Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

Help getting outer bits of brain
by Jake Freimer 31 Jul '06

31 Jul '06

I ran through autorecon1 and 2 for two subjects using the dicom images. One came out ok, but one is still missing some brain (as seen in the attached screen shots). I was wondering if there was a way to change the settings autorecon uses, because our scanner makes the inside so much brighter, or a way to batch convert rather than edit control points on all our subjects. Thanks -- -Jake

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skullstrip
by dasoscia＠buffalo.edu 31 Jul '06

31 Jul '06

I keep getting this error when trying to skullstrip a scan... *************************WATERSHED************************** preflooding height equal to 25 percent Sorting... T1-weighted MRI image modification of the preflooding height to 15 percent Count how many 110 voxels are present : 53463 Find the largest 110-component... heap usage = 133076 Kbytes. removing small segments (less than 1 percent of maxarea).done And identify it as the main brain basin...done Main component: 46289 voxels first estimation of the COG coord: x=124 y=107 z=123 r=86 first estimation of the main basin volume: 2722274 voxels ******************************************* *********************************************** *********************************************** White matter intensity 4 is lower than CSF intensity 24. Please examine input images. Will terminate ... *********************************************** *********************************************** *********************************************** ********************************************************** MRIstripSkull failed. ************************************************************ Linux localhost.localdomain 2.6.9-5.ELsmp #1 SMP Wed Jan 5 19:29:47 EST 2005 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Mon Jul 31 11:25:35 EDT 2006 Attached are some slices from my T1 images, numbered according to coronal slice number. I noted that they do look a little odd/different than previous scans. Suggestions? Thanks Dave

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caudate/putamen values for mri_segstats
by Nguyen, Thang Q 28 Jul '06

28 Jul '06

Hello all, I used mri_segstats to get subcortical volumes my subjects. However, for some of the regions like the putamen and caudate, I get values of zero. I have been told that these values are either no longer in use or have not been in use yet. Is there a way of manually getting values for these regions? Thank you for all the help, -Thang

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Total Brain Volume
by Anil Roy 28 Jul '06

28 Jul '06

Hello All, Does freesurfer generate a file with total brain volume after the recon-all procedure? Where can this be accessed? Thanks, AR.

3 2

GLIBCXX
by Chacko Cherian 28 Jul '06

28 Jul '06

Hello all, Could someone please clarify why this library cannot provide the correct 'GLIBCXX_3.4'. Thanks in advance. Chacko. mri_watershed -keep brainmask.auto.mgz brainmask.mgz brainmask.mgz T1.mgz brainmask.auto.mgz mri_watershed: /usr/lib/libstdc++.so.6: version `GLIBCXX_3.4' not found (required by mri_watershed) Linux ibmlnx4 2.4.21-32.0.1.ELsmp #1 SMP Tue May 17 17:52:23 EDT 2005 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Fri Jul 28 09:35:51 MST 2006 __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Freesurfer reconstruction- MPRAGE with iPAT On
by Nandita Shetty 28 Jul '06

28 Jul '06

Hi, I had a question regarding the MPRAGE sequences. Does freesurfer work effectively with sequences that have iPAT on? If yes, could you tell me which one of the MPRAGE sequences (available at MGH) has the shortest acquisition time? Nandita

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RE: [Freesurfer] Edit label
by Goradia, Dhruman D 27 Jul '06

27 Jul '06

Hello Rahul, Thank you for your reply. I tried to combine the different regions to create one label for each lobe but could not figure it out. Can you suggest how I can combine different regions using tksurfer? Is there a wiki page where the steps are explained? Thank you -Dhruman -----Original Message----- From: Rahul Desikan [mailto:rahul@nmr.mgh.harvard.edu] Sent: Thursday 27 July 2006 15:15 To: Goradia, Dhruman D Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Edit label Hi Dhruman, If you are interested in lobe-wise comparisons, you can indeed add up the individual regions of a specific lobe, create one massive label for that lobe, and get statistics on those. For example, if you were interested in the temporal lobe, you could combine: lateral occipital cuneus lingual pericalcarine and generate an *h.occiptal.label (you can use tksurfer to combine the regions). You could do the same for the other labels and thus create a 'lobe based' parcellation. Once you are done, you can use mris_anatomical_stats to generate stats on the new labels you have generated. best, Rahul On Thu, 27 Jul 2006, Goradia, Dhruman D wrote: > Hi all, > > I am interested in lobe wise surface measurement. I read Desikan et al. > paper to understand that their atlas divides the lobes into different > region and freesurfer uses that atlas to gets measurement for each > region. Is it possible to load the Desikan label and edit it to fuse all > the region belonging to each lobe and create a new label, which I could > use to get surface measurement? Thanks in advance. > > Dhruman > > --

4 3

Edit label
by Goradia, Dhruman D 27 Jul '06

27 Jul '06

Hi all, I am interested in lobe wise surface measurement. I read Desikan et al. paper to understand that their atlas divides the lobes into different region and freesurfer uses that atlas to gets measurement for each region. Is it possible to load the Desikan label and edit it to fuse all the region belonging to each lobe and create a new label, which I could use to get surface measurement? Thanks in advance. Dhruman

2 2

About FreeSurfer
by M SAMANTA 27 Jul '06

27 Jul '06

Hello, I am interested in using FreeSurfer for my task. I have read the site about getting started. I would like to know if FreeSurfer is supported by SGI IRIX and if it is raster based imaging or understands it? I need to know specifically if TIFF images can be supported by FreeSurfer. Thanks, Ruma

2 1

recon-all exited with errors
by Chacko Cherian 27 Jul '06

27 Jul '06

Hello all, I was running recon-all for one of my images and this happened to be the error that i got.Could someone please clarify, Thanks in advance Chacko. "mri_watershed: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory Linux elmo 2.6.12.1 #2 Thu Jul 14 11:14:31 MST 2005 i686 unknown unknown GNU/Linux recon-all exited with ERRORS at Wed Jul 26 13:09:41 MST 2006" __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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