Freesurfer August 2013

freesurfer@nmr.mgh.harvard.edu

145 participants
268 discussions

Re: [Freesurfer] [tracula] error running trac-all -prep
by Borsodi Florian 20 Aug '13

20 Aug '13

Hi Anastasia, Thank you for your help. I changed the commas in "/dmri/bvecs" to dots and reran trac-all. But the command "xfmrot" changed the dots back to commas. So, I changed our system language from de_AUT.UTF-8 to en_US.UTF-8 and reran trac-all. After changing the system language everything was genereted correctly and trac-all -prep ran without any errors. I'm so glad. Then, I started the next step "trac-all -bedp" and got a syntax error "/usr/local/freesurfer/bin/bedpostx_mgh: 131: /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected. " I also attached the the logfile. I was reading about this error in the mail archive. Would I have to run "bedpostx" outside of tracula ? Sincerely, Florian >>> Anastasia Yendiki 19.08.13 17.54 Uhr >>> Hi Florian - Can you please change the decimal commas to points and try again? a.y On Mon, 19 Aug 2013, Borsodi Florian wrote: > Hi Anastasia, > > Here are the bvec and bval files you asked me about. > > Sincerely, > Florian > > >>> Anastasia Yendiki 18.08.13 22.52 Uhr >>> > > Hi Florian - Can you please also attach the bvecs/bvals files from the > dmri directory? > > Thanks, > a.y > > On Sun, 18 Aug 2013, Borsodi Florian wrote: > > > Hi Anastasia, > > > > Thanks for your help. I renamed the directories and reran trac-all. It > > worked for the moment. > > However, then I got another error: "bvecs and bvals don't have the same > > number of entries." > > I don't know why, because they actually have the same number of entries. > > > > I attached the logfile so that you may see what is going on. The error > > occours at line 1463. > > > > Thank you in advance for your help. > > > > Sincerely, > > Florian > > > > > > >>> Anastasia Yendiki 15.08.13 18.01 Uhr >>> > > > > Hi Florian - I see what's going on. Can you please rename the directory > > /data/physics/florian/nii into something that doesn't include "nii", and > > rerun? Because "nii" is a file extension, this confuses some of the > > scripts. > > > > Thanks, > > a.y > > > > On Thu, 15 Aug 2013, Borsodi Florian wrote: > > > > > Hi Anastasia > > > > > > I ran the command you sent me and it runs without any errors. > > > I also attached the command line for you. > > > > > > Furthermore i ran data with 12 diffusion directions and i keep getting the > > > same kind of problems. > > > > > > sincerely > > > Florian > > > > > > >>> Anastasia Yendiki 02.08.13 19.59 Uhr > > >>> > > > > > > Hi Florian - Can you please run this command directly on the command line > > > and see if there are any errors? > > > > > > flip4fsl > > > /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.nii.gz > > > /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig_flip.nii.gz > > > > > > Thanks, > > > a.y > > > > > > On Fri, 2 Aug 2013, Borsodi Florian wrote: > > > > > > > Hi Anastasia > > > > > > > > Thank you for your answer. > > > > > > > > Yes, those files exist. > > > > I also extracted the bvec an bval files with anotther software then > > > dcm2nii > > > > and i keep getting the same kind of error. > > > > Also, about the 6 diffusion direction, those data i sent you, are just > > > > testdata for running tracula. > > > > > > > > sincerely > > > > Florian > > > > > > > > >>> Anastasia Yendiki 02.08.13 0.41 Uhr > > >>> > > > > > > > > Hi Florian - Do these files exist? > > >>/data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.mghdti.bvec > > s > > > > > > > > > >>/data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.mghdti.bval > > s > > > > > > > > > > > > > > > The format of the bvecs and bvals that you sent seems fine, but (and > > this > > > > has nothing to do with the error you're getting) I have to warn you that > > > > you may not be able to get good results running probabilistic > > tractography > > > > on this data. It looks like you're acquiring the same 6 diffusion > > > > directions, repeated 8 times. Six directions is the absolute minimum for > > > > reconstructing the tensor model, but will probably not be sufficient for > > > > the crossing fiber model that bedpostx reconstructs (and is used by > > > > tracula). Your scan time is better spent acquiring 48 different > > > > directions, rather than the same 6 directions 8 times. > > > > > > > > a.y > > > > > > > > On Mon, 29 Jul 2013, Borsodi Florian wrote: > > > > > > > > > Hello, > > > > > > > > > > I have been trying to run tracula on my data and i keep getting the > > same > > > > > kind of error repeatedly. > > > > > For my imput I am using dicoms from a Siemens scanner with a stadard > > > > > diffusion protocol. However, tracula cannot read the bvec and bval > > data > > > > out > > > > > of the dicom header. Therefore, I implemented bvec and bval files into > > > the > > > > > config file. > > > > > After doing so, I got the error which says that tracula cannot find > > the > > > > > "dwi_orig_flip.mghdti.bvecs" and "dwi_orig_flip.mghdti.bvals" files. > > > > > I have tried many options, but still cannot find a solution. > > > > > I am hoping to get some troubleshooting help. > > > > > > > > > > I have atteched my log- and config- files, as well as my bvec and bval > > > > > files. > > > > > To uphold patient confidentiality, I have encode the name patient's > > data > > > > as > > > > > "AAAAAA". > > > > > > > > > > I believe the problems are the bvec and bval files or their > > structures. > > > > The > > > > > log-file lete me assume this, especially the lines 202 - 205, 264 - > > 268 > > > > and > > > > > 1480 - 1484. > > > > > > > > > > Thank you in advance for your help, and your speedy response. > > > > > > > > > > With kind regards, > > > > > > > > > > Florian Borsodi > > > > > Department of Neurology > > > > > Medical University of Graz > > > > > > > > > > > > > > > > > > > > > > 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(a)nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Fornix labelled as corpus callosum in patient with periventricular leukomalacia
by Corinna Bauer 20 Aug '13

20 Aug '13

Hi Bruce, I was just wondering if you had any suggestions on how to fix the corpus callosum labels? Corinna On Wed, Aug 14, 2013 at 11:49 AM, Corinna Bauer <corinnab83(a)gmail.com>wrote: > In general, it mostly looks ok. There are regions which are labelled as > hypointensities, but should be CSF or gray matter, particularly around the > parieto-occipital fissure (see attached). Much of the fornix and corpus > callosum is also just labelled as left/right cerebral white matter. > > > > > On Wed, Aug 14, 2013 at 11:37 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu > > wrote: > >> Hi Corinna >> >> how does the rest of the aseg.mgz look? Is it accurate? >> Bruce >> >> On Wed, 14 Aug 2013, Corinna Bauer wrote: >> >> Hello all, >>> I am examining diffusion tracking in the corpus callosum of individuals >>> with >>> periventricular leukomalacia (PVL). The corpus callosum is particularly >>> small and the anterior and mid-anterior labels are being applied to the >>> fornix (see attached Fornix_labelled_as_CC.png). The midposterior and >>> posterior look ok, while the central is very small, maybe one voxel in >>> size. >>> >>> The wm segmentation, seen with ?l.white, also shows segmentation defaults >>> with the anterior corpus callosum (see attached images). I tried to >>> correct >>> this using control points, which you can see did not fix the >>> segmentation. >>> >>> Any suggestions? >>> >>> Corinna >>> >>> >>> >>> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/**complianceline<http://www.partners.org/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. >> >> >

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Track stats and covariates
by Alan Francis 20 Aug '13

20 Aug '13

Hi Anastasia: Just a quick question. When comparing FA, AD, RD etc between 2 groups, do we need to use covariates like Intra Cranial volume or AGE? If the answer is no, should I do an ANOVA or will T tests be sufficient? thank you, Alan

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ribbon.mgz, -1) : could not open file ERROR
by Pedro Rosa 20 Aug '13

20 Aug '13

Hi experts, I am processing several subjects, and they all ended up with the same error at the autorecon2: ribbon.mgz could not be opened. I ran at first the autorecon1 to check the skull striping, and then autorecon2 and 3. Autorecon3 always finished without error. I attached a log file. Any help is appreciated. Regards, Pedro Rosa.

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Fwd: calloc error
by Arno Klein 20 Aug '13

20 Aug '13

please ignore the previous post -- the calloc errors i was getting were restricted to only certain files that somehow got corrupted. cheers, @rno

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Fwd: calloc error
by Arno Klein 19 Aug '13

19 Aug '13

i have tried running the centos 4 & 6 versions of freesurfer on ubuntu 12.04, and with either i am getting a memory error when i simply run mri_info on an mgz file (this does not happen on my osx machine for the same file , and the license file is fine): """ znzTAGskip: tag=1667787808, failed to calloc 606085120 bytes! Cannot allocate memory """ any help would be appreciated. cheers, @rno

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mergecontrasts-sess - Comparisons between subjects
by preciado＠nmr.mgh.harvard.edu 19 Aug '13

19 Aug '13

Is it possible to do a conjunction analysis between subjects using one contrast? So far I've been able to do comparisons between contrasts within subjects but not between subjects. Thanks, -Ronny

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Re: [Freesurfer] [Tracula] error running trac-all –path –c Configuration_file.txt
by Anastasia Yendiki 19 Aug '13

19 Aug '13

Hi Francesco - The bedpostx files are created when you run trac-all -bedp. Then you need to run trac-all -path to reconstruct the paths under dpath/... as the final step. Did you run this? a.y On Mon, 19 Aug 2013, Francesco Siciliano wrote: > Thank you! > > Is it normal, however, not to have a dpath folder with summary statistics? I have all of the bedpostx output files, however, I seem to be missing the dpath folder as well as a script confirming that -path was completed. > > Thanks, > Francesco > ________________________________________ > From: Anastasia Yendiki [ayendiki(a)nmr.mgh.harvard.edu] > Sent: Monday, August 19, 2013 1:56 PM > To: Francesco Siciliano > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] [Tracula] error running trac-all –path –c Configuration_file.txt > > Hi Francesco - There's a list of bedpostx output files here: > http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/fdt/fdt_bedpostx.html > > The best way to determine if bedpostx finished running properly is to > check if those files were created in the dmri.bedpostX directory. > > a.y > > On Mon, 19 Aug 2013, Francesco Siciliano wrote: > >> Hello, >> I received an error on several terminals running trac-all –path –c Configuration_file.txt >> >> 55 slices processed >> 56 slices processed >> 56 slices processed >> 57 slices processed >> 57 slices processed >> 58 slices processed >> 59 slices processed >> 60 slices processed >> 61 slices processed >> Queuing post processing stage >> 70 slices processed >> For some reason the bedpostX process DOES NOT appear >> to have successfully completed. Please examine your >> results carefully. >> /Users/jonathanposner/Desktop/MRI_Software/FSL_installer/fsl/bin/bedpostx: line 262: kill: (15849) - No such process >> >> Is this an indication that the processing did not finish? Could this have anything to do with limited computer >> memory? >> >> > > > 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. > > >

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Curvature/folding stats
by Michael Kranz 19 Aug '13

19 Aug '13

Hi all, What's the difference between the curvature and folding measures outputted in the aparc stats files (i.e. mean, gaussian, folding index, and curvature index)? Additionally, which measures are the most reliable for individual differences? Thanks, Mike Michael Kranz Graduate Research Assistant |Beckman Institute University of Illinois 314-323-1329

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Re: [Freesurfer] trac-all inquiry
by Anastasia Yendiki 19 Aug '13

19 Aug '13

Hi David - Thank you very much for your kind words. Does the DWI volume for this subject have 65 frames (as many as the entries in bvecs/bvals)? You can check this by running: mri_info dmri/dwi.nii.gz a.y On Fri, 16 Aug 2013, David Soto wrote: > hi Anastasia, I am pleased that trac-all > has completed and the output looks pretty cool > so thanks for this amazing piece of software! > Just an issue with one subject, the preprocessing > stage is giving an error data and bvals/bvecs do not contain the same number > of entries, however I checked the files and do seem to > have the same number (all files attached). > Related or unrelated to this issue, not all the dlabel/diff output files > are generated, only these ... any advise appreciated, cheers - ds > anat_brain_mask.bbr.nii.gz > lh.cst_AS_avg33_mni_bbr_cpts_6.nii.gz > rh.cst_AS_avg33_mni_bbr_cpts_6.nii.gz > anat_brain_mask-vent.bbr.nii.gz > lh.cst_AS_avg33_mni_bbr_cpts_6_std.txt > rh.cst_AS_avg33_mni_bbr_cpts_6_std.txt > aparc+aseg+2mm.bbr.nii.gz > lh.cst_AS_avg33_mni_bbr_cpts_6.txt > rh.cst_AS_avg33_mni_bbr_cpts_6.txt > aparc+aseg.bbr.nii.gz > lh.ilf_AS_avg33_mni_bbr_cpts_5.nii.gz > rh.ilf_AS_avg33_mni_bbr_cpts_5.txt > aparc+aseg_mask.bbr.nii.gz > lh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt > White-Matter.bbr.nii.gz > cortex+2mm.bbr.nii.gz > lh.ilf_AS_avg33_mni_bbr_cpts_5.txt > White-Matter++.bbr.nii.gz > cortex+2mm+bs.bbr.nii.gz > lowb_brain_mask.nii.gz > cortex.bbr.nii.gz > notventricles.bbr.nii.gz > > http://www1.imperial.ac.uk/medicine/people/d.soto/ > On 12/08/13 09:57, David Soto wrote: > Thanks Anastasia, understood - the issue is that would be very > time consuming at this stage for several reasons.. > I found the issue with MRIConverter can be solved just by > doing fslmaths on the diffusion output image > fslmaths output data > This should not change the diffusion image yet is fine for processing > in FS > cheers > d.s. > http://www1.imperial.ac.uk/medicine/people/d.soto/ > > On 10 Aug 2013, at 00:43, Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > > I didn't mean run mri_convert on the nifti output of > another program. I meant run mri_convert directly on the > original dicom to convert it to nifti: > mri_convert yourimage.dcm yourimage.nii.gz > > On Fri, 9 Aug 2013, Soto, David wrote: > > I see - as said the diffusion output.nii from > MRIConverter > http://lcni.uoregon.edu/~jolinda/MRIConvert/ > [to not confound it with mri_converter) > is not read by Freeview and mri_converter does > not like it either > --------------------------------------------------------------------------- > ------------ > MD00071523-2:RSDTI_WMGUI/ACH_AMO/diff] dsoto% > mri_convert output.nii data.mgz > mri_convert output.nii data.mgz > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 > 21:55:16 mreuter Exp $ > reading from output.nii... > nifti1Read(): unsupported slice timing pattern > 5 in > /Users/dsoto/Documents/fMRI/RSDTI_WMGUI/ACH_AMO/diff/output.nii > No such file or directory > --------------------------------------------------------------------------- > ------------ > > NOW, I find that if I use FSL and run bet with > a fractional intensity threshold of 0, > I get an output file which is read by > Freeview- which should allow me to proceed > with all the necessary preprocessing steps in > trac-all > > would this be fine? I dont think the bet I run > will affect the image > > cheers > ds > http://www1.imperial.ac.uk/medicine/people/d.soto/ > > ________________________________________ > From: Anastasia Yendiki > [ayendiki(a)nmr.mgh.harvard.edu] > Sent: 09 August 2013 23:15 > To: Soto, David > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] trac-all inquiry > > When you apply a rotation to the DWIs (as > eddy_correct does), you need to > apply the same rotation to the corresponding > gradient vectors. See for > example: Leemans, A., Jones, D. K., Jun 2009. > The B-matrix must be rotated > when correcting for subject motion in DTI > data. Magn Reson Med 61 (6), > 1336–49. > > If you don't want to pass the dicoms to > trac-all directly, you can use > mri_convert to convert from dicom to nifti. > > On Fri, 9 Aug 2013, Soto, David wrote: > > hi - am afraid not because I am > feeding to trac-all > already eddycorrected images then > in the config file > I have > > # Perform registration-based > eddy-current compensation? > # Default: 1 (yes) > set doeddy = 0 > # Rotate diffusion gradient > vectors to match eddy-current > compensation? > # Only used if doeddy = 1 > # Default: 1 (yes) > > is this critical?? > > unfortunately, this is the only > way I manage to get it to work > as said my diffusion outputs from > mriconverter > are not read by FS, only through > mediation > of some FSL operation on the > files, then FS > likes those. > > I could start from scratch using > dicoms but would prefer > not to as the data is already > well organised > > cheers > ds > http://www1.imperial.ac.uk/medicine/people/d.soto/ > > ________________________________________ > From: Anastasia Yendiki > [ayendiki(a)nmr.mgh.harvard.edu] > Sent: 09 August 2013 22:44 > To: Soto, David > Subject: Re: [Freesurfer] > trac-all inquiry > > Are you rotating the gradient > vectors accordingly? This is done > in > trac-all after running > eddy_correct. > > On Fri, 9 Aug 2013, Soto, David > wrote: > > Hi Anastasia, stuff is > running smoothly at > last one quick > question, is there > any 'disadvantage' in > using FSL to do the > eddy correct and then > feed > those images to > trace-all ? > cheers > ds > http://www1.imperial.ac.uk/medicine/people/d.soto/ > > On 9 Aug 2013, at > 15:33, David Soto > <dsoto(a)imperial.ac.uk> > wrote: > > hi, for some > reason FS does not > like the > nii file from > Mriconverter, ( I saw > a post about this > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19526.ht > ml > ) but does like > the nii.gz > outputs from FSL... > > I'll try to debug > the bepostx error > > thanks! > > ds > > http://www1.imperial.ac.uk/medicine/people/d.soto/ > On 09/08/13 14:26, > Anastasia Yendiki > wrote: > > There is no > reason to conevrt to > .mnc. You should use > your > original .nii, if > that shows up > correctly in freeview. > > As for the > bedpostx error, this > is an Ubuntu issue > that > has come to my > attention very > recently. In Ubuntu > /bin/sh > is not a bash > shell any more. To get > around this, you'll > have to edit the > first line of the > scripts > $FREESURFER_HOME/bin/bedpostx_mgh > and > $FREESURFER_HOME/bin/fsl_sub_mgh. > You'll have to replace > "/bin/sh" with > "/bin/bash" on the > first line of those > two > scripts. > > On Fri, 9 Aug > 2013, David Soto > wrote: > > hi- I tried > to convert from nii to > mnc becos > that is > what i did when > I did > recon-all > > but I also > tried with nii at the > beggining and > got the > same issues. > In fact in > my last post (pasted > below > again)the > input was a nii file > could you > please check the stuff > below? > thanks! ds > > > Hi, further > to my prior email > I made some > progress. I noted that > nii2mnc > does not > seem to work on the > diffusion > output.nii > that I got from > Mriconverter as the > output.mnc > brain has parts > chopped in > Freeview. > > (I think > there may be something > funny about > this, as > the recon-all does > like the T1 output > form > Mriconverter) > > HENCE I > tried use the output > of eddycorrect > from FSL > (which I already run > for other thing) > Then I > created a new folder > where i placed the > output of > FSL eddycorrect and in > the > configuration > file I did > (i) set > dcmlist = > (fsleddycorrectoutput.nii.gz) > (ii) turned > 'set doeddy = 0' > > then run it > trac-all -c > traculatest.txt -prep > -log > trac_from_fsleddy > > > it seemed > to complete without > errors (log > attached)n > and I checked the > preprocessing > outputs in > Freeview (FA, masks > and > aparc+asegs) > and all seemed > fine. > > However > when I attempt the > next stage in > trac-all > i.e. > trac-all -c > traculatest.txt -bedp > -log > trac_from_fsleddy_bedp > it fails > saying the following > /usr/local/freesurfer/bin/bedpostx_mgh: > 131: > /usr/local/freesurfer/bin/bedpostx_mgh: > Syntax > error: "(" > unexpected > > > the log is > also attached. > > any advise > appreciated! > > cheers > ds > http://www1.imperial.ac.uk/medicine/people/d.soto/ > http://www1.imperial.ac.uk/medicine/people/d.soto/ > On 09/08/13 > 14:02, Anastasia > Yendiki wrote: > > Why > are you converting > from .nii > to > .mnc? Why are you not > using the > .nii > directly? > > On > Fri, 9 Aug 2013, David > Soto > wrote: > > hi > - thanks for the > feedback > > weirdly, > the nii2mnc > transform > of the > diffusion > data > falters, I get a > part > of the brain > chopped > have > no idea why this > is > the case, as it > worked > fine > before > for the T1 for > recon-all...I > am using > Ubuntu > 12.04 > > anyway > am trying to > sort > this out now, if > you > have any > advise > that would much > appreciated!! > cheers > ds > > > http://www1.imperial.ac.uk/medicine/people/d.soto/ > On > 08/08/13 17:03, > Anastasia > Yendiki > wrote: > > Hi > David - > The > fact > that > it's > taking > so > many > tries > to > initialize > the > left > ILF > tells > me > that > something > has > gone > wrong > with > the > data, > either > with > the > T1 > to DWI > registration, > or > with > the > mask, > or > something > like > that. > Have > you > looked > at > any > of the > output > files > of > the > pre-processing? > The > FA > map, > the > aparc+aseg, > etc? > > a.y > > On > Wed, 7 > Aug > 2013, > Soto, > David > wrote: > > Hi > Anastasia, > I > checked > the > becs > and > bvals > files, > there > was > a > bug > in > the > transposition > of > the > columns > into > 3 > rows > in > the > bvecs. > But > i > still > have > problems.. > I > rerun > trac-all > -prep > and > seemed > fine > but > ended > with > a > Segmentation > fault > (core > dumped) > which > however > is > not > present > in > the > last > line > of > the > trac-all.log > (Attached). > Writing > output > files > to/home/dsoto/Documents/fmri/rsdtianawmg > ui/02ST/dlabel/mni/lh.ilf_AS_avg33_mn > i_bbr_* > Writing > spline > volume > to/home/dsoto/Documents/fmri/rsdtianawmg > ui/02ST/dlabel/mni/lh.ilf_AS_avg33_mn > i_bbr_cpts_5.nii.gz > Segmentation > fault > (core > dumped) > Just > in > case > I > tried > trac-all > -bedp > complains > like > these > below, > any > advise > appreciated, > cheers > - > ds > /home/dsoto/Documents/fmri/rsdtianawmgui > /02ST/diffree/tracula02ST.txt > -bedp > INFO: > SUBJECTS_DIR > is > /home/dsoto/Documents/fmri/rsdtianawmgui > > INFO: > Diffusion > root > is > /home/dsoto/Documents/fmri/rsdtianawmgui > > Actual > FREESURFER_HOME > /usr/local/freesurfer > WARN: > Running > FSL's > bedbost > locally > - > this > might > take > a > while > WARN: > It > is > recommended > to > run > this > step > on > a > cluster > bedpostx_mgh > -n > 2 > /home/dsoto/Documents/fmri/rsdtianawmgui > /02ST/dmri > /usr/local/freesurfer/bin/bedpostx_mgh: > 131: > /usr/local/freesurfer/bin/bedpostx_mgh: > Syntax > error: > "(" > unexpected > http://www1.imperial.ac.uk/medicine/peop > le/d.soto/ > > ________________________________________ > > From: > Anastasia > Yendiki > [ayendiki(a)nmr.mgh.harvard.edu] > Sent: > 07 > August > 2013 > 17:22 > To: > Soto, > David > Cc: > freesurfer(a)nmr.mgh.harvard.edu > Subject: > RE: > [Freesurfer] > trac-all > inquiry > > Hi > David > - > Every > time > you > run > trac-all, > the > results > get > appended > to > this > file, > so > you > need > to > look > for > error > messages > only > in > the > more > recent > invocation > of > trac-all. > The > first > error > there > seems > to > be: > > > Error: > bvecs > and > bvals > don't > have > the > same > number > of > entries > > Do > you > have > the > same > number > of > b-values > and > gradient > vectors > and > volumes > in > your > DWI > series? > > a.y > > On > Tue, > 6 > Aug > 2013, > Soto, > David > wrote: > > hi > > I > upgraded > to > FS > 5.3 > but > still > encountering > issues > with > trac-all > prep. > > The > log > is > attached, > things > I > noted > after > inspecting > it > > 1) > INFO: > FreeSurfer > build > stamps > do > not > match > Subject > Stamp: > freesurfer-Linux-centos4_x86_64-st > able-pub-v5.1.0 > Current > Stamp: > freesurfer-Linux-centos4_x86_64-st > able-pub-v5.3.0 > > 2) > Error: > input > image > /home/dsoto/Documents/fmri/rsdtian > awmgui/02ST/dmri/lowb > not > valid > 3) > Image > Exception > : > #22 > :: > ERROR: > Could > not > open > image > /home/dsoto/Documents/fmri/rsdtian > awmgui/02ST/dmri/lowb_brain > 4) > Image > Exception > : > #22 > :: > ERROR: > Could > not > open > image > /home/dsoto/Documents/fmri/rsdtian > awmgui/02ST/dlabel/diff/White-Matter++. > 5) > ERROR: > Could > not > read > /home/dsoto/Documents/fmri/rsdtian > awmgui/02ST/dmri/dtifit_FA.nii.gz > but > despite > all > this > it > says: > trac-preproc > finished > without > error > at > Tue > Aug > 6 > 21:27:30 > BST > 2013 > > thanks > for > your > help > > cheers > ds > > http://www1.imperial.ac.uk/medicin > e/people/d.soto/ > > > > > __________________________________ > ______ > From: > Anastasia > Yendiki > [ayendiki(a)nmr.mgh.harvard.edu] > Sent: > 06 > August > 2013 > 19:30 > To: > Soto, > David > Cc: > freesurfer(a)nmr.mgh.harvard.edu > Subject: > RE: > [Freesurfer] > trac-all > inquiry > > I > see, > you're > using > the > old > version > of > tracula > (from > freesurfer > 5.1). > In > that > version, > you > had > to > define > the > number > of > low-b > images > in > the > configuration > file. > I > strongly > recommend > updating > to > freesurfer > 5.3. > A > lot > of > things > have > improved > in > tracula > since > then. > > Also, > in > the > future > please > attach > any > log > files > as > separate > attachments > instead > of > pasting > them > into > the > body > of > your > email > - > this > causes > the > body > of > the > email > to > exceed > the > limit > allowable > on > the > list. > > Thanks, > a.y > > > 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/compliance > line > . > 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. > > > > > > > > > > > > > > > > > > > > > >

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Freesurfer August 2013