Freesurfer

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19 participants
30132 discussions

question 2 about using control points
by Mehul Sampat 24 May '10

24 May '10

Hi Folks, We noticed that some WM was left out from the yellow surface. But when we look at wm.mgz these values of these voxels are in the range 80-95 (shown in the figure) In such cases should we remove these voxels from wm.mgz (using the right click option) and then include them again ? That is, this would change the voxel values from 80-95 to 255.. I ask this because sometimes, we see that the yellow surface is clipped but there is nothing to include in the wm.mgz since the corresponding voxels do have some intensity values in the range 75-90. Please let me know if you need more information/clarification about this question. thanks Mehul

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question 1 about using control points
by Mehul Sampat 24 May '10

24 May '10

Hi Folks, One of my colleagues had the following issue while using control points. He re-processed the case after adding some control points (shown in the first figure), but after doing so, the WM was still not included. Is this a typical case, where it would be better to edit wm.mgz instead of adding control points. thanks Mehul

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wm correction issues
by Ilana Hairston 24 May '10

24 May '10

Hi there. we have been doing some white matter corrections, based on the wiki instructions. After filling in some missing voxels we ran ...autorecon2-wm autorecon3 ... but it doesn't look like the white matter was corrected. See the attached to images with the wm.mgz and brainmask after the autorecon steps. the corrected area is marked with a red circle thanks ilana

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Error message in opening OSX 10.5 version image disk of FS
by Danilo Scelfo 24 May '10

24 May '10

Hi there, I'm using a Mac OS X 10.6.3. I tried to install the freesurfer-Darwin-leopard-i686-stable-pub-v4.5.0-full.dmg but I'm not allowed/able to open it, getting the error message "invalid checksum". Is it something up to the image disk version (i.e. do I need to use a *v4.6.3-full.dmg image?) or is it something up to my Mac? Thanks for your interest. Sincerely, Danilo Scelfo.

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Creating annotation file for lobar regions...
by Rudolph Pienaar 24 May '10

24 May '10

Hi all -- Is there a simple way to create an annotation for frontal/temporal/occipital/parietal lobes based off the ?h.aparc.annot files in a FS 'label' dir? Ideally speaking, I'd like to have a ?h.lobar.annot with corresponding lobar.annot.ctab. Apologies if this question has come up before... a quick google didn't reveal anything. Many thanks -=R -- Rudolph Pienaar, M.Eng, D.Eng / email: rudolph(a)nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA

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recon-all ERROR reading wm.seg.mgz when doing routine correction processing
by Stacey M Schaefer 24 May '10

24 May '10

Hello Freesurfer List Gurus, We're at the stage of making white matter edits and adding control points, but one of my subjects recently produced the following error: zcat: /study/midus/data/mri/processed/freesurfer/subject057/mri/wm.seg.mgz: unexpected end of file mghRead(/study/midus/data/mri/processed/freesurfer/subject057/mri/wm.seg.mgz): could not read 65536 bytes at slice 90 mri_segment: could not read file wm.seg.mgz to preserve edits Linux cashew.keck.waisman.wisc.edu 2.6.18-164.6.1.el5 #1 SMP Tue Nov 3 23:11:58 EST 2009 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Tue May 18 21:04:35 CDT 2010 Any suggestions on how to fix? This subject has already had a great deal of hands on processing in terms of adding control points, editing the white matter, and running recon_all to fix, with multiple passes to get it as perfect as possible. Also, I've TRIED just rerunning recon-all on it, but the errors persist. (Each time, we're running the following command: recon-all -autorecon2-cp -autorecon3 -subjid subject057) Any and all info on how to salvage this subject's data without have to start from scratch will be much appreciated! Thank you. Stacey Schaefer --------------------------------------------------- Stacey M. Schaefer, Ph.D. Waisman Laboratory for Brain Imaging and Behavior University of Wisconsin - Madison 1500 Highland Ave Rm T127 Madison, WI 53705 Waisman Phone: 608-263-9321 Laboratory for Affective Neuroscience UW Psychology Dept, Brogden 1202 W Johnson St Rm 392 Madison, WI 53706 Brogden Phone: 608-262-9937

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release v5.0.0
by Jose Luis Cantero Lorente 24 May '10

24 May '10

Hi there, does anybody know when the Freesurfer release v5.0.0 will be downloadable? Best, Jose --- Jose L. Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor(a)upo.es http://www.upo.es/neuroaging/en/

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up-sampling by mri_convert
by EDSB EDSB 24 May '10

24 May '10

Hi all, I have a question on the mri_convert command. I should up-sample my dataset (a list of COR files contained in the folder T1) that has a matrix of 256 x 256 x 256 and a voxel size of 1 mm. I'm using the command mri_convert --in_orientation LIA -ois 0.1 -ojs 0.1 -oks 0.1 T1 T1_resampled.nii In effect I obtained the resampled image but the final dimension is still 256 x 256 x 256, so my image result cropped. how can I obtain the entire field of view? Thanks in advance for your help Paolo Landini _________________________________________________________________ Spazio gratis di 25 Gigabyte per archiviare ciò che vuoi http://www.windowslive.it/skyDrive.aspx

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FW: labels don't match with tkmedit and tksurfer
by Prapti Gautam 23 May '10

23 May '10

Dear all, Reposting the following question again, Thanks, To: freesurfer(a)nmr.mgh.harvard.edu Subject: labels don't match with tkmedit and tksurfer Dear FreeSurfers, I am having some problems creating a label in tksurfer and subsequently converting it into a volume file. I have created a custom label in a test subject using tksurfer which loads correctly onto the surface when viewed with tksurfer. However, when I load the label into tkmedit in the same subject - it seems to be labelling regions that are not on the surface of the brain, but lie somewhat haphazardly in the cortex near the surface. Do you know why this is happening? I further need to convert the label into a volume file and have used mri_label2vol to do this. Mri_label2vol -- label subject/label/pfc.label -temp subject/mri/brainmask.mgz --o subject/label/pfc.mgz However, perhaps since I can see that the label does not sit correctly on the surface in tkmedit, the volume file is also not on the cortical surface, but runs below it. Can anyone point me in the right direction as to where I might be going wrong? Thanks, Prapti

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Re: [Freesurfer] Roi label mapping
by Lena Palaniyappan 23 May '10

23 May '10

Dear Martin I believe QDEC design currently allows only DODS for my model nevertheless, will this produce gross differences as I am observing? Thanks for your help Lena On 23/05/2010 18:42, "Martin Kavec" <martin.kavec(a)gmail.com> wrote: > Hi Lena, > > One can do a DODS (different offset different slope) and DOSS (different > offset same slope) GLM analysis in qdec. Did you take this into account in > your ROI analysis? > > Cheers, > > Martin > > On Sun, May 23, 2010 at 7:09 PM, Lena Palaniyappan > <Lena.Palaniyappan(a)nottingham.ac.uk> wrote: >> While doing an age corrected qdec comparison between two groups, the analysis >> resulting from ¹Does the average thickness differ between two gps¹ showed >> some potential areas of interest. I then created labels from these areas and >> mapped them back to all subjects. But when I extracted thickness values and >> looked at the means, I could not see the same direction of effect why could >> this be? Is this a problem with smoothing (I used FWHM 20 for looking at >> whole brain comparisons) >> >> Cheers >> Lena >> >> _______________________________________________________ >> Lena Palaniyappan >> PhD student & Honorary StR | Division of Psychiatry ( University of >> Nottingham) >> South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH >> >> >> >> This message has been checked for viruses but the contents of an attachment >> may still contain software viruses which could damage your computer system: >> you are advised to perform your own checks. Email communications with the >> University of Nottingham may be monitored as permitted by UK legislation. >> >> _______________________________________________ >> 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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