Freesurfer

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30132 discussions

integrating FSL and Freesurfer
by noam Schneck 29 Aug '11

29 Aug '11

Hi, I am trying to use reg-feat2anat to register my Feat analyses to anatomical images and running into a number of problems. 1) When I check the registration of the mean_func to the anatomical in tkregister2 it looks fine. But when I overlay the fsl statmaps onto the anatomical brain they extend outside of boundaries of the anatomical brain. 2) Also, before using reg-feat2anat. I was trying to do the EPI_2_structural registration in FLIRT with the fsl.mat produced by BBR. When I try this the registered image is rotated 90 degrees from the original image. Why does that happen? 3) I also noticed that if I look at the header information for an image in fslhd and mri_info the orientations are flipped. If the fslhd orientation is RAS it will be LPI in mri_info. Could this be related to what is happening in question (2)? Best, Noam

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use MNI152 normalized images in segmentation
by tony han 29 Aug '11

29 Aug '11

Dear all, I'm just learning Freesurfer and want to import output files of Freesurfer into Carat so that I can generate individual surface. I already have my functional and anatomical images preprocessed (realign, coregister, segment and normalize) in spm5. So the anatomical have been normalized into MNI152 space. Is it ok if I keep these anatomical images normalized in spm5 without using MNI305 during segmentation in Freesurfer ? Or I have to go through all autorecon processing stages? If it's ok, could you tell me specifically how to do this? all the best, Tony

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Fwd: Re: Defining an mrs voxel in the anatomical dataset for partial volume correction
by _andreia_＠sapo.pt 29 Aug '11

29 Aug '11

Hello all! I got no answer on this email, thus I'm posting these questions again, hoe someone can help: Hello! About synthesising a volume using mri_volsynth with direction cosines and RAS from mrs header: In the mrs header I have: - VOI position in the 3 views (sag, cor and tra) which are from the left upper corner of the voxel (these are the RAS coordinates that I need to feed into mri_volsynth, correct?) - position vectors [0] [1] [2] - row and columns vectors (but I think that these are not the ones used to get the direction cosines, is that right?) - VOIRotationInPlane - and I know that my voxel is 3x3x3 cm How do I introduce these infos in mri_volsynth to have a 3x3x3 cube to coregister with the anatomical? Typing mri_volsynth --help I got lots of asked information and I don't know how to feed into it. Also, for defining the geometry the "center" voxel and the first voxel are needed. Shouldn't it be only the RAS of the corner of the voxel? Also, all these infos are in the scanner space, and the anatomical image processed in FS is spacially transformed. What should I use to coregister the synthesized volume to the processed anatomical to get the same transformation in the 3x3x3 volume? Can you give me an example of how this process is done? Thank you very much! Andreia > Hi Doug, > > Ok. Thank you! :) > > Andreia > > Citando Douglas N Greve <greve(a)nmr.mgh.harvard.edu>: > >> Yes, that should work. You will need a registration matrix to give to >> mri_compute_volume_fractions. You can get this from tkregister2: >> >> tkregister2 --mov mrs.vol.nii --s subject --regheader --reg register.dat >> >> when you run this, hit the compare button to make sure that the mrs box >> falls on the part of the anatomical you think it should be. Then hit >> "Save" to save the registration. >> >> doug >> >> _andreia_(a)sapo.pt wrote: >>> Hi Doug, >>> >>> This already sheds some light on the issue! I didn't know >>> mri_volsynth, I'm a begginer in FS. Lets see if I got it right. I have >>> the anatomical and the MRS data acquired in the same session, so I >>> won't need the EPI. If I manage to create the MRS volume using the >>> header info and mri_volsynth I only need to coregister my anatomical >>> with the synthetised volume and then run mri_compute_volume_fractions >>> through the synthesed volume and the identity matrix (?) (since my >>> data are from the same session) to get the % of the different tissue >>> types only inside the voxel. Of course I'll need more advice on this >>> later, but one thing at a time. >>> >>> Thanks! >>> Andreia >>> >>> >>> >>> Citando Douglas N Greve <greve(a)nmr.mgh.harvard.edu>: >>> >>>> Sorry, I don't know anyone who can help with that. As you note, people >>>> do it, so there must be people around who can extract the relevant >>>> information out of the header. The information you need are the >>>> direction cosines and RAS of the corner of the voxel. You can feed this >>>> into mri_volsynth. >>>> >>>> To register to FS, you'll need to have a whole-brain volume collected >>>> during the same session. If you collected the anatomical analyzed in FS >>>> at the same time, then you don't need another. If you did not, you can >>>> literally use any whole brain acquisition, eg, a single TR of an EPI >>>> (less than 10 sec to acquire). You can then register the EPI to the >>>> anatomical with bbregister. This gives you a "register.dat". You can >>>> then concatenate that with the EPI-MRS registration (I can show you >>>> how). After that, you can run mri_compute_volume_fractions passing it >>>> the synthesized volume and the register.dat (or identity matrix if same >>>> session). >>>> >>>> Another alternative is to collect an actual MRI volume that spans your >>>> MRS volume. You can then substitute that for the synthetic volume. Note >>>> that the actual pixel content of this volume is irrelevant -- it's just >>>> used to get geometry information out of it. This will be the easiest if >>>> you can do it. >>>> >>>> doug >>>> >>>> _andreia_(a)sapo.pt wrote: >>>>> Hi Doug, >>>>> >>>>> Do you know who can help me with this? That's exactly what I think >>>>> that I need to do... The thing is that, unfortunately, I can't find >>>>> anyone who can describe how the creation of an MRI "volume" from the >>>>> MRS voxel is done, although this approach is present in many many >>>>> papers. >>>>> >>>>> About the second part, how do I register the synthetized MRI "volume" >>>>> to the FS anatomical? And how can I get the volumes of only that >>>>> "volume"? >>>>> >>>>> (Hopefully I'll find a way to do the first part...) >>>>> >>>>> Thanks, >>>>> Andreia >>>>> >>>>> >>>>> >>>>> >>>>> Citando Douglas N Greve <greve(a)nmr.mgh.harvard.edu>: >>>>> >>>>>> Hi Andreia, I've done this before using information in the >>>>>> spectroscopy >>>>>> header, then synthesizing an MRI "volume" with one voxel that >>>>>> covers the >>>>>> size of your spectroscopy voxel, then registering that to the FS >>>>>> anatomical, then computing the partial volume fractions from the >>>>>> anatomical. The hard part is the first step, which I can't really >>>>>> advise >>>>>> you on. >>>>>> >>>>>> doug >>>>>> >>>>>> _andreia_(a)sapo.pt wrote: >>>>>>> Dear list, >>>>>>> >>>>>>> I am performing single-voxel and multivoxel spectroscopy analysis and >>>>>>> I need to do partial volume correction. I found a thread on the list >>>>>>> of someone asking if it possible to achieve this using Freesurfer >>>>>>> (see >>>>>>> below), but there is no answer saying how it is done. My question is >>>>>>> how can I define the voxel (for single-voxel) and the chosen voxels >>>>>>> (for multivoxel) in the anatomical data set to use the >>>>>>> segmentation of >>>>>>> only that defined voxel? I'm using a Siemens TrioTim 3T. All >>>>>>> acquisitions are in the same session. The anatomical dataset is an >>>>>>> average of 2 MPRAGEs which I've already processed using FS, and the >>>>>>> spectra files are .rda. The header of the MRS data has info on >>>>>>> vectors, but I don't know how to use them. >>>>>>> >>>>>>> >>>>>>> >>>>>>> "Re: [Freesurfer] need info for beginner >>>>>>> >>>>>>> Bruce Fischl >>>>>>> Thu, 26 Apr 2007 11:17:01 -0700 >>>>>>> >>>>>>> Hi Pom, >>>>>>> >>>>>>> yes, people here are using it for spectroscopy and for partial volume >>>>>>> correction (also for voxel placement). >>>>>>> >>>>>>> cheers, >>>>>>> Bruce >>>>>>> >>>>>>> On Thu, 26 Apr 2007 [EMAIL PROTECTED] wrote: >>>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> I am about to install FREE SURFER for my Spectroscopy work. >>>>>>> I want to use the software to perform GM/WM segmentation on my >>>>>>> single voxel data sets. >>>>>>> >>>>>>> I am wondering if any one on this mailing list is currently >>>>>>> doing this task. I would like to get comments. >>>>>>> >>>>>>> My study is on a GE 3T scanner. >>>>>>> >>>>>>> thank you, >>>>>>> >>>>>>> Pom" >>>>>>> >>>>>>> >>>>>>> >>>>>>> Any advice, please? >>>>>>> >>>>>>> Thank you! >>>>>>> >>>>>>> Andreia >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> >>>>>>> Andreia Pereira, MSc student >>>>>>> Visual Neuroscience Laboratory >>>>>>> IBILI-Faculdade de Medicina >>>>>>> Azinhaga de Santa Comba >>>>>>> 3000-354 Coimbra Portugal >>>>>>> Phone +(351) 239480220 >>>>>>> Fax +(351) 239480280 >>>>>>> >>>>>>> ------------------------------------------------------------------------ >>>>>>> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> 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 >>>> >>>> _______________________________________________ >>>> 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 >> > > > > -- > > Andreia Pereira, MSc student > Visual Neuroscience Laboratory > IBILI-Faculdade de Medicina > Azinhaga de Santa Comba > 3000-354 Coimbra Portugal > Phone +(351) 239480220 > Fax +(351) 239480280 -- Andreia Pereira, MSc student Visual Neuroscience Laboratory IBILI-Faculdade de Medicina Azinhaga de Santa Comba 3000-354 Coimbra Portugal Phone +(351) 239480220 Fax +(351) 239480280

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ERROR: Option ‐‐hemi unknown for mri_surf2surf
by xian zhang 29 Aug '11

29 Aug '11

Dear Freesurfers: mri_surf2surf  ‐‐hemi  lh  ‐‐s  fsaverage  ‐‐sval  att-lh-thickness.mgh ‐‐fwhm  10  ‐‐tval  att-lh-thickness.10.mgh I got error " command not found" or "ERROR: Option  ‐‐hemi unknown" although I can do mri_surf2surf  ‐‐help with not problem I checked fsaverage, OK but my att-lh-thickness.mgh is not inside the fsaverage folder the result of unix "ls" command is att-lh-thickness.mgh fsaverage Is there a tutorial data so that I can go through group analysis step by step? Thanks!

2 1

Cortical thickness - again
by Ed Gronenschild 29 Aug '11

29 Aug '11

Hi, How do you compute the cortical thickness for each structure as listed in the ?h.aparc.stats file? Is it equal to the thickness at each vertex averaged over all vertices within the structure? Ed

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two questions regarding qdec and conjunction analysis is FS
by Tetiana Dadakova 29 Aug '11

29 Aug '11

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. 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? Thank you for your time and help, Tanja.

3 2

Accuracy of FreeSurfers gray matter segmentation
by Lucas Eggert 29 Aug '11

29 Aug '11

Dear List, I recently posted the message you see below. I currently compare the segmentation results of different segementation algorithms and FreeSurfer always yields the least accurate results. Because I still have difficulties to decide which of the labels in the aseg.mgz files should be considered gray matter, I have the feeling, the bad results I am getting for FreeSufer might be caused by not including all relevant gray matter segments. So, I would very much appreaciate any help on deciding which of the labels in the aseg.mgz file belong to gray matter! With kind regards Lucas Eggert -------- Original-Nachricht -------- Betreff: [Freesurfer] How to determine gray matter in the aseg.mgz Datum: Tue, 03 May 2011 17:26:55 +0200 Von: Lucas Eggert <leggert(a)Uni-Osnabrueck.DE> An: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Dear Experts, I would like to generate a gray matter mask using the aparc+aseg.mgz file. Now, my question is whether there exists a file in addition to the FreeSurferColorLUT.txt file, which more explicitly, i. e., withouth the abbreviations, explains the labels, because I find it hard to decide whether, e. g., "Left-VentralDC", "Line1", "LeftmOg", or "Left-Interior" belong to gray matter, or not (to name only a few of those labels I cannot clearly classify). Or is there a easier way to create a gray matter mask? Thank you very much in advance! Best regards, Lucas Eggert -- Lucas Eggert, M.Sc. Institute of Cognitive Science University of Osnabrueck Albrechtstrasse 28 D-49076 Osnabrueck Germany Phone: +49-541-969-44-28 Website: http://www.cogsci.uni-osnabrueck.de/~leggert/

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Correlation cortical thickness and lgi
by dolphinede＠aol.com 29 Aug '11

29 Aug '11

Dear freesurfer experts, I have finsihed my lgi analyzes with qdec. In the next step I want to make a correlation between lgi and cortical thickness. Is this possible with qdec and if it is how can I do that? Best regards and thanks a lot. Daniel Klein

3 2

problem with selxavg3
by Maryam Vaziri Pashkam 29 Aug '11

29 Aug '11

Hi, I am encountering a memory allocation error with selxavg3-sess and I am not sure how to get around it: Here is the lines that I am running mkanalysis-sess -analysis FHPDM_noauto -TR 2 -paradigm allpara.par -designtype event-related -funcstem fmc -motioncor -runlistfile FHPDM_runlist.txt -inorm -nconditions 8 -timewindow 20 -TER 2 -polyfit 2 -mcextreg -noautostimdur -force selxavg3-sess -s 110821_xu_FHPDM_02 -df sessdir -analysis FHPDM_noauto It is a single subject data with 12 runs, event related design that each event last for about 4 seconds and the total experiment time is 328 seconds( at TR=2 is equal to 164 TRs) My computer is a MAC with 4 gb of ram. and I am running freesurfer 4.5. I have ran similar analysis on the same number of runs but much longer events (12 sec) before and have not had a problem. This is the first time I am analyzing data for this particular experiment though. Here is the error line that I get: mri_fwhm(2138) malloc: *** mmap(size=16777216) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(70, 70, 33): could not allocate 19600 bytes for 49364th slice voxelvolume 35.3062 mm3 Loading mask /Users/maryam/mri-space/studies/FHPDM/unpackdata/110821_xu_FHPDM_02/bold/FHPDM_noauto/mask.nii Search region is 60647 voxels = 2141216.616840 mm3 Polynomial detrending, order = 0 Detrending Cannot allocate memory [dhcp-0170571539-df-00:st Can anyone help? Thanks, Maryam

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FW: Cortical Flattening
by Tax, C.M.W. 29 Aug '11

29 Aug '11

Dear all, Would it be possible to create a virtual CentOS environment on Ubuntu? Since the computer is used in clinic, it's hard to change. I hope there is some easier solution... Thank you in advance! -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: maandag 29 augustus 2011 15:38 To: Tax, C.M.W. Subject: RE: [Freesurfer] Cortical Flattening Hi Chantal, can you post this to the list so that Nick or Krish (or others) can answer? thanks Bruce On Mon, 29 Aug 2011, Tax, C.M.W. wrote: > Dear Bruce, > > Would it be possible to create a virtual CentOS environment on Ubuntu? Since the computer is used in clinic, it's hard to change... > > Thank you > > -----Original Message----- > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Sent: donderdag 25 augustus 2011 14:41 > To: Tax, C.M.W.; Nick Schmansky; Krish Subramanian > Subject: Re: [Freesurfer] Cortical Flattening > > Nick and Krish: any ideas? > > > > On Aug 25, 2011, at 2:03 AM, "Tax, C.M.W." <c.m.w.tax(a)student.tue.nl> wrote: > >> Dear Bruce, >> >> Thank you for your response. I'm working on ubuntu version 10.04 indeed, one computer 32b and the other 64b. Is there any way how I could solve this problem? >> >> Regards, >> Chantal >> ________________________________________ >> Van: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] >> Verzonden: woensdag 24 augustus 2011 23:23 >> Aan: Tax, C.M.W. >> CC: freesurfer(a)nmr.mgh.harvard.edu >> Onderwerp: Re: [Freesurfer] Cortical Flattening >> >> Louis just pointed out to me what the thread was about. What operating >> system are you running on? This seems to be a problem in the depths of >> openGL on ubuntu. We haven't seen it on CentOS or red hat. >> >> Bruce >> On Wed, 24 Aug >> 2011, Bruce Fischl wrote: >> >>> Hi Chantal, >>> >>> what went wrong? Sorry, I've lost this thread. >>> >>> cheers >>> Bruce >>> >>> >>> On Wed, 24 Aug 2011, Tax, C.M.W. wrote: >>> >>>> Dear Doug, >>>> >>>> Tank you for your response. The freesurfer wikipage I was following: http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOccipitalFlattenedPatch >>>> Do I have to do some additional steps? >>>> >>>> Thank you in advance, >>>> Regards, >>>> Chantal >>>> _______________________________________________ >>>> 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 >>> >>> >>> >> >> >> 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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