Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30132 discussions

Analyze 7.5 hdr into .mat file
by SG KIM 09 Apr '10

09 Apr '10

I want to import anlayze75 with a right direction (still). I have those files: subject.hdr subject.img And got warnings as: -------------------------- INFO: could not find ~/subject.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in ~/subject.mat file -------------------------- I know the orientation info should be provided somehow; but I don't know how to do it. I just tried to make a corresponding MAT file containing header info by simply saving whole header info as >>HRD=analyze75info('subject.hdr'); >>save subject.mat HDR But I got another error as ----------- unsupported matlab format 262149 (unknown) MatrixMultiply: m1 cols 1 does not match m2 rows 4 Segmentation fault ----------- *Does someone who handled Analyze75 format before know how to create a corresponding MAT file?* SG. +I firstly tried import without MAT file, then I worked but with a wrong direction (fig1). I checked the header file. It says 'Transverse unflipped' as default, which is also perplexing because the import was made using the default orientation 'Transverse unflipped' anyway.

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Retinotopy with bow ties
by Peter Jes Kohler 08 Apr '10

08 Apr '10

Hello Everyone, I am a new FreeSurfer user, trying to do retinotopy. My stimulus has the following configurations: - 96 TRs in total per run, including 8 blanks in the beginning and 8 in the end - Polar angle: - bowtie checkerboard wedges - 16 unique positions - 5 repetitions per run - 2 TRs per position per run = 80 stimulus TRs per run. - counterclockwise or clockwise rotation - Eccentricity - checkerboard annuli - 16 unique eccentricities - 5 repetitions per run - 2 TRs per position per run = 80 stimulus TRs per run - expanding on contracting I have 3 runs of CCW wedges, 3 runs of CW wedges, 2 runs of expanding annuli and 2 runs of contracting annuli. I have used this guide by Xu Cui as a template for directory structure and analysis: http://www.alivelearn.net/?p=65 I I have made appropriate .par-files and placed them in the folder for every run. In mk-analysis-sess.new I set ncycles to 5 (because I have 5 repetitions per run). After I paint the results on the flattened map the eccentricity map looks like other maps I've seen, but this the polar map looks awful - like random spray paint on the flattened surfaces, and with a lot of space with no coloring, even close to the calcarine. The field sign maps are completely empty, not even the flattened surface shows up (I don't know how they are supposed to look, but its all black). I have tried several solutions: a) removing the blank TRs from my functional data files, so that only stimulus TRs are included in my analysis. b) setting ncycles to 10 (because we essentially have two polar wedges on the screen at each position). But none of this has helped. I am also somewhat unclear on the settings inside surf-sess. For example, what do I set the values in phase encoded data display at? I would be grateful for any suggestions that might help - if you need to know anything else about my stimulus or analysis, please let me know. Best, Peter K.

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implementation of topology correction
by Jerald Zhao 08 Apr '10

08 Apr '10

Hi freesurfer experts, I have some volumes, which are grey matter surface, to be corrected. So I want to compare the performance of various topology correction methods. Can I only implement the topology correction method in freesurfer? thanks in advance, Jerald

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Covariate for results of cortical parcellation
by Liukarl 08 Apr '10

08 Apr '10

Hello, Freesurfer experts: I noticed for analyzing the results from autorecon2, the intracranial volume are controlled as covariate in some publications. Is there any corresponding covariate for cortical results from autorecon3, cortical thickness, surface, and volume? In my current study, there are two group: one is a group with less optimal developmental environment and the other is control. I noticed that without any covariate, the r square from cortical measure and group variable was really low, only accounting for 2%. Is any standard way to analyze the cortical data? Thanks! Karl _________________________________________________________________ MSN十年回馈，每位用户可免费获得价值25元的卡巴斯基反病毒软件2010激活码，快来领取！ http://kaba.msn.com.cn/?k=1

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tksurfer: Load multiple overlays from command line
by Dickinson, Annelise (NIH/NIMH) [F] 08 Apr '10

08 Apr '10

Hi all, What would be the syntax for loading multiple significance maps into different tksurfer overlay layers from the command line? I tried: tksurfer D14 lh.inflated -overlay lh.Tstat1.mgh -overlay lh.Tstat2.mgh --overlay lh.Tstat3.mgh And tksurfer D14 lh.inflated -overlay lh.Tstat1mgh lh.Tstat2.mgh lh.Tstat3.mgh But neither of those worked. Thanks so much for your consideration! ***************************************************** Annelise Dickinson Post-Bac IRTA Laboratory of Brain and Cognition, NIMH/NIH/DHHS Building 10, Room 4C212 10 CENTER DR MSC 1366 BETHESDA MD 20892-1366 ***************************************************** Phone: (301) 435-4941 FAX: (301) 402-0921 E-Mail : dickinsona(a)mail.nih.gov

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submitting manual Talairached data into FreeSurfer pipeline
by Jenessa Price 08 Apr '10

08 Apr '10

Hello, We've noticed that FreeSurfer has been doing a poor job with our data on the first few steps prior to segmentation. All of our data has been aligned and Talairached manually for another project, and we were wondering if it is possible to submit that data into the FreeSurfer pipeline so that it can be segmented from there. If so, what is the command? Thank you, Jenessa -- Jenessa S. Price, B.A. Graduate Student, Clinical Psychology and Neuropsychology University of Cincinnati

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Problems segmenting monkey brain
by Srihasam, Krishna 08 Apr '10

08 Apr '10

Hi, I have a (0.35 mm)^3 resolution monkey brain which I am trying to segment. I am unable to get the frontal cortex to segment properly. My WM.mgz looks good ( I think), but after I do "recon-all -autorecon2-wm ", the surf that gets created has no frontal cortex. I have attached two pictures of one slice, with generated surface overlaid on WM.mgz ( WM_Surf133.jpg) and the same generated surface on T1 image (NU-Surf133.jpg). I tried adding control points, I manually edited the WM.mgz and nothing works. Any help will be appreciated.. regards, Krishna Srihasam Postdoctoral Fellow Livingstone Lab 220 Longwood Avenue, WAS 232 Boston, MA 02115

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Re: [Freesurfer] Freesurfer Digest, Vol 74, Issue 13
by Sebastian Moeller 07 Apr '10

07 Apr '10

Hi Krishna, how does your brainmask look? In my experience, if you use bet to create a brainmask for monkeys, occasionally the brain center is positioned to far posterior. This seems to cause to a loss of frontal gray & white matter in the brainmask. That in turn, would "crop" these parts away from what is considered for the reconstruction. Then since I have no clue about your workflow an procedere this might not actually be helpful... Nevertheless Best Regards Sebastian On Apr 7, 2010, at 1:05 PM, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Message: 2 > Date: Wed, 7 Apr 2010 16:06:31 -0400 > From: "Srihasam, Krishna" <Krishna_Srihasam(a)hms.harvard.edu> > Subject: [Freesurfer] Problems segmenting monkey brain > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <97172F7B8A916A44BF05EA8D13905ECE50C293CA0F(a)ITCCRMAIL02.MED.HARVARD.EDU> > > Content-Type: text/plain; charset="us-ascii" > > Hi, > > I have a (0.35 mm)^3 resolution monkey brain which I am trying to segment. I am unable to get the frontal cortex to segment properly. My WM.mgz looks good ( I think), but after I do "recon-all -autorecon2-wm ", the surf that gets created has no frontal cortex. I have attached two pictures of one slice, with generated surface overlaid on WM.mgz ( WM_Surf133.jpg) and the same generated surface on T1 image (NU-Surf133.jpg). I tried adding control points, I manually edited the WM.mgz and nothing works. Any help will be appreciated.. > > > regards, > Krishna Srihasam > Postdoctoral Fellow > Livingstone Lab > 220 Longwood Avenue, WAS 232 > Boston, MA 02115 > >

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Re: [Freesurfer] Pial Surfaces Cutting off Gyri
by Sherri Novis 07 Apr '10

07 Apr '10

Thank you Bruce. I've had this prob randomly before - but recently it's been each of the last 10 datasets - so I think its a process issue that I introduced - but would love help from any direction. If I use the upload site - which files to you need? will send wm.mgz, ?h.orig surface - any others? Thank you - Sherri -----Original Message----- >From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >Sent: Apr 7, 2010 1:15 PM >To: Sherri Novis <echotalk(a)earthlink.net> >Cc: Sita Kakunoori <sita(a)nmr.mgh.harvard.edu>, freesurfer(a)nmr.mgh.harvard.edu >Subject: Re: [Freesurfer] Pial Surfaces Cutting off Gyri > >Hi Sherri, > >you may also have a topological defect near those control points, which >is causing the surfaces to lose the wm (and hence the gm also). What does >the wm.mgz look like there? Is the wm segmented correctly but not >included in the ?h.orig surface? If you upload this data we can take a >look, if you want. >Bruce > > >On Wed, 7 Apr 2010, Sherri Novis wrote: > >> Thanks Sita. I have struggled with how to capture very ghostly gray matter. Sometimes throwing a CP in it works (I understand now this may be hosing it sometimes) - if AR2-cp w/CPs in white matter is not driving the pial surfaces to capture all the gray - is the only way to capture the ghostly gray matter to directly edit the pial surface? >> >> I was trying to avoid that. I was told don't ever edit the pial surfaces - not sure why though. Will manual edits of the pial surfaces cause other problems in getting surface segmentation stats? >> >> Thank you - >> Sherri >> >> -----Original Message----- >>> From: Sita Kakunoori <sita(a)nmr.mgh.harvard.edu> >>> Sent: Apr 7, 2010 12:55 PM >>> To: Sherri Novis <echotalk(a)earthlink.net> >>> Cc: freesurfer(a)nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] Pial Surfaces Cutting off Gyri >>> >>> >>> Hi Sherri, >>> >>> one of the control points seems to be in gray matter, which is probably >>> causing this. Please try deleting it and rerunning autorecon2-cp. >>> >>> Sita. >>> >>> >>> On Tue, 6 Apr 2010, Sherri Novis wrote: >>> >>>> Hello brilliant and generous FS people, >>>> >>>> I have introduced a problem I cannot solve. I am simply trying to capture as much gray matter as possible. We have some very bad constrast images (ghostly edeges where the gray matter should be). I'm adding control points to try to capture - however, now when I run AR2-cp, the pial surfaces go haywire on the superior borders of the slices. >>>> >>>> Attached are two images displaying the problem. >>>> >>>> I have edited wm.mgz to fill in the ventricles because I was getting islands, and I manually edited the brainmask to remove some vasculature that was being included in the pial surfaces. >>>> >>>> Can you tell me where I introduced this instability? >>>> >>>> Best Regards, >>>> Sherri >>> >>> >>> 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 >> >> >>

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Re: [Freesurfer] Pial Surfaces Cutting off Gyri
by Sherri Novis 07 Apr '10

07 Apr '10

Thanks Sita. I have struggled with how to capture very ghostly gray matter. Sometimes throwing a CP in it works (I understand now this may be hosing it sometimes) - if AR2-cp w/CPs in white matter is not driving the pial surfaces to capture all the gray - is the only way to capture the ghostly gray matter to directly edit the pial surface? I was trying to avoid that. I was told don't ever edit the pial surfaces - not sure why though. Will manual edits of the pial surfaces cause other problems in getting surface segmentation stats? Thank you - Sherri -----Original Message----- >From: Sita Kakunoori <sita(a)nmr.mgh.harvard.edu> >Sent: Apr 7, 2010 12:55 PM >To: Sherri Novis <echotalk(a)earthlink.net> >Cc: freesurfer(a)nmr.mgh.harvard.edu >Subject: Re: [Freesurfer] Pial Surfaces Cutting off Gyri > > >Hi Sherri, > >one of the control points seems to be in gray matter, which is probably >causing this. Please try deleting it and rerunning autorecon2-cp. > >Sita. > > >On Tue, 6 Apr 2010, Sherri Novis wrote: > >> Hello brilliant and generous FS people, >> >> I have introduced a problem I cannot solve. I am simply trying to capture as much gray matter as possible. We have some very bad constrast images (ghostly edeges where the gray matter should be). I'm adding control points to try to capture - however, now when I run AR2-cp, the pial surfaces go haywire on the superior borders of the slices. >> >> Attached are two images displaying the problem. >> >> I have edited wm.mgz to fill in the ventricles because I was getting islands, and I manually edited the brainmask to remove some vasculature that was being included in the pial surfaces. >> >> Can you tell me where I introduced this instability? >> >> Best Regards, >> Sherri > > >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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