Freesurfer January 2014

freesurfer@nmr.mgh.harvard.edu

130 participants
211 discussions

pial_lgi in QDEC
by Sophie Maingault 13 Jan '14

13 Jan '14

Dear FS experts, I followed this page to measure LGI : http://freesurfer.net/fswiki/LGI I wanted to use it in QDEC, so after running recon-all cache for pial_lgi, I created the $SUBJECTS_DIR/qdec/.Qdecrc with MEASURE1 = pial_lgi but I don't see it in the measures menu. Do you know why ? Best regards. Sophie Maingault

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Fwd: Re: problem with bvecs file with new (12/13) TRACULA code
by Salil Soman 13 Jan '14

13 Jan '14

---------- Forwarded message ---------- From: "Salil Soman" <salsoman(a)stanford.edu> Date: Jan 12, 2014 1:28 PM Subject: Re: problem with bvecs file with new (12/13) TRACULA code To: "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> Cc: Hi, > > Thank you for your email. Taking the .bval and bvec files outputed by > dcm2nii (which are row format) and transposing them to column format was > resulting in the blank rows that were causing troubles. Running this > command got rid of the problems and allowed trac-all prep / bedp / and path > to complete without errors: > > sed '/^\s*$/d' > > > Thanks, > > Sal > > > On Fri, Jan 10, 2014 at 3:57 PM, Anastasia Yendiki < > ayendiki(a)nmr.mgh.harvard.edu> wrote: > >> >> Hi Sal - It looks like a problem with the spaces at the end of the lines >> of the bvecs file. If you remove those spaces, it should work. Thanks for >> bringing this to my attention - the row-formatted bvecs files are new in >> this version and I'll make sure to allow them to have spaces at the end of >> the lines in the future. >> >> a.y >> >> >> On Thu, 9 Jan 2014, Salil Soman wrote: >> >> Hi, >>> >>> I am re-running GE acquired 3T product DTI data which ran without >>> trouble through the older tracula code. >>> However, now when I run the code, the bvec file that gets generated has >>> an extra 0 placed at the very end, >>> and then trac-all -prep eventually fails because it complains the bvec >>> and bvals files have non-matching >>> number of entries. I do have the dorotbvecs option set to 1 (as I had >>> before). Any suggestions on what I am >>> doing incorrectly would be greatly appreciated. I have attached the bvec >>> and bval files I am providing a >>> input. >>> >>> Best wishes, >>> >>> Sal >>> -- >>> 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 >>> >>> >>> >> >> 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. >> > > > > -- > 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 >

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DOSS or DODS
by amirhossein manzouri 13 Jan '14

13 Jan '14

Hello all, I am using Qdec (version5.1) to study cortical thickness differences between groups having Age as nuisance covariate. I do not have assumption if the groups are different or not . Using DODS and DOSS gives me completely different results. We have three groups including 41, 39, and 24 subjects in each. My question is which results design matrix type is more reliable for such a study? And also what if I include a covariate of interest in my comparison? Thanks in advance, Best regards, Amirhossein Manzouri

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Tracula Error: bvecs and bvals don't have the same number of entries
by Francesco Baldacchini 13 Jan '14

13 Jan '14

Hi everybody, I'm trying to run the* trac all -prep *command but after some times I get this error "bvecs and bvals don't have the same number of entries". I've checked my bvals and bvecs, which are in attach, but they seems to be formatted in the right way. What can I do? Thanks, Francesco Baldacchini

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Sphere vertices
by Chris McNorgan 13 Jan '14

13 Jan '14

Hi, I wanted to confirm whether spherical inflation generates meshes with the same number of vertices across individuals? Or would you have to use something like mri_surf2surf to map everyone's sphere to a template sphere? Thanks, Chris

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b value for TRACULA
by Roschinski, Benjamin 13 Jan '14

13 Jan '14

Dear Anastasia, in the FS Tutorial/Running Freesurfer you say TRACULA uses bedpostX to fit the ball-and-stick model to the DWI data. So with TRACULA we use a high angular resolution diffusion imaging model and you give the recommendation in "Introduction to diffusion MRI" to set the b value for HARDI ~ 10,000 sec/mm² with a few of 100´s of gradient directions. The b values in your published articles are much less than what you adviced and you also used much less gradient directions. What does it mean? Why do you suggest a higher b value although you use a much less one? Is it because of the upper likelihood of motion effects and the longer scan time or did I misunderstand the relationship between TRACULA and HARDI? kind regards Benjamin AG Ehrlich Medizinische Fakultät Carl Gustav Carus TU Dresden

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Re: [Freesurfer] data uploaded
by charujing123 12 Jan '14

12 Jan '14

Hi Louis, I'm sorry to reply so late. I resolved my question. Thanks. All the best. Rujing Zha 2014-01-13 charujing123 发件人：Louis Nicholas Vinke <vinke(a)nmr.mgh.harvard.edu> 发送时间：2014-01-09 23:38 主题：Re: Re: Re: [Freesurfer] data uploaded 收件人："Rujing Zha"<charujing123(a)163.com> 抄送："Bruce Fischl"<fischl(a)nmr.mgh.harvard.edu> Hi Rujing, Sorry I missed this thread, it got clumped in with other fs list emails. Has the problem you were having since been resolved? If you zip the recon folders for each subject separately there should be no upload limitation. On Windows OS, just click on the subject recon folder, right-click, Send to -> Compress (zipped) folder. Upload those to FTP again and send me a note. -Louis On Wed, 18 Dec 2013, Rujing Zha wrote: > Hi Bruce, > Ok. > Thanks Bruce and Louis. Any problem about my data itself can be sent to me. > All the best. > Rujing > > > 2013-12-18 > > ____________________________________________________________________________ > Rujing Zha > > ____________________________________________________________________________ > 发件人：Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > 发送时间：2013-12-18 10:21 > 主题：Re: Re: [Freesurfer] data uploaded > 收件人："Rujing Zha"<charujing123(a)163.com> > 抄送："Louis Vinke"<vinke(a)nmr.mgh.harvard.edu> > > Hi Rujing > > I'll leave it to Louis to see if he can get to the bottom of it > Bruce > On Wed, 18 > Dec 2013, Rujing Zha wrote: > > > Hi Bruce, > > Thanks for your attention and help. > > I have 2 folders for 2 subjects. I zipped the folder LJH_error into a > > multi-part achive as its size beyond 500M in Windows. So did the other > > folder. > > I want to know if "subject" folder unzip successfully? If so, LJH_error.z > 02 > > may be the cause. > > Bruce, I try to unload the LJH_error.z02 again now. > > Thanks. > > All the best. > > > > 2013-12-18 > > > > _________________________________________________________________________ > ___ > > Rujing Zha > > > > _________________________________________________________________________ > ___ > > 发件人：Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > > 发送时间：2013-12-18 01:27 > > 主题：Re: [Freesurfer] data uploaded > > 收件人："Rujing Zha"<charujing123(a)163.com> > > 抄送："Louis Vinke"<vinke(a)nmr.mgh.harvard.edu> > > > > Hi Rujing > > > > oe of the files (LJH_error.z02) is zero length, so probably didn't > > transfer correctly. Are they all in zip format? They have extensions like > > ?? ?*.z01. Wehn I try to unzip them I get > > > > unzip /cluster/incoming/LJH_error.zip > > Archive: /cluster/incoming/LJH_error.zip > > warning [/cluster/incoming/LJH_error.zip]: zipfile claims to be last dis > k > ?? ? > > of a multi-part archive; > > attempting to process anyway, assuming all parts have been concatenate > d > ?? ? together in order. Expect "errors" and warnings...true multi-part ?? ? > > support > > doesn't exist yet (coming soon). > > file #1: bad zipfile offset (local header sig): 4 > > file #2: bad zipfile offset (local header sig): 44 > > file #3: bad zipfile offset (local header sig): 22699 > > file #4: bad zipfile offset (local header sig): 44867 > > file #5: bad zipfile offset (local header sig): 66337 > > file #6: bad zipfile offset (local header sig): 87301 > > file #7: bad zipfile offset (local header sig): 107456 > > > > do they need to be concatenated? Louis: can you take a look and see if yo > u > ?? ? > > can help Rujing with this? > > > > thanks > > Bruce > > > > On Tue, 17 Dec 2013, Rujing Zha wrote: > > > > > Hi Bruce, > > > I uploaded the data to your server. > > > All files can be divided into 2 subjects. And one subject has incorrect > s > > egmentation (subject), the other has a multiframe > > > ERROR(LJH_error). > > > Thanks. > > > All the best. > > > > > > 2013-12-17 > > > > > > _______________________________________________________________________ > __ > > ________________________________________________________ > > > Rujing Zha > > > > > > > > > > > > The information in this e-mail is intended only for the person to whom it > i > > s > > addressed. If you believe this e-mail was sent to you in error and the e- > ma > > il > > contains patient information, please contact the Partners Compliance Help > Li > > ne at > > http://www.partners.org/complianceline . If the e-mail was sent to you in > e > > rror > > but does not contain patient information, please contact the sender and p > ro > > perly > > dispose of the e-mail. > > > > > > > >

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Question regarding Qdec
by Dusan Hirjak 12 Jan '14

12 Jan '14

Dear Freesurfer experts, I'm using qdec to perform a statistical analysis in Freesurfer. Could someone explain the meaning of the dependent measures (which can be used in qdec) to me? What does the "volume", "sulc" and "curv" etc. mean??? What kind of information do they convey??? Thanks! Best regards, DH

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Surface colour tksurfer
by matteo.diano＠unito.it 12 Jan '14

12 Jan '14

Dear Freesurfer experts, I would like to change the colour of the surface in tksurfer (e.g. from "grey" brain to "blue" brain). How can i obtain it? Thank you very much in advance! Regards Matteo

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manual editing: skull strip
by irene saviozzi 12 Jan '14

12 Jan '14

Hello, I'm learning to use freesurfer. I would understand if the tissue that is not brain (i.e. meninges, vessel and skull), which is not automatically included in pial, must be deleted with the manual editing or not. I send you some screenshots as exemple. In this cases, I can ignore skull and vessel out of the pial surface or I have to delete them? In this page ( http://freesurfer.net/fswiki/Edits ) they wrote : "Skull, dura and blood vessels might interfere with surface formation and need to be erased". Elsewhere they wrote that, in manual editing, leaving meninges it's not a skull strip error. In the manual editing of the brainmask.mgz, I obtain different values of volumes (in the aseg.stats) if I delete skull, meninges and vessel or not. thank you, Irene

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Freesurfer January 2014