Freesurfer

freesurfer@nmr.mgh.harvard.edu

30088 discussions

Skull strip
by Vincent 28 Mar '12

28 Mar '12

Hi, I have an image that is completing the skull strip with a lot of skull/dura remaining and it is affecting the surfaces. I've tried lowering the watershed threshold as low as 5 and I've tried adding the -gcut option, but the low threshold by itself does not eliminate the skull and gcut not only fails to remove the dura affecting my surfaces but it removes cerebellum as well. There is enough skull/dura left that I am hesitant to try manual edits, but I don't know any other options. I believe a good source of my trouble comes from my own confusion about how much remaining dura/skull is acceptable and how much cerebellum can be missing without affecting the rest of the data. I've uploaded the file (AL.zip) to the FTP server. If anybody has the time I would greatly appreciate it if I could have it looked at. Thank you very much. --Vincent

1 0

(no subject)
by Antonella Kis 28 Mar '12

28 Mar '12

Dear FS experts, I would like to know if for a Diffusion tensor imaging (DTI) tractography study with TRACULA I can use my previous results from FSTutorial/Diffusion more exactly my results after running dt_recon and registrations on the CVS space. If not can you please advise me if for a DTI probabilistic tractography using my previous results as mentioned above I can use TracVis. Thank you.Antonell

1 0

Re: [Freesurfer] volume mapping
by Douglas N Greve 28 Mar '12

28 Mar '12

And what coordinate system are the xyz in? doug ps. Please post questions to the list and not to me personally. Thanks! On 03/27/2012 04:10 PM, Johnson wrote: > Hi > I have the tracts in (x,y,z) format not as an nii file > regards > JG > On 03/27/2012 11:25 AM, Douglas N Greve wrote: >> Hi Johnson, try something like this: >> >> mri_label2vol --seg tracts.nii --temp orig.mgz --o tracts-in-fs.nii >> --regheader tracts.nii >> >> doug >> >> >> On 03/26/2012 03:29 PM, Johnson wrote: >>> OK >>> T1 space is the space acquired from the machine, original anatomical >>> space >>> regards >>> JG >>> >>> On 03/26/2012 2:25 PM, Bruce Fischl wrote: >>>> can you post to the list so others can answer? And can you clarify >>>> what you mean by "T1" space? >>>> >>>> On Mon, 26 Mar 2012, Johnson wrote: >>>> >>>>> Hi >>>>> well, I had to transfer the fiber tracts coordinates from DWI space >>>>> to T1 space, I used the b0 and the T1 for the registration process, I >>>>> got the transformation matrix and applied it onto the tracts and they >>>>> fit very well. >>>>> Now I want to transform the tracts from T1 space to the freesurfer >>>>> space, I need to know the transformation matrix that was used during >>>>> the processing if it was saved in any of the logs >>>>> thanks >>>>> Johnson >>>>> On 03/26/2012 2:09 PM, Bruce Fischl wrote: >>>>>> Hi Johnson >>>>>> >>>>>> what T1 did you register to? Most of the ones we generate (T1.mgz, >>>>>> brainmask.mgz, ...) are in a common coordinate system and you >>>>>> shouldn't >>>>>> have to transform from one to another. >>>>>> cheers >>>>>> Bruce >>>>>> >>>>>> >>>>>> On Mon, 26 Mar 2012, Johnson wrote: >>>>>> >>>>>>> Hi >>>>>>> Let me re-phrase my question: >>>>>>> I already did registration from DWI to T1, this step is OK. >>>>>>> Now I want to go from T1 to FreeSurfer space (aparc+aseg.mgz >>>>>>> file not >>>>>>> the aparc+aseg-in-rawavg file). I know I have two choices: >>>>>>> 1) do registration using bbregister >>>>>>> 2) since Freesurfer during processing have already done this >>>>>>> step, the >>>>>>> transformation matrix is there somewhere, the question is where to >>>>>>> find >>>>>>> it? which log or which file? this choice is better since it is more >>>>>>> accurate. >>>>>>> >>>>>>> Thanks >>>>>>> JG >>>>>>> >>>>>>> On 03/26/2012 12:41 PM, Anastasia Yendiki wrote: >>>>>>>> If you want to register your DWI to T1, you should register to >>>>>>>> mri/brain.mgz. You can do this with bbregister, or with any affine >>>>>>>> registration tool of your choice. >>>>>>>> >>>>>>>> On Mon, 26 Mar 2012, Johnson wrote: >>>>>>>> >>>>>>>>> Hi >>>>>>>>> I found it in a 256x256x256 space while the T1 we use is in >>>>>>>>> different >>>>>>>>> space, I found this page on the registration step: >>>>>>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat >>>>>>>>> I wish to know how this script work? >>>>>>>>> >>>>>>>>> mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o >>>>>>>>> aseg-in-rawavg.mgz >>>>>>>>> --regheader aseg.mgz >>>>>>>>> >>>>>>>>> what is the transformation used ? >>>>>>>>> JG >>>>>>>>> >>>>>>>>> >>>>>>>>> On 03/26/2012 12:24 PM, Anastasia Yendiki wrote: >>>>>>>>>> Hi Johnson - The aparc+aseg.mgz is in the same space as >>>>>>>>>> the T1 >>>>>>>>>> used as >>>>>>>>>> input to freesurfer. >>>>>>>>>> >>>>>>>>>> a.y >>>>>>>>>> >>>>>>>>>> On Mon, 26 Mar 2012, Johnson wrote: >>>>>>>>>> >>>>>>>>>>> Hi FS expert >>>>>>>>>>> I need to know the transformation matrix itself since I >>>>>>>>>>> will do >>>>>>>>>> the> transformation in matlab. >>>>>>>>>>> I successfully transformed white matter fibers >>>>>>>>>>> coordinates to T1 >>>>>>>>>> using> AIR 5.0 from LONI lab. >>>>>>>>>>> They provide a transformation matrix. >>>>>>>>>>> Now I want to transform the coordinates from T1 to >>>>>>>>>>> Freesurfer >>>>>>>>>> space, so >>>>>>>>>>> my question is: what is the transformation matrix that >>>>>>>>>>> relates >>>>>>>>>> the T1 >>>>>>>>>>> which FS have used for parcellation and segmentation >>>>>>>>>>> with the> >>>>>>>>>> aparc+aseg.mgz file? >>>>>>>>>>> I searched the logs but couldn't find such matrix. >>>>>>>>>>> I don't want to do a registration step since it will be >>>>>>>>>>> less >>>>>>>>>> accurate> than the one that was generated during the >>>>>>>>>> segmentation >>>>>>>>>> process. >>>>>>>>>>> Also is it just one transformation or a combination of >>>>>>>>>> transformations? >>>>>>>>>>>> thanks >>>>>>>>>>>> >>>>>>>>>> The information in this e-mail is intended only for the >>>>>>>>>> person to >>>>>>>>>> whom it >>>>>>>>>> is >>>>>>>>>> addressed. If you believe this e-mail was sent to you in >>>>>>>>>> error >>>>>>>>>> and the >>>>>>>>>> e-mail >>>>>>>>>> contains patient information, please contact the Partners >>>>>>>>>> Compliance >>>>>>>>>> HelpLine at >>>>>>>>>> http://www.partners.org/complianceline . If the e-mail was >>>>>>>>>> sent to >>>>>>>>>> you in >>>>>>>>>> error >>>>>>>>>> but does not contain patient information, please contact the >>>>>>>>>> sender >>>>>>>>>> and >>>>>>>>>> properly >>>>>>>>>> dispose of the e-mail. >>>>>>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>> > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

2 4

Re: [Freesurfer] conjunction analysis in FS
by Douglas N Greve 28 Mar '12

28 Mar '12

Add " --cwsig cwsig.mgh", then load cwsig.mgh as an overlay in tksurfer. Set the threshold to 1.3 (cluster p < .05). doug On 03/28/2012 07:48 AM, Tetiana Dadakova wrote: > Hello Doug, > > I cancel my first question, I realized CWP values are in the same file. > > Regarding second question, my cluster is quite big, so it goes beyond > just one atlas region. I would like to see what regions it cover, but > for this I need to overlay atlas at the surface (desirably the same as > I overlay cluster) in tksurfer. Can I somehow do it? > > Thank you for your time, > Tanja. > > On Tue, Mar 27, 2012 at 9:55 AM, Tetiana Dadakova<tetiana.d(a)gmail.com> wrote: >> Hello Doug, >> >> thank you so much for your reply. >> >> Could you please answer two more questions: >> >> I used the following line >> mri_surfcluster --in conjunction_sig.mgh --thmin 1.3 --thmax 5 --sign >> abs --subject fsaverage --hemi lh --annot aparc --minarea 0 --csd >> /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm10/abs/th13/mc-z.csd >> --cwsig summary_sig.mgh --sum summary_sig.txt >> >> I get a table summary_sig.txt with all the clusters uncorrected for >> multiple comparisons. Also, I get the corrected clusters >> summary_sig.mgh, which I can visualize with tksurfer. >> >> My questions are: >> 1) Can I get a txt file with corrected (for multiple comparisons) clusters? >> 2) Can I overlay a Desikan-Killiany Atlas in tksurfer? >> >> Thank you again for your help. >> Tanja. >> >> On Mon, Mar 26, 2012 at 8:38 PM, Douglas N Greve >> <greve(a)nmr.mgh.harvard.edu> wrote: >>> You can view it with tksurfer (instead of qdec). You can run the clustering >>> program (mri_surfcluster) to determine the location, max value, and >>> cluster-wise significance. You can run mri_surfcluster with --help to get >>> details, but you'll need to run it something like: >>> >>> mri_surfcluster --in conjunction_sig.mgh --thmin 2 --sign abs --subject >>> fsaverage --hemi lh --annot aparc --csd path/to/csdfile --sum sum.dat >>> >>> where --thmin 2 means to use p<.01 as the voxel-wise cluster-forming >>> threshold, --sign abs means to consider pos or negative values when forming >>> the threshold, sum.dat is the output. The tricky part will be to get the >>> right CSD file. The path will be something like >>> >>> $FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/cortex/fwhm12/abs/th20/mc-z.cdf >>> >>> where "th20" corresponds to "--thmin 2", and "abs" corresponds to "--sign >>> abs" and "fwhm12" means that the fwhm.dat file in the qdec output directory >>> has a value between 11 and 12. >>> >>> doug >>> >>> >>> >>> On 03/21/2012 11:00 AM, Tetiana Dadakova wrote: >>>> Thank you, Doug, for your explanation about conjunction analysis in >>>> FreeSurfer. >>>> >>>> I did everything as you said using sig maps, and now I have a >>>> conjunction_sig.mgh, which I don't know how to look at. >>>> Is it possible to load it in qdec (my purpose is to see where the >>>> conjunction clusters are located and what is their size, max value, >>>> significance)? >>>> >>>> Best wishes, >>>> Tanja >>>> >>>> On Mon, Aug 29, 2011 at 7:01 PM, Douglas N Greve >>>> <greve(a)nmr.mgh.harvard.edu> wrote: >>>>> For #1, Donald is right about FS -- you have to exclude the subject. For >>>>> #2, >>>>> you can use mri_concat with the --conjunct option (using sig or t or z >>>>> maps >>>>> as input). >>>>> >>>>> the Conjunction option takes the min of the abs across frames >>>>> at each voxel. The output value at the voxel is the min, >>>>> including the true sign of the min. Eg, if the two frames are: >>>>> +2.1 and +3.4 --> +2.1 >>>>> -2.1 and -3.4 --> -2.1 >>>>> +2.1 and -3.4 --> +2.1 >>>>> -2.1 and +3.4 --> -2.1 >>>>> See: Nichols, Brett,Andersson, Wager, and Poline >>>>> NeuroImage, Volume 25, Issue 3, 15 April 2005, 653-660. >>>>> >>>>> doug >>>>> >>>>> >>>>> MCLAREN, Donald wrote: >>>>>> See inline responses.On Wed, Aug 24, 2011 at 7:35 AM, Tetiana Dadakova >>>>>> <tetiana.d(a)gmail.com<mailto:tetiana.d@gmail.com>> wrote: >>>>>> >>>>>> Dear FS experts, >>>>>> >>>>>> I have two questions: >>>>>> >>>>>> 1. In qdec.table.dat file I am specifying several continuous factors, >>>>>> e.g factor1 and factor2. For some subjects factor2 is missing, >>>>>> therefore I leave empty space in those cells. When I load a >>>>>> qdec.table.dat into qdec, the whole line of the subject with missing >>>>>> factor2 is omitted. >>>>>> I was wondering if I can make some input into the empty cell, so that >>>>>> qdec recognizes that for this subject the value is missing only for >>>>>> factor2, and the value for factor1 is present. >>>>>> >>>>>> >>>>>> I'm not sure about Freesurfer, but in all my work with neuroimaging data >>>>>> across platforms, missing data in X requires that the subject to be >>>>>> excluded. The reason is the Y=X1*B+X2*B. Since you don't know X2, you >>>>>> can't >>>>>> find predicted Y and thus you can't find the error associated with that >>>>>> subject. Programs that all allow you to keep the subject often impute >>>>>> the >>>>>> value of the missing data to get the full X matrix or do not use the >>>>>> General >>>>>> Linear Model to find the solution. The GLM approach inverts the X matrix >>>>>> and >>>>>> you can't invert a matrix with an empty cell, as far as I know. >>>>>> >>>>>> >>>>>> 2. Is it possible to do conjunction analysis in FreeSurfer, I mean >>>>>> looking at common differences in two groups as compared to the third >>>>>> group? >>>>>> >>>>>> >>>>>> When I do conjunctions, I use a logical AND. There are other ways, but >>>>>> there are statistical issues. The logical AND will show where group A> >>>>>> group C and where group B> group C. >>>>>> To do this, I load the thresholded surfaces into matlab, make them both >>>>>> binary, multiply one of them by 2, then add the two datasets together. >>>>>> Then >>>>>> write the data back out to the surface. The new values will be 0 for no >>>>>> difference in either group, 1 or 2 for a difference in one of the group >>>>>> comparison, 3 where both groups are different from the third. >>>>>> >>>>>> >>>>>> >>>>>> Thank you for your time and help, >>>>>> Tanja. >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)nmr.mgh.harvard.edu<mailto: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. >>>>>> >>>>>> >>>>>> Best Regards, Donald McLaren >>>>>> ================= >>>>>> D.G. McLaren, Ph.D. >>>>>> Postdoctoral Research Fellow, GRECC, Bedford VA >>>>>> Research Fellow, Department of Neurology, Massachusetts General Hospital >>>>>> and >>>>>> Harvard Medical School >>>>>> Office: (773) 406-2464 >>>>>> ===================== >>>>>> This e-mail contains CONFIDENTIAL INFORMATION which may contain >>>>>> PROTECTED >>>>>> HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is >>>>>> intended only for the use of the individual or entity named above. If >>>>>> the >>>>>> reader of the e-mail is not the intended recipient or the employee or >>>>>> agent >>>>>> responsible for delivering it to the intended recipient, you are hereby >>>>>> notified that you are in possession of confidential and privileged >>>>>> information. Any unauthorized use, disclosure, copying or the taking of >>>>>> any >>>>>> action in reliance on the contents of this information is strictly >>>>>> prohibited and may be unlawful. If you have received this e-mail >>>>>> unintentionally, please immediately notify the sender via telephone at >>>>>> (773) >>>>>> 406-2464 or email. >>>>>> ------------------------------------------------------------------------ >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> -- >>>>> Douglas N. Greve, Ph.D. >>>>> MGH-NMR Center >>>>> greve(a)nmr.mgh.harvard.edu >>>>> Phone Number: 617-724-2358 Fax: 617-726-7422 >>>>> >>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve(a)nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

1 0

Re: [Freesurfer] Failure to convert DICOM files
by Ed Gronenschild 28 Mar '12

28 Mar '12

Hi Doug, These are Siemens DICOMs and I really don't know what happened to these T1 files, we just got them in this format. Only one out of 32 datasets went wrong, so I consider it as an incident. The workaround with dcm2nii worked fine. Nevertheless, if you are interested I can upload the dataset. Ed On 28 Mar 2012, at 15:47, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Message: 2 > Date: Tue, 27 Mar 2012 12:14:11 -0400 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Failure to convert DICOM files > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <4F71E753.3040504(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Is it a siemens dicom? If so, what happened to the ascii header? > Did you > do something to the file? What are the contents of the image? Eg, a > T1? > doug > > On 03/27/2012 05:35 AM, Ed Gronenschild wrote: >> Hi, >> >> I got an error during the first step in recon-all (Mac OS 10.6.8, >> FreeSurfer v5.1.0). The eror message in the log file is: >> >> WARNING: file ...../MR. >> 1.3.12.2.1107.5.2.18.41016.201008031106017688438785.dcm does not >> contain a Siemens ASCII header >> has this file been anonymized? >> ERROR: cannot unpack mosiacs without ASCII header. >> >> This is strange because it is no mosaic file and all the files can >> be converted >> without any problems with e.g., dcm2nii and viewed with OSIRIX. >> >> Cheers, >> Ed >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >

1 0

Research Fellow/Postdoc in Pain Neuroimaging, University of Michigan, Ann Arbor, MI
by Dasilva, Alexandre 28 Mar '12

28 Mar '12

Research Fellow/Postdoc in Pain Neuroimaging University of Michigan, Ann Arbor, MI The Headache and Orofacial Pain Effort (H.O.P.E.) requests applications for Research fellow/Postdoc. The research ranges from neuroimaging to non-invasive brain stimulation for primary headaches and orofacial pain. The projects are funded by grants from governmental, private and industry sectors. Knowledge of Linux/UNIX operating systems as well as programming experience is required, as is a good level of comfort with novel computer applications. Previous research experience, including positron emission tomography (mu-opioid and dopamine) and MRI-based neuroimaging methods and analyses, is highly desirable. We are also seeking applicants with strong self-motivation to work in a highly innovative, altruistic, and mentoring environment. Hence, the applicant should feel comfortable working with chronic pain patients (e.g., migraine, fibromyalgia and trigeminal neuralgia patients), and a multidisciplinary group of clinical and research collaborators. H.O.P.E. is a multidisciplinary collaborative effort at University of Michigan to investigate the brain as a research and therapeutic target for headaches and orofacial pain disorders. The University of Michigan is an equal opportunity affirmative action employer. Initially a curriculum vitae and letter of intent should be sent to: Alexandre F. M. DaSilva, DDS, DMedSc Director, Headache and Orofacial Pain Effort (H.O.P.E.) TM Biologic & Material Sciences, School of Dentistry The Molecular & Behavioral Neuroscience Institute (MBNI) adasilva(a)umich.edu<file:///x-msg/::71:adasilva@umich.edu>

1 0

wm edits
by Tetiana Dadakova 28 Mar '12

28 Mar '12

Dear FS list, After recon-all -all we had some wm missing in temporal part of the brain (fig. wm_missing1). We edited wm.mgz and re-run recon-all -autorecon2 -autorecon3. After this, the wm.mgz looks as fig. wm_missing2, but the surfaces still look as fig. wm_missing1. What can be the reason that wm.mgz edits didn't affect the surfaces? Thank you, Tanja.

3 7

Re: [Freesurfer] Error in fast_selxavg3 (line 254) XCond = cond(XtX);
by Douglas N Greve 27 Mar '12

27 Mar '12

You will have to mri_convert all the .nii files so that they have the proper TR. On 03/27/2012 12:51 PM, Kiley Seymour wrote: > Hi Doug. I just made a dummy folder with an eccen run. It got around > the error XCond = cond(XtX) but took me back to the original error : > TR mismatch error despite me re-doing the preprocessing and re- > mri_concat-enating my SPM nii files into a 4D file for each run. > > Do you think using mri_concat with --regheader could be the problem? > Or perhaps the fact that dicoms were converted to nii files in a > program that was not freesufer? > > K > > > On Tue, Mar 27, 2012 at 6:35 PM, Kiley Seymour > <kileyseymour(a)googlemail.com> wrote: >> no I don't. >> >> On Tue, Mar 27, 2012 at 6:17 PM, Douglas N Greve >> <greve(a)nmr.mgh.harvard.edu> wrote: >>> Do you not have any eccen runs? >>> doug >>> >>> On 03/27/2012 06:55 AM, Kiley Seymour wrote: >>>> Dear Doug, >>>> >>>> I am aware I am becoming a regular pain. But I now encounter the >>>> following problem when running selxavg3-sess -a rtopy.self.lh -s >>>> CMRU1711. I have also attached my analysis.info and Xtmp.mat files >>>> >>>> Thanks for all of your suggestions. >>>> >>>> K >>>> >>>> #@# CMRU1711 ############################### >>>> /media/sf_DATA1/RETINOTOPY/CMRU1711 >>>> ------------------------- >>>> $Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $ >>>> /home/virtualuser/freesurfer/fsfast/toolbox/fast_selxavg3.m >>>> /home/virtualuser/freesurfer/fsfast/toolbox/fast_ldanaflac.m >>>> /home/virtualuser/freesurfer/matlab/MRIread.m >>>> ------------------------- >>>> outtop = /media/sf_DATA1/RETINOTOPY >>>> Extension format = nii.gz >>>> nruns = 3 >>>> autostimdur = >>>> >>>> >>>> outanadir = /media/sf_DATA1/RETINOTOPY/CMRU1711/bold/rtopy.self.lh >>>> Found 138599/149490 (92.7) voxels in mask >>>> Creating Design Matrix >>>> ... creation time = 0.008 sec >>>> DoMCFit = 1 >>>> ntptot = 369, nX = 33, DOF = 336 >>>> Saving X matrix to >>>> /media/sf_DATA1/RETINOTOPY/CMRU1711/bold/rtopy.self.lh/Xtmp.mat >>>> Error using svd >>>> Input to SVD must not contain NaN or Inf. >>>> >>>> Error in cond (line 39) >>>> s = svd(A); >>>> >>>> Error in fast_selxavg3 (line 254) >>>> XCond = cond(XtX); >>>> >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve(a)nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)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. >>> > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

3 2

Re: [Freesurfer] Cortical Normalization Questions
by jorge luis 27 Mar '12

27 Mar '12

I think we must be careful about including noisy large scale measurements as global nuisance covariates in the General Linear Model (GLM). The GLM assumes that the independent variables are measured almost without error (eg. see http://en.wikipedia.org/wiki/Errors-in-variables_models) For instance, mean cortical thickness or mean global activity in fMRI (as the mean of many values) should not be as noisy as Intracranial Volume estimates (or the estimated volume of any neuroanatomical structure). -Jorge > > > >>________________________________ >> De: Anderson Winkler <andersonwinkler(a)hotmail.com> >>Para: freesurfer(a)nmr.mgh.harvard.edu >>Enviado: Lunes 26 de marzo de 2012 13:56 >>Asunto: Re: [Freesurfer] Cortical Normalization Questions >> >>Hi Jeff and all, >> >>For normalization (i.e., divide the measurement under study by some >>global measurement), I would not argue favourably, as this procedure can >>bias the results in the opposite direction if a global effect is present. >> >>Instead, include it as a covariate is not as harmful. My suggestion is, >>when there is no clear approach about using or not a global measurement >>as a nuisance, the relationships between the measurement under study, >>the independent variable, and the putative nuisance should be >>calculated, and models with and without the nuisance should be analysed >>and presented. The discussion should consider both analyses together, >>and enough information should be presented so that the final >>interpretation is left to the reader. >> >>Specifically for area, I suggest analysing and presenting two models: >>(1) without any global measurement and (2) with global area as nuisance. >> >>If brain volume (whichever way it is measured) is to be considered a >>potential nuisance for the disorder you are analysing, it can be >>included in the model #2 above, even given that they are not orthogonal >>to each other, and are related to global area. Non-orthogonality >>between the nuisance variables is not a problem as it is when effects of >>interest are involved. >> >>Hope this helps! >> >>All the best, >> >>Anderson >> >> >>On 23/03/12 11:29, Michael Harms wrote: >>> Our reply to that is here >>> http://bjp.rcpsych.org/content/196/5/414.2.long >>> >>> which reminded me of other papers that have also used a global thickness >>> measure to covary for mean cortical thickness and thereby "address whether >>> any regional thickness differences were in excess of global cortical >>> thickness differences between groups" -- see references [1,4] in our >>> Reply. >>> >>> cheers, >>> -MH >>> >>>> Hi Michael and others, >>>> >>>> maybe it's this one: >>>> >>>> http://bjp.rcpsych.org/content/196/5/414.1.long >>>> >>>> best, >>>> -joost >>>> >>>> >>>> On Fri, Mar 23, 2012 at 2:15 AM, Michael Harms >>>> <mharms(a)conte.wustl.edu>wrote: >>>> >>>>> Hi Jeff, >>>>> I personally like the idea of using average thickness as a covariate to >>>>> control for a reduction in "whole brain" thickness, and have used that >>>>> approach in a paper. If the Abstract that you mentioned indicated that >>>>> this is flawed, I'd be curious to know what the reason was... >>>>> >>>>> cheers, >>>>> -MH >>>>> >>>>> On Thu, 2012-03-22 at 21:00 -0400, Bruce Fischl wrote: >>>>>> Hi Jeff >>>>>> >>>>>> yes, I think this is still our recommendation for thickness, although >>>>>> perhaps David Salat can verify. As far as surface area, you might get >>>>>> Anderson Winkler to send you a preprint of his newly accepted paper on >>>>>> surface area comparisons and how to do them properly. I would have >>>>> said >>>>>> normalize by the 2/3 root of ICV (maybe David can comment on this as >>>>> well) >>>>>> cheers >>>>>> Bruce >>>>>> >>>>>> >>>>>> On Thu, 22 Mar 2012, Jeff Sadino wrote: >>>>>> >>>>>>> Hello, >>>>>>> For cortical thickness normalizations, Bruce said not to normalize >>>>> based on a HBM >>>>>>> abstract >>>>>>> ( >>>>> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06646.html) >>>>> Is >>>>>>> this still the consensus? >>>>>>> >>>>>>> For cortical volume, it is pretty standard to normalize to eTIV. >>>>>>> >>>>>>> For cortical surface area (jacobian), I couldn't find any >>>>> information >>>>> on the wiki. >>>>>>> Does anyone have any recommendations? >>>>>>> >>>>>>> Thank you, >>>>>>> Jeff >>>>>>> >>>>>>> >>>>>> _______________________________________________ Freesurfer mailing >>>>> list >>>>> Freesurfer(a)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(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 >>> >>> >> >>_______________________________________________ >>Freesurfer mailing list >>Freesurfer(a)nmr.mgh.harvard.edu >>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > >

2 1

Re: [Freesurfer] ERROR: could not determine file fieldsign
by Douglas N Greve 27 Mar '12

27 Mar '12

Did you run fieldsign-sess? If you don't have an eccen run you can't compute a fieldsign. doug ps. Please post emails to the list and not to me personally. Thanks! On 03/27/2012 04:07 PM, Kiley Seymour wrote: > Dear Doug, > > Thanks for all of your help today. I think I am almost there with this > retinotopy analysis. But the error below has halted me. I have > fieldsign folder, but only a fsig.nii.gz exists (i.e. no fieldsign > file) though. > > % tksurfer-sess -a rtopy.self.lh -s IFEE2211 -fieldsign > Surface self lh > Map Surface self lh > $Id: tksurfer-sess,v 1.16.2.1 2011/04/05 22:25:15 greve Exp $ > Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 > UTC 2009 i686 GNU/Linux > Tue Mar 27 15:46:22 EDT 2012 > /home/virtualuser/freesurfer/tktools/tksurfer > > list fieldsign > ERROR: could not determine file for > /media/sf_DATA1/RETINOTOPY/IFEE2211/bold/rtopy.self.lh/fieldsign/fieldsign > child process exited abnormally > > > On Tue, Mar 27, 2012 at 7:28 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu> wrote: >> You will have to mri_convert all the .nii files so that they have the proper >> TR. >> >> >> On 03/27/2012 12:51 PM, Kiley Seymour wrote: >>> Hi Doug. I just made a dummy folder with an eccen run. It got around >>> the error XCond = cond(XtX) but took me back to the original error : >>> TR mismatch error despite me re-doing the preprocessing and re- >>> mri_concat-enating my SPM nii files into a 4D file for each run. >>> >>> Do you think using mri_concat with --regheader could be the problem? >>> Or perhaps the fact that dicoms were converted to nii files in a >>> program that was not freesufer? >>> >>> K >>> >>> >>> On Tue, Mar 27, 2012 at 6:35 PM, Kiley Seymour >>> <kileyseymour(a)googlemail.com> wrote: >>>> no I don't. >>>> >>>> On Tue, Mar 27, 2012 at 6:17 PM, Douglas N Greve >>>> <greve(a)nmr.mgh.harvard.edu> wrote: >>>>> Do you not have any eccen runs? >>>>> doug >>>>> >>>>> On 03/27/2012 06:55 AM, Kiley Seymour wrote: >>>>>> Dear Doug, >>>>>> >>>>>> I am aware I am becoming a regular pain. But I now encounter the >>>>>> following problem when running selxavg3-sess -a rtopy.self.lh -s >>>>>> CMRU1711. I have also attached my analysis.info and Xtmp.mat files >>>>>> >>>>>> Thanks for all of your suggestions. >>>>>> >>>>>> K >>>>>> >>>>>> #@# CMRU1711 ############################### >>>>>> /media/sf_DATA1/RETINOTOPY/CMRU1711 >>>>>> ------------------------- >>>>>> $Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $ >>>>>> /home/virtualuser/freesurfer/fsfast/toolbox/fast_selxavg3.m >>>>>> /home/virtualuser/freesurfer/fsfast/toolbox/fast_ldanaflac.m >>>>>> /home/virtualuser/freesurfer/matlab/MRIread.m >>>>>> ------------------------- >>>>>> outtop = /media/sf_DATA1/RETINOTOPY >>>>>> Extension format = nii.gz >>>>>> nruns = 3 >>>>>> autostimdur = >>>>>> >>>>>> >>>>>> outanadir = /media/sf_DATA1/RETINOTOPY/CMRU1711/bold/rtopy.self.lh >>>>>> Found 138599/149490 (92.7) voxels in mask >>>>>> Creating Design Matrix >>>>>> ... creation time = 0.008 sec >>>>>> DoMCFit = 1 >>>>>> ntptot = 369, nX = 33, DOF = 336 >>>>>> Saving X matrix to >>>>>> /media/sf_DATA1/RETINOTOPY/CMRU1711/bold/rtopy.self.lh/Xtmp.mat >>>>>> Error using svd >>>>>> Input to SVD must not contain NaN or Inf. >>>>>> >>>>>> Error in cond (line 39) >>>>>> s = svd(A); >>>>>> >>>>>> Error in fast_selxavg3 (line 254) >>>>>> XCond = cond(XtX); >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> -- >>>>> Douglas N. Greve, Ph.D. >>>>> MGH-NMR Center >>>>> greve(a)nmr.mgh.harvard.edu >>>>> Phone Number: 617-724-2358 >>>>> Fax: 617-726-7422 >>>>> >>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)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. >>>>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer