
Re: [Freesurfer] TRACULA tract path failure
Hi Arman - Have you ruled out any issues with the gradient directions? In situations where the problem is wide-spread, this seems to be the usual suspect. If you've checked the eigenvectors and they're ok, can you send an example case where the problem persists? You can use this page to upload a tar ball of all the tracula-related directories of the subject: https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Thanks! a.y On Mon, 26 Nov 2012, Arman Eshaghi wrote: Dear all, I have difficulty sorting out the problem with some tracts in several subjects, tracts are incomplete or missing. As it has come up quite a few times on the list, for this sort of problem I have first set "reinit=1" and then increased control points to 7, and re-ran trac-all with "-prior" flag. This has worked for some tracts in several subjects, however there are a few subjects that still have this problem. It would be great if someone could let me know what else I might be able to do in order to correct missing/faulty tracts in my subjects. (The problem is not limited to a specific tract, it varies in different subjects) All the best, -Arman ___ 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] SEEDING in Tracula
Hi Durai - Tracula is not for exploratory tractography, i.e., to answer questions like "what is this region connected to"? It uses prior anatomical information on known pathways to reconstruct those specific pathways. The anatomical information comes from the FreeSurfer anatomical segmentation of the same subject, and it's not just a seed region, but rather the probability of the pathway to go through each label in the anatomical segmentation at each point along the pathway's trajectory. Hope this helps, a.y On Sat, 29 Mar 2014, Durai Arasan wrote: Hi Freesurfer experts, So I have seen studies where tracula was used to examine one of the 18 major tracts. However can tracula perform seed based probabilistic tractography? i.e. can I seed ANY region and specify targets etc? I guess I am asking if it can do LOCAL tractography of any kind? 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] Freesurfer version after 5.3.0 from May 2013?
Hi Janosch - The December 9th tracula update is just that, an update to the tracula code without any changes to the rest of freesurfer. a.y On Tue, 1 Apr 2014, Janosch Linkersdörfer wrote: Hi all, I am a little confused about what the latest Freesurfer version is. I thought that v5.3.0 from May 15, 2013 would be the latest, but today I saw in the Tracula update list that there is apparently a version from December 9, 2013. Could you please clear that up for me? Thanks, Janosch ___ 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] SEEDING in Tracula
Hi Emily - I don't remember off the top of my head where this is mentioned, but it probably refers to the FA, MD, etc maps. An ROI-based analysis would be one where you average the FA in an ROI, so it doesn't refer to tractography. Hope this helps, a.y On Mon, 31 Mar 2014, ebell...@uwm.edu wrote: Hi Anastasia, Although the website says: In addition to the tract-based analysis that can be performed on the tract-based averages of anisotropy and diffusivity, the same maps could also be used for other voxel-based and ROI-based group analyses. So this makes me think that this type of group based ROI analysis is possible? Emily - Original Message - From: ebell...@uwm.edu To: "Freesurfer support list" Sent: Monday, March 31, 2014 10:53:08 PM Subject: Re: [Freesurfer] SEEDING in Tracula Hi Anastasia, On a related note, with tracula, you can't let's say track the amygdala to the vmpfc (there is a study already demostrating that there is a white matter tract that connects these two structures). Can I do something like that...take the amygdala as the seed and the vmpfc as the target? Based on your response I am guessing no? Thanks, Emily - Original Message - From: "Anastasia Yendiki" To: "Freesurfer support list" Sent: Monday, March 31, 2014 6:32:17 PM Subject: Re: [Freesurfer] SEEDING in Tracula Hi Durai - Tracula is not for exploratory tractography, i.e., to answer questions like "what is this region connected to"? It uses prior anatomical information on known pathways to reconstruct those specific pathways. The anatomical information comes from the FreeSurfer anatomical segmentation of the same subject, and it's not just a seed region, but rather the probability of the pathway to go through each label in the anatomical segmentation at each point along the pathway's trajectory. Hope this helps, a.y On Sat, 29 Mar 2014, Durai Arasan wrote: Hi Freesurfer experts, So I have seen studies where tracula was used to examine one of the 18 major tracts. However can tracula perform seed based probabilistic tractography? i.e. can I seed ANY region and specify targets etc? I guess I am asking if it can do LOCAL tractography of any kind? 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. ___ 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 longitudinal stream - length of Center variable
Hi Vincent - I suspect that this problem would be fixed by some recent changes that I've implemented for the longitudinal stream of tracula, and that I'm in the process of testing. As soon as we can get a new dev version built, I'll let you know so you can test it. Thank you for your patience! a.y On Fri, 4 Apr 2014, Vincent Brunsch wrote: > Dear TRACULA experts, > > I have used the longitudinal version and find that for some subjects' > tracts Len_Min is larger than Len_Center. How is this possible? (An > extreme example is Len_Min: 36, Len_Max: 75, Len_Center: 4.) > > Best, Vincent > > --- > This email is free from viruses and malware because avast! Antivirus > protection is active. > http://www.avast.com > > ___ > 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 libnetcdf
Hi Satra - We've been talking about a 5.3.1, yes. On my end, it would include the tracula updates that are currently available and possibly some more (I've been working on some improvements to longitudinal tracula). Not sure about libnetcdf but this is a good time to add things to the wish list :) a.y On Fri, 4 Apr 2014, Satrajit Ghosh wrote: hi folks, we are setting up freesurfer on a new cluster and trying to be as modular as possible in terms of dependencies. at present we are only installing 5.3.0 + tracula updates. will libnetcdf (required by tracula) be included in freesurfer? or is it considered a dependency? and talking of which, is there a patch (a 5.3.1) in the horizon which will include the tracula updates and perhaps netcdf in the freesurfer download. cheers, satra On Wed, Feb 5, 2014 at 11:07 PM, Satrajit Ghosh wrote: update: the lack of libnetcdf eventually makes it fail. i found a libnetcdf.so.7 on the cluster and soft linked it to libnetcdf.so.6 and added the path to LD_LIBRARY_PATH. that let trac-all -prep run to completion. cheers, satra On Wed, Feb 5, 2014 at 9:02 PM, Satrajit Ghosh wrote: hi a.y., when running trac-preproc i'm getting this error (for dmri_motion and dmri_group), but it continues running: /software/freesurfer/bin/dmri_motion: error while loading shared libraries: libnetcdf.so.6: cannot open shared object file: No such file or directory what will this fail to do? also is libnetcdf now a dependency for freesurfer? the reason i ask is that i'm running this on a remote cluster for which i don't have admin privileges. cheers, satra ___ 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 longitudinal stream - length of Center variable
Hi Vincent - Overall measures for the whole tract would not be affected by this type of error. a.y On Fri, 4 Apr 2014, Vincent Brunsch wrote: > Great, thank you! > > Do you maybe know if these changes will only affect the "center > variables"? I have almost completed my soon-due report about the > longitudinal analysis of "weighted average variables" (overall not > byvoxel along the MAP) and now I fear that results are maybe not correct > because after all the MAP is a part of all sampled paths. > > Best, Vincent > > Am 4/4/2014 11:49 AM, schrieb Anastasia Yendiki: >> Hi Vincent - I suspect that this problem would be fixed by some recent >> changes that I've implemented for the longitudinal stream of tracula, and >> that I'm in the process of testing. As soon as we can get a new dev >> version built, I'll let you know so you can test it. >> >> Thank you for your patience! >> >> a.y >> >> On Fri, 4 Apr 2014, Vincent Brunsch wrote: >> >>> Dear TRACULA experts, >>> >>> I have used the longitudinal version and find that for some subjects' >>> tracts Len_Min is larger than Len_Center. How is this possible? (An >>> extreme example is Len_Min: 36, Len_Max: 75, Len_Center: 4.) >>> >>> Best, Vincent >>> >>> --- >>> This email is free from viruses and malware because avast! Antivirus >>> protection is active. >>> http://www.avast.com >>> >>> ___ >>> 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 >> >> > > > --- > This email is free from viruses and malware because avast! Antivirus > protection is active. > http://www.avast.com > > ___ > 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] SNR on DTI data
Hi Yuko - As long as you define in your paper how you calculated SNR, you'll be fine reporting these values. a.y On Mon, 7 Apr 2014, Yuko Yotsumoto wrote: Hi Anastasia and freesurfers, I have more questions regarding SNR on DTI data. I masked the low-b images by the white matter label (aseg), then calculated the SNR ( mean / standard deviation within the label). The mean values ranged for 250-350 across subjects, and the sd ranged for 60-140 across subjects. As a result, I got the SNR ranged for 2.5-4.0 ish. When I compared these values with the ones reported in other studies, I realized that my values are much smaller. http://www.ncbi.nlm.nih.gov/pubmed/21591016 http://www.scirp.org/journal/PaperInformation.aspx?paperID=370#.U0JSS8dLFAI They reported SNR to be around 20-50. It looks like they used different calculations, so probably I should not make direct comparisons, but still the difference worries me. My questions are: (1) Do our values look valid to you? (2) Are there any article that reported SNR as mean low-b / sd in the white matter aseg mask? Thank you in advance! Yuko Yotsumoto Mar 18, 2014 1:26 PM、Anastasia Yendiki のメール： Signal-to-noise ratio = mean / standard deviation On Tue, 18 Mar 2014, Yuko Yotsumoto wrote: Anastasia, Thank you so much for your reply. So I should calculate the mean and s.d. of the values of the low-b within the white matter region for each subject, and compare those numbers between groups. Is it correct to say that the higher mean values indicate larger SNR? Yuko On Mar 18, 2014, at 12:53 AM, Anastasia Yendiki wrote: Hi Yuko - You can use the low-b images and compute the SNR of those images inside a mask of the white matter. Because dt_recon computes a registration from the diffusion to the structural data, you can use that registration to map the white matter label from the freesurfer segmentation (aseg) to the diffusion data. Then calculate the mean and standard deviation of the values of the low-b images inside that white matter mask. Hope this helps, a.y On Mon, 17 Mar 2014, Yuko Yotsumoto wrote: Hello Freesurfers, I have DTI data for two groups of subjects, and were asked SNR for each group. I did ROI analysis on FA values, therefore, I do not have the averaged DTI data. I am wondering if there is any way to compute SNR from dt_recon output. It doesn't have to be the ROI specific SNR values, I just need SNR for the whole DTI data for each group. Any suggestions will be appreciated! Yuko Yotsumoto --- - Yuko Yotsumoto, Ph. D. Associate Professor The University of Tokyo, Department of Life Sciences Bldg #2, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902 Japan phone : (+81)-3-5454-4332 E-mail: cy...@mail.ecc.u-tokyo.ac.jp ___ 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] Questions about byvoxel statistics from Tracula
Bonsoir Emilie - Tracula draws a large number of path samples, which in the end are added up to produce the path probability distribution. "FA" shows the values of FA at each point along the path sample with the greatest probability, i.e., along a single 1D curve. "FA_Avg" averages the FA from all the path samples at corresponding points along their trajectory. Because it is an average of many values rather than a single value, FA_Avg will tend to be less noisy and more reliable. Currently there is no way to average other values along the path, but you can trick the software into doing it. Find the "dmri_pathstats" command line corresponding to the tract that you want in trac-all.log. Rename "dmri/dtifit_FA.nii.gz" to something else temporarily, and rename the volume that you want to get values along the tract from as "dmri/dtifit_FA.nii.gz". Now when you run the same dmri_pathstats command, the pathstats.byvoxel.txt file will contain the values from the new volume in the FA/FA_Avg columns, instead of the values from the FA volume. The coordinates in the stats files are in the subject's native DWI space. Hope this helps, a.y PS: For combining the pathstats.byvoxel.txt files across subjects, get the latest tracula update, if you haven't: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula/#Updates On Wed, 9 Apr 2014, Emilie Poirion wrote: Hello I'm using Tracula to analyse our DWI-images. Freesurfer reconstructions of the corresponding T1-images have been perfomed before. Respectively, the version used are 1.53 and 5.3. The Tracula process works fine and I have extracted the statistics for all tracts. About this statistics, I wanted to know what is the difference between FA and FA_Avg ? An other question about the values extracted is about the coordinates in the file "byvoxel.txt". Are they correspind with the coordinates of the voxel in the dtifit image were the values were extracted? The last question, can we extracted the same by tract statistics from an other image like a PET registered to the DWI with your code? Thanks for your answer -- Emilie Poirion Master 1 Informatique Industrielle et Imagerie Industrielle Université Pierre et Marie Curie (Paris 6) ___ 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 lesions
Hi Florian - Tracula has certain expectations for what aparc+aseg labels each tract goes through or next to, and it'll skip areas that don't match those expectations. If the voxels in the lesions get labeled in the aparc+aseg, e.g. as white-matter hypointensities instead of white matter, you can switch those voxels to the white matter label, and then tracula will treat them like the rest of white matter. I should probably add an option for trac-all to be able to do that in the next version. For now, you can change those voxels in mri/aparc+aseg.mgz (first keep a copy of the original file under another name for all other intents and purposes!) and then rerun trac-all. You can skip the trac-all steps before -masks, that's the step where it grabs the aparc+aseg to use in subsequent steps. Hope this helps, a.y On Wed, 16 Apr 2014, Florian Borsodi wrote: > Dear Freesurfer TRACULA Experts, > > We are trying to run TRACULA on patients with lesions and found out, that > TRACULA had problems tracking streamlines trough the lesions, which is > understandable. The problem is, if TRACULA gets lost in the lesions, the > whole streamline is not considered, even if the streamline until the lesion > might be correct! > > Is there any possibility to hand TRACULA lesionmasks, so that the regions > with lesions are ignored? If not, is there a possibility to maintain the lost > streamlines, or at least parts of it? > > Thank you in advance for your help. > > With kind regards, > > Florian Borsodi, Lukas Pirpamer > Department of Neurology > Medical Universtiy of Graz > > > ___ 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] openmp/mkl support in tracula
Hi Satra - Sorry, no. a.y On Fri, 25 Apr 2014, Satrajit Ghosh wrote: > hi a.y., > is there any part of tracula that currently benefits from openmp or mkl > availability? > > cheers, > > satra > > ___ 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-Tracula Error
Hi Elia - This issue was fixed in the last update: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula/#Updates FYI, there will be another tracula update soon (after ISMRM) that will further improve the longitudinal stream specifically. a.y On Fri, 9 May 2014, Elia S. wrote: Dear Freesurfer Staff, I encountered the following error while running tracula - longitudinal: ERROR: flag ; unrecognized The exact command line i ran is the following one: trac-all -prep -c '/home/elia/scripts/Tracula/LCL/dcmTimePoints_tar-2/tracula.config' I will attach the complete error log as well as my dmrirc file (which I called in this case tracula.config). Best, Elia --- --- Freesurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Linux Distribution: Ubuntu 12.04 precise - Ubuntu 12.04.4 LTS Environment/Version: Linux king-ubuntu 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 09:20:45 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux My Current Working Directory: /home/elia ___ 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 preprocessing error, FreeSurfer 5.2.0
Hi Colm - The final version used is bvecs. The eddy current correction step registers each DWI to the first b=0 image, and the same transformation is applied to the corresponding gradient vector. This is a standard procedure when doing eddy current correction by registration. Hope this helps, a.y On Fri, 16 May 2014, McGinnity, Colm wrote: Hi Anastasia, Many thanks for your help. I did reply but don't see the email on the forum. I have began using FreeSurfer 5.3.0 instead, thanks. However, I'm a bit confused - I've created a 3-column bvecs format file (I had been using for version 5.2.0). After running several I've noticed the 'bvecs' file in the dmri folder is slightly different from the input file, whereas the 'bvecs.norot' file matches the input file extactly. For example: File 2: 0.9200842 0.3251221 0.2185593 File 2: 0.919 0.3311 0.2141 Can you please clarify which is used, and if these differences can be ignored? Thanks and best wishes, Colm. -----Original Message- From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] Sent: 11 March 2014 00:39 To: McGinnity, Colm Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] TRACULA preprocessing error, FreeSurfer 5.2.0 Hi Colm - Note that the information in the tutorial (particularly the part where gradient tables can be formatted in 3 rows or 3 columns) pertains to the latest tracula update: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates You're using an older version that only supports the 3-column format. I have no idea if this is what's causing the error without looking at your trac-all.log, but this would be a first guess. a.y On Mon, 10 Mar 2014, McGinnity, Colm wrote: Dear Experts, I am very new to TRACULA, I apologise for what is probably a silly question. I’ve got the following error on running trac-all –prep (FreeSurfer 5.2.0): awk: cmd. line:1: fatal: cannot open file `0' for reading (No such file or directory) mri_concat --i /home/k1193186/FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz --mean --o /home/k1193186/ FreeSurfer/TRACULA/ROLAND03A/dmri/lowb.nii.gz niiRead(): error opening file /home/k1193186/ FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz ninputs = 1 Checking inputs ERROR: reading /home/k1193186/FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz Can anyone tell me what this means and how to fix this, please? I’m guessing I’ve set up my configuration wrong or have the files in the wrong place? Many thanks! Best wishes, Colm. King's College London 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] Compatibility Tracula v.5.3 and recon v.5.2 longitudinal
Hi Yoonho - Tracula did not change at all between the 5.2 and 5.3 releases. It was recon-all that changed, and in fact 5.3 was released to correct a bug in 5.2, so it is not recommended to use 5.2 recon-all. For info about tracula versions, see: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates Hope this helps, a.y On Wed, 21 May 2014, Chung, Yoonho wrote: > Hi Anastasia, > > I have a large set of freesurfer recons (T1) already processed through > FS version 5.2 longitudinal stream while ago. However, I see now that > there is an advantage of using Tracula 5.3 longitudinal stream for DTI > longitudinal analysis. Do you know if I run the DWI data using 5.3 > TRACULA longitudinal stream - if it will work with recons that are > processed with 5.2? Thanks! > > Y > ___ > 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] Compatibility Tracula v.5.3 and recon v.5.2 longitudinal
Hi Yoon - If you are getting an error from longitudinal tracula, do check the tracula updates at the link that I gave you in my previous email. As for 5.2 recon-all, others can chime in here, but like I said it is not recommended to use it. Sorry about that. a.y On Thu, 22 May 2014, Yoonho Chung wrote: > Thanks for the quick response! > > If I already have all the T1 data processed using recon-all with FS v5.2, do > you think it is okay to switch the stream to FS v.5.3 and run Tracula? - > without having to do the recon-all again for the T1 data? It is because I am > also experiencing DTI longitudinal error due to the OS issue (according to > other threads). And if possible, I would like to avoid having to redo all the > recons if we have to switch it to v5.3. > > Thanks again! > Yoon ___ 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] Compatibility Tracula v.5.3 and recon v.5.2 longitudinal
Hi Yoon - No, in the current code the assumption is that the b-values are the same for all subjects in the study. One scenario where this wouldn't be the case is if different DWI volumes are removed for different subjects because of excessive motion, and we'll be able to handle this in the next version. a.y On Fri, 30 May 2014, Chung, Yoonho wrote: > Thanks for the tip. Another question. > > In the dmrirc file, can we also define multiple bval file? (like how in the > example-dmrirc long- you can set multiple bvecs.txt using 'set bveclist'? > In the example, option for specifying multiple bval files is not shown. > > Thank you > Yoon > > > > On May 22, 2014, at 5:37 PM, Anastasia Yendiki > wrote: > >> >> Hi Yoon - If you are getting an error from longitudinal tracula, do check >> the tracula updates at the link that I gave you in my previous email. >> >> As for 5.2 recon-all, others can chime in here, but like I said it is not >> recommended to use it. Sorry about that. >> >> a.y >> >> On Thu, 22 May 2014, Yoonho Chung wrote: >> >>> Thanks for the quick response! >>> >>> If I already have all the T1 data processed using recon-all with FS v5.2, >>> do you think it is okay to switch the stream to FS v.5.3 and run Tracula? - >>> without having to do the recon-all again for the T1 data? It is because I >>> am also experiencing DTI longitudinal error due to the OS issue (according >>> to other threads). And if possible, I would like to avoid having to redo >>> all the recons if we have to switch it to v5.3. >>> >>> Thanks again! >>> Yoon >> >> >> 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: ERROR in -qa Flag
Hi Shantanu - The -qa flag was added in the update to tracula that was
posted after the 5.3 release.
http://freesurfer.net/fswiki/Tracula/#Updates
Martinos Center users can simply switch to the dev version of freesurfer
to take advantage of these updates, in which case you don't need to
download anything.
a.y
On Mon, 2 Jun 2014, Shantanu Ghosh wrote:
> Dear Anastasia and Freesurfer experts,
>
> I am trying to set up an analysis of motion parameters using the flag -q
> from a set of DTI Dicoms located on the Martinos cluster, but I am facing
> problems -- it says "ERROR: flag -qa unrecognized". My .tcshrc is set to
> Freesurfer5.3 and FSL.
>
> What am I doing wrong?
>
> My config file is attached and here are my commands.
>
> cd /autofs/space/glia_001/users/shantanu/dtistudy/
> setenv PATH /usr/pubsw/packages/python/epd/bin:${PATH}
> setenv FSENV_KEEP_PROMPT
> setenv MNE_ROOT /usr/pubsw/packages/mne/stable
> setenv SUBJECTS_DIR /autofs/space/calvin_001/marvin/1/users/MRI/WMA/recons
> setenv FSL_DIR /usr/pubsw/packages/fsl/5.0.0
> source /usr/local/freesurfer/nmr-stable53-env
> source /usr/pubsw/packages/mne/stable/bin/mne_setup
>
> My console output-
> glia:shantanu[120] mynmr53
> freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> WARNING: /autofs/space/calvin_001/marvin/1/users/MRI/WMA/recons does not
> exist
> FREESURFER_HOME /usr/local/freesurfer/stable5_3_0
> FSFAST_HOME /usr/local/freesurfer/stable5_3_0/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR /autofs/space/calvin_001/marvin/1/users/MRI/WMA/recons
> MNI_DIR /usr/local/freesurfer/stable5_1_0/mni
> FSL_DIR /usr/pubsw/packages/fsl/5.0.0
>
> MNE software location set to:/usr/pubsw/packages/mne/stable
> MATLAB software not available
>
> /usr/pubsw/packages/mne/stable/bin already in PATH
> /usr/pubsw/packages/mne/stable/lib added to LD_LIBRARY_PATH
> /usr/pubsw/packages/mne/stable/share/app-defaults/%N added to
> XUSERFILESEARCHPATH
>
> Note: Remember to set SUBJECTS_DIR and SUBJECT environment variables
> correctly.
> Note: FreeSurfer environment is needed to access tkmedit from mne_analyze.
>
> glia:shantanu[121] trac-all -qa -s 008801 -c
> /autofs/space/glia_001/users/shantanu/dtistudy/dticonfigfile.txt
> ERROR: flag -qa unrecognized
> -qa -s 008801 -c
> /autofs/space/glia_001/users/shantanu/dtistudy/dticonfigfile.txt
> glia:shantanu[122]
>
>
> Thanks in advance for all help.
> Shantanu
>
>
>
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Re: [Freesurfer] trac-all -stat option
Hi Kathryn - The -stat option was added in the latest tracula update, see here: http://freesurfer.net/fswiki/Tracula/#Updates You need to download this update, after installing freesurfer 5.3, to be able to do what is described in the tutorials. a.y On Wed, 4 Jun 2014, Kathryn Cullen wrote: > Hello, I am trying to examine FA along the trajectory of the white matter > tract, as described in the wiki: > http://freesurfer.net/fswiki/FsTutorial/TraculaStatistics (half way down the > page). > > I am using the FreeSurfer version 3.0. > > The wiki says: > > The pathstats.byvoxel.txt files will generally not contain the same number > of positions (rows) for each subject because the tracts are reconstructed in > each subject's native diffusion space and not in a template space. Thus they > are not ready for performing group analyses yet. To combine these files from > multiple subjects, interpolating the anisotropy and diffusivity values at > corresponding positions along the tract for all subjects, run the following: > > trac-all -stat -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial > > However, when I try to use the -stat option, it says it is not recognized. > There is no -stat option described in the help, either. > > Am I using the wrong version, or do I need to upload something differently? > > Thanks very much, > > Katie > > -- > Kathryn R. Cullen, M.D. > Assistant Professor > University of Minnesota Medical School > Department of Psychiatry > Division of Child and Adolescent Psychiatry > F268 West Building > 2450 Riverside Avenue > Minneapolis, MN 55454 > (612) 273-9762 > > > ___ 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] possible to enable openmp with tracula cvsreg?
Hi Sal - There is no way to do this through trac-all, sorry. a.y On Fri, 6 Jun 2014, Salil Soman wrote: > Hi, > I noticed in the output for tracula -prep I am currently running using > cvsreg it mentions openmp=1, I was wondering if there is a way to enable > more than 1 core for openmp for tracula-prep? > > Thanks, > > -- > Salil Soman, MD, MS > Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory > Fellow - Palo Alto War Related Illness and Injury Study Center > WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System > > ___ 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 in -qa Flag
The right one to source is /usr/local/freesurfer/nmr-dev-env
On Fri, 13 Jun 2014, Shantanu Ghosh wrote:
> Hi Anastasia,
>
> Thanks for the reply.
>
> After I edit my .tcshrc file to source the dev, I still get an error message.
>
> glia:shantanu[64] mynmr53
>
> MNE software location set to:/usr/pubsw/packages/mne/stable
> MATLAB software not available
>
> /usr/pubsw/packages/mne/stable/bin added to PATH
> /usr/pubsw/packages/mne/stable/lib added to LD_LIBRARY_PATH
> /usr/pubsw/packages/mne/stable/share/app-defaults/%N added to
> XUSERFILESEARCHPATH
>
> Note: Remember to set SUBJECTS_DIR and SUBJECT environment variables
> correctly.
> Note: FreeSurfer environment is needed to access tkmedit from mne_analyze.
>
> glia:shantanu[65] fslview
> fslview: Command not found.
>
>
>
> Can you tell me if this is the right one to source?
> /autofs/cluster/freesurfer/centos6_x86_64/dev
>
> Or do I have to make further changes to my .tcshrc to access the dev version?
>
> Thanks in advance.
> Shantanu
>
>
> On Fri, June 13, 2014 12:02 pm, Anastasia Yendiki wrote:
>>
>> Hi Shantanu - The -qa flag was added in the update to tracula that was
> posted after the 5.3 release.
>> http://freesurfer.net/fswiki/Tracula/#Updates
>>
>> Martinos Center users can simply switch to the dev version of freesurfer
> to take advantage of these updates, in which case you don't need to
> download anything.
>>
>> a.y
>>
>> On Mon, 2 Jun 2014, Shantanu Ghosh wrote:
>>
>>> Dear Anastasia and Freesurfer experts,
>>> I am trying to set up an analysis of motion parameters using the flag
> -q
>>> from a set of DTI Dicoms located on the Martinos cluster, but I am facing
>>> problems -- it says "ERROR: flag -qa unrecognized". My .tcshrc is set
> to
>>> Freesurfer5.3 and FSL.
>>> What am I doing wrong?
>>> My config file is attached and here are my commands.
>>> cd /autofs/space/glia_001/users/shantanu/dtistudy/
>>> setenv PATH /usr/pubsw/packages/python/epd/bin:${PATH}
>>> setenv FSENV_KEEP_PROMPT
>>> setenv MNE_ROOT /usr/pubsw/packages/mne/stable
>>> setenv SUBJECTS_DIR
>>> /autofs/space/calvin_001/marvin/1/users/MRI/WMA/recons
>>> setenv FSL_DIR /usr/pubsw/packages/fsl/5.0.0
>>> source /usr/local/freesurfer/nmr-stable53-env
>>> source /usr/pubsw/packages/mne/stable/bin/mne_setup
>>> My console output-
>>> glia:shantanu[120] mynmr53
>>> freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514
>
>>> Setting up environment for FreeSurfer/FS-FAST (and FSL)
>>> WARNING: /autofs/space/calvin_001/marvin/1/users/MRI/WMA/recons does
> not
>>> exist
>>> FREESURFER_HOME /usr/local/freesurfer/stable5_3_0
>>> FSFAST_HOME /usr/local/freesurfer/stable5_3_0/fsfast
>>> FSF_OUTPUT_FORMAT nii.gz
>>> SUBJECTS_DIR
> /autofs/space/calvin_001/marvin/1/users/MRI/WMA/recons
>>> MNI_DIR /usr/local/freesurfer/stable5_1_0/mni
>>> FSL_DIR /usr/pubsw/packages/fsl/5.0.0
>>> MNE software location set to:/usr/pubsw/packages/mne/stable MATLAB
> software not available
>>> /usr/pubsw/packages/mne/stable/bin already in PATH
>>> /usr/pubsw/packages/mne/stable/lib added to LD_LIBRARY_PATH
>>> /usr/pubsw/packages/mne/stable/share/app-defaults/%N added to
>>> XUSERFILESEARCHPATH
>>> Note: Remember to set SUBJECTS_DIR and SUBJECT environment variables
> correctly.
>>> Note: FreeSurfer environment is needed to access tkmedit from
>>> mne_analyze.
>>> glia:shantanu[121] trac-all -qa -s 008801 -c
>>> /autofs/space/glia_001/users/shantanu/dtistudy/dticonfigfile.txt ERROR:
> flag -qa unrecognized
>>> -qa -s 008801 -c
>>> /autofs/space/glia_001/users/shantanu/dtistudy/dticonfigfile.txt
> glia:shantanu[122]
>>> Thanks in advance for all help.
>>> Shantanu
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>
>
>
___
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addressed. If you believe this e-mail was sent to you in error and the e-mail
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Re: [Freesurfer] Tracula preprocessing error ( set dob0 = 1 )
Hi Elia - It looks like this file didn't get created: /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz The command that was supposed to create it was epidewarp.fsl. You can find the command line that begins with "epidewarp.fsl" in the log file that you sent me. When you run that whole line directly from the unix command line, do you get any errors? a.y On Thu, 12 Jun 2014, Elia S. wrote: Dear Freesurfer community, Whenever i try to launch the tracula preprocessing, using "set dob0 = 1 " and the following command line: trac-all -prep -no-isrunning -c '/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/tracula.config It stops, giving me errors like these: niiRead(): error opening file /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz ERROR: reading /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_frame0.nii.gz While setting "dob0 = 0" everything runs smoothly. Can you help me please? I'll attach the log + dmrirc (tracula.config) Best, Elia. --- --- Freesurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Linux Distribution: Ubuntu 12.04 precise - Ubuntu 12.04.4 LTS Environment/Version: Linux king-ubuntu 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 09:20:45 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux ___ 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 preprocessing error ( set dob0 = 1 )
Hi Elia - This could very well be the case. Does the epidewarp.fsl command give you any specific error message, or does it just not create an output? a.y On Tue, 17 Jun 2014, Elia S. wrote: Hi Anastasia, Yes, launching the same command line from terminal produced the same error, but at the same time we realized we were using the wrong magnetic/phase dicoms.which weren't magnetic/phase images at all. Could that be the cause of the failure? I would answer the question myself but right now I don't have the correct images to test it. Best, Elia. Date: Sun, 15 Jun 2014 07:21:28 -0400 From: ayend...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula preprocessing error ( set dob0 = 1 ) Hi Elia - It looks like this file didn't get created: /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz The command that was supposed to create it was epidewarp.fsl. You can find the command line that begins with "epidewarp.fsl" in the log file that you sent me. When you run that whole line directly from the unix command line, do you get any errors? a.y On Thu, 12 Jun 2014, Elia S. wrote: > Dear Freesurfer community, > Whenever i try to launch the tracula preprocessing, using "set dob0 = 1 " and the follow ing command > line: > > trac-all -prep -no-isrunning -c '/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/trac ula.config > > It stops, giving me errors like these: > > niiRead(): error opening file > /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz > > ERROR: reading > /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_frame0.nii.g z > > While setting "dob0 = 0" everything runs smoothly. > > Can you help me please? I'll attach the log + dmrirc (tracula.config) > > Best, > Elia. > > - -- > --- > > Freesurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 > > Linux Distribution: Ubuntu 12.04 precise - Ubuntu 12.04.4 LTS > > Environment/Version: Linux king-ubuntu 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 09:20:4 5 UTC 2013 > x86_64 x86_64 x86_64 GNU/Linux > > ___ 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] Tracula preprocessing error ( set dob0 = 1 )
Check the email archives for a recent message about epidewarp.fsl from Doug, there is a newer version that works with FSL 5. On Tue, 17 Jun 2014, Elia S. wrote: Hi Anastasia, The epidewarp.fsl gives me the following output: FSLVersion 5.0.6 FSLVerMaj 5 FSL Version is 5.0.6, must be 3.X or 4.X Either from script or command line. Best, Elia. Date: Tue, 17 Jun 2014 09:17:58 -0400 From: ayend...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula preprocessing error ( set dob0 = 1 ) Hi Elia - This could very well be the case. Does the epidewarp.fsl command give you any specific error message, or does it just not create an output? a.y On Tue, 17 Jun 2014, Elia S. wrote: > Hi Anastasia, > Yes, launching the same command line from terminal produced the same error, but at the sa me > time we realized we were using the wrong magnetic/phase dicoms.which weren't > magnetic/phase images at all. > Could that be the cause of the failure? I would answer the question myself but right now I > don't have the correct images to test it. > > Best, > Elia. > > > Date: Sun, 15 Jun 2014 07:21:28 -0400 > From: ayend...@nmr.mgh.harvard.edu > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Tracula preprocessing error ( set dob0 = 1 ) > > > Hi Elia - It looks like this file didn't get created: > /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz > > The command that was supposed to create it was epidewarp.fsl. You can find > the command line that begins with "epidewarp.fsl" in the log file that you > sent me. When you run that whole line directly from the unix command line, > do you get any errors? > > a.y > > On Thu, 12 Jun 2014, Elia S. wrote: > > > Dear Freesurfer community, > > Whenever i try to launch the tracula preprocessing, using "set dob0 = 1 " and the foll ow > ing command > > line: > > > > trac-all -prep -no-isrunning -c '/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/tr ac > ula.config > > > > It stops, giving me errors like these: > > > > niiRead(): error opening file > > /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz > > > > ERROR: reading > > /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_frame0.nii .g > z > > > > While setting "dob0 = 0" everything runs smoothly. > > > > Can you help me please? I'll attach the log + dmrirc (tracula.config) > > > > Best, > > Elia. > > > > --- -- > -- > > --- > > > > Freesurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 > > > > Linux Distribution: Ubuntu 12.04 precise - Ubuntu 12.04.4 LTS > > > > Environment/Version: Linux king-ubuntu 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 09:20 :4 > 5 UTC 2013 > > x86_64 x86_64 x86_64 GNU/Linux > > > > > > ___ Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurf er > The information in this e-mail is intended only for the person to whom it is addressed. I f > 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. ___ 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 (segmentation fault?)
Hi Durai - You cannot run all 3 steps of trac-all at the same time. The 3 steps need to be run separately. Please check the tutorial on the wiki for more details. a.y On Tue, 24 Jun 2014, Durai Arasan wrote: Hi Freesurfer experts, I tried running trac-all with my config file and received the following error : Segmentation fault Linux 129-x-xx-xxx 3.4.33-2.24-desktop #1 SMP PREEMPT Tue Feb 26 03:34:33 UTC 2013 (5f00a32) x86_64 x86_64 x86_64 GNU/Linux trac-paths exited with ERRORS at Tue Jun 24 11:15:12 EDT 2014 Any help would be greatly appreciated! I am attaching the config file, log and error files. Thank you! Durai ___ 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: fMRIframe: frame >= nframes
Hi Jun - It's failing at the point where it tries to extract the low-b images from the DWI series. I suspect that the number of frames in the 4D DWI volume that is extracted from your dicom does not match the number of frames that it expects to find based on how many gradient vectors or b-values it's looking for. So I'd check these DWI, gradient vector and b-value files to make sure they are all consistent. Hope this helps, a.y On Mon, 30 Jun 2014, Jun Shinozaki wrote: > Dear All, > > I am trying to run a single subject in TRACULA (trac-all -prep -c > dmrirc), but exited with ERRORS. > > ERROR: fMRIframe: frame >= nframes > > The attached file is a log file. > > Can anyone help me? > Thank you in advance. > > Regards, > Jun Shinozaki. > ___ 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: fMRIframe: frame >= nframes
Hi Jun - By a simple word count on these files: % wc -w bvals bvecs 65 bvals 198 bvecs 263 total As you can see, there are 3 extra entries in the bvecs file. If you then open the file, you'll see that there is an extra column of zeros in the end. Not sure if that's what's causing the problem, but you might want to look for empty lines at the end of your original gradient table. a.y On Tue, 1 Jul 2014, Jun Shinozaki wrote: > Hi Anastasia, > Thank you for your e-mail. > I took 65 DWIs (5 b0 volumes and 60 direction DWIs). > > I checked dwi.nii.gz in the dmri folder, and dwi.nii.gz had 65 images. > Also, I checked bvals and bvecs in the dmri folder, and they have 65 counts. > It seems consistent. > I attach bvals and bvecs. These files were created by freesurfer > automatically. > > Regards, > Jun Shinozaki > > 2014-06-30 18:38 GMT+09:00 Anastasia Yendiki : >> >> Hi Jun - It's failing at the point where it tries to extract the low-b >> images from the DWI series. I suspect that the number of frames in the 4D >> DWI volume that is extracted from your dicom does not match the number of >> frames that it expects to find based on how many gradient vectors or >> b-values it's looking for. So I'd check these DWI, gradient vector and >> b-value files to make sure they are all consistent. >> >> Hope this helps, >> a.y >> >> On Mon, 30 Jun 2014, Jun Shinozaki wrote: >> >>> Dear All, >>> >>> I am trying to run a single subject in TRACULA (trac-all -prep -c >>> dmrirc), but exited with ERRORS. >>> >>> ERROR: fMRIframe: frame >= nframes >>> >>> The attached file is a log file. >>> >>> Can anyone help me? >>> Thank you in advance. >>> >>> Regards, >>> Jun Shinozaki. >>> >> ___ >> 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 ERROR: fMRIframe: frame >= nframes
There are probably some empty spaces at the end of the lines of the original files that confuses it into introducing those zeros. If you attach the original files, I can take a look at them. On Wed, 2 Jul 2014, Jun Shinozaki wrote: > Hi Anastasia, > > I created bvals.txt and bvecs.txt using dcm2nii. > These original files were text files and set in dmrirc profile as > "set bvalfile = /path/to/bvals.txt". > > I checked word count for these files > # wc -w bvals.txt bvecs.txt > 65 bvals.txt > 195 bvecs.txt > 260 total > > However, when I run "trac-all -prep -c dmrirc", then freesurfer creates > bvals and bvecs automatically in dmri folder. > > Then, I check word count > # wc -w bvals bvecs > 65 bvals > 198 bvecs > 263 total > > Now, freesurfer adds 3 extra entries in the bvecs file. > As you said, there is an extra column of zeros in the end. > > So, I cannot fix the error. > > Regards, > Jun Shinozaki > > 2014-07-01 15:56 GMT+09:00 Anastasia Yendiki : >> >> Hi Jun - By a simple word count on these files: >> >> % wc -w bvals bvecs >>65 bvals >> 198 bvecs >> 263 total >> >> As you can see, there are 3 extra entries in the bvecs file. If you then >> open the file, you'll see that there is an extra column of zeros in the >> end. Not sure if that's what's causing the problem, but you might want to >> look for empty lines at the end of your original gradient table. >> >> a.y >> >> On Tue, 1 Jul 2014, Jun Shinozaki wrote: >> >>> Hi Anastasia, >>> Thank you for your e-mail. >>> I took 65 DWIs (5 b0 volumes and 60 direction DWIs). >>> >>> I checked dwi.nii.gz in the dmri folder, and dwi.nii.gz had 65 images. >>> Also, I checked bvals and bvecs in the dmri folder, and they have 65 counts. >>> It seems consistent. >>> I attach bvals and bvecs. These files were created by freesurfer >>> automatically. >>> >>> Regards, >>> Jun Shinozaki >>> >>> 2014-06-30 18:38 GMT+09:00 Anastasia Yendiki : >>>> >>>> Hi Jun - It's failing at the point where it tries to extract the low-b >>>> images from the DWI series. I suspect that the number of frames in the 4D >>>> DWI volume that is extracted from your dicom does not match the number of >>>> frames that it expects to find based on how many gradient vectors or >>>> b-values it's looking for. So I'd check these DWI, gradient vector and >>>> b-value files to make sure they are all consistent. >>>> >>>> Hope this helps, >>>> a.y >>>> >>>> On Mon, 30 Jun 2014, Jun Shinozaki wrote: >>>> >>>>> Dear All, >>>>> >>>>> I am trying to run a single subject in TRACULA (trac-all -prep -c >>>>> dmrirc), but exited with ERRORS. >>>>> >>>>> ERROR: fMRIframe: frame >= nframes >>>>> >>>>> The attached file is a log file. >>>>> >>>>> Can anyone help me? >>>>> Thank you in advance. >>>>> >>>>> Regards, >>>>> Jun Shinozaki. >>>>> >>>> ___ >>>> 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 > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] DTI FA Values in Diffusion Space vs. Standard Space
Hi Emily - Depends on what you're doing. If you're doing an ROI-based or tractography-based analysis, where you extract average FA in a part of white matter, there is no need to warp. If you're doing a voxel-based analysis, obviously all the subjects need to be in a common space to compare their FA values voxel-by-voxel. a.y On Tue, 1 Jul 2014, ebell...@uwm.edu wrote: > Hello, > > I was wondering if it is better to keep the FA results from a DTI > analysis in diffusion space for group analysis or if you should warp > them into standard space as you would typically do with functional MRI > data. > > Emily > ___ > 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: fMRIframe: frame >= nframes
Hi Pedro - Have you specified not to do eddy current compensation? It looks like it's being skipped. In that case, you need to also skip the QA step (by adding -noqa to your trac-all command line). That's because the QA step requires the output of the eddy current compensation to assess how much motion there is in the data. Hope this helps, a.y On Thu, 3 Jul 2014, Pedro Rosa wrote: > Anastasia, > I was finding the same error as Jun, and your help fixed it. Thank you very > much. > However, I am now finding a new error (attached). > Can you help me? > Thank you again. > Regards, > Pedro Rosa. > > On Wednesday, July 2, 2014 at 10:49 PM, Jun Shinozaki wrote: > > Hi Anastasia, > > You are right! There are empty spaces at the end of the lines in > original bvecs and bvals. > I could fix the error and finish trac-preproc without error by > eliminating these spaces. > Thank you so much! > > Regards, > Jun Shinozaki > > 2014-07-02 15:21 GMT+09:00 Anastasia Yendiki : > > There are probably some empty spaces at the end of the lines of the > original files that confuses it into introducing those zeros. If you > attach the original files, I can take a look at them. > > On Wed, 2 Jul 2014, Jun Shinozaki wrote: > > Hi Anastasia, > > I created bvals.txt and bvecs.txt using dcm2nii. > These original files were text files and set in dmrirc profile as > "set bvalfile = /path/to/bvals.txt". > > I checked word count for these files > # wc -w bvals.txt bvecs.txt > 65 bvals.txt > 195 bvecs.txt > 260 total > > However, when I run "trac-all -prep -c dmrirc", then freesurfer creates > bvals and bvecs automatically in dmri folder. > > Then, I check word count > # wc -w bvals bvecs > 65 bvals > 198 bvecs > 263 total > > Now, freesurfer adds 3 extra entries in the bvecs file. > As you said, there is an extra column of zeros in the end. > > So, I cannot fix the error. > > Regards, > Jun Shinozaki > > 2014-07-01 15:56 GMT+09:00 Anastasia Yendiki > : > > Hi Jun - By a simple word count on these files: > > % wc -w bvals bvecs > 65 bvals > 198 bvecs > 263 total > > As you can see, there are 3 extra entries in the bvecs file. If you > then > open the file, you'll see that there is an extra column of zeros in > the > end. Not sure if that's what's causing the problem, but you might > want to > look for empty lines at the end of your original gradient table. > > a.y > > On Tue, 1 Jul 2014, Jun Shinozaki wrote: > > Hi Anastasia, > Thank you for your e-mail. > I took 65 DWIs (5 b0 volumes and 60 direction DWIs). > > I checked dwi.nii.gz in the dmri folder, and dwi.nii.gz had > 65 images. > Also, I checked bvals and bvecs in the dmri folder, and they > have 65 counts. > It seems consistent. > I attach bvals and bvecs. These files were created by > freesurfer automatically. > > Regards, > Jun Shinozaki > > 2014-06-30 18:38 GMT+09:00 Anastasia Yendiki > : > > Hi Jun - It's failing at the point where it tries to > extract the low-b > images from the DWI series. I suspect that the number > of frames in the 4D > DWI volume that is extracted from your dicom does not > match the number of > frames that it expects to find based on how many > gradient vectors or > b-values it's looking for. So I'd check these DWI, > gradient vector and > b-value files to make sure they are all consistent. > > Hope this helps, > a.y > > On Mon, 30 Jun 2014, Jun Shinozaki wrote: > > Dear All, > > I am trying to run a single subject in TRACULA > (trac-all -prep -c > dmrirc), but exited with ERRORS. > > ERROR: fMRIframe: frame >= nframes > > The attached file is a log file. > > Can anyone help me? > Thank you in advance. > > Regards, > Jun Shinozaki. > > ___ > 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
Re: [Freesurfer] Tracula ERROR: fMRIframe: frame >= nframes
The error message is "data and bvals/bvecs do not contain the same number of entries". This doesn't necessarily mean that the bvecs and bvals don't agree with each other, but that the bvecs and bvals don't agree with the DWI data. Based on this line in the log file, there are 130 frames in the DWI dicoms, so I suspect that you may have two repetitions of your 65 directions: INFO: (120 120 50), nframes = 130, ismosaic=0 You can confirm this my looking at the images. If that is the case, you need to have two repetitions in the bvecs/bvals files too. On Thu, 3 Jul 2014, Pedro Rosa wrote: Hi! Thanks! It helped, but now I have another error… I attached the log, and both the bvec and bval files that served as inputs (without any empty space in the end) and the ones generated by the script in the $subject/dmri (which turns out to have empty spaces in the end). All these 4 files have 65 entries (bval with 65 for each one of the three sequences). Can you spot the error? Regards Pedro Rosa On Thursday, July 3, 2014 at 3:05 AM, Anastasia Yendiki wrote: Hi Pedro - Have you specified not to do eddy current compensation? It looks like it's being skipped. In that case, you need to also skip the QA step (by adding -noqa to your trac-all command line). That's because the QA step requires the output of the eddy current compensation to assess how much motion there is in the data. Hope this helps, a.y On Thu, 3 Jul 2014, Pedro Rosa wrote: Anastasia, I was finding the same error as Jun, and your help fixed it. Thank you very much. However, I am now finding a new error (attached). Can you help me? Thank you again. Regards, Pedro Rosa. On Wednesday, July 2, 2014 at 10:49 PM, Jun Shinozaki wrote: Hi Anastasia, You are right! There are empty spaces at the end of the lines in original bvecs and bvals. I could fix the error and finish trac-preproc without error by eliminating these spaces. Thank you so much! Regards, Jun Shinozaki 2014-07-02 15:21 GMT+09:00 Anastasia Yendiki : There are probably some empty spaces at the end of the lines of the original files that confuses it into introducing those zeros. If you attach the original files, I can take a look at them. On Wed, 2 Jul 2014, Jun Shinozaki wrote: Hi Anastasia, I created bvals.txt and bvecs.txt using dcm2nii. These original files were text files and set in dmrirc profile as "set bvalfile = /path/to/bvals.txt". I checked word count for these files # wc -w bvals.txt bvecs.txt 65 bvals.txt 195 bvecs.txt 260 total However, when I run "trac-all -prep -c dmrirc", then freesurfer creates bvals and bvecs automatically in dmri folder. Then, I check word count # wc -w bvals bvecs 65 bvals 198 bvecs 263 total Now, freesurfer adds 3 extra entries in the bvecs file. As you said, there is an extra column of zeros in the end. So, I cannot fix the error. Regards, Jun Shinozaki 2014-07-01 15:56 GMT+09:00 Anastasia Yendiki : Hi Jun - By a simple word count on these files: % wc -w bvals bvecs 65 bvals 198 bvecs 263 total As you can see, there are 3 extra entries in the bvecs file. If you then open the file, you'll see that there is an extra column of zeros in the end. Not sure if that's what's causing the problem, but you might want to look for empty lines at the end of your original gradient table. a.y On Tue, 1 Jul 2014, Jun Shinozaki wrote: Hi Anastasia, Thank you for your e-mail. I took 65 DWIs (5 b0 volumes and 60 direction DWIs). I checked dwi.nii.gz in the dmri folder, and dwi.nii.gz had 65 images. Also, I checked bvals and bvecs in the dmri folder, and they have 65 counts. It seems consistent. I attach bvals and bvecs. These files were created by freesurfer automatically. Regards, Jun Shinozaki 2014-06-30 18:38 GMT+09:00 Anastasia Yendiki : Hi Jun - It's failing at the point where it tries to extract the low-b images from the DWI series. I suspect that the number of frames in the 4D DWI volume that is extracted from your dicom does not match the number of frames that it expects to find based on how many gradient vectors or b-values it's looking for. So I'd check these DWI, gradient vector and b-value files to make sure they are all consistent. Hope this helps, a.y On Mon, 30 Jun 2014, Jun Shinozaki wrote: Dear All, I am trying to run a single subject in TRACULA (trac-all -prep -c dmrirc), but exited with ERRORS. ERROR: fMRIframe: frame >= nframes The attached file is a log file. Can anyone help me? Thank you in advance. Regards, Jun Shinozaki. ___ 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 HelpLin
Re: [Freesurfer] Tracula ERROR: fMRIframe: frame >= nframes
ERROR: Found 130 b-values but 108.333 gradient vectors If the b-value table has 130 entries, then the gradient table should have 130*3 entries (one x,y,z direction vector for each b-value). This error means that there are fewer entries in the gradient table than there should be. Run wc -w on these text files to check for yourself. On Fri, 4 Jul 2014, Pedro Rosa wrote: Thank you once again! Yes, that is true. The bval and bvec file were doubled, so I removed half the values (and also the empty spaces) and the fMRIframe: frame >= nframes stopped from happening. A converted the dcm to nii using dcm2nii software, and used its bval and bvec files as input to TRACULA. Is it frequent to have a repetition of directions? I now included the doubled bvec and bval files, but it seems I have another error: [server:/MRI/Tracula-test] pedrogomesrosa% trac-all -prep -c config -no-isrunning INFO: SUBJECTS_DIR is /MRI/Tracula-test INFO: Diffusion root is /MRI/Tracula-test Actual FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer INFO: current FREESURFER_HOME does not match that of previous processing. Current: /Applications/Freesurfer5.3/freesurfer Previous: /Volumes/Data/Freesurfer_5.3/freesurfer trac-preproc -c /MRI/Tracula-test/ESNA149/scripts/dmrirc.local -log /MRI/Tracula-test/ESNA149/scripts/trac-all.log -cmd /MRI/Tracula-test/ESNA149/scripts/trac-all.cmd -no-isrunning #- /Applications/Freesurfer5.3/freesurfer/bin/trac-preproc #- #@# Image corrections Fri Jul 4 07:00:19 BRT 2014 mri_convert/MRI/Tracula-test/149/1.3.12.2.1107.5.2.31.30747.2012061308004376537404155. dcm /MRI/Tracula-test/ESNA149/dmri/dwi_orig.nii.gz mri_convert/MRI/Tracula-test/149/1.3.12.2.1107.5.2.31.30747.2012061308004376537404155. dcm /MRI/Tracula-test/ESNA149/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from/MRI/Tracula-test/149/1.3.12.2.1107.5.2.31.30747.2012061308004376537404155. dcm... Getting Series No INFO: Found 6607 files in /MRI/Tracula-test/149 INFO: Scanning for Series Number 3 Scanning Directory INFO: found 6500 files in series INFO: loading series header info. RunNo = 2 INFO: sorting. INFO: (120 120 50), nframes = 130, ismosaic=0 PE Dir COL COL AutoAlign matrix detected AutoAlign Matrix - 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FileName/MRI/Tracula-test/149/1.3.12.2.1107.5.2.31.30747.2012061308004780512604280. dcm Identification NumarisVer syngo MR B15 ScannerModel Espree PatientName XX Date and time StudyDate 20120613 StudyTime 074845.171000 SeriesTime 080047.531000 AcqTime 080046.267500 Acquisition parameters PulseSeq *ep_b0 Protocol DIF 64 2NEX 2.7mmX2mm Trigger (Ax Puro) PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 110 InversionTime -1 RepetitionTime 8000 PhEncFOV 240 ReadoutFOV 240 Image information RunNo 2 SeriesNo 3 ImageNo 1 NImageRows 120 NImageCols 120 NFrames 130 SliceArraylSize 50 IsMosaic 0 ImgPos 116.6747 79.4248 -34.6722 VolRes 2. 2. 2.7000 VolDim 120 120 50 Vc -1. -0. 0. Vr -0. -1. -0.0052 Vs -0. -0.0052 1. VolCenter -3.3253 -40.9270 32.1985 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) INFO: no Siemens slice order reversal detected (good!). TR=8000.00, TE=110.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.86, -0.00523596) k_ras = (-0, -0.00523596, 0.86) writing to /MRI/Tracula-test/ESNA149/dmri/dwi_orig.nii.gz... mri_probedicom --i/MRI/Tracula-test/149/1.3.12.2.1107.5.2.31.30747.2012061308004376537404155. dcm > /MRI/Tracula-test/ESNA149/dmri/dcminfo.dat cp /MRI/Tracula-test//bvec.bvec /MRI/Tracula-test/ESNA149/dmri/dwi_orig.mghdti.bvecs cp /MRI/Tracula-test//bval2.bval /MRI/Tracula-test/ESNA149/dmri/dwi_orig.mghdti.bvals ERROR: Found 130 b-values but 108.333 gradient vectors Darwin server.macbookpro.com 13.2.0 Darwin Kernel Version 13.2.0: Thu Apr 17 23:03:13 PDT 2014; root:xnu-2422.100.13~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Fri Jul 4 07:04:02 BRT 2014 Pedro Rosa On Friday, July 4, 2014 at 5:18 AM, Anastasia Yendiki wrote: The error message is "data and bvals/bvecs do not contain the same number of entries". This doesn't necessarily mean that the bvecs and bvals don't agree with each other, but that the bvecs and bvals don't agree with the DWI data. Based on this line in the log file, there are 130 frames
Re: [Freesurfer] Tracula
Hi Emily, 1. That's fine because the BET-based mask is not used by default in the the tractography. The brain mask from the freesurfer segmentation of the structural scan is used instead. 2. To check the diffusion-to-anatomical registration, you can look at the aparc+aseg registered into diffusion space, i.e., from the dlabel/diff directory, overlaid onto the FA map. It's also important to check that the gradient table is correct by looking at dtifit_V1 (the primary eigenvector of the tensors) displayed as lines. Assuming the protocol is the same for all subjects, you just need to do this latter check for one of your subjects only. 3. TRACULA doesn't do whole-brain tractography. It reconstructs a set of specific tracts. Information on the anatomical regions that these tracts go through or next to is derived from a set of training subjects. See our paper for more info: http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2011.00023/abstract Hope this helps, a.y On Thu, 10 Jul 2014, ebell...@uwm.edu wrote: > Hello, > > I have a few questions about Tracula. I am very new to DTI, so I hope you can > bare with me. > > 1.) I have been checking my registration at the prep stage. I am very new to > this so it may be that I am not looking at the right files. > > I looked at my eddy current corrected diffusion data (which I believe is in > data.nii.gz in the dmri folder) with the no_dif_brain_mask.nii, and noticed > that the no_dif_brain_mask does not cover very well for some of my subjects. > Should I individually tailor the Fractional Intensity Threshold for BET mask > extraction from low-b images at the prep stage? > > > 2.) In general what files should I be checking at each phase (prep, bedpost, > path)? > > 3.)How do you generate the whole-brain ROIS to guide the tractography (is the > white matter mask that is generated at the prep phase involved)? > > Thanks, > > Emily > ___ > 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
Hi Emily - When a mask is used as input to bedpostx, all voxels outside that mask will be zero in all bedpostx output volumes. So it makes sense to use the same mask for any subsequent processing. Is the mask that you're referring to a symbolic link to another volume? You can run ls -l to see what volume it points to. a.y On Mon, 14 Jul 2014, ebell...@uwm.edu wrote: > Hi Anastasia, > > Thank you so much, this is really helpful. > > I have one other question. So, at the bedpost stage, the no_dif_brain mask is > used correct (looking at the fsl webpage), or at this stage the freesurfer > segmentation is used as well? > > If in addition to using tracula, lets say if I also wanted to look into doing > local probablistic tractography in FSL (using probtractx). I know that > probtractx uses the output from the fsl bedpost stage. In this case then, > would I need to adjust the no_dif_brain mask since it was used in the bedpost > stage? I planned on using the output from the bedpost stage in tracula into > FSL's probtractx to also try some local probablistic tractography. > > Emily > > - Original Message - > From: "Anastasia Yendiki" > To: "Freesurfer support list" > Sent: Monday, July 14, 2014 4:14:49 AM > Subject: Re: [Freesurfer] Tracula > > > Hi Emily, > > 1. That's fine because the BET-based mask is not used by default in the > the tractography. The brain mask from the freesurfer segmentation of the > structural scan is used instead. > > 2. To check the diffusion-to-anatomical registration, you can look at the > aparc+aseg registered into diffusion space, i.e., from the dlabel/diff > directory, overlaid onto the FA map. It's also important to check that the > gradient table is correct by looking at dtifit_V1 (the primary eigenvector > of the tensors) displayed as lines. Assuming the protocol is the same for > all subjects, you just need to do this latter check for one of your > subjects only. > > 3. TRACULA doesn't do whole-brain tractography. It reconstructs a set of > specific tracts. Information on the anatomical regions that these tracts > go through or next to is derived from a set of training subjects. See our > paper for more info: > > http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2011.00023/abstract > > Hope this helps, > a.y > > On Thu, 10 Jul 2014, ebell...@uwm.edu wrote: > >> Hello, >> >> I have a few questions about Tracula. I am very new to DTI, so I hope you >> can bare with me. >> >> 1.) I have been checking my registration at the prep stage. I am very new to >> this so it may be that I am not looking at the right files. >> >> I looked at my eddy current corrected diffusion data (which I believe is in >> data.nii.gz in the dmri folder) with the no_dif_brain_mask.nii, and noticed >> that the no_dif_brain_mask does not cover very well for some of my subjects. >> Should I individually tailor the Fractional Intensity Threshold for BET mask >> extraction from low-b images at the prep stage? >> >> >> 2.) In general what files should I be checking at each phase (prep, bedpost, >> path)? >> >> 3.)How do you generate the whole-brain ROIS to guide the tractography (is >> the white matter mask that is generated at the prep phase involved)? >> >> Thanks, >> >> Emily >> ___ >> 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] trac-all -prep error field map error
Hi Eileen - That step is run with the program epidewarp.fsl, which you can run on the command line to see the available options. The input phase map volume is expected to have either 2 frames (2 separate phase maps) or 1 frame (the difference phase map). This error from trac-all means that it found that your input phase map has something other than 1 or 2 frames, so it doesn't know how to handle it. Hope this helps, a.y On Sat, 12 Jul 2014, Eileen Moore wrote: Hi - I'm using freesurfer 5.3 on an Ubuntu operating system. I'm tyring to run tracula on some images acquired from a GE scanner. I am running into problems when I try to perform the registration-based B0-inhomogeneity compensation, getting an error in the terminal output: "ERROR: Unrecognized format of phase map". However, trac-all -prep runs fine when I skip the B0-inhomogeneity compensation step. Is there something else I need to do to use field map correction? I've attached the trac-all.log and a copy of the terminal output. Thanks, Eileen. ___ 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 Emily - Sorry for the confusion. The mask in the bedpostx output directory is a copy of whichever mask was input to bedpostx. By default, tracula uses the anatomical mask for this. If that mask doesn't cover the brain well, I would check for diffusion-to-anatomical miregistration. Probtrackx will use whichever mask you specify as its input. a.y On Mon, 14 Jul 2014, ebell...@uwm.edu wrote: > Hi Anastasia, > > So probtractx uses the output from the bedpost stage (which I ran in > Tracula). I noticed that the bedpost stage (in the dmri.bedpostx folder) also > outputs a no_dif_brain mask. I guess what I am worried about is that if > bedpost creates this no_dif_brain mask, that is what will be utilized in > probtractx instead of the Freesurfer brain mask. > > When bedpost is conducted in Tracula, is the brain mask from the freesurfer > segmentation of the structural scan utilized? > > I am sorry. I know I am making this confusing! > > Thanks, > > Emily > > - Original Message - > From: "Anastasia Yendiki" > To: "Freesurfer support list" > Sent: Monday, July 14, 2014 10:18:11 AM > Subject: Re: [Freesurfer] Tracula > > > Hi Emily - When a mask is used as input to bedpostx, all voxels outside > that mask will be zero in all bedpostx output volumes. So it makes sense > to use the same mask for any subsequent processing. Is the mask that > you're referring to a symbolic link to another volume? You can run ls -l > to see what volume it points to. > > a.y > > On Mon, 14 Jul 2014, ebell...@uwm.edu wrote: > >> Hi Anastasia, >> >> Thank you so much, this is really helpful. >> >> I have one other question. So, at the bedpost stage, the no_dif_brain mask >> is used correct (looking at the fsl webpage), or at this stage the >> freesurfer segmentation is used as well? >> >> If in addition to using tracula, lets say if I also wanted to look into >> doing local probablistic tractography in FSL (using probtractx). I know that >> probtractx uses the output from the fsl bedpost stage. In this case then, >> would I need to adjust the no_dif_brain mask since it was used in the >> bedpost stage? I planned on using the output from the bedpost stage in >> tracula into FSL's probtractx to also try some local probablistic >> tractography. >> >> Emily >> >> - Original Message - >> From: "Anastasia Yendiki" >> To: "Freesurfer support list" >> Sent: Monday, July 14, 2014 4:14:49 AM >> Subject: Re: [Freesurfer] Tracula >> >> >> Hi Emily, >> >> 1. That's fine because the BET-based mask is not used by default in the >> the tractography. The brain mask from the freesurfer segmentation of the >> structural scan is used instead. >> >> 2. To check the diffusion-to-anatomical registration, you can look at the >> aparc+aseg registered into diffusion space, i.e., from the dlabel/diff >> directory, overlaid onto the FA map. It's also important to check that the >> gradient table is correct by looking at dtifit_V1 (the primary eigenvector >> of the tensors) displayed as lines. Assuming the protocol is the same for >> all subjects, you just need to do this latter check for one of your >> subjects only. >> >> 3. TRACULA doesn't do whole-brain tractography. It reconstructs a set of >> specific tracts. Information on the anatomical regions that these tracts >> go through or next to is derived from a set of training subjects. See our >> paper for more info: >> >> http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2011.00023/abstract >> >> Hope this helps, >> a.y >> >> On Thu, 10 Jul 2014, ebell...@uwm.edu wrote: >> >>> Hello, >>> >>> I have a few questions about Tracula. I am very new to DTI, so I hope you >>> can bare with me. >>> >>> 1.) I have been checking my registration at the prep stage. I am very new >>> to this so it may be that I am not looking at the right files. >>> >>> I looked at my eddy current corrected diffusion data (which I believe is in >>> data.nii.gz in the dmri folder) with the no_dif_brain_mask.nii, and noticed >>> that the no_dif_brain_mask does not cover very well for some of my >>> subjects. Should I individually tailor the Fractional Intensity Threshold >>> for BET mask extraction from low-b images at the prep stage? >>> >>> >>> 2.) In general what files should I be checking at each phase (prep, >>> bedpost, path)? >>> >>> 3.)How do y
Re: [Freesurfer] Tracula : Path not entirely in the white matter
Hi Emily - This is not necessarily a problem. To make sure, you can check the output path.pd.nii.gz file from that specific tract. If it got stuck somewhere (e.g., because the brain mask is missing a bit of brain that this tract should go through) then the path.pd.nii.gz will look like a single curve rather than a more diffuse volumetric distribution. Hope this helps, a.y On Wed, 16 Jul 2014, ebell...@uwm.edu wrote: > Hello, > > I was looking at a trac-all log file to get my bearings on what is being done > and making sure things were done successfully, > > I did not get any errors for this subject but when I was looking at the right > uncinate fasciculus: It would say "Path from initial control points not > entirely in the white matter" and then it attempted to perturb control points. > > I noticed that for this tract, it did not say that it did not say sucess > after how ever many control points. It just said that it reverted back to the > initial control points. > > Do I then need to be concerned about the validity of this particular tract > for this subject? > > Thanks, > > Emily > ___ > 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 field map error
Hi Eileen - All image formats that mri_convert (and thus any freesurfer program) can read will do, you don't need dicom. Try giving trac-all the phase difference maps you have and let's see what happens. Best, a.y On Wed, 16 Jul 2014, Eileen Moore wrote: > Hi Anastasia, > > OK - our imaging physicists had developed a wrapper script around epidewarp > which takes our dicom images and converts them into the phase difference map > (it is based on the script that was authored by Doug Greve for the fBIRN > consortium). It looks like the tracula script requires dicom images. Is > there a way for me to do epidewarp manually and then follow through with the > remaining steps using trac-all? > > Thanks, > Eileen. > > > Date: Mon, 14 Jul 2014 11:23:47 -0400 (EDT) > From: Anastasia Yendiki > Subject: Re: [Freesurfer] trac-all -prep error field map error > To: Freesurfer support list > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > > Hi Eileen - That step is run with the program epidewarp.fsl, > which you can > run on the command line to see the available options. The input > phase map > volume is expected to have either 2 frames (2 separate phase > maps) or 1 > frame (the difference phase map). This error from trac-all means > that it > found that your input phase map has something other than 1 or 2 > frames, so > it doesn't know how to handle it. > > Hope this helps, > a.y > > On Sat, 12 Jul 2014, Eileen Moore wrote: > > > Hi - I'm using freesurfer 5.3 on an Ubuntu operating system. > I'm tyring to > > run tracula on some? images acquired from a GE scanner. I am > running into > > problems when I try to perform the registration-based > B0-inhomogeneity > > compensation, getting an error in the terminal output: "ERROR: > Unrecognized > > format of phase map". However, trac-all -prep runs fine when I > skip the > > B0-inhomogeneity compensation step. Is there something else I > need to do to > > use field map correction? > > > > I've attached the trac-all.log and a copy of the terminal > output. > > > > Thanks, > > Eileen. > > > > > > > > > > > > ___ 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 AD weighted average
Hi Cat - AD_AVG_Weight weighs the AD value at each voxel with the probability value of the tract going through that voxel. So it's the proper definition of the expected (mean) value from probability theory. a.y On Fri, 18 Jul 2014, Cat Chong wrote: Dear Anastasia, Another quick question: We found significant differences in two subject groups for the AD_AVG as well as the AD_AVG_Weight, which is stated as the "weighted average over the entire path distribution'. Could you tell me how the average weight is calculated and why it would be better to use than the AD_AVG perhaps? Thank you very much, Cat ___ 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] dwi_motion Tracula
Hi Cat - Just install the update and run trac-all -qa. This will produce the motion measures. Check the tutorial for where to find the output. a.y On Mon, 21 Jul 2014, Cat Chong wrote: Hello Anastasia, I ran Tracula on Freesurfer 5.3 but without the 2013 Tracula updates. Now, I would like to use the command "dwi_motion" on my data. I have installed the updates, but will I have to completely reprocess my data inducing steps trac-all -prep, trace-all -bedp, and trac-all path in order to use dwi_motion? cheers, Cat ___ 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] Diffusion analysis qs - gradient matrix
It'd be nice if things were that simple, but! Although the pre-processing is done with FSL tools, tractography is done with locally written code. Some gradient sets may appear to work with FSL, but they won't work for us. For example, some dicom converters may perform a L-R flip as preparation for feeding the gradient vectors into FSL. We need the unflipped vectors because, instead of flipping vectors, we convert both vectors and images to LAS orientation. This ensures that they work both for FSL and for us, and that you can view things correctly in both freeview and fslview, without the subject looking like it's hanging upside down from its bat cave or some such awkward arrangement. In the end, the best way of knowing that the gradient table is correct is to run one example subject through and view the eigenvectors of the tensors as lines to see if they're pointing in the right direction. (Even though the tensors themselves aren't used for tractography, they're good for troubleshooting.) On Mon, 21 Jul 2014, Harms, Michael wrote: FS uses FSL tools under the hood, so you want to use the bvecs that are rotated into the axes of the scan. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: Rotem Saar Reply-To: Freesurfer support list Date: Monday, July 21, 2014 1:54 PM To: "freesurfer@nmr.mgh.harvard.edu" Subject: [Freesurfer] Diffusion analysis qs - gradient matrix Dear freesurfer experts, For diffusion analysis in freesurfer - I want to know which gradient matrix freesurfer expects. The thing is - when I look at the gradient matrix created using a MATLAB script that reads the directions from the dicom header - I get one table, but the bvecs file created in MRIconvert (for converting dicoms to nifti) looks different. This is the situation when an angle is applied during the acquisition of the dMRI scans, which means that each subject has its own gradient matrix. So my question is which table should I use for diffusion analysis in freesurfer? The one that was created from the dicom header or the one created for NIFTI format using MRIconvert ? Thanks Rotem Saar-Ashkenazy Department of Brain and Cognitive Science Ben Gurion University of the Negev, Beer-Sheva, 84105 School of Social Work Ashkelon Academic College, Ashkelon, 78211 Israel The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return 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] DTImap
Hi Shantanu - What do you mean by compatible? Are you trying to import an output from the other software into tracula or vice versa? a.y On Mon, 21 Jul 2014, Shantanu Ghosh wrote: > Hi FS experts, > > Is the DtiMap software (www.kennedykrieger.org) compatible with > Freesurfer/Tracula? > > Thanks > Shantanu > > > ___ 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] DTImap
Can DTImap read nifti volumes? The output of tracula includes one nifti volume with the probability distribution of each of the 18 pathways in each subject. On Tue, 22 Jul 2014, Shantanu Ghosh wrote: > Hi Anastasia, > > By `compatible' I meant whether I could export tracula outputs into a > format recognized by DtiMap, with the LAS coordinates preserved. > > My goal for this project is to use tracula outputs to prepare > probabilistic segmentations of the white matter including deep structures. > > I was thinking of using Mori group's WM Fiber tract based atlases, but if > tracula has this capability, then it would be ideal. > > Shantanu > > > > > On Tue, July 22, 2014 2:35 am, Anastasia Yendiki wrote: >> >> Hi Shantanu - What do you mean by compatible? Are you trying to import an >> output from the other software into tracula or vice versa? >> >> a.y >> >> On Mon, 21 Jul 2014, Shantanu Ghosh wrote: >> >>> Hi FS experts, >>> >>> Is the DtiMap software (www.kennedykrieger.org) compatible with >>> Freesurfer/Tracula? >>> >>> Thanks >>> Shantanu >>> >>> >>> >> ___ >> 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] ERROR: Could not open [..]/bvals for reading
Hi Elia - Have you searched for the libnetcdf error in the archives? I do believe that a few people were getting that error when 5.3 was first released. a.y On Tue, 22 Jul 2014, Elia S. wrote: Dear Freesurfer Community, Running Tracula preprocessing produces this error: ERROR: Could not open /home/elia/scripts/Tracula/LCL/dcmTimePoints_tar/T13D/timePoint1/dmri/bvals for reading I think the error described is the same as here: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg34169.html And as suggested here(https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-February/035935.h tml) I swapped the dmri_motion from the centos4 updates with the dmri_motion from the centos6 updates, and it works. Now here's the situation, I need to run tracula on machines where is not possibile to install the centos6 updates, since the message i get is this: error while loading shared libraries: libnetcdf.so.6: cannot open shared object file: No such file or directory Do you have any advice for me? Thanks in advance, Elia. -- - Freesurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Linux Distribution: Ubuntu 12.04 precise - Ubuntu 12.04.4 LTS Environment/Version: Linux king-ubuntu 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 09:20:45 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux My Current Working Directory: /home/elia ___ 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] dwi_motion Tracula
Hi Cat - I'll have to see your trac-all.log, I can't tell what is going on just from that one line. a.y On Tue, 22 Jul 2014, Cat Chong wrote: Dear Anastasia, With the new Tracula update installed, I ran the command: trac-all –qa –c dmrirc_file with location of bval specified and received the following error after ‘Loading volume-to-baseline affine transformations’ Could not open ../dmri/ dwi.ecclog for reading. It seems like all subjects do have the dwi.ecclog in their /dmri/ directories. Any ideas of what might have gone wrong? Cheers, Cat On Monday, July 21, 2014 1:53 PM, Anastasia Yendiki wrote: Hi Cat - Just install the update and run trac-all -qa. This will produce the motion measures. Check the tutorial for where to find the output. a.y On Mon, 21 Jul 2014, Cat Chong wrote: > Hello Anastasia, > > I ran Tracula on Freesurfer 5.3 but without the 2013 Tracula updates. Now, > I would like to use the command "dwi_motion" on my data. I have installed > the updates, but will I have to completely reprocess my data inducing steps > trac-all -prep, trace-all -bedp, and trac-all path in order to use > dwi_motion? > > cheers, > Cat > > ___ 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] Looking at dtifit_V1 in freeview
Hi Emily - Actually, there is a bug in the 5.3 version of freeview in that specific feature. But you can use fslview - you select the V1 file, click on the (i) button and choose Display as: Lines. a.y On Tue, 22 Jul 2014, ebell...@uwm.edu wrote: > Hi all, > > I was wondering how you go about looking at dtifit_V1 (the primary > eigenvector of the tensors) displayed as lines in freeview? > > Emily > ___ > 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] Pathstat.byvoxel.txt question
Hi Sarina - It's linear interpolation. a.y On Wed, 23 Jul 2014, Sarina Sacco wrote: > > Hi all freesurfer experts , > I have a question about the command trac-all-stat-c ,what is the > interpolation that uses? > > > ___ 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] Diffusion analysis qs
Hi Rotem - The FA values are actually invariant to a rotation of the gradient vectors. You can test that yourself. If, however, you get different FA maps with the different gradient tables, then something else is going on and not a simple rotation. a.y On Wed, 23 Jul 2014, Rotem Saar wrote: Dear Anastasia & Michael, Thank u for your answers (I attached my last email and your answers at the end of this email. I still want to specify my question. If I only want to extract FA values using the following script (see script below), and I know that an angle was applied during the dMRI scans, should I use the rotated gradient matrix ? When I first analyzed 20 subjects with the gradient matrix that is published for a T3 Philips magnet (I also read the gradients from the dicom header - they were the same) I got reasonable results - but now I don't know what to think of them... ___ ___ source ~/Desktop/fs_script dt_recon --i /usr/local/freesurfer/subjects/Anatomy0207/DTI/I160.dcm --s Anatomy0207 --o /usr/local/freesurfer/subjects/Anatomy0207/DTI --b /usr/local/freesurfer/subjects/Anatomy0207/DTI/bvals.bval /usr/local/freesurfer/subjects/Anatomy0207/DTI/bvecs.bvec To check results, run: tkregister2 --mov /usr/local/freesurfer/subjects/Anatomy0207/DTI/lowb.nii --reg /usr/local/freesurfer/subjects/Anatomy0207/DTI/register.dat --surf tkregister2 --s fsaverage --surf white --reg /usr/local/freesurfer/subjects/Anatomy0207/DTI/mask-tal.nii.reg --mov /usr/local/freesurfer/subjects/Anatomy0207/DTI/mask-tal.nii tkregister2 --s fsaverage --surf white --reg /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-tal.nii.reg --mov /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-tal.nii freeview -v /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii /usr/local/freesurfer/subjects/Anatomy0207/DTI/adc.nii freeview -v /usr/local/freesurfer/subjects/Anatomy0207/mri/brain.mgz/usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii:reg=register.dat:colo rmap=heat:heatscale=.2,.2,1 tkmedit Anatomy0207 orig.mgz -aux brain.mgz -seg wmparc.mgz -reg /usr/local/freesurfer/subjects/Anatomy0207/DTI/register.dat -overlay /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii -fthresh 0.2 -fmax 1 mri_vol2vol --mov /usr/local/freesurfer/subjects/Anatomy0207/DTI/lowb.nii \ --targ /usr/local/freesurfer/subjects/Anatomy0207/mri/wmparc.mgz \ --inv --interp nearest --o /usr/local/freesurfer/subjects/Anatomy0207/mri/wmparc2diff.mgz \ --reg /usr/local/freesurfer/subjects/Anatomy0207/DTI/register.dat --no-save-reg mri_vol2vol --mov /usr/local/freesurfer/subjects/Anatomy0207/DTI/lowb.nii \ --targ /usr/local/freesurfer/subjects/Anatomy0207/mri/aparc+aseg.mgz \ --inv --interp nearest --o /usr/local/freesurfer/subjects/Anatomy0207/mri/aparc+aseg2diff.mgz \ --reg /usr/local/freesurfer/subjects/Anatomy0207/DTI/register.dat --no-save-reg freeview -v /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii \ /usr/local/freesurfer/subjects/Anatomy0207/mri/aparc+aseg2diff.mgz:colormap =lut mri_mask /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii \ /usr/local/freesurfer/subjects/Anatomy0207/mri/wmparc2diff.mgz \ /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-masked.mgz freeview -v /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-masked.mgz/usr/local/freesurfer/subjects/Anatomy0207/mri/aparc+aseg2diff.mgz:colormap =lut mri_segstats --seg /usr/local/freesurfer/subjects/Anatomy0207/mri/wmparc2diff.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-masked.mgz --sum /usr/local/freesurfer/subjects/Anatomy0207/stats/all_stats_fa-masked ___ ___ It'd be nice if things were that simple, but! Although the pre-processing is done with FSL tools, tractography is done with locally written code. Some gradient sets may appear to work with FSL, but they won't work for us. For example, some dicom converters may perform a L-R flip as preparation for feeding the gradient vectors into FSL. We need the unflipped vectors because, instead of flipping vectors, we convert both vectors and images to LAS orientation. This ensures that they work both for FSL and for us, and that you can view things correctly in both freeview and fslview, without the subject looking like it's hanging upside down from its bat cave or some such awkward arrangement. In the end, the best way of knowing that the gradient table is correct is to run one example subject through and view the eigenvectors of the tensors as lines to see if they're pointing in the right direction. (Even though the tensors themselves aren't used for tractography, they're good for troubleshooting.) On Mon, 21 Jul 2014, Harms, Michael wrote: > > FS uses FSL tools under the
Re: [Freesurfer] Compatibility Tracula v.5.3 and recon v.5.2 longitudinal
Hi Yoon - The update is here: http://freesurfer.net/fswiki/Tracula#Updates There will also be a new freesurfer release in the next couple of months, but I don't anticipate making more changes to longitudinal tracula before that, so this should be the same as in the future 5.4 version. a.y On Wed, 23 Jul 2014, Yoonho Chung wrote: > Thank you for your input. Before we go ahead and reprocess our recon and DTI > data with FS v 5.3 we were wondering if you plan an update on the TRACULA DTI > longitudinal stream anytime soon. > I think I saw somewhere in the email chain that this is likely to happen soon > with additional features and bug fixes. If so, I think it would be worth the > wait. > > Thank you! > > Yoon > > > > > On May 22, 2014, at 5:37 PM, Anastasia Yendiki > wrote: > >> >> Hi Yoon - If you are getting an error from longitudinal tracula, do check >> the tracula updates at the link that I gave you in my previous email. >> >> As for 5.2 recon-all, others can chime in here, but like I said it is not >> recommended to use it. Sorry about that. >> >> a.y >> >> On Thu, 22 May 2014, Yoonho Chung wrote: >> >>> Thanks for the quick response! >>> >>> If I already have all the T1 data processed using recon-all with FS v5.2, >>> do you think it is okay to switch the stream to FS v.5.3 and run Tracula? - >>> without having to do the recon-all again for the T1 data? It is because I >>> am also experiencing DTI longitudinal error due to the OS issue (according >>> to other threads). And if possible, I would like to avoid having to redo >>> all the recons if we have to switch it to v5.3. >>> >>> Thanks again! >>> Yoon >> >> >> 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 : Path not entirely in the white matter
Hi Emily - Yes, this is fine. I just meant that it shouldn't look like a single line. a.y On Thu, 24 Jul 2014, ebell...@uwm.edu wrote: > Hi Anastasia, > > Just to be clear, is this what you mean by a more diffuse volumetric > distribution. Here is a snapshot of the right inferior longitudinal > fasiculous. > > I am just getting a better sense of what to look for in terms of bad vs. good > tracts. > > Emily > > - Original Message - > From: "Anastasia Yendiki" > To: "Freesurfer support list" > Sent: Wednesday, July 16, 2014 4:54:29 PM > Subject: Re: [Freesurfer] Tracula : Path not entirely in the white matter > > > Hi Emily - This is not necessarily a problem. To make sure, you can check > the output path.pd.nii.gz file from that specific tract. If it got stuck > somewhere (e.g., because the brain mask is missing a bit of brain that > this tract should go through) then the path.pd.nii.gz will look like a > single curve rather than a more diffuse volumetric distribution. > > Hope this helps, > a.y > > On Wed, 16 Jul 2014, ebell...@uwm.edu wrote: > >> Hello, >> >> I was looking at a trac-all log file to get my bearings on what is being >> done and making sure things were done successfully, >> >> I did not get any errors for this subject but when I was looking at the >> right uncinate fasciculus: It would say "Path from initial control points >> not entirely in the white matter" and then it attempted to perturb control >> points. >> >> I noticed that for this tract, it did not say that it did not say sucess >> after how ever many control points. It just said that it reverted back to >> the initial control points. >> >> Do I then need to be concerned about the validity of this particular tract >> for this subject? >> >> Thanks, >> >> Emily >> ___ >> 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] dmri_trk2trk issue
Hi Tommi - The input reference volume (--inref) should be in the same
space as the input .trk file, i.e., your individual's diffusion space. It
seems that you're using the individual's T1 space instead?
a.y
On Fri, 25 Jul 2014, r...@nmr.mgh.harvard.edu wrote:
> Hi,
>
> I am attempting to morph deterministic tractography results (.trk file)
> from the individual diffusion space into the average brain
> cvs_avg35_inMNI152. However, something goes wrong, as the output trk file
> is greatly misplaced / strongly distorted / wrongly sized.
>
> The input file (dsi60.trk, a TrackVis trk file with an angle threshold of
> 60 degrees) loads fine in Trackvis, as do the inref and outref volumes (in
> .nii format). The rigid body (.mat) and nonlinear (.m3z) registrations
> also appear ok. The mat file (or more precisely, the corresponding
> register.dat file) looked fine with tkregister2 and the latter was
> successfully used to morph the corresponding probabilistic tractography
> results from the individual diffusion space to cvs_avg35_inMNI152 (= the
> same transformation I am trying to do here).
>
> Any suggestions what I am doing wrong? For example, could this be related
> to inref/outref voxel sizes or coordinate systems?
>
> Just in case, I already tried using the inverse rigid registration
> (anat2diff.mat) and the FDT-generated files inside DSI.bedpostX/xfms
> (diff2str.mat and its inverse) but the results were in all cases very much
> wrong, just in different ways.
>
> FS 5.3 (nmr-std-env)
> on machine avml
> cd $SUBJECTS_DIR
>
> dmri_trk2trk \
> --in $SUBJECT/DSI/dsi60.trk \
> --out TMSDSIGA_19Jul14/${SUBJECT}inCVS35MNI152_dsi60.trk \
> --inref $SUBJECT/mri/norm.mgz \
> --outref $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri/norm.mgz \
> --reg $SUBJECT/DSI/${SUBJECT}_diff2anat.mat \
> --regnl $SUBJECT/cvs_CVS35MNI152/final_CVSmorph_tocvs_avg35_inMNI152.m3z \
>
> reg (.mat) was computed as follows:
> bbregister --mov dsi_b0.nii --frame 0 --bold --s $SUBJECT --init-fsl --reg
> DSIregister.dat --fslmat ${SUBJECT}_anat2diff.mat
>
> I would be happy to copy the data to a location of your choosing if you
> would like to replicate the error. Thanks!
>
> Tommi
>
> ---
> Tommi Raij, MD, PhD
> MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
> Bldg 149, 13th St
> Charlestown, MA 02129
> U.S.A.
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
___
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
dispose of the e-mail.
Re: [Freesurfer] Diffusion analysis qs
Hi Rotem - It's hard to tell without zooming into some key areas, like corpus callosum and cingulum for example. The colors look ok (red and green, respectively) but it's hard to see how the lines look. a.y On Mon, 28 Jul 2014, Rotem Saar wrote: Dear Anastasia, I followed your suggestion: I calculated the FA maps in freesurfer using the script below (see last message): I did it with both the rotated and the not rotated gradient table. The FA maps were identical as u said. BUT ! - when I used the rotated gradient table in FSL and tried to create the FA & MD maps (as in the first step of tracula), I got the attached results: http://tinypic.com/r/skzwqa/8 Does this map seems ok to u ? I think that something is wrong but can't specify what. I will appreciate your help here again:) Hi Rotem - The FA values are actually invariant to a rotation of the gradient vectors. You can test that yourself. If, however, you get different FA maps with the different gradient tables, then something else is going on and not a simple rotation. a.y On Wed, 23 Jul 2014, Rotem Saar wrote: > Dear Anastasia & Michael, > > Thank u for your answers (I attached my last email and your answers at the > end of this email. > > I still want to specify my question. If I only want to extract FA values > using the following script (see script below), and I know that an angle was > applied during the dMRI scans, should I use the rotated gradient matrix ? > > When I first analyzed 20 subjects with the gradient matrix that is published > for a T3 Philips magnet (I also read the gradients from the dicom header - > they were the same) I got reasonable results - but now I don't know what to > think of them... > > source ~/Desktop/fs_script > > dt_recon --i /usr/local/freesurfer/subjects/Anatomy0207/DTI/I160.dcm --s > Anatomy0207 --o /usr/local/freesurfer/subjects/Anatomy0207/DTI --b > /usr/local/freesurfer/subjects/Anatomy0207/DTI/bvals.bval > /usr/local/freesurfer/subjects/Anatomy0207/DTI/bvecs.bvec > > To check results, run: > > tkregister2 --mov /usr/local/freesurfer/subjects/Anatomy0207/DTI/lowb.nii > --reg /usr/local/freesurfer/subjects/Anatomy0207/DTI/register.dat --surf > > tkregister2 --s fsaverage --surf white --reg > /usr/local/freesurfer/subjects/Anatomy0207/DTI/mask-tal.nii.reg --mov > /usr/local/freesurfer/subjects/Anatomy0207/DTI/mask-tal.nii > > tkregister2 --s fsaverage --surf white --reg > /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-tal.nii.reg --mov > /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-tal.nii > > freeview -v /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii > /usr/local/freesurfer/subjects/Anatomy0207/DTI/adc.nii > > freeview -v/usr/local/freesurfer/subjects/Anatomy0207/mri/brain.mgz/usr/local/freesurfer/subje cts/Anatomy0207/DTI/fa.nii:reg=register.dat:colo > rmap=heat:heatscale=.2,.2,1 > > tkmedit Anatomy0207?orig.mgz -aux brain.mgz -seg wmparc.mgz -reg > /usr/local/freesurfer/subjects/Anatomy0207/DTI/register.dat -overlay > /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii -fthresh 0.2 -fmax 1 > > mri_vol2vol --mov /usr/local/freesurfer/subjects/Anatomy0207/DTI/lowb.nii \ > ??? --targ /usr/local/freesurfer/subjects/Anatomy0207/mri/wmparc.mgz > \ > ??? --inv --interp nearest --o > /usr/local/freesurfer/subjects/Anatomy0207/mri/wmparc2diff.mgz \ > ??? --reg > /usr/local/freesurfer/subjects/Anatomy0207/DTI/register.dat --no-save-reg > > mri_vol2vol --mov /usr/local/freesurfer/subjects/Anatomy0207/DTI/lowb.nii \ > ??? --targ > /usr/local/freesurfer/subjects/Anatomy0207/mri/aparc+aseg.mgz \ > ??? --inv --interp nearest --o > /usr/local/freesurfer/subjects/Anatomy0207/mri/aparc+aseg2diff.mgz \ > ??? --reg > /usr/local/freesurfer/subjects/Anatomy0207/DTI/register.dat --no-save-reg > > freeview -v /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii \ >???/usr/local/freesurfer/subjects/Anatomy0207/mri/aparc+aseg2diff.mgz:color map > =lut > > > mri_mask /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii \ > /usr/local/freesurfer/subjects/Anatomy0207/mri/wmparc2diff.mgz \ > /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-masked.mgz > > > freeview -v/usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-masked.mgz/usr/local/freesurfer/s ubjects/Anatomy0207/mri/aparc+aseg2diff.mgz:colormap > =lut > > mri_segstats --seg > /usr/local/freesurfer/subjects/Anatomy0207/mri/wmparc2diff.mgz --ctab > $FREESURFER_HOME/FreeSurferColorLUT.txt --i > /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-masked.mgz --sum > /usr/local/freesurfer/subjects/Anatomy0207/stats/all_stats_fa-masked > > It'd be nice if things were that simple, but! > > Although the pre-processing is done with FSL tools, tractography is done > with locally written code. Some gradient sets may appear to work with FSL, > but they won't work for us. For example, some dicom converters may perfo
Re: [Freesurfer] trac-all -prep problem
Hi Shantanu - It's stuck trying to initialize one of the tracts. You can check which tract it is, and then check the data to see if there's something wrong that would affect that particular tract (for example, if part of the brain that this tract goes through is cut off in the mask). a.y On Fri, 1 Aug 2014, Shantanu Ghosh wrote: > Hi Freesurfer experts, > > I ran the command > > on a bunch of subjects and all of them finished in ~90 minutes except one. > This subject keeps on going into a seemingly endless loop. It has been > running for almost 12 hours now. A section of the console output is > reproduced below. > > What is the issue here, and how can this be solved? > I am using the dev version on a Linux box. > > Thanks in advance for all help. > Shantanu > > -- > SAMPLE CONSOLE OUTPUT > -- > INFO: Distances between consecutive points in test subject's space are 11 > 11 10 10 10 > WARN: Could not find satisfactory control point fit - try 1831 > Finding center streamline > INFO: Step is 5 voxels > WARN: Turning off deviation check for center streamline > INFO: Step is 5 voxels > WARN: Turning off FA check for center streamline > INFO: Step is 5 voxels > INFO: Length of center streamline is 91 voxels > Selecting 6 points on center streamline > INFO: Minimum allowable distance between dominant points is 9 > INFO: Minimum allowable curvature at a dominant point is 0.0283381 > INFO: Points where local peeks in curvature occur are > 106 105 67 (curv = 0.0284049) > 112 108 77 (curv = 0.0450985) > 115 108 98 (curv = 0.0526145) > 113 104 116 (curv = 0.0460477) > 107 103 128 (curv = 0.0759711) > INFO: Intermediate dominant points are > 103 98 50 > 112 108 77 > 114 108 89 > 115 108 98 > 107 103 128 > 105 106 145 > INFO: Final dominant points are > 103 98 50 > 112 108 77 > 114 108 89 > 115 108 98 > 107 103 128 > 105 106 145 > WARN: Defaulting to equidistant dominant points > WARN: Defaulting to equidistant control points > INFO: Selected control points are > 103 98 50 > 108 106 69 > 114 108 89 > 114 105 108 > 108 103 126 > 105 106 145 > INFO: Distances between consecutive points are 21 21 19 19 19 > INFO: Selected control points in test subject's space are > 80 62 23 > 81 66 31 > 84 68 40 > 84 66 48 > 82 64 56 > 81 65 64 > INFO: Distances between consecutive points in test subject's space are 9 > 10 8 8 8 > WARN: Could not find satisfactory control point fit - try 1832 > Finding center streamline > INFO: Step is 5 voxels > WARN: Turning off deviation check for center streamline > INFO: Step is 5 voxels > WARN: Turning off FA check for center streamline > INFO: Step is 5 voxels > > > > > ___ 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 Missing Statistics
Hi Emily - The weighted average is the most reliable in practice, and it is also the proper statistical definition of mean (expected) value. It weighs the value of FA etc at each voxel with the probability of the tract going through that voxel. The cases that are missing stats may need to be rerun. I'm guessing that those will look like single curves if you view the path.pd.nii.gz volume. You can rerun them by using "set reinit = 1" in the config file, and also specifying in the config file to run only the specific tract and specific subject. You'd have to rerun the -prior and -path steps only. a.y On Sun, 3 Aug 2014, Emily Louise Belleau wrote: > > > Hello Tracula Experts, > > I noticed that for a few of my subjects, I am missing all "Center" statistics > for FA, MD etc. for certain tracts like the left uncinate fasciculus for > example. > > I am assuming this means that an optimal pathway was unable to be found? I > do have the average and weighted statistics for these subjects. Should I > consider excluding these subjects or should I try analyzing them again with > different parameters? > > Additionally, I noticed that for a couple of my subjects, the "Length Center" > (length of the highest probability pathway) is unusually short compared to > the rest of the subjects? Is this a problem and do I consider excluding or > tweaking the parameters for these subjects? > > Also, do individuals usually report in publications just the average > statistics or are the weighted average or center statistics used? > > Attached are the stats of the problematic subjects. Any advice would be > greatly appreciated! > > Emily ___ 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] DTI Statistics
Weighted average recommended, see my previous email. On Tue, 5 Aug 2014, Emily Louise Belleau wrote: Hello all, I was just wondering if in publications/papers it is more common to report the average FA statistics, the weighted average statistics, or the center statistics (the average of the highest probability pathway). These are the statistics provided by Tracula. Thanks, Emily ___ 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 longitudinal
Hi Kevin - The names should be the cross-sectional IDs, i.e., without the .long.basename suffix. Note that the version of longitudinal tracula originally included in freesurfer 5.3 uses the cross-sectional aparc+aseg from freesurfer, whereas the latest updated version (recommended) uses the longitudinal aparc+aseg of each time point. But in either case what I said above about how to specify the names in the config file applies. http://freesurfer.net/fswiki/Tracula#Updates a.y On Wed, 6 Aug 2014, Dabbs (Kevin) wrote: Getting ready to run longitudinal tracula. Does the sublist entries in the dmrirc.long file refer to the cross-sectional or longitudinal processed subject time points? set subjlist = ( huey-scan1 \ huey-scan2 \ dewey-scan1 \ dewey-scan2 \ louie-scan1 \ louie-scan2 ) Thanks, Kevin Dabbs Department of Neurology University of Wisconsin-Madison ___ 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] Steps for Longitudinal trac-all
Hi Yoon - Sorry, the config file is necessary for anything that doesn't use default settings for trac-all, and that includes running it in longitudinal mode. What kind of cluster do you have? I'm working on making running trac-all easier on clusters that are not currently supported, as part of the 5.4 release. a.y On Tue, 12 Aug 2014, Chung, Yoonho wrote: > Dear FS experts. > > I am trying run trac-all - the longitudinal version - on the cluster and not > by using the dmrirc file. I am looking at the 'trac-all -help' and also the > wiki, but I couldn't find a flag or option where I could specify the use of > unbiased-template (e.g. [subjectID-base]) and other steps that may be > necessary for the longitudinal analysis. Could someone please provide the > steps that is required for running the longitudinal stream using 'trac-all' ? > Thank you very much. > > Best, > Yoon > > > ___ 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] download link broken?
Hi Wynn - There is a scheduled outage of the Martinos Center storage cluster today and tomorrow. a.y On Mon, 18 Aug 2014, Wynn Legon wrote: Hi,Trying to download freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz. Link gives 550 error and terminal error is: No such directory 'pub/dist/freesurfer/5.3.0' Please advise -- --- -Wynn Legon PhD Assistant Professor Department of Physical Medicine and Rehabilitation School of Medicine University of Minnesota R398 - 426 Church St. E Minneapolis, MN 55455 USA Ph. (612) 626-1183 ___ 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] downloads of freesurfer from website doesn't work
Hi Lau - There is a scheduled outage of the Martinos Center storage cluster all day today. Please try again later, it has nothing to do with your system. a.y On Tue, 19 Aug 2014, Lau Møller Andersen wrote: Dear List I get the following error: „550 Failed to change directory.” I tried on two operating systems. The wget also doesn’t work. Says the file doesn’t exist. Do you get the same errors, or is it specific to my system? Best Lau ___ 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 update link not working
Hi Kirstie - This was a glitch related to yesterday's storage cluster maintence. It's been fixed now, so please try again. a.y On Wed, 20 Aug 2014, Kirstie Whitaker wrote: > Hi, > > I apologise if this is only on my end but I can't seem to download any of the > updates from http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula. I was > successful last week > so I wonder if something's changed? > > Thanks > Kx > > -- > Kirstie Whitaker, PhD > Research Associate > > Department of Psychiatry > University of Cambridge > > Mailing Address > Brain Mapping Unit > Department of Psychiatry > Sir William Hardy Building > Downing Street > Cambridge CB2 3EB > > Phone: +44 7583 535 307 > Website: www.kirstiewhitaker.com > > ___ 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] Some notes on getting Tracula to work for newbies
Thanks a lot, Kirstie. Nice job on finding solutions in the archives! You
are a model user :)
On Wed, 20 Aug 2014, Kirstie Whitaker wrote:
> Hi Anastasia and the freesurfer list,
>
> I've been working on getting the latest version of tracula to run and I
> thought I would post here the errors that I've worked around. It's all been
> based on looking
> through the mailing list archives but I thought it would be useful to add
> them here all in one place! The goal of this email is simply to save time for
> others in the
> future (including myself when I forget all these things!)
>
> [Note that if I've written something between < > then it will be specific to
> your files/directories etc]
>
> When running trac-all on an input nii file with corresponding bval and bvec
> files:
>
> 1) If you're getting an error that says:
>
> nifti1Read(): unsupported slice timing pattern 5 in FILE>
>
> Try running the command:
>
> fslmaths
>
> eg: fslmaths dti.nii.gz dti.nii.gz
>
> I'm really not clear on what exactly is wrong with my files (created using an
> in house dicom converter) but taking in the file and writing it straight back
> out again
> gets rid of this problem for me.
>
> 2) If you're getting an error that says
>
> ERROR: Could not open //dmri/bvals for reading
>
> Then you're probably using the centos4 update at
> http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula. You have two options - if
> the centos6 update works then switch to
> that, otherwise all other steps in trac-all -prep work *except* for the
> quality control. So you can run trac-all -prep -noqa and all should be well.
>
> To install the update just download it (I used wget )
> and the untar it (tar -zxvf ). Copy the files
> inside the folder
> you've created into the $FREESURFER_HOME/bin/ directory.
>
> 3) If you're getting an error that says (something along the lines of)
>
> mri_convert --frame 0 14 27 41 54 68 //dmri/dwi.nii.gz
> //dmri/lowb.nii.gz
>
> mri_convert: extra arguments ("41" and following)
>
> type mri_convert -u for usage
>
> Then you're probably using an old version of trac-all. Double check that
> you've replaced the appropriate files in your $FREESURFER_HOME/bin directory
> with those
> contained in the appropriate update at
> http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula. (See my instructions at
> point 2).
>
>
> Some fun facts from my experience:
> * You can have decimal points (not commas though) in your bvals files.
> * You can run trac-all in either a bash or tcsh shell.
> (These were not the droids I was looking for)
>
> Thanks again for the really excellent software. And please correct anything
> that I've written here if it's wrong!
>
> Kx
>
> --
> Kirstie Whitaker, PhD
> Research Associate
>
> Department of Psychiatry
> University of Cambridge
>
> Mailing Address
> Brain Mapping Unit
> Department of Psychiatry
> Sir William Hardy Building
> Downing Street
> Cambridge CB2 3EB
>
> Phone: +44 7583 535 307
> Website: www.kirstiewhitaker.com
>
>
___
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] Some notes on getting Tracula to work for newbies
Hi Kirstie - Your work-around works, but I should've actually included the
new mri_convert in the update. I've included it now, so you'll find it if
you download the last tracula update again. This should make things run
smoothly without changing any scripts.
Let me know if this solves it and sorry for the confusion! And I stand by
my statement on the model user - it's not about not ever running into
problems but about not being afraid to troubleshoot them! :)
a.y
On Wed, 20 Aug 2014, Kirstie Whitaker wrote:
On 20 August 2014 14:27, Anastasia Yendiki wrote:
Thanks a lot, Kirstie. Nice job on finding solutions in the archives!
You
are a model user :)
Thank youalthough unfortunately not quite the best user - I still have
problems...
I think I lied in my earlier email - I think that the mri_convert problem (#3
below) is actually in the newest version of trac-preproc. (I didn't do a great
job of keeping track of my version because I was being lazy! More fool me.)
Here's the part of the code which in the May 2014 update ('$Id: trac-preproc,v
1.49 2014/03/22 03:31:22 ayendiki Exp $' ) that is leading to the error:
#=
# Make diffusion brain mask
if ($#nb0 > 0) then
set lowblist = ()
@ k = 0
while ($k < $nb0)
set lowblist = ($lowblist $k)
@ k = $k + 1
end
else
set bmin = `grep -v ^$ $dwidir/dwi_orig.mghdti.bvals \
| sort --numeric-sort | head -1`
set lowblist = `cat $dwidir/dwi_orig.mghdti.bvals \
| awk -v bmin=$bmin '{if ($1 == bmin) print NR-1}'`
endif
if (! $#lowblist) then
echo "ERROR: Cannot detect low-b volumes"
goto error_exit
endif
set cmd = mri_convert
set cmd = ($cmd --frame $lowblist)
set cmd = ($cmd $dwidir/dwi.nii.gz)
set cmd = ($cmd $dwidir/lowb.nii.gz)
echo $cmd |& tee -a $LF |& tee -a $CF
if ($RunIt) then
$cmd |& tee -a $LF
if ($status) goto error_exit
endif
#=
Which leads to this command:
> mri_convert --frame 0 14 27 41 54 68
/scratch/kw401/UCHANGE_INTERIM/SUB_DATA/10778/SURFER/MRI0/dmri/dwi.nii.gz
/scratch/kw401/UCHANGE_INTERIM/SUB_DATA/10778/SURFER/MRI0/dmri/lowb.nii.gz
And then to this error:
> mri_convert: extra arguments ("41" and following)
I made the following changes to the code (trac-preproc) and everything seems to
run just fine.
#=
OLD
> set cmd = ($cmd --frame $lowblist)
NEW
< set cmd = ($cmd --frame ${lowblist[1]})
#=
What do you think? Is this just an odd-ness for me, or is it a helpful fix? One
thing that I haven't been able to ascertain is whether I have an old version of
mri_convert that should be able to concatenate the six listed volumes! (The next
section of code seems to look like its trying to concatenate volumes so it might
be expecting a 4D file? Or multiple lowb.nii.gz volumes?)
I hope this all makes sense! Thank you again for all your hard work!
Kx
On Wed, 20 Aug 2014, Kirstie Whitaker wrote:
> Hi Anastasia and the freesurfer list,
>
> I've been working on getting the latest version of tracula to run
and I thought I would post here the errors that I've worked around.
It's all been based on looking
> through the mailing list archives but I thought it would be useful
to add them here all in one place! The goal of this email is simply
to save time for others in the
> future (including myself when I forget all these things!)
>
> [Note that if I've written something between < > then it will be
specific to your files/directories etc]
>
> When running trac-all on an input nii file with corresponding bval
and bvec files:
>
> 1) If you're getting an error that says:
>
> nifti1Read(): unsupported slice timing pattern 5 in
>
> Try running the command:
>
> fslmaths
>
> eg: fslmaths dti.nii.gz dti.nii.gz
>
> I'm really not clear on what exactly is wrong with my files
(created using an in house dicom converter) but taking in the file
and writing it straight back out again
> gets rid of this problem for me.
>
> 2) If you're getting an error that says
>
> ERROR: Could not open //dmri/bvals for reading
>
> Then you're probably using the centos4 update at
http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula. You have two
options - if the centos6 update works then switch
Re: [Freesurfer] tracula: bvec-error
Hi Robby - It looks like in your config file "setbveclist" is one word, instead of "set bveclist". This may be why you're getting the "Badly placed ()'s." error at the very beginning of your trac-all output. And it would explain why it can't find the files. Hope this helps, a.y On Thu, 21 Aug 2014, Robby De Pauw wrote: Dear FreeSurfer, When I try to use TRACULA I keep getting the following error: mv -f /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig_flip.mghdti.bvecs /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/bvecs mv: rename /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig_flip.mghdti.bvecs to /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/bvecs: No such file or directory after entering the following command: $ trac-all -prep -c dmrirc.preproc I tried to specify my bval and bvec in the config file, but that doesn’t seem to help. My data was assessed using a Siemens-scanner. Attached you can find the config-file. Thank you in advance, Best regards, Robby — the complete output can be found here: ~/Desktop/SUBJECTS_FS $ trac-all -prep -c dmrirc.preproc Badly placed ()'s. INFO: SUBJECTS_DIR is /Users/rdpauw/Desktop/SUBJECTS_FS/T1 INFO: Diffusion root is /Users/rdpauw/Desktop/SUBJECTS_FS/T1 Actual FREESURFER_HOME /Applications/freesurfer INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: current FREESURFER_HOME does not match that of previous processing. Current: /Applications/freesurfer Previous: /apps/gent/SL6/sandybridge/software/FreeSurfer/5.3.0-centos4_x86_64 trac-preproc -c /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/scripts/dmrirc.local -log /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/scripts/trac-all.log -cmd /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/scripts/trac-all.cmd #- /Applications/freesurfer/bin/trac-preproc #- #@# Image corrections Thu Aug 21 15:59:52 CEST 2014 mri_convert /Users/rdpauw/Desktop/SUBJECTS_FS/Diffusion/INP_080_LISA_V_1/1.IMA /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig.nii.gz mri_convert /Users/rdpauw/Desktop/SUBJECTS_FS/Diffusion/INP_080_LISA_V_1/1.IMA /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Users/rdpauw/Desktop/SUBJECTS_FS/Diffusion/INP_080_LISA_V_1/1.IMA... INFO: this looks like a dicom, not an old Siemens .ima file, so I'm going to unpack it as a dicom. If this fails, run mri_convert with -it dicom Getting Series No INFO: Found 71 files in /Users/rdpauw/Desktop/SUBJECTS_FS/Diffusion/INP_080_LISA_V_1 INFO: Scanning for Series Number 5 Scanning Directory INFO: found 65 files in series INFO: loading series header info. RunNo = 4 WARNING: Run 1 appears to be truncated Files Found: 65, Files Expected (lRep+1): 1 FileName /Users/rdpauw/Desktop/SUBJECTS_FS/Diffusion/INP_080_LISA_V_1/1.IMA Identification NumarisVersyngo MR B17 ScannerModel TrioTim PatientName Sabbe^Linde Date and time StudyDate 20140422 StudyTime 164616.578000 SeriesTime171854.765000 AcqTime 171832.007500 Acquisition parameters PulseSeq *ep_b0 Protocol DTI64dir_1av_b1200_2.5x2.5x2.5_sfs PhEncDir COL EchoNo1 FlipAngle 90 EchoTime 83 InversionTime -1 RepetitionTime10800 PhEncFOV 240 ReadoutFOV240 Image information RunNo 4 SeriesNo 5 ImageNo 1 NImageRows768 NImageCols768 NFrames 65 SliceArraylSize 60 IsMosaic 1 ImgPos961.3685 959.9193 107.7635 VolRes 2.5000 2.5000 2.5000 VolDim 96 96 60 Vc -1. -0.0011 0.0062 Vr 0. -0.9841 -0.1774 Vs 0.0063 -0.1774 0.9841 VolCenter 0. 0. 0. TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: ( 96 96 60), nframes = 65, ismosaic=1 Could not parse NUMARIS version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 10800, TR = 10800 ms PE Dir COL COL AutoAlign matrix detected AutoAlign Matrix - 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FileName /Users/rdpauw/Desktop/SUBJECTS_FS/Diffusion/INP_080_LISA_V_1/1.IMA Identification NumarisVer
Re: [Freesurfer] error in pre-processing in TRACULA
Hi Anri - What text editor did you use to create the configuration file? It looks like the last line (which specifies the b-value file) has no end-of-line, and so that line is not executed, hence the failure to find the b-value file. Can you please press "enter" at the end of that line, so that you move to the next line, then save the configuration file and try again? a.y On Fri, 22 Aug 2014, 渡辺杏里 wrote: Dear TRACULA experts Hello. I am running TRACULA, but it exited an error very early in pre-processing. My data is not a format in DICOM but .nii, does this cause the error? I set the dcmlist to .nii file (in attachment). Could anyone help me? This is the error log and I attached the configuration file. -error log- [watanabeanris-Mac-Pro:mybook/Anri/diffusion_tutorial] watanabeanri% trac-all -prep -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial INFO: SUBJECTS_DIR is /volumes/mybook/Anri/diffusion_recons INFO: Diffusion root is /volumes/mybook/Anri/diffusion_tutorial Actual FREESURFER_HOME /Applications/freesurfer trac-preproc -c /volumes/mybook/Anri/diffusion_tutorial/HC_025/scripts/dmrirc.local -log /volumes/mybook/Anri/diffusion_tutorial/HC_025/scripts/trac-all.log -cmd /volumes/mybook/Anri/diffusion_tutorial/HC_025/scripts/trac-all.cmd #- /Applications/freesurfer/bin/trac-preproc #- #@# Image corrections Fri Aug 22 11:03:45 JST 2014 mri_convert /volumes/mybook/Anri/diffusion_tutorial/HC_025/orig/00.nii /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig.nii.gz mri_convert /volumes/mybook/Anri/diffusion_tutorial/HC_025/orig/00.nii /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /volumes/mybook/Anri/diffusion_tutorial/HC_025/orig/00.nii... TR=7175.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.996496, -0.0735924, -0.0397398) j_ras = (-0.0756091, 0.995787, 0.0518831) k_ras = (-0.0357542, -0.0547061, 0.997862) writing to /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig.nii.gz... cp /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/bvecs /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig.mghdti.bvecs flip4fsl /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig.nii.gz /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -8 fslswapdim /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig.nii.gz x y z /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig_flip.nii.gz fslorient -forceradiological /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig_flip.nii.gz INFO: found /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig_flip.mghdti.bvecs /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/bvecs mv -f /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig_flip.mghdti.bvals /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/bvals mv: rename /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig_flip.mghdti.bvals to /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/bvals: No such file or directory Darwin watanabeanris-Mac-Pro.local 13.1.0 Darwin Kernel Version 13.1.0: Wed Apr 2 23:52:02 PDT 2014; root:xnu-2422.92.1~2/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Fri Aug 22 11:03:46 JST 2014 Many thanks for your help. Best Wishes, Anri WATANABE ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** WATANABE ANRI Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ** ___ 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] anatorig vs anat in dlabel
Hi Kirstie - That's correct. The only difference between the anatorig and anat is in the orientation, where the latter is always in LAS so it looks straight if you open it in fslview. For the purposes of freeview and every other freesurfer program, the two are indistinguishable, and they should align with the volumes in your subject's mri/... a.y On Fri, 22 Aug 2014, Kirstie Whitaker wrote: > Hi > > I have a very minor question about the naming scheme for tracula output. > > I have the folders anat and anatorig in the dlabel folder. Am I right that: > * anatorig is the T1 image in "freesurfer space" (256 x 256 x 256; LIA) > * anat is a rotated version of the T1 image in freesurfer space that lines > up with the standard orientation > used by FSL (256 x 256 x 256; LAS) > > So neither is actually in the same space as the *original* file that was > passed to recon-all (176 x 240 x 256; > LAS)? > > I ran mri_label2vol with dlabel/anat/anat_brain_mask.nii.gz as the --temp > argument and the labels didn't line > up nicely. They did line up with anatorig though. Is this what you'd expect? > > Kx > > -- > Kirstie Whitaker, PhD > Research Associate > > Department of Psychiatry > University of Cambridge > > Mailing Address > Brain Mapping Unit > Department of Psychiatry > Sir William Hardy Building > Downing Street > Cambridge CB2 3EB > > Phone: +44 7583 535 307 > Website: www.kirstiewhitaker.com > > ___ 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: bvec-error
Hi Robby - Which version of tracula are you using? In general it's hard to guess what's going on just by seeing the error message. Please attach the entire log file (scripts/trac-all.log). a.y On Mon, 25 Aug 2014, Robby De Pauw wrote: Hi Anastasia Thanks for your quick reply. I’ve changed the command and I got one step further. Now I get another error: mv -f /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig_flip.mghdti.bvecs /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/bvecs mv: rename /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig_flip.mghdti.bvecs to /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/bvecs: No such file or directory Darwin ge24p176.ugent.be 13.3.0 Darwin Kernel Version 13.3.0: Tue Jun 3 21:27:35 PDT 2014; root:xnu-2422.110.17~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Mon Aug 25 14:23:03 CEST 2014 Somehow the folder bvecs was not created? Regards, Robby Hi Robby - It looks like in your config file "setbveclist" is one word, instead of "set bveclist". This may be why you're getting the "Badly placed ()'s." error at the very beginning of your trac-all output. And it would explain why it can't find the files. Hope this helps, a.y On Thu, 21 Aug 2014, Robby De Pauw wrote: Dear FreeSurfer, When I try to use TRACULA I keep getting the following error: mv -f /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig_flip.mghdti.bvecs /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/bvecs mv: rename /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig_flip.mghdti.bvecs to /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/bvecs: No such file or directory after entering the following command: $ trac-all -prep -c dmrirc.preproc I tried to specify my bval and bvec in the config file, but that doesn’t seem to help. My data was assessed using a Siemens-scanner. Attached you can find the config-file. Thank you in advance, Best regards, Robby — the complete output can be found here: ~/Desktop/SUBJECTS_FS $ trac-all -prep -c dmrirc.preproc Badly placed ()'s. INFO: SUBJECTS_DIR is /Users/rdpauw/Desktop/SUBJECTS_FS/T1 INFO: Diffusion root is /Users/rdpauw/Desktop/SUBJECTS_FS/T1 Actual FREESURFER_HOME /Applications/freesurfer INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: current FREESURFER_HOME does not match that of previous processing. Current: /Applications/freesurfer Previous: /apps/gent/SL6/sandybridge/software/FreeSurfer/5.3.0-centos4_x86_64 trac-preproc -c /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/scripts/dmrirc.local -log /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/scripts/trac-all.log -cmd /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/scripts/trac-all.cmd #- /Applications/freesurfer/bin/trac-preproc #- #@# Image corrections Thu Aug 21 15:59:52 CEST 2014 mri_convert /Users/rdpauw/Desktop/SUBJECTS_FS/Diffusion/INP_080_LISA_V_1/1.IMA /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig.nii.gz mri_convert /Users/rdpauw/Desktop/SUBJECTS_FS/Diffusion/INP_080_LISA_V_1/1.IMA /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Users/rdpauw/Desktop/SUBJECTS_FS/Diffusion/INP_080_LISA_V_1/1.IMA... INFO: this looks like a dicom, not an old Siemens .ima file, so I'm going to unpack it as a dicom. If this fails, run mri_convert with -it dicom Getting Series No INFO: Found 71 files in /Users/rdpauw/Desktop/SUBJECTS_FS/Diffusion/INP_080_LISA_V_1 INFO: Scanning for Series Number 5 Scanning Directory INFO: found 65 files in series INFO: loading series header info. RunNo = 4 WARNING: Run 1 appears to be truncated Files Found: 65, Files Expected (lRep+1): 1 FileName /Users/rdpauw/Desktop/SUBJECTS_FS/Diffusion/INP_080_LISA_V_1/1.IMA Identification NumarisVersyngo MR B17 ScannerModel TrioTim PatientName Sabbe^Linde Date and time StudyDate 20140422 StudyTime 164616.578000 SeriesTime171854.765000 AcqTime 171832.007500 Acquisition parameters PulseSeq *ep_b0 Protocol DTI64dir_1av_b1200_2.5x2.5x2.5_sfs PhEncDir COL EchoNo1 FlipAngle 90 EchoTime 83 InversionTime -1 RepetitionTime10800 PhEncFOV 240 ReadoutFOV240 Image information RunNo 4 SeriesNo 5 ImageNo 1 NImageRows768 NImageCols768 NFrames 65 SliceArraylSize
Re: [Freesurfer] Tracula - May update version
Hi Peggy, 1. All anatomical volumes used in the last update of longitudinal tracula are in the same space as the *.long.* freesurfer volumes, i.e., the within-subject base template. 2. There are no changes to the bedpostx step. 2a. The brain mask should be the same across all steps of trac-all, i.e., either use a mask based on the anatomical segmentation throughout, or use a mask based on the low-b diffusion volumes throughout. Whether you want to use the anatomical or diffusion brain mask for another analysis with FSL is up to you. 3. You can't skip the tensor fit step. Even if it weren't used it in the -prior step, the -path step would need it because it calculates average FA and other such measures for each tract that it reconstructs. In any case, skipping the tensor fit step would not save you much time. Hope this helps, a.y On Mon, 25 Aug 2014, Peggy Skelly wrote: I have a few questions about the May 2014 update to Tracula: 1. Between the 2013-12-04 trac-all version 1.53 and 2014-05-26 trac-all version 1.56, the longitudinal stream now uses the aparc+aseg.mgz from the *.long.* directories, and all output is saved there, too. Are the .long./dlabel/anat and anatorig transformed into the base space like other images from the longitudinal recon-all, or are they in the original space of the timepoint T1 image? 2. Are there any changes to the bedpostX step, other than using a different mask? I've already run bedpostx in the Dec 2013 version (with lowb_brain_mask). Can the results be used with the new version by moving the /dmri.bedpostX directory to .long.base/dmri.bedpostX? 2a. (Maybe pertains to both versions) The link to .../dmri/nodif_brain_mask.nii.gz seems to be made during the -prep stage using .../dlabel/diff/aparc+aseg_mask.bbr.nii.gz or lowb_brain_mask.nii.gz depending on usemaskanat's value in the dmrirc file. The bedpost stage seems to use the target file as its mask no matter what usemaskanat is in the dmrirc file used when calling trac-all -bedp. (I'm trying to use aparc+aseg_mask for -prep and -path, but lowb_brain_mask for -bedp in anticipation of using the bedpostx output for other seed-base tracking in FSL.) 3. May 2014 version: trac-all -prep -notensor fails when it gets to computing the priors because dmri_train includes the --fa flag and the dtifit_FA.nii.gz is not present. Running trac-all -prior without a computed FA also fails the same way. I could compute the tensor, but thought I would save some time. I didn't realize computing the priors would use it. Does it improve the accuracy? Thanks, Peggy ___ 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: bvec-error
Hi Robby - The option to specify a different gradient table for each scan (with bveclist) was introduced more recently. See: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula/#Updates The version that you're using doesn't recognize bveclist. Hope this helps, a.y On Tue, 26 Aug 2014, Robby De Pauw wrote: Hi Anastasia, I’m using this version of tracula. trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp I’ve attached the log-file you requested. Robby De Pauw, dra. Ghent University Department of Physiotherapy and Rehabilitation Sciences 3B3 De Pintelaan 185 B-9000 Ghent robby.dep...@ugent.be ___ 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 field map error
Hi Eileen - In b0plist you can give files that contain either 2 phase maps (a volume with 2 frames), or the difference of 2 phase maps (a volume with only 1 frame). Depending on whether the volume that you specified has 2 or 1 frame, trac-all will assume which of the above you're giving it. Your error seems to be that mri_convert doesn't recognize the format of your volume: mri_convert /home/image/FASD/call1285/call1285_dti_021210/proc/b0pha.nii /home/image/FASD/Shared/freesurfer/tracula/CIFASDII_T1-DTI/call1285_CIFASDII _T1_021210/dmri/b0pha.nii.gz niiRead(): unsupported datatype 32 (with scl_slope != 0) in /home/image/FASD/call1285/call1285_dti_021210/proc/b0pha.nii Can you view the volume in freeview, for example? If freesurfer tools can't recognize the format of your file, then it's not a tracula-specific problem. In that case, it's best to send a new email on the list about the mri_convert error, so that you get responses from the appropriate experts. a.y On Wed, 27 Aug 2014, Eileen Moore wrote: Anastasia, I'm not sure how I can give tracula the phase difference maps, can you provide an example? As a reminder, I've run a wrapper script around epidewarp which takes our dicom images and converts them into a phase difference map (it is based on the script that was authored by Doug Greve for the fBIRN consortium). In the tutorial dmrirc example I see only the 'set b0mlist' and 'set b0plist' options, and am unsure where I could give it the phase difference map. I've also tried converting the dicom magnitude and phase maps to nifti format and inputting these into the dmrirc file but I am still getting an error. (See attached log file). Thanks, Eileen. -- Message: 10 Date: Thu, 17 Jul 2014 04:14:16 -0400 (EDT) From: Anastasia Yendiki Subject: Re: [Freesurfer] trac-all -prep error field map error To: Freesurfer support list Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Hi Eileen - All image formats that mri_convert (and thus any freesurfer program) can read will do, you don't need dicom. Try giving trac-all the phase difference maps you have and let's see what happens. Best, a.y On Wed, 16 Jul 2014, Eileen Moore wrote: > Hi Anastasia, > > OK - our imaging physicists had developed a wrapper script around epidewarp > which takes our dicom images and converts them into the phase difference map > (it is based on the script that was authored by Doug Greve for the fBIRN > consortium). It looks like the tracula script requires dicom images. Is > there a way for me to do epidewarp manually and then follow through with the > remaining steps using trac-all? > > Thanks, > Eileen. > > > Date: Mon, 14 Jul 2014 11:23:47 -0400 (EDT) > From: Anastasia Yendiki > Subject: Re: [Freesurfer] trac-all -prep error field map error > To: Freesurfer support list > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > > Hi Eileen - That step is run with the program epidewarp.fsl, > which you can > run on the command line to see the available options. The input > phase map > volume is expected to have either 2 frames (2 separate phase > maps) or 1 > frame (the difference phase map). This error from trac-all means > that it > found that your input phase map has something other than 1 or 2 > frames, so > it doesn't know how to handle it. > > Hope this helps, > a.y > > On Sat, 12 Jul 2014, Eileen Moore wrote: > > > Hi - I'm using freesurfer 5.3 on an Ubuntu operating system. > I'm tyring to > > run tracula on some? images acquired from a GE scanner. I am > running into > > problems when I try to perform the registration-based > B0-inhomogeneity > > compensation, getting an error in the terminal output: "ERROR: > Unrecognized > > format of phase map". However, trac-all -prep runs fine when I > skip the > > B0-inhomogeneity compensation step. Is there
Re: [Freesurfer] problems with tracula pre-processing (bvecs)
Hi Michelle - Your column-formatted gradient table (original_columns.bvec) shows up as having only 2 rows in unix (e.g. with the cat command). That's sometimes the case for text files saved from Excel or other non-unix applications. When I open your file in TextEdit on a mac and then copy-paste it into a unix text editor, it shows up fine. For row-formatted gradient tables, you have to make sure you have the latest version of tracula, as that option was added more recently: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula/#Updates Hope this helps, a.y On Thu, 28 Aug 2014, Michele Cavallari wrote: > Hi, > I'm having some problems with the first command of the tracula pipeline. > I am using FreeSurfer 5.3 on a mac (OS 10.9). > The problem seems to be related to the bvecs file. I received the following > error message: > niiRead(): error opening file /path/to/dmri/dwi_frame.nii.gz > > I read some threads available on your website, but couldn't figured out a > solution yet. I tried to organize the bvecs in columns, as opposed to the > original configuration in rows. By doing that and re-launching the > pre-processing command I obtained a differente error message: > Error: bvecs and bvals don't have the same number of entries > > The original bvals and bvecs files seem to have the same numbers of entries > to me. But the bvecs file produced by the processing - both the bvecs.norot > and the bvecs files in the dmri folder - don't have all the information of > the vectors. > > I am enclosing a zip folder with attachments: > 1) original bvecs and bvals files organized in rows and columns > 2) bvecs and bvals files generated by tracula > 3) error logs > > Let me know if you need any other information. > Thanks in advance for your help. > ___ 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: bvec-error
Hi Barbara - If your version is the same as Robby's, then you're trying to use an option (different gradient table for each scan) that was added in a tracula update. Older versions only allowed a single gradient table for all scans. See: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula/#Updates a.y On Mon, 1 Sep 2014, Barbara Kreilkamp wrote: Dear all, Robby, are you still having the problem? Did you solve it? I am really having the same problem, just that I am using nifti files instead of dicoms. I am using the same version as Robby. Please find my command+output, trac-all.log and configuration file in the attachment. I would also appreciate any help. Thank you, Barbara On Tue, Aug 26, 2014 at 8:21 AM, Robby De Pauw wrote: Hi Anastasia, I’m using this version of tracula. trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp I’ve attached the log-file you requested. Robby De Pauw, dra. Ghent University Department of Physiotherapy and Rehabilitation Sciences 3B3 De Pintelaan 185 B-9000 Ghent robby.dep...@ugent.be ___ 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] problems with tracula pre-processing (bvecs)
Hi Michelle - Based on your recon-all.log, your SUBJECTS_DIR that contains the freesurfer recon of your subject is /PHShome/my738/FSout. But based on you trac-all.log, you're using: SUBJECTS_DIR /Users/michele/Desktop/tracula/sages_diff_test_tracula So tracula cannot find the freesurfer recon of your subject. This is what's causing the latest error. About the confusion with the gradient table formats: The tutorials refer to the latest version of tracula, which has been updated since the 5.3 release. The newer features included in those updates are described here: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula/#Updates Hope this helps, a.y On Wed, 3 Sep 2014, Michele Cavallari wrote: Hi Barbara,thanks again for your help. I checked the bvecs file using the 'more' command, and (as you pointed out) there was some extra text. This was likely due to MS-excel formatting, which I have used to reshape the bvecs file from row to column configuration. Such extra text was not part of the original bvecs file organized in rows though, but tracula was not giving errors as well. So, take home message#1 It is not true that FreeSurfer 5.3 allows both rows and columns configuration of the bvecs (as stated in the wiki page). Or at least that's not true for all the scanners. I'd recommend a column configuration of the bvecs, even with FreeSurfer 5.3. Also - take home message#2 verify that there's no extra text due to excel formatting in the reshaped bvecs file. That said, now this lead me to the next error! It seems that there's a problem with the recon-all output that I'm using (?). However, both the log file and the output of the recon-all processing seem fine to me. Here is the detail of the error message I am getting ERROR: fio_pushd: path/to/dlabel/mni And attached are the log files of both tracula pre-processing (with errors) and recon-all (apparently without errors). Any help/suggestions? Thanks. On Mon, Sep 1, 2014 at 5:51 AM, Barbara Kreilkamp wrote: Hi Michele, This might be the solution - try the command 'more' in unix on your column bvec and bval, they should each have one (bval) and three (bvec) columns and no strange symbols. But you have these symbols in the bvec-file (probably because you have extra formatting information, that is not needed and an obstacle to Tracula). more original_columns.bval 0 0 0 0 0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 NEURO-222:tracula_help NEURO-222$ more original_columns.bvec 0 0 0 0 0 0 ^M0 0 0 ^M0 0 0 ^M0 0 0 ^M-1 0 0 ^M-0.166 0.986 0 ^M0.11 0.664 0.74 ^M-0.901 -0.419 -0.11 ^M0.169 -0.601 0.781 ^M0.815 -0.386 0.433 ^M-0.656 0.366 0.66 ^M^M-0.582 0.8 0.143 ^M-0.9 0.259 0.35 ^M-0.693 -0.698 0.178 ^M-0.357 -0.924 -0.14 ^M-0.543 -0.488 -0.683 ^M0.525 -0.396 0.753 ^M0.639 0.689 0.341 ^M0.33 -0.013 -0.944 ^M0.524 -0.783 0.335 ^M-0.609 -0.065 -0.791 ^M-0.22 -0.233 -0.947 ^M0.004 -0.91 -0.415 ^M0.511 0.627 -0.589 ^M-0.414 0.737 0.535 ^M0.679 0.139 -0.721 ^M-0.884 -0.296 0.362 ^M-0.262 0.432 0.863 ^M-0.088 0.185 -0.979 ^M-0.294 -0.907 0.302 ^M-0.887 -0.089 -0.453 ^M-0.257 -0.443 0.859 ^M-0.086 0.867 -0.491 ^M-0.863 0.504 -0.025 You are ending up with multiple columns in the second row, please make sure they are 3 columns. Good luck, Barbara On Mon, Sep 1, 2014 at 10:36 AM, Barbara Kreilkamp wrote: Hi Michele, Do you use the dicoms or the nifti files as input to TRACULA? Also, I think the complete trac-all.log could be even more helpful. I am a newbie myself but I am having a similar problem, so I am trying to find a solution as well :). Best, Barbara On Fri, Aug 29, 2014 at 4:48 PM, Michele Cavallari wrote: Hi Barbara, thanks for your reply. I checked the dwi series on a viewer and it looks fine: I have 1960 dicoms, corresponding to 56 slices x 35 directions specified in the bval/bvec. Also, I was able to obtain the FA and MD maps through fsl using the very same dicoms and bval/bvec. Any suggestion? Thanks On Thu, Aug 28, 2014 at 7:30 PM, Barbara Kreilkamp wrote: Dear Michele, I cannot find anything wrong with your bvec and bval files. Seeing as you had an errormessage related to the dwi (the one about the dwi_frame.nii.gz): Did you check that your dwi data have the same amount of volumes as entries in bvec and bval? Good luck, Barbara On 28/08/2014 22:47, Michele Cavallari wrote: Hi, I'm having some problems with the first command of the tracula pipeline. I am using FreeSurfer 5.3 on a mac (OS 10.9). The problem seems to be related to the bvecs file. I received the following error message: niiRead(): e
Re: [Freesurfer] problems with tracula pre-processing (bvecs)
Hi Michelle - Try replacing this line: setenv /Users/michele/Desktop/tracula/sages_diff_test_tracula/SD40_1/FSout_P0401_e20130813_s002_Cor7minMDEFT_T1_b with: setenv SUBJECTS_DIR /PHShome/my738/FSout (Or whatever the location of your freesurfer recons is.) a.y On Wed, 3 Sep 2014, Michele Cavallari wrote: Hi Barbara,I checked the path. The folder with the trac-all output is is the very same folder of the dwi dicoms. Attached is the dmrirc file I am using, with all the specs. Thanks On Wed, Sep 3, 2014 at 12:59 PM, Barbara Kreilkamp wrote: Hi Michele, You would have to make sure that the files are written to the same folder for both commands (recon-all and trac-all) Right now it seems you wrote the output of recon-all to /PHShome/my738/FSout/FSout_P0401_e20130813_s002_Cor7minMDEFT_T1_b/ and trac-all output to /Users/michele/Desktop/tracula/sages_diff_test_tracula/SD40_1/ This is what the code was looking for but did not find: Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz What path did you specify for the T1 segmentations (by recon-all) in your configuration file? Hope it helps, All the best, Barbara On 03.09.14 17:31, Michele Cavallari wrote: Hi Barbara, thanks again for your help. I checked the bvecs file using the 'more' command, and (as you pointed out) there was some extra text. This was likely due to MS-excel formatting, which I have used to reshape the bvecs file from row to column configuration. Such extra text was not part of the original bvecs file organized in rows though, but tracula was not giving errors as well. So, take home message#1 It is not true that FreeSurfer 5.3 allows both rows and columns configuration of the bvecs (as stated in the wiki page). Or at least that's not true for all the scanners. I'd recommend a column configuration of the bvecs, even with FreeSurfer 5.3. Also - take home message#2 verify that there's no extra text due to excel formatting in the reshaped bvecs file. That said, now this lead me to the next error! It seems that there's a problem with the recon-all output that I'm using (?). However, both the log file and the output of the recon-all processing seem fine to me. Here is the detail of the error message I am getting ERROR: fio_pushd: path/to/dlabel/mni And attached are the log files of both tracula pre-processing (with errors) and recon-all (apparently without errors). Any help/suggestions? Thanks. On Mon, Sep 1, 2014 at 5:51 AM, Barbara Kreilkamp wrote: Hi Michele, This might be the solution - try the command 'more' in unix on your column bvec and bval, they should each have one (bval) and three (bvec) columns and no strange symbols. But you have these symbols in the bvec-file (probably because you have extra formatting information, that is not needed and an obstacle to Tracula). more original_columns.bval 0 0 0 0 0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 NEURO-222:tracula_help NEURO-222$ more original_columns.bvec 0 0 0 0 0 0 ^M0 0 0 ^M0 0 0 ^M0 0 0 ^M-1 0 0 ^M-0.166 0.986 0 ^M0.11 0.664 0.74 ^M-0.901 -0.419 -0.11 ^M0.169 -0.601 0.781 ^M0.815 -0.386 0.433 ^M-0.656 0.366 0.66 ^M^M-0.582 0.8 0.143 ^M-0.9 0.259 0.35 ^M-0.693 -0.698 0.178 ^M-0.357 -0.924 -0.14 ^M-0.543 -0.488 -0.683 ^M0.525 -0.396 0.753 ^M0.639 0.689 0.341 ^M0.33 -0.013 -0.944 ^M0.524 -0.783 0.335 ^M-0.609 -0.065 -0.791 ^M-0.22 -0.233 -0.947 ^M0.004 -0.91 -0.415 ^M0.511 0.627 -0.589 ^M-0.414 0.737 0.535 ^M0.679 0.139 -0.721 ^M-0.884 -0.296 0.362 ^M-0.262 0.432 0.863 ^M-0.088 0.185 -0.979 ^M-0.294 -0.907 0.302 ^M-0.887 -0.089 -0.453 ^M-0.257 -0.443 0.859 ^M-0.086 0.867 -0.491 ^M-0.863 0.504 -0.025 You are ending up with multiple columns in the second row, please make sure they are 3 columns. Good luck, Barbara On Mon, Sep 1, 2014 at 10:36 AM, Barbara Kreilkamp wrote: Hi Michele, Do you use the dicoms or the nifti files as input to TRACULA? Also, I think the complete trac-all.log could be even more helpful. I am a newbie myself but I am having a similar problem, so I am trying to find a solution as well :). Best, Barbara On Fri, Aug 29, 2014 at 4:48 PM, Michele Cavallari wrote: Hi Barbara, thanks for your reply. I checked the dwi series on a viewer and it looks fine: I have 1960 dicoms, corresponding to 56 slices x 35 directions specified in the bval/bvec. Also, I was able to obtain the FA and MD maps through fsl using the very same dicoms and bval/bvec. Any suggestion? Thanks On Thu, Aug 28, 2014 at 7:30 PM, Barbara Kreilkamp wrote: Dear Michele, I cannot find anything wr
Re: [Freesurfer] Tracula
Hi Emily - Is your amygdala seed ROI in MNI space? Only in that case the seed-to-diffusion transformation would be the MNI-to-diffusion transformation. a.y On Wed, 3 Sep 2014, Emily Louise Belleau wrote: > Hello, > > I did all of my DTI preprocessing through tracula. I now am using FSL > probtractx (which utilizes the bedpost stage output) to explore pathways from > the amygdala to the ventromedial prefontal cortex. > > When I used FSL's probtractx, when I viewed the tract. The tract was in the > wrong area of the brain. > > So, I think this may have something to do with the transfromation matrices I > gave it via tracula. > > *FSL asks for the seed to diffusion transformation matrix so that it can > convert your seed masks from MNI space to diffusion space. I gave the > transformation matrix in the dmri folder under xfms, titled > mni2diff.bbr.mat. I have a feeling this may be the issue. > > * I then tried to use the FLIRT registration tool through FSL to get the > appropriate transformation matrices. It asks for the bedpost directory. I > got an error saying it could not read my no_dif_brain_mask.nii. > > I am not sure what transformation matrix to give and was wondering if you > could give me some guidance. > > Thanks, > > Emily > > > ___ > 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] From bedpostX and recon-all to tracula
Hi Kate - There is an example configuration file for tracula in your freesurfer distribution ($FREESURFER_HOME/bin/dmrirc.example). The same file is also here: http://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc If you attach your configuration file and the log file (scripts/trac-all.log), we can try to troubleshoot. a.y On Wed, 3 Sep 2014, Katherine Damme wrote: > Hello Freesurfer Community! > I have sucessfully completed diffusion preprocessing in FSL and the > recon-all of the structural image and would like to use tracula for the > tract reconstruction. I keep having trouble with my configuration file. > > Does anyone have a bedpostX tracula config file they could share as an > example? > > Thank you! > > Kate > > ___ 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
Certainly you can, and it's a good idea for troubleshooting this. In FSL you can do it with: flirt -in your_label_in_MNI_space.nii.gz -out your_label_in_diff_space.nii.gz -ref dmri/lowb.nii.gz -applyxfm -init dmri/xfms/mni2diff.bbr.mat -interp nearestneighbour Then you can overlay the transformed label on some of the other inputs that you're giving probtrackx (e.g. a volume from the bedpostx directory) to make sure they look right in fslview. On Thu, 4 Sep 2014, Emily Louise Belleau wrote: > Hi Anastasia, > > Yes my amygdala seed is in MNI space. When I used the MNI to diffusion.mat > file in the dmri folder and placed it into FSL's probtractx, I developed a > track that was in the wrong area of the brain, so I am thinking there is > something wrong happening with the transformation to diffusion space. > > Can I transform the amygdala mask into diffusion space prior to putting it > into FSL's probtrackx viz bb register. If so, how might I go about doing that? > > Thanks so much for your help, > > Emily > > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Anastasia Yendiki > > Sent: Thursday, September 04, 2014 4:26 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Tracula > > Hi Emily - Is your amygdala seed ROI in MNI space? Only in that case the > seed-to-diffusion transformation would be the MNI-to-diffusion > transformation. > > a.y > > On Wed, 3 Sep 2014, Emily Louise Belleau wrote: > >> Hello, >> >> I did all of my DTI preprocessing through tracula. I now am using FSL >> probtractx (which utilizes the bedpost stage output) to explore pathways >> from the amygdala to the ventromedial prefontal cortex. >> >> When I used FSL's probtractx, when I viewed the tract. The tract was in the >> wrong area of the brain. >> >> So, I think this may have something to do with the transfromation matrices I >> gave it via tracula. >> >> *FSL asks for the seed to diffusion transformation matrix so that it can >> convert your seed masks from MNI space to diffusion space. I gave the >> transformation matrix in the dmri folder under xfms, titled >> mni2diff.bbr.mat. I have a feeling this may be the issue. >> >> * I then tried to use the FLIRT registration tool through FSL to get the >> appropriate transformation matrices. It asks for the bedpost directory. I >> got an error saying it could not read my no_dif_brain_mask.nii. >> >> I am not sure what transformation matrix to give and was wondering if you >> could give me some guidance. >> >> Thanks, >> >> Emily >> >> >> ___ >> 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] problems with tracula pre-processing (bvecs)
Hi Ludy - If your gradient table is formatted in 3 rows you need to either: 1. Convert it to 3 columns so you can use it with the 5.3 version of tracula, which requires the gradient table to be formatted in columns OR 2. Download the tracula update that can use gradient tables formatted in rows Hope this helps, a.y On Thu, 4 Sep 2014, ls...@bidmc.harvard.edu wrote: > Hi, > > I was having similar errors as Michele Cavallari regarding "error reading > /path/to/subject/dmri/dwi_frame," but I'm not sure it's related to my bvecs > file. I did try reconfiguring my bvecs file into columns instead of row just > in case, but that didn't solve the problem. It really just looks like it > can't find the dwi_frame file after the mri_concat command. > > I am attaching my trac-all.log and config file. > > Running Freesurfer 5.3 on Macbook OS 10.7.5. The bvecs files were generated > after I converted my dicoms to nifti using dcm2niigui (GE scanner). > > Can anyone tell me how dwi_frame is generated? > > > Ludy > > This message is intended for the use of the person(s) to whom it may be > addressed. It may contain information that is privileged, confidential, or > otherwise protected from disclosure under applicable law. If you are not the > intended recipient, any dissemination, distribution, copying, or use of this > information is prohibited. If you have received this message in error, please > permanently delete it and immediately notify the sender. 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] Tracula
To view your label over the MNI average brain: fslview $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz your_label_in_MNI_space.nii.gz -l Red There are no settings, other than choosing a different color for the label. On Fri, 5 Sep 2014, Emily Louise Belleau wrote: > Hi Anastasia, > > I am still having a bit of trouble understanding how to properly view my > tract through fsl view. > > What is the appropriate underlay to use/settings? > > Thanks again for your continued help! > > Emily > > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Anastasia Yendiki > > Sent: Thursday, September 04, 2014 4:54 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Tracula > > Certainly you can, and it's a good idea for troubleshooting this. In FSL > you can do it with: > > flirt -in your_label_in_MNI_space.nii.gz -out your_label_in_diff_space.nii.gz > -ref dmri/lowb.nii.gz -applyxfm -init dmri/xfms/mni2diff.bbr.mat -interp > nearestneighbour > > Then you can overlay the transformed label on some of the other inputs > that you're giving probtrackx (e.g. a volume from the bedpostx directory) > to make sure they look right in fslview. > > > On Thu, 4 Sep 2014, Emily Louise Belleau wrote: > >> Hi Anastasia, >> >> Yes my amygdala seed is in MNI space. When I used the MNI to diffusion.mat >> file in the dmri folder and placed it into FSL's probtractx, I developed a >> track that was in the wrong area of the brain, so I am thinking there is >> something wrong happening with the transformation to diffusion space. >> >> Can I transform the amygdala mask into diffusion space prior to putting it >> into FSL's probtrackx viz bb register. If so, how might I go about doing >> that? >> >> Thanks so much for your help, >> >> Emily >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> on behalf of Anastasia Yendiki >> >> Sent: Thursday, September 04, 2014 4:26 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] Tracula >> >> Hi Emily - Is your amygdala seed ROI in MNI space? Only in that case the >> seed-to-diffusion transformation would be the MNI-to-diffusion >> transformation. >> >> a.y >> >> On Wed, 3 Sep 2014, Emily Louise Belleau wrote: >> >>> Hello, >>> >>> I did all of my DTI preprocessing through tracula. I now am using FSL >>> probtractx (which utilizes the bedpost stage output) to explore pathways >>> from the amygdala to the ventromedial prefontal cortex. >>> >>> When I used FSL's probtractx, when I viewed the tract. The tract was in the >>> wrong area of the brain. >>> >>> So, I think this may have something to do with the transfromation matrices >>> I gave it via tracula. >>> >>> *FSL asks for the seed to diffusion transformation matrix so that it can >>> convert your seed masks from MNI space to diffusion space. I gave the >>> transformation matrix in the dmri folder under xfms, titled >>> mni2diff.bbr.mat. I have a feeling this may be the issue. >>> >>> * I then tried to use the FLIRT registration tool through FSL to get the >>> appropriate transformation matrices. It asks for the bedpost directory. I >>> got an error saying it could not read my no_dif_brain_mask.nii. >>> >>> I am not sure what transformation matrix to give and was wondering if you >>> could give me some guidance. >>> >>> Thanks, >>> >>> Emily >>> >>> >>> ___ >>> 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 > > ___ > 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] Tracula
If your label is in diffusion space, then replace the MNI brain with any volume that's in diffusion space. On Fri, 5 Sep 2014, Emily Louise Belleau wrote: > Hi Anastasia, > > This would be in diffusion space though. Since I converted all of my seeds to > diffusion space. > > Emily > > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Anastasia Yendiki > > Sent: Friday, September 05, 2014 11:32 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] Tracula > > To view your label over the MNI average brain: > > fslview $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz > your_label_in_MNI_space.nii.gz -l Red > > There are no settings, other than choosing a different color for the > label. > > On Fri, 5 Sep 2014, Emily Louise Belleau wrote: > >> Hi Anastasia, >> >> I am still having a bit of trouble understanding how to properly view my >> tract through fsl view. >> >> What is the appropriate underlay to use/settings? >> >> Thanks again for your continued help! >> >> Emily >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> on behalf of Anastasia Yendiki >> >> Sent: Thursday, September 04, 2014 4:54 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] Tracula >> >> Certainly you can, and it's a good idea for troubleshooting this. In FSL >> you can do it with: >> >> flirt -in your_label_in_MNI_space.nii.gz -out >> your_label_in_diff_space.nii.gz -ref dmri/lowb.nii.gz -applyxfm -init >> dmri/xfms/mni2diff.bbr.mat -interp nearestneighbour >> >> Then you can overlay the transformed label on some of the other inputs >> that you're giving probtrackx (e.g. a volume from the bedpostx directory) >> to make sure they look right in fslview. >> >> >> On Thu, 4 Sep 2014, Emily Louise Belleau wrote: >> >>> Hi Anastasia, >>> >>> Yes my amygdala seed is in MNI space. When I used the MNI to diffusion.mat >>> file in the dmri folder and placed it into FSL's probtractx, I developed a >>> track that was in the wrong area of the brain, so I am thinking there is >>> something wrong happening with the transformation to diffusion space. >>> >>> Can I transform the amygdala mask into diffusion space prior to putting it >>> into FSL's probtrackx viz bb register. If so, how might I go about doing >>> that? >>> >>> Thanks so much for your help, >>> >>> Emily >>> >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> on behalf of Anastasia Yendiki >>> >>> Sent: Thursday, September 04, 2014 4:26 PM >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] Tracula >>> >>> Hi Emily - Is your amygdala seed ROI in MNI space? Only in that case the >>> seed-to-diffusion transformation would be the MNI-to-diffusion >>> transformation. >>> >>> a.y >>> >>> On Wed, 3 Sep 2014, Emily Louise Belleau wrote: >>> >>>> Hello, >>>> >>>> I did all of my DTI preprocessing through tracula. I now am using FSL >>>> probtractx (which utilizes the bedpost stage output) to explore pathways >>>> from the amygdala to the ventromedial prefontal cortex. >>>> >>>> When I used FSL's probtractx, when I viewed the tract. The tract was in >>>> the wrong area of the brain. >>>> >>>> So, I think this may have something to do with the transfromation matrices >>>> I gave it via tracula. >>>> >>>> *FSL asks for the seed to diffusion transformation matrix so that it can >>>> convert your seed masks from MNI space to diffusion space. I gave the >>>> transformation matrix in the dmri folder under xfms, titled >>>> mni2diff.bbr.mat. I have a feeling this may be the issue. >>>> >>>> * I then tried to use the FLIRT registration tool through FSL to get the >>>> appropriate transformation matrices. It asks for the bedpost directory. I >>>> got an error saying it could not read my no_dif_brain_mask.nii. >>>> >>>> I am not sure what transformation matrix to give and was wondering if you >>>> could give me some guidance. >>>> >>>> Thanks, >>>> >>>> Emily >>>> >>>> >>>>
Re: [Freesurfer] help extracting Brodmann areas masks
Hi David - On the difference between .thresh and "not .thresh" labels: The BA labels come from averaging histologically derived labels from a set of post mortem brains. The non-thresholded version is just the sum of the corresponding labels from the different brains in fsaverage space. So vertices are included even if only one of the brains had their BA in that vertex, which means that these labels are going to be rather large. In the thresholded version, a threshold has been applied to the average BA label, to make it have an area as close as possible to the average area of the individual BA labels. I hope this makes sense. a.y On Mon, 8 Sep 2014, David Provencher wrote: > Hi Bruce, > > First of all, thanks for the reply! There was a typo in my initial question, > so I > rewrote it to make it clearer : > > # convert labels to annotation (outputs lh.myAnnot.annot & rh.myAnnot.annot) > mris_label2annot --s --h lh --l lh.V1.label --l lh.V2.label --l > lh.label --ct > ab BA.ctab --a myAnnot > mris_label2annot --s --h rh --l rh.V1.label --l rh.V2.label --l > rh.label --ct > ab BA.ctab --a myAnnot > > # convert ?h.myAnnot.annot files to volume > mri_aparc2aseg --s --annot myAnnot.annot --o mySeg.mgz > > > I had not noticed the ?h.BA.annot and ?h.BA.thresh.annot files so I was > trying to create > an annotation with the labels I was interested in (V1, V2, MT). Maybe I > misunderstood > what an annotation is, but I thought it was just a collection of labels. I'm > not sure > what the difference is between .thresh and "not .thresh" labels. Anyway, > whether I run > the code above or just the following : > > # convert ?h.BA.annot to volume > mri_aparc2aseg --s --annot BA --o BAseg.mgz > > when I open the .mgz file in freeview, something is obviously wrong (see > https://www.dropbox.com/s/evthp4sx40azost/BAseg.png?dl=0 and > https://www.dropbox.com/s/s5s7wcwywlaq68o/mySeg.png?dl=0). > In comparison, when I convert either the ?h.myAnnot.annot or ?h.BA.annot > files using > mri_label2vol, it seems fine (see > https://www.dropbox.com/s/avo1ot8bitbaeeo/BAlabels.png?dl=0). > > regards, > David > > On 14-09-08 10:37 AM, Bruce Fischl wrote: > > p.s. probably you should use the ?h.BA.thresh.annot, which is the annot > containing the labels thresholded to have the correct area > > cheers > Bruce > > > On Mon, 8 Sep 2014, Bruce Fischl wrote: > > Hi David > > what is the annot you are using in mris_label2annot? is it the > ?h.BA.annot? > > cheers > Bruce > On Mon, 8 Sep 2014, David Provencher wrote: > > Hi, > > I am new to freesurfer and I am trying to figure our how to extract 3d > masks in native space for the visual cortex (BA 17,18,19) of individual > subjects. I have looked at other threads similar to this, but there are > still a few things I can't figure out in generating the masks (the > conversion to native space should be fine). > > 1- I ran recon-all and I have V1, V2 and MT labels. My knowledge of > brain anatomy is very limited, but if I understand correctly, this > equates to BA 17, 18 and V5, so I don't have access to all of B19 (V3, > V4 and V5), right? > > 2- I managed to convert V1, V2 and MT labels to 3d masks using > mri_label2vol and it seems to work at first glance when I looked at the > generated file with freeView. However, I read in the mailing list that > mri_label2vol produces "patchy" volumes and that it is preferable to use > mri_aparc2aseg instead. That's what I can't figure out. From what I > understand, mri_aparc2aseg aims to map the surface labels of interest to > the segmented volumes? I tried doing the following (I altered some file > names/paths for readability): > > # convert labels to annotation (outputs lh.myAnnot.annot & > rh.myAnnot.annot)) > mris_label2annot --s --h lh --l lh.V1.label --l lh.V2.label > ---l lh.label --ctab BA.ctab --a annot > mris_label2annot --s --h rh --l rh.V1.label --l rhV2.label > ---l rh.label --ctab BA.ctab --a annot > > # convert to volume > mri_aparc2aseg --s --annot myAnnot.annot --o lh.asegTest.mgz > > When I look at the asegTest.mgz file in freeView, I only see segmented > cortical volumes and I can't see anything related to V1, V2 or MT, so I > assume that I don't use mri_aparc2aseg correctly, but I can't manage to > make it work. > > Any help would be appreciated! > David > > > ___ > 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.
Re: [Freesurfer] does Tracula correct for CSF contamination
Hi Laura - Apologies, I just found your email and realized I hadn't answered earlier. Which tract are you concerned about being contaminated by CSF? a.y On Wed, 27 Aug 2014, Laura Christine Anderson wrote: Dear Tracula users, does anyone know whether or not Tracula uses any corrections for CSF contamination? Thanks for your time, Laura -- Laura Anderson, B.A. Graduate Student Clinical / Developmental Psychology University of Maryland College Park, MD 20742 BPS 0112 ___ 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 reconstructed tracts quality
Hi Peggy - It's hard to diagnose the problem by seeing only the tracts and not the rest of the data, but this does look very strange. 1.5T is not a problem, but anisotropic resolution is not optimal for tractography, as it can bias the amount of diffusion measured in the direction that the voxels are larger. If you upload the entire data set (all the tracula directories: dmri, dmri.bedpostX, dlabel, dpath) for me here, I'll take a closer look. https://gate.nmr.mgh.harvard.edu/filedrop2/ a.y On Mon, 8 Sep 2014, Peggy Skelly wrote: > Hello Tracula experts, > I was wondering if you could comment on the quality of the tracts > reconstructed with our > 1.5T data. These 2 files are from the same subject at 2 timepoints, processed > in the > longitudinal stream. > > Is much of the non-smooth look of the tracts due to the resolution of the dwi > scans > (1.8x1.8x4mm)? > What could be the source of the diagonal lines/gaps in the tracts seen in tp1 > when > viewed from above? > > Thanks, > Peggy > > > ___ 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.
