Freesurfer August 2011

freesurfer@nmr.mgh.harvard.edu

124 participants
212 discussions

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

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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. >> >> >> > > >

1 0

patch present-label missing
by maahmed＠mappi.helsinki.fi 29 Aug '11

29 Aug '11

Hi, I did the recon-all using the same case and the same freesurfer edition twice. The second processing I did was missing the label : Medial_wall-rh.label I have the same problem with 20 other cases. I uploaded an image of the first and second attempt here : http://tinyurl.com/3p52zrj You will notice that in the second one, the patches definition is poor around the medial surface of the hemisphere.Is this the problem ?and if so, how can i tackle it ? Can i label the medial patch manually ? Thank you, Mostafa Abdelgawad

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tkmedit: Extending white matter and pial surfaces
by Michelle Umali 27 Aug '11

27 Aug '11

Hi Freesurfers, When looking at the surfaces in tkmedit, I noticed that quite a bit of the tip of the temporal lobe was not included in pial/wm surfaces. I need to extend both surfaces. In what order does one do the edits? Does one paint in wm voxels first or pial first? Thanks. Michelle

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Re: [Freesurfer] Hippocampal volumes measured by Freesurfer 4.3.0 vs 4.5
by Thomas Yeo 27 Aug '11

27 Aug '11

I might be wrong, but it's generally not recommended to compare data across different freesurfer versions. --Thomas On Sat, Aug 27, 2011 at 5:08 PM, Thomas Yeo <yeoyeo02(a)gmail.com> wrote: > I might be wrong, but it's generally not recommended to compare data across > different freesurfer versions. > > --Thomas > > On Sat, Aug 27, 2011 at 6:59 AM, Bayley, Peter J. <Peter.Bayley(a)va.gov>wrote: > >> Hi,**** >> >> ** ** >> >> I would like to merge two datasets containing volumetric data from two >> different versions of Freesurfer (4.3.0 and 4.5). I am only interested in >> looking at volumes of hippocampus, entorhinal cortex, and whole brain. A >> cursory look at the release notes for versions 4.4 and 4.5 suggests that v. >> 4.3.0 and v. 4.5 are quite similar as most updates involved bug fixes. >> However, v 4.5 involved an updated C.Destrieux atlas. Does anyone know of >> any problems when comparing data generated by v. 4.3.0 and v. 4.5 ?**** >> >> ** ** >> >> Thanks**** >> >> ** ** >> >> Peter Bayley**** >> >> _______________________________________________ >> 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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Hippocampal volumes measured by Freesurfer 4.3.0 vs 4.5
by Bayley, Peter J. 26 Aug '11

26 Aug '11

Hi, I would like to merge two datasets containing volumetric data from two different versions of Freesurfer (4.3.0 and 4.5). I am only interested in looking at volumes of hippocampus, entorhinal cortex, and whole brain. A cursory look at the release notes for versions 4.4 and 4.5 suggests that v. 4.3.0 and v. 4.5 are quite similar as most updates involved bug fixes. However, v 4.5 involved an updated C.Destrieux atlas. Does anyone know of any problems when comparing data generated by v. 4.3.0 and v. 4.5 ? Thanks Peter Bayley

1 0

about correction of inhomogeneity
by Xiaoying Tang 26 Aug '11

26 Aug '11

Hi All, I am now trying to do inhomogeneity correction for T1 images. I find that there are two commands: nu_correct and mri_nu_correct.mni in Freesurfer. I am not sure about the difference between these two commands. To me, they seem to be the same.... I would be glad if someone could answer my question. Best, Xiaoying

1 0

Freesursfer versions and Linux CentOS versions
by Alexopoulos, Dimitrios 26 Aug '11

26 Aug '11

I have a few questions related to Freesursfer versions and Linux CentOS versions. We have we processed some data (i.e. generated surfaces using -autorecon 1 -autorecon2, and then GM and WM surface-based volumes using mris_anatomical_stats and mris_wm_volume, respectively), using the build 'freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0' on our linux server that was running CentOS 4. We have recently upgraded the server OS to CentOS 5.6. We now would like to modify the segmentations/surfaces and was wondering whether we can use the same build (freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0) on CentOS5.6 or do we need to install 'freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0' ? Are there any issues with processing data using 'freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0' on CentOs4 then modifying this data with 'freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 on CentOs5 Comments? Thanks. The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email.

2 1

DTI and Fresurfer
by Antonella Kis 26 Aug '11

26 Aug '11

Dear All, I would like to do DTI analysis on my subjects data. I finished the pre-processing using recon-all and also I used GLm for the group study. Can you please let me know how I can do DTI analysis using FSL in Freesurfer? What steps I need to follow? Many thanks, Antonella

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Freesurfer August 2011