Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30133 discussions

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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Error: bvecs and bvals don't have the same number of entries (tracula error in step 1.6)
by christian buhl 11 Jan '14

11 Jan '14

Hi I would like to use tracula for analysis of our dataset of DWI-images. Freesurfer reconstructions of the corresponding T1-images have been performed. Our DWI-dicom-images have been aquired using a Philips 1.5T scanner (E_sDW_SSh). I have used MRICRON to extract the bvals and bvecs. (I attach these original b-files, x20080912...) The Trac-all prep step works fine until the tensor fit in step 1.6 where the run stops with: "Error: bvecs and bvals don't have the same number of entries" The Bvals-file has to be flipped in order to run tracula (not getting the "missing 1000 file"-error=. I guess that bvec-file should be in either 3-row or 3-column format. Flipping this file doesn't help. In the .tschrc-file I have set the language to english as proposed here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19747.html This didn't help. I attach my log-file for the tracall-prep, the configuration-file and the bvecs.txt and bvals.txt used. In the configuration-file I have set the run list to only the first subject. The files bvals and bvecs from the output/dmri - directory are also attached. They are quite different from the original files? Any input and help will be warmly appreciated. Best regards Christian Christian Buhl Medical Doctor (MD), PhD-student Aarhus University Denmark

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wmparc.mgz and aparc.a2009s+aseg.mgz
by sujith vijayan 11 Jan '14

11 Jan '14

Hi All I am using wmparc.mgz and aparc.a2009s+aseg.mgz to determine the closest grey matter region for electrodes in some human epileptic patients; I have the RAS coordinates of the electrodes. I have a couple of questions: 1) When the electrode (its RAS coordinate) is close to the midline and out of the grey matter it won't give me the closest grey matter label (like wmparc does with the white matter). Is there someway to get this in a principled manner? For example, is there a way to get a file with all the RAS coordinates and the parcellation labels, so I could find the closest neighbor in Matlab? 2) The recons for three subjects were done between 2008 and 2010 using freesurfer. Therefore files like aparc.a2009s+aseg.mgz, wmparc.mgz, lh.aparc.a2009s.annot are missing. Is there a simple way just to recreate these set of files (one command would be great, even if it takes a little bit of time)? Or does the entire recon have to be done again? Thanks, Sujith

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Change in Tracula ability to use bvec / bval file containing zeros for b0 images?
by Salil Soman 10 Jan '14

10 Jan '14

Hi, I have been trying to rerun cases through the new (12/13) tracula code, which I had successfully ran through the pre 12/13 code. While I am still trying to sort out the libnetcdf.so.6 issue on our cluster, I also noticed that cases which I ran using the bvec and bval files including 0's for the b0 files were processed with the old code, but result in a xx:subscript out of range error in the current code. Removing the b0 entries fixed the problem and the remainder of the processing (other than the part requiring libnetcdf.so.6) works. I did notice that the bvecs and bval files in the diffusion tutorial do include the b0 0. Does the current version of tracula require the b0 entries to be removed? If not, any suggestions on what I may be doing incorrectly would be great. Thank you. 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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problem with bvecs file with new (12/13) TRACULA code
by Salil Soman 10 Jan '14

10 Jan '14

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

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Pooling data across experiments
by Cesar Echavarria 10 Jan '14

10 Jan '14

Hi freesurfers, I have run 2 separate blocked fMRI experiments ,each on a different pool of subjects, with couple of conditions identical in both experiments. I would like to pool the data for the conditions in common across these 2 experiments/group of subjects. I was wondering if anyone had any insight as to whether this is statistically valid or if there are any complications I should take into consideration when interpreting the pooled data. Thanks in advance for your help Cesar

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Freesurfer